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Alleviates microbial threats

Alleviates microbial threats

When animals threags given antibiotics, resistant bacteria in their intestines can continue to survive and grow. Analysis of soil nutrient status and Alpeviates stoichiometry characteristics of Coenzyme Q and cholesterol regulation planting in Guizhou. brevis microgial Gambierdiscus Coenzyme Q and cholesterol regulation and a Preventive dentistry Pseudonitzschia Alleviatse toxins with Height-weight chart variety of neurologic, gastrointestinal, respiratory and irritating effects. Sampling schematic. food supply and the burden of illness associated with foodborne threats to health; considered the spectrum of food-borne threats as well as illustrative case studies; reviewed existing research, policies, and practices to prevent and mitigate foodborne threats; and, identified opportunities to reduce future threats to the nation's food supply through the use of a "One Health" approach to food safety. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP.

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Applying fertilizer is key in maintaining and improving the fertility of agricultural soils. The nutrient content of farmland soil changes with fertilization.

These changes alter the soil C, N, and P stoichiometry, and greatly affect the C, N, and P of soil enzyme activities and microbial biomass 1328 The imbalance between soil microbial demand and soil substrate supply affects C, N, and P nutrient cycling 9. N is usually the key nutrient limiting the net primary productivity of agroecosystems 30and applying organic fertilizer can aggravate 5 or diminish 6 N limitation.

For example, Shen et al. In arid and semi-arid regions, organic fertilizer alone or in combination with N fertilizer diminishes N limitation 6. Recent studies have shown that P limitation is common in agroecology 3132and applying organic N to replace chemical fertilizer N helps relieve soil microbial C and P limitations Tobacco is an important commercial crop in Yunnan Province, and its yield and quality are affected by many factors, including climate, fertilization management, crop rotation pattern, soil properties, and soil microorganisms 3435 Previous studies on C, N, and P stoichiometry were used to reflect flue-cured tobacco soil fertility levels However, to our knowledge, only a few studies have elucidated the effects of different fertilization treatments on microbial resource limitations in tobacco-planting soils 13 In contrast, many studies have confirmed that using microbial fertilizers rather than chemical fertilizers promotes the absorption and transformation of soil-available nutrients while reducing environmental pollution and improving soil fertility Nevertheless, fertilizer-mediated changes in the microbial nutrient limitations of tobacco-planted soil are poorly understood.

Therefore, it is important to further understand how microbial nutrient limitations respond to different fertilization strategies. The ecological stoichiometric properties of soil C, N, and P in different ecosystems are significantly affected by the sampling period. Qi et al. Jin et al. These studies demonstrated that it would be helpful to determine the stoichiometric characteristics of C, N, and P during different sampling periods to better reflect soil nutrient requirements and understand how the plant elements change during different growth periods.

In this study, we investigated C, N, and P stoichiometric and microbial nutrient limitations by measuring the C, N, and P contents of available soil resources, microbial biomass, and soil hydrolytic enzyme activities during the tobacco growing season, and studied the response of microbial resource limitation to applications of microbial fertilizer.

We addressed the following two questions: 1 Does applying microbial fertilizer lead to changes in the stoichiometric ratio of soil and microbial biomass C, N, and P, compared to conventional fertilizer applications?

Based on the known relationship between ecological stoichiometry and microbial resource limitations, we hypothesized that 1 soil microbial biomass stoichiometry would be strictly homeostatic and would not change with soil C:N:P; 2 different fertilizer applications would lead to changes in microbial resource limitations; and 3 microbial resource limitations would vary among growth periods.

The authors affirm that all methods were performed following the relevant guidelines and regulations.

The average annual rainfall, temperature, and sunshine hours were The soil type was red soil and the previous crop was wheat. The major soil properties of the field before transplanting were: pH 6.

The microbial fertilizer was used as the base dressing before transplanting and the compound fertilizer was applied at transplant. The test variety was the local main variety K Base and top-dressing fertilizer applications, picking, and backing were done in line with local management methods The row spacing of the tobacco plants was 1.

Rhizosphere soil samples were collected according to the method of Wang et al. The rhizosphere soils from three similar growing tobacco plants for each fertilization treatment were mixed, sieved to 2 mm after removing impurities, stored in a sealed bag, and transported back to the laboratory for preservation within 24 hours.

Soil pH was measured in water The soil microbial biomass contents of C, N, and P MBC, MBN, and MBP were measured according to the chloroform-fumigation-extraction method 40and the conversion factor E values of microbial biomass C, N, and P were 0. We measured the activities of four common C, N, and P-related hydrolytic enzymes, including β-1,4-glucosidase BGβ-1,4- N -acetyl-glucosaminidase NAGleucine aminopeptidase LAPand acid phosphatase ACP.

BG and NAG activities were determined according to a previously described method LAP and ACP activities were measured using a physiological assay kit Suzhou Keming Biological Technology Co. Finally, we calculated the vector angle and the ratio of C, N, and P enzyme activity to characterize the enzyme stoichiometry 46and we calculated microbial stoichiometric homeostasis 747 A logarithmic or reciprocal transformation was carried out for the indicators that did not conform to a normal distribution.

Differences between groups were detected using the Kruskal—Wallis nonparametric test for the indicators that could not be transformed.

One-way analysis of variance and Tukey's honestly significant difference HSD test were used to determine differences in soil basic physicochemical properties, soil, microbial, and related enzyme C, N, P stoichiometric ratios, and microbial resource limitation-related indicators between the fertilization treatments at the same sampling time Statistical analysis and graphing were completed using RStudio software package v.

SOC, TN and TP were not affected by the interaction between the sampling period and the fertilization treatment, or by either alone Table 1.

TN and TP were highest in the T2 treatment during the H period Table 2. SWC and soil pH were significantly affected by sampling time and were lowest during the H period. Except for N-acq, all other microbial traits were affected by the sampling time Table 1. MBC was highest during the F period, and MBN and MBP were highest during the H period Table 2.

C:N:P stoichiometry of soil, microbial biomass and related enzyme activities during the sampling periods under different fertilization treatments. R, F, M, and H indicate the root extending, flourishing, maturation, and harvesting sampling periods, respectively.

The ratio of soil C, N, and P related enzyme activities to microbial biomass C, N, and P specific enzyme activity per microbial biomass unit: microbial enzyme activity coefficient during the different sampling periods under different fertilization treatments.

In contrast, almost all of the soil enzyme stoichiometry points were above the line except for some samples from the R period Fig. None of the soils was limited by C and N co-limitation or C and P co-limitation Fig. The vector angle A and soil extracellular enzyme stoichiometry BC. The PCA results showed that axes 1 and 2 explained The differences in the soil and microbial C, N, and P indices at the different sampling times were greater than the differences between fertilization treatments Fig.

The differences during the R and F periods were higher than those during the M and H periods Fig. The difference in CK was lower than that in the other treatments with added microbial fertilization Fig.

Principal component analysis PCA of soil resources, soil microbial biomass, and enzyme-related stoichiometric ratios of C, N and P AB and correlation between the soil physicochemical and microbial indicators C. Blue and red represent positive and negative correlations, respectively. The darker the color, the stronger the relationship.

The stoichiometric balance in soil resources is critical for maintaining microbial metabolism and a dynamic balance among the elements, which reflecting the ability of microorganisms to decompose soil organic matter and release P and indicating the supply of soil nutrients during plant growth 828 Tian et al.

Microbial resource limitations describe microbial growth and activity that is limited by nutrient availability and energy Ecological stoichiometry theory suggests that the C:N:P ratio of soil microbial biomass is more stable relative to the soil C, N, and P stoichiometry ratio and reflects the state of microbial C, N, and P demand Our results indicate no significant correlation between the microbial biomass stoichiometric ratio and the soil resources stoichiometric ratio Fig.

The strict homeostasis of soil microbial biomass between the fertilization treatments and different sampling times also confirmed the stability of microbial stoichiometry 7 Table 3which supports our first hypothesis.

This result indicates that soil microorganisms have a weak tendency to assimilate soil available P, and the ability to absorb P results from competition with plants In contrast to a previous study, Qi et al.

: Alleviates microbial threats

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Citation: Mylonakis E Frontiers in bacteriology: Challenges and opportunities. Received: 28 July ; Accepted: 22 August ; Published: 10 February Copyright © Mylonakis. This is an open-access article distributed under the terms of the Creative Commons Attribution License CC BY.

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Export citation EndNote Reference Manager Simple TEXT file BibTex. Check for updates. FIELD GRAND CHALLENGE article. Bacterial drug resistance and the challenges ahead Antibacterial agents, combined with infection prevention measures, have allowed for medical treatments and procedures, such as cancer chemotherapy and transplantation.

Another important limitation in the interpretation of diversity data from human-impacted environments is our incomplete knowledge of the biogeography of marine microorganisms and the relevant environmental factors determining their distribution. In recent years, there have been some efforts aiming to explain the distribution of marine bacterioplankton and sediment microorganisms Bowman et al.

This background knowledge is very important for the interpretation of data from human-impacted environments.

A typical result from diversity surveys, including those in polluted environments, is the retrieval of sequence types highly related to sequences from other environments as well as site-specific ones.

It is usually impossible to determine whether or not these site-specific sequence types are related to the particular stress found in the site. The direct comparison of these site-specific sequences retrieved in different studies in global, or for a particular ecosystem i.

water column, sediment, estuarine, coastal, etc. or stressor i. nutrient input, chemical pollution, etc. might help to determine whether or not there are microorganisms that could be systematically associated with human-derived impact. This would allow the definition of indicator microorganisms, as is currently done for higher organisms, to help in the assessment of environmental quality.

Finally, if we really aim to evaluate the effect of anthropogenic perturbations on marine microbial communities at a more global scale i. So far, we do not know whether the results obtained with the small-scale studies i.

with small water volumes of few grams of sediments, taken at relatively small distances and at specific time points are really representative of larger water bodies or extensive sediment areas, or whether they are representative at long temporal series.

To solve this problem, the way forward is the use of remote ocean-observing systems equipped with appropriate sensors, which allow for a continuous, real-time observation of oceanic systems Paul et al.

For example, satellite imaging can be used to track pollution hazards at the ocean surface over broad spatial scales, i.

oil spills, sewage effluents, river discharges or algal blooms. For higher resolution, there are moorings and mobile platforms equipped with sensors, which provide data at a smaller spatial scale Zielinski et al.

Multiple sensors are available, such as CTD conductivity, temperature, depth , pH, oxygen, redox potential, light, turbidity, chlorophyll and accessory pigments, nitrate, nitrite, ammonium, phosphate, silicate, sulphide, heavy metals copper, lead, cadmium, zinc, manganese, iron , radionuclides or petroleum hydrocarbons see Zielinski et al.

All these parameters are very relevant for the functioning of microbial communities. For example, optical methods for the in situ detection of blooms from the toxin-producing dinoflagellate Karenia brevis have been developed Paul et al.

Moreover, a field-deployable system called Environmental Sample Processor ESP can perform remote molecular analyses of prokaryotic plankton and harmful algal species based in sandwich hybridization assay with a battery of probes with different specificities, and can analyse the presence of the toxin domoic acid in water by a competitive enzyme-linked immunosorbent assay.

The device contains also physical and chemical detectors for measurements of basic environmental conditions Scholin et al. Another device for performing remote molecular analyses of marine microorganisms is the Autonomous Microbial Genosensor AMG Fries et al. It is being tested for the detection of active cells of toxin-producing dinoflagellate K.

These platforms, plus further developments that might lie ahead, represent very powerful tools for the in situ and continuously operating analysis of microbial parameters such as changes in composition, functionality or presence of toxins in seawater, which are relevant to analyse anthropogenic impact.

Throughout the text, the term nutrient enrichment is used in a broad sense to refer to the increase of nutrient inputs to the marine system due to human activities mainly organic and inorganic forms of nitrogen and phosphorus.

As shown in Table 1 , nutrient enrichment is the result of different practices, such as agriculture, urban development, industries, tourism or aquaculture, and it is one of the most important causes of human-derived impact in the marine environment.

In coastal areas, nutrients are discharged either directly or by river and groundwater flow. They can also reach the marine environment through atmospheric deposition Jickells, Besides, due to the movement of water masses, nutrient enrichment can have only local effects or affect distant locations Sarà et al.

The risk posed by nutrient enrichment is greatest in enclosed bays or seas with limited water exchange, in shallow waters and in estuaries, where differences in water density limit the vertical mixing of the water column Cloern et al.

In general, nutrient inputs increase levels of phytoplankton production, stimulate bacterial production and increase oxygen demand and sedimentation rates of particulate material. The development of hypoxic or anoxic conditions does not have a detrimental effect on the abundance and activity of bacterioplankton but causes changes in composition and function, as has been demonstrated in waters from the Chesapeake Bay Crump et al.

Thus, in the absence of oxygen, microorganisms able to use alternative terminal electron acceptors i. nitrate, manganese and iron oxides and sulphate started to proliferate. At early stages of the development of anoxia, bacterial communities still resembled those in oxic waters, which evidenced that important members of the bacterioplankton in this estuary SAR11, SAR86 clusters and the picocyanobacterium Synechococcus have a certain tolerance to anoxia.

But, as the most energetically favourable terminal electron acceptors were consumed i. oxygen, nitrate and sulphate reduction became the predominant respiratory process, there was a dramatic change in bacterial community composition. Phylotypes similar to groups described in sediments, in low-oxygen environments and related to sulphur-oxidizing Gammaproteobacteria were found in the anoxic water Crump et al.

In sediments, the accentuation of anoxic conditions alters the biogeochemistry and might contribute to increase the flux of inorganic nutrients, i.

ammonium, silicate and phosphate, from the sediment again to the water column. Some of the well-studied coastal areas suffering from eutrophication have been reviewed in recent publications: the Baltic Sea, the northern Gulf of Mexico, the East China Sea, the Northern Adriatic Sea, the Chesapeake Bay and the Neuse River estuary Paerl, ; Paerl et al.

Interventions to reduce diffuse nutrient loads in coastal areas have been carried out but they do not seem to have an immediate effect on the ecosystem, although they have alleviated the problems in some cases Ho et al. In the following subsections, we discuss some examples of the effect of nutrient enrichment due to human activity, where the experimental design allowed the comparison of samples subjected to different levels of impact.

Several comparative analyses of microbial diversity along pollution gradients in water and sediments of coastal areas receiving high nutrient inputs have been published in the last years Paerl et al.

A common characteristic to many of these environments is the presence of point sources of pollution i. discharges from sewage treatment plants, industries, etc. as well as diffuse sources of nutrients such as river discharges, runoff from land, harbour activity, atmospheric deposition, etc.

Often, these are transitional environments where we find strong gradients in important variables such as salinity ranging from that typical of freshwater to those characteristically marine , as for example in estuaries whose high productivity is in part due to the nutrient load received from river discharge.

Because of the natural heterogeneity of estuaries, it is difficult to relate the observed changes in microbial community only to nutrient enrichment in these environments.

This complexity is well exemplified by the impossibility of finding common trends in the composition of microbial communities in estuaries studied worldwide, as discussed by Kan et al. These authors interpreted that the high spatial and temporal variability of communities in estuaries probably reflect strong regional or physiographic components.

Therefore, in order to simplify the number and complexity of variables involved in determining the composition of microbial communities in nutrient-enriched environments, only examples of environments where truly marine samples were analysed along gradients of nutrients will be presented.

A particularly interesting study has been conducted in VH in Hong Kong because it has allowed the comparison of environmental data before and after the implementation of sewage treatment to water discharged to the harbour.

The area is also a good example of coastal development and exploitation; it is located next to the big city of Hong Kong and includes one of the busiest ports in the world.

Up to November , it received untreated local sewage effluents discharged in VH [over 1. In addition, this area receives high nutrient loads i. nitrate and silicate from Pearl River, particularly during the rainy season summer.

The predominant wind conditions in summer push the river plume towards VH and also cause upwelling of deep coastal water, intensifying eutrophication. The situation is the opposite in winter, when rainfall is low, predominant winds push the river plume away from the area of VH and cause downwelling of surface waters Ho et al.

The discharge of preliminary-treated sewage water caused an increase in ammonium and phosphate concentrations in the area around VH throughout the year 7—20 μM ammonium and 0. However, these values represented an average decrease of 2—10 μM of ammonium and 0.

There was also an increase in the concentration of dissolved oxygen in deep waters, which indicated better water quality in the area of VH. The impact of nutrient load was also evident in the sediments. Thus, organic matter content, exchangeable ammonia NH 3 -N and available phosphorus were also higher in sediments of the harbour samples Zhang et al.

These sediments also contained higher amounts of other pollutants such as polyaromatic hydrocarbons PAHs and heavy metals Zhang et al. Redox potential was more negative in VH sediments as we could expect from nutrient-enriched environments.

This, together with the higher amounts of acid volatile sulphide and total sulphur measured in VH sediments, indicated higher sulphate reduction rates in the polluted sediments.

Microbial communities in seawater and sediments of VH area were analysed in the same period — , about 2. In agreement with the higher nutrient concentration at VH, the number of prokaryotic cells in seawater and sediments was higher.

Bacterial communities in VH seawater were different from those at the neighbouring sites and the same was true for the sediments Zhang et al. Seasonal variation in the bacterioplankton composition was observed in these samples, mainly driven by changes in temperature, with the exception of the Western part of VH site VHW , which did not show the typical seasonal trend.

At site VHW, which is the one receiving the impact of the sewage effluents more directly, the main drivers of bacterioplankton dynamics were factors indicative of impact such as the amount of dissolved oxygen, phosphate and organic content Zhang et al.

Parameters indicative of pollution were also important in determining the composition of bacterial communities in sediments and they influenced temporal variability as well Thiyagarajan et al. Detailed phylogenetic analysis of 16S rRNA gene clone libraries in seawater identified sequences related to potential human pathogens, such as Arcobacter or with likely faecal origin Bacteroides in the harbour Zhang et al.

Other distinctive characteristics of the bacterioplankton in the harbour were the dominance of sequences of Gammaproteobacteria with a high proportion of Oceanospirillales , Alteromonadales , Enterobacteriales and Vibrionales over those of Alphaproteobacteria , which is usually the main group in seawater, and the lack of sequences of typical coastal marine microorganisms such as the SAR11 group Zhang et al.

This assemblage differs remarkably from those described in coastal environments Pommier et al. Significantly different microbial assemblages also developed in the most polluted sediments and there were also differences in the composition within the functional group of the sulphate-reducing bacteria SRB Zhang et al.

Diversity was high, both in water and sediment of VH, and therefore, pollution did not seem to cause a decrease in the overall diversity, but the contrary. In fact, high diversity and high equitability seem to be a common feature in water and sediments of other human-impacted environments Nogales et al.

Recent studies conducted in the eutrophicated Venice lagoon also highlight areas with different trophic status, some of them under the strong influence of tributaries and point discharges of urban and industrial effluents Solidoro et al. These studies also demonstrate differences in the microbial community composition under different levels of anthropogenic impact Borin et al.

The main driver affecting community composition in sediments seemed to be, as in VH, the discharge of urban waste, which in this case favoured the development of Vibrionaceae Borin et al.

In contrast, differences in microbial composition along the pollution gradient were not evident in the water column because the temporal variation in bacterioplankton composition in seawater was higher than that observed at the spatial scale when comparing assemblages from areas with different levels of pollution Celussi et al.

This lack of spatial resolution might be due to the particular hydrologic characteristics of the Venice lagoon, which is highly dynamic, or to the methods used to explore diversity. What seems to be true is that the lagoon holds particular bacterioplankton communities, different from those in incoming water from the North Adriatic Sea.

These communities, as in the case of VH, are enriched in copiotrophic microorganisms such as gammaproteobacterial genera Vibrio , Alteromonas and Pseudoalteromonas as well as members of the Bacteroidetes Simonato et al.

Interestingly, bacterial activity measured as bacterial production and hydrolytic ectoenzymatic activities inside the lagoon appears to be relatively constant despite seasonal differences in community composition and water parameters Celussi et al.

The examples just reported, together with estuaries, are complex and variable ecosystems with many factors besides nutrient enrichment interacting and having an effect on microbial communities and high nutrient loads.

However, some of the trends observed in these environments, in particular in relation to microbial composition, also hold for simpler environments. An example of those is a small oligotrophic bay, Cala Penyes Rotges Mallorca Island, Spain , which is exploited for tourist purposes during the summer season; it receives the impact of housing development of the neighbouring coast, the use of a small beach and of a nearby recreational marina, but no discharges of sewage treatment plants, agriculture, aquaculture or river discharges Nogales et al.

In this case, nutrient loads are low compared with the environments discussed above and the ecosystem is far from being eutrophicated. However, as in the more complex environments Zhang et al. At times when perturbation was higher i. summer , the composition of bacterial communities deviated clearly from that of the reference sites: a high proportion of sequences from the Gammaproteobacteria and Bacteroidetes , as well as a reduction of Alphaproteobacteria , was observed; typical oligotrophic groups such as SAR11 or SAR86 decreased or disappeared, and the main alphaproteobacterial species belonged to the Roseobacter clade Nogales et al.

These patterns are the same as those found in VH and the Venice lagoon Zhang et al. Therefore, independently of the particular phylotypes observed in each site which appeared to be different after sequence comparison , there seems to be a general response of microbial communities to nutrient enrichment, at least in seawater, which seems to be independent of the absolute magnitude of the nutrient load.

Thus, there seems to be a counter-selection against typical oligotrophic microorganisms and the proliferation of copiotrophic bacteria able to grow and respond to increased nutrient concentrations, such as certain groups of Gammaproteobacteria i. Alteromonadales , Pseudoalteromonas , Pseudomonadales , OM60 group , members of the division Bacteroidetes and representatives of the Roseobacter clade in the Alphaproteobacteria.

All these groups have been associated with experimental nutrient enrichment or algal blooms in marine environments Eilers et al. These microorganisms probably react directly to nutrient enrichment by increasing their growth rate and their biomass, following the typical strategy of fast growers.

None of the studies conducted so far have explored at the same time the diversity of phytoplankton and bacterioplankton in nutrient-enriched environments, and, therefore, this aspect remains unknown. A good model for studying more directly the effect of nutrient enrichment in marine ecosystems without the presence of additional stressors is aquaculture.

Fish production in aquaculture farms is a growing economical sector worldwide but has the drawback of releasing high amounts of organic matter resulting from uneaten fish food and faecal material to the seawater and the sediments below the cages.

Because aquaculture has been shown to have an effect on environmental quality and health, there are numerous studies addressing this issue. Meta-analysis of published ecological data from the water column, as well as studies conducted in particular locations, have shown that fish farms have a significant local effect on the pools of particulate and dissolved organic and inorganic nutrients, such as particulate organic phosphorus, particulate organic nitrogen, dissolved organic nitrogen, dissolved organic carbon, ammonium and nitrite La Rosa et al.

Usually, no effects are observed on the concentration of phosphate and silicate. As in most complex environments nutrient enrichment from fish cages causes a significant increase in bacterioplankton abundance and heterotrophic production Sakami et al.

Although increases in phytoplankton abundance is not always evident from chlorophyll data, a stimulatory effect of fish cages on autotrophic eukaryotic phytoplankton has been observed as well, although this does not lead to the development of phytoplankton blooms because there seem to be a tight control by grazing Navarro et al.

Hydrology is probably also playing a role because fish farms are usually located in areas with good water exchange. Despite all these important perturbations of the marine microbial food web, few studies have reported which are the changes in microbial communities that occur under fish cages in comparison with control areas.

In a study performed in farms of milkfish Chanos chanos in the Philippines, Garren et al. There were few phylogenetic groups represented in libraries from the fish pens and the proportion of clones affiliated to the Cyanobacteria , the Proteobacteria and the Bacteroidetes were high.

The results of this study would indicate a reduction in the bacterioplankton diversity near fish cages in comparison with surrounding areas, contradicting the findings reported above about microbial diversity in nutrient-enriched coastal areas.

This apparent reduction in bacterial diversity due to aquaculture should be confirmed in other systems because it might not be a general finding.

For example, Wei et al. However, it should be taken into account that fish pens and ponds are completely different aquaculture systems and therefore the effect on microbial communities might also be different.

On the other hand, if we take into account the fact that the perturbation caused by a fish farm is more constant in amount, composition and periodicity of additions i. fish food and fish faeces , we can hypothesize that this might lead to the development of microbial communities highly specialized in processing this particular type of organic load, maybe dominated by a few very efficient microorganisms, and therefore less diverse.

The most dramatic effect of the nutrient load from fish farms occurs in sediments below the cages. There, the high organic load, mainly in the form of particulate organic matter, increases oxygen demand and alters the biogeochemistry of the sediments.

The benthic biomass in environments affected by fish farms becomes dominated by microbial components, and bacterial abundance increases significantly compared with control areas Mirto et al.

In contrast, fish farms cause a decline of some groups of benthic fauna and seagrasses Mirto et al. With respect to functionality, the organic load of fish farming stimulates microbial anaerobic respiration processes in sediments below fish farms, such as sulphate, iron and manganese reduction, denitrification, methanogenesis and fermentation Christensen et al.

By far the most important anaerobic process in fish-farm sediments, as in other nutrient-enriched environments, is sulphate reduction because sulphate is usually present in nonlimiting concentrations in marine sediments Holmer et al.

The production of high amounts of hydrogen sulphide by sulphate reduction, concomitant with a decrease in oxygen, might lead to the inhibition of important microbial processes in the nitrogen cycle such as nitrification oxidation of ammonium to nitrate , and hence, to lower the rates of coupled denitrification reduction of nitrate to nitrogen gas , which requires oxidized forms of nitrogen.

Coupled nitrification—denitrification is important for reducing the high nitrogen load of fish-farm sediments and for controlling the efflux of ammonium from the sediments to the water column McCaig et al.

However, in reduced fish-farm sediments, the process of dissimilatory nitrate reduction to ammonium, which also needs oxidized forms of nitrogen, can be quantitatively more important than denitrification.

As a result of reduced nitrification, there is less nitrogen removed from the sediment as nitrogen gas ultimately released to the atmosphere and a higher efflux of ammonium to the water column, which stimulates primary production and maintains the nitrogen in the system Christensen et al. But even if nitrification is not inhibited, it might be insufficient to oxidize all the ammonium resulting from the organic load to nitrate, and consequently there is a net flux of ammonium to the water column Bissett et al.

The bacterial composition in sediments under fish farms along gradients of organic pollution, and hence sulphide and oxygen concentrations, have been analysed by 16S rRNA gene-based approaches in Japan Asami et al.

Significant differences in composition of clone libraries from fish-farm and reference sediments are usually observed, both at a broad and at a fine phylogenetic resolution Bissett et al.

These studies have also shown that bacterial community composition changes significantly after cessation of production, such as in periods of fallowing, but the communities do not revert to the composition before the impact, i. they are not resilient Bissett et al. A distinctive characteristic composition of bacterial communities in fish-farm sediments cannot be easily drawn due to the high microbial diversity found in marine sediments Asami et al.

However, even when these farm sediments were located in different areas and they were dedicated to the production of different fish species, there were some common findings that allow the formulation of certain general trends.

For example, an increase in the abundance of Deltaproteobacteria which includes most of the sulphate-reducing genera is generally observed. This has been proven by a higher proportion of deltaproteobacterial 16S rRNA gene clones in fish-farm libraries Castine et al.

Besides, in agreement with a high production of sulphide by sulphate reduction, a characteristically high proportion of clone sequences of putative sulphur-oxidizing Gammaproteobacteria Asami et al. Sequences of the Epsilonproteobacteria are also abundant Bissett et al.

This group is also related to the metabolism of reduced sulphur compounds and it is usually found in sulphide-rich sediments Campbell et al. The proportion of clones affiliated to the division Bacteroidetes Flavobacteria in particular , which are supposed to play a role in biopolymer degradation, tends to be high in fish-farm sediments as well, and the phylotypes recovered are different from those in control areas Asami et al.

Finally, clone sequences related to betaproteobacterial nitrifiers are usually not recovered in libraries from fish-farm sediments targeting total bacterial diversity Bissett et al. However, using molecular tools targeting selectively this bacterial group, several authors have demonstrated a different composition of the betaproteobacterial nitrifiers in fish-farm sediments compared with control sites McCaig et al.

These changes in the composition of microorganisms participating in the degradation of the organic load and in the sulphur and nitrogen cycles, together with the changes in process rates i. sulphate reduction , provide good evidence of an altered functionality of the microbial communities in sediments below fish farms.

The perturbation is likely to have an effect on archaeal groups too, but the composition of archaeal communities or their role in biogeochemical processes such as ammonia oxidation or methanogenesis in these environments has not been explored so far.

Taking together the results of the studies conducted in environments receiving point and diffuse nutrient inputs, some general effects of nutrient enrichment on microbial community composition and function can be proposed Fig. Thus, despite the composition of the microbial assemblage developing at a particular site, it seems clear that the structure of the microbial food web will be affected as well as important biogeochemical cycles, such as the nitrogen, carbon and sulphur cycles.

General effects of two examples of human-derived stressors on marine microbial communities. Persistent organic pollutants, such as herbicides aldrin, DDT, hexachlorobenzene, etc. They reach the marine environment by direct discharges from coastal areas or dumping into the sea , runoff from land, river discharges or atmospheric deposition.

They also adsorb to floating and stranded plastics, which contributes to their transport and persistence in the environment Rios et al.

Among the different pollutants entering the marine environment, the effect of hydrocarbon pollution on marine microbial communities has been the subject of numerous studies, mainly driven by the concerns caused by tanker accidents such as that of the Exxon Valdez in Alaska or the more recent accident of the Prestige tanker in Spain.

Most of these studies have focused on analysing the effect of crude oil spills on microbial diversity, the changes in response to bioremediation trials usually involving the addition of nutrients and the extent of hydrocarbon biodegradation in polluted environments.

These topics are covered in excellent recent review articles Head et al. The results obtained show that the microbial communities developing in response to events of hydrocarbon contamination differ in composition although the efficacy in hydrocarbon removal is similar Head et al.

Events of acute contamination cause a reduction of microbial diversity in the short term. This is due to two main reasons: the disappearance of certain groups of microorganisms i. archaea and cyanobacteria and the strong selection for specialist hydrocarbon-degrading marine bacteria i.

Alcanivorax , Cycloclasticus , which become predominant particularly when nutrients are added to stimulate hydrocarbon degradation Head et al. In contrast, microbial diversity is usually high in chronically or long-term hydrocarbon-polluted marine environments Hernandez-Raquet et al.

This behaviour is exactly the same as that observed in environments polluted chronically with nutrients Zhang et al.

Typically, 16S rRNA gene sequences related to known hydrocarbon degraders [i. Alcanivorax , Cycloclasticus , etc. Yakimov et al. This might indicate that those hydrocarbon degraders are minor components of these communities, and therefore are missed because of method limitation, although they become predominant in bioremediation trials.

For example, sequences affiliated to Alcanivorax were not observed in mesocosms prepared with seawater from Messina Harbour but they became predominant 15 days after the addition of oil and nutrients Cappello et al.

Also, most-probable-number counts of hydrocarbon degraders in two marinas in the United States were shown to be low Piehler et al. Recent studies conducted in areas polluted after the Prestige tanker oil spill sampled one year after the accident revealed the importance of members of the suborder Corynebacterineae i.

Rhodococcus and the family Sphingomonadaceae in the degradation of the alkane and aromatic fraction of this heavy oil, respectively Alonso-Gutiérrez et al.

These results show the wide diversity of bacterial hydrocarbon degraders in environmental samples and the importance of certain groups i. Actinobacteria as hydrocarbon degraders in rough environments i. rocks polluted with heavy oil.

Alternatively, there might be novel, uncharacterized degraders in these polluted environments Paissé et al. We have experimental evidence supporting this hypothesis coming from an analysis of aromatic ring-hydroxylating dioxygenase genes ARHD in polluted coastal sediments from Patagonia in Argentina Lozada et al.

Sequences representative of the already known phnAc -like genes of Alcaligenes faecalis AFK2, phnAI -like genes of Cycloclasticus spp. and nahAc -like genes of Pseudomonas spp. These novel ARHDs contained the conserved residues of bacterial ring-hydroxylating dioxygenase α-subunits Lozada et al.

We have a biased perception of the risk associated to hydrocarbon pollution towards contamination caused by tanker accidents and this has motivated most of the research on hydrocarbon pollution and bioremediation studies conducted so far.

However, the contribution of tanker accidents to total hydrocarbon contamination in the sea is very low. For example, in the Mediterranean Sea, 80 tonnes of oil were spilled in accidents between and [ Environmental European Agency EEA , ].

In contrast, tonnes are discharged per year due to shipping operations i. discharges of ballast water, tank washing, oil sludge, bilge water or engine room wastes and about tonnes per year from oil terminals and routine land-based operations EEA, Therefore, it is important to take into account this type of pollution and to assess properly its effects on coastal microbial communities.

An example of a study of the effect of land-based sources of hydrocarbon pollution on microbial communities is the one done in a chronically polluted coastal retention basin in the Mediterranean Sea Etang de Berre, France. This coastal lagoon receives hydrocarbons from refineries, petrochemical plants and transportation systems.

Samples were taken along the hydrocarbon pollution gradient Hernandez-Raquet et al. This means that, although other environmental factors were determining microbial composition in the area, hydrocarbons appeared as a key factor for diversification of communities.

When the composition of bacterial communities was analysed in detail, a predominance of sequences related to Delta - and Gammaproteobacteria , as usually observed in marine sediments, was obtained, although variability in different sampling years was high as happens also in nutrient-enriched environments Hernandez-Raquet et al.

As usual, only a few sequences could be related to hydrocarbon-degrading bacteria and these included sequences related to Marinobacter spp. Therefore, anaerobic metabolism of hydrocarbons by SRB seems to be common in polluted environments.

As mentioned above, activities derived from shipping are important sources of hydrocarbon contamination in the marine environment EEA, ; Halpern et al. A good proportion of the pollution caused by ships is due to illegal discharges.

In the Mediterranean, for example, the density of spills can be correlated with major shipping routes Ferraro et al. The effect of this type of diffuse hydrocarbon pollution in the composition of seawater microbial communities has not been addressed but it might be a factor to consider for explaining the described cosmopolitan distribution of specialist hydrocarbon degraders in the marine environment Yakimov et al.

In areas exploited for tourism, there is a consistent increase in the number of hydrocarbon spill detections during the high season, correlating with the increase in boating activity Ferraro et al.

The pollution caused by maritime transport and recreational boats is likely to be a source of fuels i. diesel and synthetic lubricants to seawater and sediments.

There are few studies addressing the effect of this type of pollution. One experiment was performed in in situ mesocosms with water and sediments from a tropical estuary in Singapore, impacted by boating-derived activities.

The mesocosms were treated with diesel oil at concentrations reproducing the mean and the highest hydrocarbon concentrations measured in the area Nayar et al. The response observed was negative for eukaryotic phytoplankton and picocyanobacteria Synechococcus at higher hydrocarbon concentrations, although picocyanobacteria were stimulated at the lower concentrations.

In contrast, the number of heterotrophic bacteria and production rates increased in response to the treatment, particularly at the higher concentrations Nayar et al. These results show that there is a rapid response of microbial communities to diesel pollution in the marine environment, as demonstrated for more complex hydrocarbon mixtures such as crude oil Head et al.

A second study tested the short-term effect of diesel oil, a biodegradable lubricant and a synthetic lubricant clean and used in a field experiment in pristine Antarctic sediments Powell et al. Although the bacterial communities differed from the control in all treatments, the most significant variations were due to treatment with diesel, followed by synthetic lubricants, but not with the biodegradable lubricant Powell et al.

These results show ways of reducing the impact of lubricants in the marine environment, particularly in sensitive areas such as the poles. Maritime activities require the building of ports and recreational marinas. Because of the constant increase of maritime transport United Nations Conference on Trade and Development, and the interest in increasing tourism-derived activities European Commission, , there is a constant pressure for the development of harbours and recreational marinas, and therefore, we can expect an increase in the environmental stress posed by them.

Some of the pollutants that are commonly found in harbours are hydrocarbons i. as result of boat traffic, accidental spills or discharge of bilge oil and ballast water , detergents, surfactants or antifouling compounds i.

heavy metals, biocides , even though ports have facilities for the collection of wastes and for pollution control. Additionally, they receive nutrient inputs, either directly due to harbour activities or through discharges of rivers and sewage effluents such as VH in Hong Kong Zhang et al.

Harbour seawater and sediments have been shown to hold particular bacterial communities, different from those in adjacent areas, highly diverse and highly variable at the temporal scale Schauer et al. Despite chemical pollution, the effect of nutrient enrichment seems to be the most important factor driving the composition of bacterioplankton in harbours, and for example nutrient enrichment might explain the high abundance of sequences related to Clostridium and Vibrio in the sediments of Milazzo Harbour, subjected to high organic load Yakimov et al.

Relationships between bacterioplankton community composition and hydrocarbon pollution were only found in the study conducted in Messina Harbour, where the relative abundance of putative hydrocarbon-degrading bacteria correlated with an increase in hydrocarbons Denaro et al.

In sediments, stimulation of hydrocarbon degraders has been observed after hydrocarbon addition, indicating that there is a primed microbial community able to use these pollutants, both aerobically and anaerobically Hayes et al.

As in other hydrocarbon-polluted sediments, SRB seem to be involved in hydrocarbon degradation in harbour sediments. For example, a recent study on the composition of the active sulphate-reducing assemblages in sediments of Boston Harbour by analysing transcripts mRNAs of dsrAB genes Chin et al.

Several studies have addressed the composition of bacterial communities in marine sediments polluted with heavy metals. As in the case of other pollutants, bacterial communities in sediments with different levels of heavy-metal pollution are shown to differ Gillan et al.

The same result has been observed for archaeal and photosynthetic communities Toes et al. Different from the cases of nutrient or hydrocarbon pollution, which seem to stimulate bacterial growth, total prokaryotic cell numbers appear to be negatively correlated with heavy metals such as cadmium, copper, zinc and lead Gillan et al.

However, when the calculations were done for particular phylogenetic groups, few statistically significant correlations could be established, and they seemed to be dependent on the sample. Therefore, it is difficult to determine the effect of heavy metal on particular groups of microorganisms with the data available so far.

In highly polluted sediments of a Norwegian fjord, the abundance of Gammaproteobacteria determined by FISH counts was negatively correlated with copper and zinc, and that of Bacteroidetes with copper, zinc and cadmium.

In contrast, in Belgian sediments with lower pollution levels, the only significant correlation was found between Bacteroidetes and cadmium Gillan et al. In these two sediments, bacterial community composition was also analysed by a cloning and sequencing approach. The results evidenced the presence of the main groups typically found in marine sediments: Gamma - and Deltaproteobacteria and Bacteroidetes.

But some of the clones in the Norwegian sediment grouped with clones from an Antarctic sediment polluted with heavy metals and hydrocarbons, and a group of gammaproteobacterial sequences was found in both the Norwegian and the Belgian sediments Gillan et al.

This might indicate that certain bacterial populations might be favoured in heavy-metal-polluted sediments, although these relationships are even more difficult to draw than in the case of hydrocarbon pollution. A laboratory experiment was performed in microcosms to simulate the effect of sediment disturbance dredging in a sediment chronically polluted with heavy metals.

In addition, the effect of deposition of a 3 mm layer of polluted sediment on the surface of unpolluted sandy sediments was also analysed Toes et al. These two practices dredging and deposition onto a different location are common in the marine environment. Homogenization of the polluted sediment simulating dredging caused minor changes in the composition of microbial communities.

However, overlying of sandy sediments with polluted sediment caused significant changes in the composition in the three microbial components analysed Bacteria , Archaea and Cyanobacteria in comparison with the unpolluted control, although the effect was lower for Archaea Toes et al.

After one year of incubation, some common bacterial groups were observed in clone libraries from the artificially polluted sandy sediments in comparison with those from the chronically polluted sediment: representatives of the Roseobacter clade, the genus Vibrio and a member of the Flavobacteriaceae whose sequence was related to a clone from a heavy-metal-polluted Antarctic sediment Toes et al.

These sequences might represent microorganisms favoured by the conditions imposed by heavy-metal pollution, although to confirm this, it will be necessary to corroborate their absence or lower abundance in control, unpolluted sediments. In the environment, removal of sediments polluted with mercury, PCBs and PAHs in a location in the Baltic Sea resulted in the development of significantly different bacterial communities.

Summarizing the studies presented on chemical and heavy-metal pollution, we can conclude that, as in the case of nutrient enrichment, this type of perturbation again alters the composition of microbial communities Fig. But because this type of pollution selects for those microorganisms that are capable of degrading or chemically transforming the pollutants, and sometimes these organisms belong to particular phylogenetic groups, the studies conducted so far can point to particular types of bacteria i.

oligotrophic marine hydrocarbon-degrading Gammaproteobacteria , Actinobacteria , Sphingomonaceae or certain SRB phylotypes likely to be contributing to alleviate the problem of chemical pollution in the environment.

However, in many cases, these is only indirect evidence that does not fill the gap in knowledge on fundamental aspects of the functionality of microbial communities in chemically polluted environments. For example, novel or unrecognized microbial genera might be involved in the degradation of contaminants, most likely through metabolic cooperation with other microorganisms using degradation intermediates.

Microorganisms as such, i. forming part of degradation networks, will not be isolated as typical pollutant degraders and therefore escape our knowledge, although they are probably key players in the environment.

Other fundamental aspects, such as how pollution affects bacterial production rates, respiration rates or other microbial processes have not been analysed in chemically polluted environments, in contrast to what has been done in nutrient-enriched environments.

The broad use of high amounts of antibiotics in intensive farming to prevent or treat animal infections is also causing environmental concern see review Cabello et al. The bactericidal action of antibiotics can cause changes in the composition of natural microbial communities by selectively inhibiting susceptible bacteria.

Besides, exposure of natural communities to antibiotics might lead to the selection of resistant bacteria, which can then transfer their resistance determinants to opportunistic pathogenic bacteria in the environment.

In relation to the marine environment, there are numerous data coming from aquaculture, where administration of high amounts of a variety of antibiotics in fish farms for prophylactic or therapeutic reasons is routinely done Cabello, ; Sapkota et al.

Antibiotic treatment in fish farms leads to increased concentrations of these compounds in water and sediments below the cages as well as in the fish stock produced. As a result, there is a positive selection for antibiotic-resistant bacteria in water and sediments from fish cages, surrounding areas and among fish-associated bacteria Chelossi et al.

Often, the isolation of multiresistant bacteria i. bacteria resistant to several antibiotics is reported. This is in agreement with the simultaneous use of several types of antibiotics in fish farms Dang et al.

Antibiotic-resistant bacteria isolated from fish-farm water and sediments are diverse. Although most of them belong to the Gammaproteobacteria genera Vibrio , Photobacterium , Pseudomonas , Pseudoalteromonas , Alteromonas , Citrobacter , Salmonella , isolates from the Alphaproteobacteria , Firmicutes , Actinobacteria and Bacteroidetes have also been reported Furushita et al.

The presence of antibiotic-resistance genes in these isolates, as well as the ability of some of the isolates for transferring the resistance genes by conjugation to Escherichia coli recipient strains, have been demonstrated Rhodes et al.

Besides, closely related plasmids of the IncU group, carrying oxytetracycline-resistance determinants, have been found in isolates from hospitals in the UK and Germany and from fish-farm environments, demonstrating that plasmid transfer might occur between natural bacteria and potential human pathogens Rhodes et al.

Instead of isolating antibiotic-resistant bacteria, Hargrave et al. They measured profiles of resistance to the antibiotic oxytetracycline, widely used in aquaculture, in mixed bacterial communities from sediments around salmon aquaculture farms and in feed pellets which were proposed as the source of antibiotics.

Usually, numbers were higher in surface sediments but resistance levels were still high at intermediate depths, which mean that sediments around fish farms can constitute reservoirs for antibiotic-resistant bacteria in the marine environment Hargrave et al.

It is important to recognize that fish farms are not the only source of antibiotics in the marine environment. Thus, oxytetracycline-resistant bacteria are present in surface seawater and sediments receiving the input of sewage treatment plants, as demonstrated in Jiaozhou Bay in China and Halifax Harbour in Canada Dang et al.

The study conducted in the area of VH, where discharges of Anthropogenic use of coastal areas i. beaches also seems to have an effect on the natural abundance of antibiotic-resistant bacteria. Studies performed in sand from beaches of the Southern Baltic Sea coast showed that bacteria isolated from a recreational beach had higher resistance to antibiotics from different chemical families than those in nonrecreational areas Mudryk, ; Mudryk et al.

The level of multiresistance resistance to several antibiotics was also higher among isolates from the recreational beach. The examples presented here provide evidence of the potential health risk derived from antibiotic contamination in the marine environment because they demonstrate the selection and enrichment of multiresistant bacteria.

Some of them might be potential human pathogens i. Vibrio , Pseudomonas , Salmonella or might potentially transfer genetic determinants of resistance to pathogenic bacteria. But none of these studies have addressed how antibiotics alter the composition and functionality of microbial communities in marine environments.

Given the magnitude and worldwide extension of the problem of antibiotic pollution, it is imperative to design carefully environmental and laboratory studies to address this issue, to determine which microbial groups are affected by the presence of antibiotics in the water and how antibiotics alter the functionality of microbial communities, both in water and in sediments.

Several of the uses of coastal resources have the risk of introducing potential human pathogenic bacteria, as shown in Table 1. The highest risk is derived from direct sewage discharges, which are a source of human faecal bacteria. Therefore, sewage treatment and routine controls for faecal indicators coliforms, E.

coli , enterococci in seawater in areas dedicated to bathing are usual procedures in developed countries Stewart et al. However, sewage discharge is not the only source of faecal bacteria in marine environments.

Other human-derived sources of potential pathogens are runoff from land urban and agricultural areas , leaking septic tanks, sewer overflows, discharges from boats, etc. Stewart et al. Sources of faecal bacteria other than human i. birds, pets, wildlife, etc.

should not be disregarded Choi et al. A recent publication has presented a novel and interesting approach to assess faecal pollution in coastal watersheds using community-based indicators Wu et al.

Using PhyloChip, a phylogenetic microarray, these authors identified operational taxonomic units OTUs characteristic of faecal samples mainly belonging to the phyla Firmicutes , Proteobacteria , Bacteroidetes and Actinobacteria which were designated as faecal subsample associated OTUs FSAO.

By analysing the similarity of bacterial communities in several environmental samples from two watersheds in Santa Barbara CA to FSAO, they could identify the samples exposed to faecal sources.

The results obtained agree with traditional culture methods for the detection of faecal bacteria. In addition, they proposed a new community-based indicator to assess ecosystem health, based in the ratio of relative richness of three bacterial classes: Bacilli , Bacteroidetes and Clostridia to that of the Alphaproteobacteria BBC: A.

This ratio is higher in faecal and sewage samples and lower in samples not impacted by faecal material Wu et al. Approaches like this represent an important step forward in the analysis of faecal contamination in coastal areas because it is based in powerful molecular methods, and in the assessment of whole communities instead of using a few two or three indicator bacteria.

Faecal material is also a source of human pathogenic enteric viruses. Viruses from faecal origin belong to the families Adenoviridae adenovirus , Caliciviridae i. Norwalk virus , Picornaviridae i. poliovirus, hepatitis A and Reoviridae reoviruses and rotaviruses. These viruses cause a variety of diseases in humans, either by direct exposure to water or after ingestion of contaminated seafood Griffin et al.

Viruses are shown to persist better in the environment than the bacterial indicators used for water quality monitoring Griffin et al. Apart from causing diseases in human and other marine mammals, epidemic viral infections can cause significant economic losses in aquaculture plants for commercial production of fish and shellfish Lang et al.

In addition to discharges of faecal material, other human activities such as bathing constitute a source of potential microbial contamination. For example, enterococci and Staphylococcus aureus are transferred directly from the skin of bathers in high loads into seawater 3—6 × 10 5 and 6.

These results highlight the importance of nonenteric bacteria as potential pathogens in the environment Stewart et al. Besides the health risk posed by allochthonous microorganisms from faecal or other origin, there are several potential human pathogenic species that are indigenous to marine and estuarine environments, such as Vibrio cholerae , Vibrio vulnificus and Vibrio parahaemolyticus Thompson et al.

The first two species, V. chlolerae and V. vulnificus , can cause severe, fatal diseases. In contrast, V. parahaemolyticus infections are usually not life-threatening but they are very common worldwide, mainly due to the consumption of contaminated seafood Collins et al.

These opportunistic pathogenic bacteria have a variety of virulence factors such as haemolysins V. vulnificus and V. parahaemolyticus , toxins cholera toxin , colonization factors, etc. Thompson et al.

The presence of pathogenicity-associated genes from V. cholerae and V. parahameolyticus has been proven in environmental isolates from different Vibrio spp. In the marine environment, vibrios are usually associated to surfaces and establish symbiotic relationships with phyto- and zooplankton i.

copepods , which might constitute vectors for disease transmission and for the development of disease outbreaks Lipp et al. Therefore, conditions favouring the development of phytoplankton blooms, such as in eutrophicated environments, might favour the development of vibrios.

In fact, as mentioned previously in this review, Vibrionaceae have been found in nutrient-rich environments Yakimov et al.

In addition, vibrios proliferate at higher water temperatures and have a wide tolerance range to salinity, being able to survive well in low-salinity brackish water.

Therefore, their incidence is expected to increase in a scenario of global climate change. Different marine dinoflagellates Dinophysis spp. brevis and Gambierdiscus toxicus and a diatom Pseudonitzschia produce toxins with a variety of neurologic, gastrointestinal, respiratory and irritating effects.

Disease is usually caused by consumption of contaminated fish or shellfish, although aerosol inhalation and direct eye or skin exposure can also cause problems.

Environmental perturbations derived from human activities that might have an effect in the increased incidence of harmful algal blooms are multiple and include: nutrient enrichment eutrophication , particularly in coastal waters; destruction of coastline due to coastal exploitation i.

Potential pathogens might be disseminated in the marine environment due to long-distance transport and discharge of ship ballast water used for ship stability and trim. For example, ballast water has been shown to contain epidemic-causing serotypes of V.

coli including strain O , Enterococcus spp. Concerns of the danger of ballast water discharges, not only for the spread of microbial pathogens but also of invasive species, have resulted in the establishment of guidelines for ballast water management and the promulgation of the International Convention for the Control and Management of Ship's Ballast Water and Sediments in by the International Maritime Organization.

These numbers are highly variable and depend on many factors such as the source region of the boat, season of the year and ballast-water management, i. whether or not there had been open-ocean exchange of water Drake et al.

The changes in the microbial component of ballast water during a transoceanic voyage in tanks with and without open-ocean exchange have been studied by quantifying bacterial and viral numbers Drake et al. The results showed that containment of ballast water in boat tanks led to a decrease in the bacterial and viral load in comparison with the initial water, irrespective of performing open-ocean exchange or not Drake et al.

Bacterial communities in ballast water initially resemble those of the source seawater, which is usually from a coastal location Tomaru et al. This ballast water is replaced in the open ocean at some point during the voyage to reduce the risk of discharging invasive species in the reception port.

The open-ocean water filling the tanks has a significantly different microbial composition Tomaru et al. This means that allochthonous microorganisms from coastal regions are routinely discharged into the open ocean, and vice versa, open-ocean microorganisms are discharged into coastal regions.

However, the microbial assemblages discharged in each case are different from those in the source water because there is a change in composition during the voyage within the time frame of days Tomaru et al.

A recent study analysed bacterial diversity in ballast water in a ship anchored in Xiamen Port, and compared it with that of the receiving harbour seawater Ma et al. The source of the ballast water was Singapore and it had been partially replaced with water from the South China Sea.

The analysis of the corresponding 16S rRNA gene clone libraries revealed that ballast water contained a less diverse bacterial community, with representatives of only two classes, Alpha - and Gammaproteobacteria. There was no evidence of the presence of pathogenic bacteria.

Within these two groups, the phylotypes retrieved in ballast water were different from those in Xiamen Harbour seawater Ma et al. Thus, wherever it is done, the discharge of ballast water might potentially alter, at least transiently, the autochthonous microbial composition of the discharge site.

Whether this is significant or not has not been determined. If an open-ocean exchange is performed, we can expect that most of the coastal microorganisms will not be able to compete with the autochthonous bacteria in the more oligotrophic open ocean, and the opposite, i.

oligotrophic bacteria from the open ocean will not survive in coastal regions. Results from metagenomic studies show that microbial communities with dissimilar genomic composition i. genetic repertoire develop in different marine locations or at different depths DeLong et al. Therefore, the success of an invasive microorganism, potentially dangerous such as a pathogen, would depend on the size of the inoculum, its capability to survive in the new environment and its competitive ability in facing a microbial community adapted to the conditions at the site of discharge.

As reported by Halpern et al. Thus, the interest in studying the effect of processes such as increase of seawater temperature and ocean acidification is increasing rapidly in the last years.

No particular studies have been done targeting the microbial compartment but the information gathered so far provides clues on how microbial communities could be affected. Anthropogenic activities such as the burning of fossil fuels, deforestation, industrialization and cement production are causing increased levels of atmospheric carbon dioxide CO 2 and, consequently, an increase in dissolved CO 2 in the oceans.

The acidification of the oceans will be detrimental for calcifying organisms and will cause changes in species distribution and abundance, as well as in food-web dynamics and structure.

The increase in dissolved CO 2 has an effect in the carbon cycle of the oceans but also in the cycles of the major nutrient elements: nitrogen, phosphorus, silicon and iron for a review, see Hutchings et al. The information available indicates that three important processes in the nitrogen cycle might be affected.

For example, nitrogen fixation is predicted to increase in a high-CO 2 ocean, based on the results of experiments done with nitrogen-fixing Trichodesmium and unicellular Cyanobacteria. In contrast, a decrease in pH seems to reduce nitrification rates and the abundance of bacterial and archaeal nitrifiers in seawater Hutchings et al.

Consequently, the fluxes of oxidized nitrogen species, such as nitrate, will be affected. This in turn would have a negative effect on denitrification rates, although there can also be positive effects over this process due to the expansion of suboxic zones in the oceans.

An increase in the relative proportions of ammonium to nitrate due to decreased nitrification will cause a shift in the composition of primary producers, by favouring microbial components such as picocyanobacteria and nanoflagellates Hutchings et al.

On the other hand, global warming will lead to an increase in seawater temperatures and cause a stronger stratification of the oceans. This will limit the fluxes of nutrients from sediments and the deep sea i. phosphorus, iron , and potentially intensify problems of hypoxia and anoxia.

Changes in the climate system can also cause alterations in the abundance and global distribution i. spread from tropical areas to lower latitudes of pathogens such as Vibrio spp. The abundance of V. cholerae , the causative agent of cholera epidemics, is already shown to follow climatic patterns Lipp et al.

Higher water temperatures, together with increased nutrient levels, would also increase the frequency and severity of harmful algal blooms Moore et al.

Environmental changes due to anthropogenic activities seawater warming or increased CO 2 and nutrient supply are also suspected of being involved in the expansion of coral diseases worldwide, diseases in which microorganisms are important Sokolov et al.

In addition, strong rainfall events and flooding due to sea-level changes, both expected under a global change scenario, would result in an increase of estuarine and brackish low-salinity environments, which again would favour the growth of Vibrio spp.

Lipp et al. Moreover, floods may also cause problems of inefficient water sanitation and increase runoff from land, with the consequent increase in the risk of faecal bacterial and viral , nutrient and chemical contamination of the marine environment Kite-Powell et al.

The possibility of generating phytoplankton blooms by ocean fertilization with the aim of increasing the flux of organic matter towards the deep ocean causing carbon burial and alleviating problems of increasing CO 2 concentrations is catching the attention of companies for commercial exploitation.

IN ADDITION TO READING ONLINE, THIS TITLE IS AVAILABLE IN THESE FORMATS: Thus, microbiap the composition A,leviates the microbial assemblage developing at a thrreats site, Core strength exercises seems thrfats that Alleviates microbial threats structure Alleviates microbial threats rhreats microbial food web will threatts affected as well as important biogeochemical cycles, Support groups for individuals with depression as the nitrogen, carbon and sulphur cycles. Article CAS PubMed Google Scholar Tariq R, Pardi DS, Bartlett MG, Khanna S. You're looking at OpenBook, NAP. Currently, CDI is primarily treated with orally bioavailable antibiotics such as vancomycin or metronidazole, which further contributes to microbiome disruption, AR infections, and risk for recurrent CDI [ 111213 ]. Nature : — Acta Ecol. Compared with the control group, the relative abundance of Bacteroides was significantly increased in our study, and treatment of Rg1 effectively reverses the increase of Bacteroides.
Forum on Microbial Threats | National Academies Figure and Table provide examples of several emerging infectious diseases identified by scientists in the final decades of the twentieth century. Noroviruses formerly Norwalk-like viruses, caliciviruses. In relation to the marine environment, there are numerous data coming from aquaculture, where administration of high amounts of a variety of antibiotics in fish farms for prophylactic or therapeutic reasons is routinely done Cabello, ; Sapkota et al. Muhammad, Q. The MetaCyc database of metabolic pathways and enzymes—A update. After pair-end sequence assembly, quality filtering and singletons removal, our final dataset consisted of 7,, reads.
Antimicrobial stewardship - APIC Moreover, floods may also cause problems of inefficient water sanitation and increase runoff from land, with the consequent increase in the risk of faecal bacterial and viral , nutrient and chemical contamination of the marine environment Kite-Powell et al. Introduction Carbon C , nitrogen N , and phosphorus P play pivotal roles in regulating plant growth and soil nutrient cycling, and their interactions are closely intertwined through a series of physical, chemical, and biological processes 1 , 2. Three separate ASVs from the Akkermansia genus provided a large portion of the variation, and in some severely perturbed samples at day 0 and 7, A. Except for N-acq, all other microbial traits were affected by the sampling time Table 1. Enhancement by Adrenaline of Ginsenoside Rg1 Transport in Caco-2 Cells and Oral Absorption in Rats.
Frontiers | Frontiers in bacteriology: Challenges and opportunities Eur Alleviates microbial threats Gastroenterol Hepatol. The bacterial microbiome composition of gut tgreats was microblal towards Coenzyme Q and cholesterol regulation Zhou Y, Zhi F. This study presents taxa and microbial functional pathways that require larger datasets and further validation prior to incorporation into clinical practice. About this article.
Alleviates microbial threats

Alleviates microbial threats -

Roughly 2 million people die each year from TB worldwide WHO, c , with the vast majority of these deaths 98 percent occurring in developing countries Mukadi et al. In , approximately 8. In most countries, the average incidence of TB has recently been increasing approximately 3 percent per year; however, the increase is much higher in Eastern Europe 8 percent per year and those African countries most affected by HIV 10 percent per year.

Twenty-three countries account for 80 percent of all new TB cases. In , over half of these cases were concentrated in five countries: India, China, Indonesia, Nigeria, and Bangladesh.

Although Zimbabwe and Cambodia report fewer total cases, they possess the highest global rates per , population and , respectively WHO, a.

If present trends continue, more than 10 million new cases of TB are expected to occur in , mainly in Africa and Southeast Asia; by , nearly 1 billion people will be newly infected, million will develop the disease, and 35 million of them will die WHO, a. The global resurgence of TB is not confined to developing countries.

From to , TB rates in Russia increased by 70 percent, with more than 25, persons dying from the disease each year Netesov and Conrad, The increased incidence is compounded by the spread of multiple drug-resistant TB MDR-TB , especially in prisons, where patients typically self-administer treatment.

Because most prison clinics experience massive shortages of drugs, most patients are unable to complete their full course of treatment, thus fostering the emergence of MDR-TB. Indeed, the rate of MDR-TB among TB isolates in Russian prisons is an astonishing 40 percent, compared with 6 percent in the general population.

The overall rate of TB per capita in prison populations i. TB is the leading cause of morbidity and mortality among HIV-infected people worldwide Mukadi et al.

In , approximately one-third of HIV-infected people worldwide were also coinfected with M. tuberculosis ; the vast majority of these cases were in sub-Saharan Africa Harries and Maher, The incidence and case-fatality rate i. In some sub-Saharan countries, the case-fatality rate for HIV-posi-.

tive pulmonary TB patients can exceed 50 percent Dye et al. Malaria, caused by plasmodia parasites, is responsible for — million clinical cases and 1.

Malaria is the most prevalent vector-borne disease and is endemic in 92 countries Martens and Hall, It disproportionately affects rural populations living in housing without screens and doors, children under 5 years of age, and pregnant women. Africa accounted for nearly 90 percent of new cases reported worldwide in ; of these, 40 percent occurred in children under 5 years of age WHO, b.

Nearly all people who live in endemic areas are repeatedly exposed to mosquitoes that carry the infective agent, and those who survive malaria develop partial immunity.

Endemic areas are subject to irregular rapid increases in incidence as the warm seasons arrive, rainfall and humidity increase, and populations migrate IOM, ; WHO, b. In areas where the infection rate is low and people are rarely exposed to the disease, however, the population is generally much more susceptible to the devastation of epidemic malaria—and the number of malaria epidemics is growing worldwide.

Between and , malaria epidemics in 14 countries of sub-Saharan Africa caused a high number of deaths, many in areas previously free of the disease Nchinda, Drug resistance has been implicated as a contributing factor in the spread of malaria to new areas and the reemergence of the disease in areas where it had previously been eliminated, leading to increased morbidity and mortality Bloland, In , the Centers for Disease Control and Prevention CDC received 1, reports of malaria cases with onset of symptoms in among persons in the United States and its territories; 98 percent of these cases were classified as imported, primarily from Africa 60 percent , Asia 20 percent , and the Americas Western European countries are reporting similar statistics for imported malaria Fayer, Between and , malaria increased as much as fold in certain southern regions of the former Soviet Union; more recently, it has begun to emerge even as far north as Moscow Fayer, Only a few isolated cases or small outbreaks have occurred in the United States, in areas where individuals with imported disease have provided a reservoir of infection for local-vector mosquitoes that have subsequently transmitted the infection to persons from that locality Olliaro et al.

However, increasing global travel, immigration, and the presence of competent anopheline vectors throughout the continental United States all contribute to the growing threat of malaria transmission even in nontropical North. America, as well as other temperate regions of the world.

Indeed, two cases of locally acquired malaria were recently discovered in Loudon County, Virginia, 30 miles from Washington, D. CDC, c. The emergence of a microbial threat is a phenomenon in which something has changed—either our perception of a microbial threat, our recognition of a threat, or the true biological expansion of a microbe.

An emerging infectious disease is either a newly recognized, clinically distinct infectious disease, or a known infectious disease whose reported incidence is increasing in a given place or among a specific population. As illustrated in the previous section, HIV, TB, and malaria are certainly emerging infections, even though the latter two diseases have been around for centuries.

Figure and Table provide examples of several emerging infectious diseases identified by scientists in the final decades of the twentieth century. These and other examples of emerging infectious diseases, including STDs, nosocomial infections, and vector-borne and zoonotic diseases, are discussed in Chapter 3 , along with the major factors in their emergence.

We will inevitably see more emerging infections in the future as the factors that lead to emergence become more prevalent and converge with increased frequency. We can only guess at how many more of the microbes in the environment will eventually be found as human pathogens.

Even small, isolated events cannot be readily dismissed because of their potential to expand with time. After all, when the initial handful of cases of what would later be termed AIDS first appeared, few could foresee that their affliction would soon become a global catastrophe, threatening the security of entire nations.

Antimicrobial resistance is a paramount microbial threat of the twenty-first century. With the presence of antimicrobial resistance may come a corresponding increase in mortality and morbidity from untreatable disease, an increased risk of the global spread of drug-resistant pathogens, a rise in the health care costs associated with the need for multidrug therapy and longer and more frequent hospital stays, and the costs of research and development of alternative drugs.

For example, efforts to control each of the three major global infectious diseases discussed earlier—AIDS, TB, and malaria—are seriously thwarted by the rise of antimicrobial resistance. FIGURE Examples of recent emerging and re-emerging infectious diseases.

Reprinted with permission, from Fauci, Copyright by the Infectious Disease Society of America. Inhalation of spores; via skin contact with contaminated tissues or materials; ingestion of contaminated food.

Primarily an infection of animals; long-term persistence in contaminated soil or environment; agent of bioterrorism. Emerged in Asia in — in areas with poor sanitation; has caused large outbreaks in India and Bangladesh; prior infection with V.

cholerae O1 does not protect against O; ongoing genetic reassortment in O Close contact with person who has diphtheria or who carries Corynebacterium diphtheriae. Escherichia coli OH7 hemorrhagic colitis severe bloody diarrhea and kidney failure.

Ingestion of contaminated food or water; can be spread from person to person via fecal-oral route. Healthy cattle are primary reservoir carried in feces ; bacteria survive in acidic environment; small inoculum of bacteria can cause infection; sporadic cases and large outbreaks in U.

and other countries; vehicles of transmission have included meat, milk, fresh produce, cider, contaminated water ingested during swimming, other; mass processing and wide distribution of contaminated foods has led to widely dispersed outbreaks.

Zoonosis; rodents and deer maintain transmission cycle; common in parts of North America, Europe; also found in Asia, Australia; increase in human cases attributed to reforestation and expansion of deer populations; increased human-tick contact. Bite of infective flea; inhalation of airborne bacilli; close contact with infected animal or tissues.

Primarily a zoonosis; rodents are reservoir host; most sporadic cases and outbreaks occur in Africa but infections also occur in the Americas including the U. First emerged in U.

in ; consequence of intensive use of antimicrobials; can be spread from patient to patient in health care settings; risk of spread into the community. Multiple outbreaks in North America in s linked to imported raspberries from Guatemala; endemic in many countries.

Increasing morbidity and mortality in many areas, especially in Africa; increase linked to poor vector control and rising resistance to inexpensive antimalarial drugs, lack of resources for other drugs and other control measures.

Dengue fever and dengue hemorrhagic fever and shock syndrome ; dengue viruses, serotypes 1,2,3,4. Found in most tropical and subtropical areas worldwide, including urban areas; outbreak in Hawaii in —; epidemics are increasing in size and severity, especially in Asia and Latin America; factors in worsening situation include poor mosquito control, abundant mosquito breeding sites in growing tropical cities, travel of humans who carry the virus, and wide circulation of more than one serotype of virus.

Spread from person with acute infection by contact with blood, secretions, or other material. Repeated outbreaks with high mortality in sub-Saharan Africa; secondary spread of infection has occurred in health care settings and in households in Africa; reservoir for the virus not yet identified.

Zoonosis; rodent reservoir host; sporadic cases and outbreaks especially in North and South America; rise in reported human cases linked to factors that lead to expansion of rodent population e.

Zoonosis; 3 human cases in Australia in —; fruit bats may be reservoir host. Continued spread and rising rates of infection in some areas; emergence of resistant strains related to antiviral therapy; resistant strains can be transmitted; infected persons can be infected with second strain; HIV-associated immunosuppression contributes to increase in multiple other infections, including TB.

Major epizootics of influenza H5N1 in avian species in Hong Kong in and spread of avian virus to humans; millions of chickens killed to halt spread of infection to humans; virus infected multiple avian species; no or limited spread of H5N1 from human to human.

Zoonosis; several generations of person-to-person spread documented; outbreaks in central and western Africa; vaccination with vaccinia virus, which is protective, may have limited spread in the past; possible confusion with smallpox. Zoonosis; fruit bats are probable reservoir host; outbreaks in Malaysia started in , in areas with intensive pig farming and movement of pigs; large-scale culling of pigs was used to halt outbreaks.

Multiple large outbreaks, especially in institutions and shared environments, including nursing homes, schools, cruise ships; multiple modes of transmission, stability of virus in environment and low infectious dose favor transmission; recently emerged strain may be more transmissible.

Presumed via consumption of flesh from cattle with bovine spongiform encephalopathy BSE. First outbreak in U. in with epicenter in New York. Has subsequently spread through most of the U. and into Canada and Mexico; virus infects many species of birds and other animals; migratory birds have facilitated spread of virus.

Presumed zoonosis with rodent reservoir host; caused human deaths in California in Recent spread into some urban areas of Africa and South America; poor vector control; increase in urban tropical areas infested with mosquitoes competent to transmit virus increases risk of introduction by infected traveler; many at-risk populations not vaccinated with highly effective vaccine.

Despite the steadily increasing availability of new drugs against HIV, the management of drug-resistant HIV poses a serious worldwide challenge. Drugs that mitigate opportunistic infections have also encountered an increase in resistance, with a profound effect on the remaining life expectancy of HIV-infected individuals, as well as their quality of life.

Antimicrobial resistance may represent a more profound hindrance to TB prevention and control efforts than is the case with HIV, in that antituberculin drugs can cure the infected individual and also prevent subsequent infection of others. In more than 50 million cases of TB worldwide were resistant to one or more drugs WHO, a.

Developing countries in which TB is rampant often have limited laboratory resources to test for drug resistance. Individuals infected with drug-resistant strains, therefore, are often treated inappropriately, thus compounding the spread of MDR-TB.

As with the thwarting of efforts to control TB, drug-resistant malaria continues to expand and impair control efforts. Multiple drug-resistant strains of Plasmodium falciparum , the malaria with the highest fatality rate, are common in many parts of the world.

Resistance of P. vivax to certain antimalarials has also been described. The spread of resistance results from numerous factors, including incomplete courses of therapy, changes in vector and parasite biology, pharmacokinetics, and economics Bloland, The health challenges created by antimicrobial resistance extend far beyond the management of these three major killers.

For example, Staphylococcus aureus was the most common cause of nosocomial infections in the s Rubin et al. Methicillin or related drugs i. In , however, 15 percent of all S. aureus isolates were reported to be resistant to methicillin; in critical care units, 22 percent of all nosocomial S.

aureus isolates were methicillin-resistant Wenzel et al. CDC estimates that as many as 80, hospital patients are infected with methicillin-resistant S.

aureus MRSA each year in the United States. As of this writing , vancomycin remains the mainstay for treatment against staph infection. Yet extensive transfer of antimicrobial resistance can occur among MRSA pathogenic bacteria and normal flora residing in the human colon Shoemaker et al.

Since vancomycin resistance has been increasing substantially in enterococci Enterococcus faecium isolated from hospitalized patients, and vancomycin resistance is threatening to become a problem in S. aureus as resistant genes can be transferred to S.

aureus through horizontal spread. In , the first case of S. aureus infection with intermediate resistance to vancomycin was reported in Japan CDC, a ; the following year, the United States reported two additional cases CDC, b. In , the first case of vancomycin-resistant S.

aureus was isolated from a year-old Michigan resident with diabetes. This newly identified strain underscores the urgent need to prevent the spread of antimicrobial resistance through the appropriate and controlled use of antimicrobials, as well as the need to develop new classes of antibiotics CDC, d.

Although MRSA infections are much more likely to develop in hospitals and long-term care facilities than in the general healthy population, several recent deaths due to MRSA infection in previously healthy children show that the condition is now circulating outside of hospitals Groom et al.

Moreover, the incidence of MRSA in prison populations is unexpectedly high for non—health care settings CDC, b.

Public health officials recently reported a foodborne outbreak of community-acquired MRSA infection, which is believed to have been caused by a food handler who had recently been exposed to MRSA while visiting an elderly relative in a nursing home Jones et al.

A dramatic increase in resistance among community-acquired bacteria i. For example, evidence indicates a very clear relationship between erythromycin use and resistance among Group A streptococci; when erythromycin use is controlled, the prevalence of erythromycin-resistant isolates declines dramatically Seppala et al.

Resistance to penicillin among isolates of Streptococcus pneumoniae increased from 5 percent in Spika et al. Many penicillin-resistant pneumococci are now resistant to multiple other drugs as well; for example, fluoroquinolone-resistant pneumococci emerged as recently as the late s Chen et al.

Over the past decade, several countries—including the United States Kilmarx et al. The regional surveillance program in the Western Pacific WHO Region documented increases in the proportion of quinolone-resistant gonococci in Hong Kong.

from 3. Quinolone-resistant gonococci are now highly common greater than 80 percent in most large cities in the Peoples Republic of China Su, More than 20 percent of gonococci in Hawaii are quinolone-resistant, and similar resistant organisms are being reported in California see Figure CDC, e.

The emergence of fluoroquinolone-resistant gonococci in the Pacific rim, Hawaii, and California is a particularly bad sign because of the historical trend for resistant gonococci to move from those areas across the United States.

No isolates with reduced susceptibility were identified for persons who were younger than 15 years. Solid bars indicate an age of 15 to 64 years, and open bars an age of 65 years or older.

Data on per capita fluoroquinolone prescriptions were obtained from through , and data on the frequency of pneumococci with decreased susceptibility to fluoroquinolones in each age group were obtained in and in through No isolates with reduced susceptibility were identified in or Reprinted with permission, from Chen et al.

Copyright Massachusetts Medical Society. A growing body of evidence supports the hypothesis that infectious agents cause or contribute to many chronic diseases and cancers previously thought to be caused by genetic, environmental, or lifestyle factors see Table Cassell, ; Pisani et al.

Specific microbes claimed to be associated with chronic conditions may be cofactors with other microbes or other etiologic factors in the disease, sometimes being necessary but perhaps not sufficient elements in the causation pathway. The era of molecular biology and intensive research efforts in the field of AIDS have led to powerful advances in technology for the sensitive detection of infectious agents.

These diagnostic tools, plus the realization that organisms of otherwise unimpressive virulence can produce slowly progressive chronic disease with a wide spectrum of clinical manifestations and disease outcomes, have resulted in the discovery of new infectious agents and new concepts in the understanding of infectious diseases.

SOURCES: Campbell et al. Cases in point are the proof that many stomach ulcers are due to the bacterium Helicobacter pylori Parsonnet, ; Marshall, ; Moller et al. Recent data obtained in humans and animal models also suggest that mycoplasmas may cause some cases of chronic lung disease in newborns Cassell et al.

It has been estimated that more than 15 percent of cancers— including more than 50 percent of stomach and cervical cancers and 80 percent of liver cancers—could be avoided by preventing the associated infectious diseases WHO, Findings such as these raise the possibility that other chronic conditions may also have infectious etiologies.

Many of these culprit microbial agents are potentially treatable with existing antibiotics Cassell, , and they may even be vaccine preventable.

For example, the realization that H. pylori causes ulcers revolutionized ulcer treatment. In addition to its causal role in the development of peptic ulcers and gastritis, H.

pylori appears to play a role as well in the development of gastric maltomas i. pylori infection has been shown to result in tumor regression Wotherspoon et al.

The basic biology of those organisms implicated in chronic diseases and cancer is relatively obscure. Given that many of these diseases are among the most common in the world, a substantial.

Major advances could be made through the application of functional genomics and integrative biological technologies. Whereas a number of infectious agents—including herpes simplex virus HSV and cytomegalovirus CMV —have been implicated as causal agents of cardiovascular disease, Chlamydiae pneumoniae has been identified most frequently as a causal infectious agent Saikku et al.

pneumoniae is better known for its causal role in community-acquired pneumonia; an estimated 26 percent of all community-acquired pneumonia cases in patients over 65 years of age are due to chlamydial infection Gant and Parton, pneumoniae infections are usually mild or asymptomatic, but they can be severe, especially in the elderly Peeling and Brunham, Prevalence rates of C.

pneumoniae antibodies increase from about 50 percent in young adults to 75 percent in the elderly, suggesting that most individuals are infected and reinfected with the bacterium throughout their lives Kenny and Kuo, Compelling evidence of a link between C.

pneumoniae and heart disease has been accumulating from a variety of sources, including polymerase chain reaction PCR , immunocytochemical ICC staining, and electron microscopy studies Campbell et al. Seroepidemiologic studies have revealed consistent associations between C.

pneumoniae antibodies and both coronary heart and cerebrovascular disease, independent of other artherosclerosis risk factors i. Insofar as infection does predispose to the development of atherosclerosis, the risk of coronary artery disease is related to the aggregate number of potentially atherogenic pathogens to which an individual has been exposed Epstein et al.

In addition, infectious agents lead to an increase in other factors, such as C-reactive protein, that may play a causal role in atherosclerosis. Cervical cancer is one of the most common malignant diseases of women.

heavy metals, biocides , even though ports have facilities for the collection of wastes and for pollution control. Additionally, they receive nutrient inputs, either directly due to harbour activities or through discharges of rivers and sewage effluents such as VH in Hong Kong Zhang et al.

Harbour seawater and sediments have been shown to hold particular bacterial communities, different from those in adjacent areas, highly diverse and highly variable at the temporal scale Schauer et al. Despite chemical pollution, the effect of nutrient enrichment seems to be the most important factor driving the composition of bacterioplankton in harbours, and for example nutrient enrichment might explain the high abundance of sequences related to Clostridium and Vibrio in the sediments of Milazzo Harbour, subjected to high organic load Yakimov et al.

Relationships between bacterioplankton community composition and hydrocarbon pollution were only found in the study conducted in Messina Harbour, where the relative abundance of putative hydrocarbon-degrading bacteria correlated with an increase in hydrocarbons Denaro et al.

In sediments, stimulation of hydrocarbon degraders has been observed after hydrocarbon addition, indicating that there is a primed microbial community able to use these pollutants, both aerobically and anaerobically Hayes et al. As in other hydrocarbon-polluted sediments, SRB seem to be involved in hydrocarbon degradation in harbour sediments.

For example, a recent study on the composition of the active sulphate-reducing assemblages in sediments of Boston Harbour by analysing transcripts mRNAs of dsrAB genes Chin et al. Several studies have addressed the composition of bacterial communities in marine sediments polluted with heavy metals.

As in the case of other pollutants, bacterial communities in sediments with different levels of heavy-metal pollution are shown to differ Gillan et al. The same result has been observed for archaeal and photosynthetic communities Toes et al. Different from the cases of nutrient or hydrocarbon pollution, which seem to stimulate bacterial growth, total prokaryotic cell numbers appear to be negatively correlated with heavy metals such as cadmium, copper, zinc and lead Gillan et al.

However, when the calculations were done for particular phylogenetic groups, few statistically significant correlations could be established, and they seemed to be dependent on the sample.

Therefore, it is difficult to determine the effect of heavy metal on particular groups of microorganisms with the data available so far. In highly polluted sediments of a Norwegian fjord, the abundance of Gammaproteobacteria determined by FISH counts was negatively correlated with copper and zinc, and that of Bacteroidetes with copper, zinc and cadmium.

In contrast, in Belgian sediments with lower pollution levels, the only significant correlation was found between Bacteroidetes and cadmium Gillan et al. In these two sediments, bacterial community composition was also analysed by a cloning and sequencing approach.

The results evidenced the presence of the main groups typically found in marine sediments: Gamma - and Deltaproteobacteria and Bacteroidetes. But some of the clones in the Norwegian sediment grouped with clones from an Antarctic sediment polluted with heavy metals and hydrocarbons, and a group of gammaproteobacterial sequences was found in both the Norwegian and the Belgian sediments Gillan et al.

This might indicate that certain bacterial populations might be favoured in heavy-metal-polluted sediments, although these relationships are even more difficult to draw than in the case of hydrocarbon pollution.

A laboratory experiment was performed in microcosms to simulate the effect of sediment disturbance dredging in a sediment chronically polluted with heavy metals.

In addition, the effect of deposition of a 3 mm layer of polluted sediment on the surface of unpolluted sandy sediments was also analysed Toes et al. These two practices dredging and deposition onto a different location are common in the marine environment. Homogenization of the polluted sediment simulating dredging caused minor changes in the composition of microbial communities.

However, overlying of sandy sediments with polluted sediment caused significant changes in the composition in the three microbial components analysed Bacteria , Archaea and Cyanobacteria in comparison with the unpolluted control, although the effect was lower for Archaea Toes et al.

After one year of incubation, some common bacterial groups were observed in clone libraries from the artificially polluted sandy sediments in comparison with those from the chronically polluted sediment: representatives of the Roseobacter clade, the genus Vibrio and a member of the Flavobacteriaceae whose sequence was related to a clone from a heavy-metal-polluted Antarctic sediment Toes et al.

These sequences might represent microorganisms favoured by the conditions imposed by heavy-metal pollution, although to confirm this, it will be necessary to corroborate their absence or lower abundance in control, unpolluted sediments. In the environment, removal of sediments polluted with mercury, PCBs and PAHs in a location in the Baltic Sea resulted in the development of significantly different bacterial communities.

Summarizing the studies presented on chemical and heavy-metal pollution, we can conclude that, as in the case of nutrient enrichment, this type of perturbation again alters the composition of microbial communities Fig. But because this type of pollution selects for those microorganisms that are capable of degrading or chemically transforming the pollutants, and sometimes these organisms belong to particular phylogenetic groups, the studies conducted so far can point to particular types of bacteria i.

oligotrophic marine hydrocarbon-degrading Gammaproteobacteria , Actinobacteria , Sphingomonaceae or certain SRB phylotypes likely to be contributing to alleviate the problem of chemical pollution in the environment.

However, in many cases, these is only indirect evidence that does not fill the gap in knowledge on fundamental aspects of the functionality of microbial communities in chemically polluted environments. For example, novel or unrecognized microbial genera might be involved in the degradation of contaminants, most likely through metabolic cooperation with other microorganisms using degradation intermediates.

Microorganisms as such, i. forming part of degradation networks, will not be isolated as typical pollutant degraders and therefore escape our knowledge, although they are probably key players in the environment.

Other fundamental aspects, such as how pollution affects bacterial production rates, respiration rates or other microbial processes have not been analysed in chemically polluted environments, in contrast to what has been done in nutrient-enriched environments.

The broad use of high amounts of antibiotics in intensive farming to prevent or treat animal infections is also causing environmental concern see review Cabello et al. The bactericidal action of antibiotics can cause changes in the composition of natural microbial communities by selectively inhibiting susceptible bacteria.

Besides, exposure of natural communities to antibiotics might lead to the selection of resistant bacteria, which can then transfer their resistance determinants to opportunistic pathogenic bacteria in the environment.

In relation to the marine environment, there are numerous data coming from aquaculture, where administration of high amounts of a variety of antibiotics in fish farms for prophylactic or therapeutic reasons is routinely done Cabello, ; Sapkota et al. Antibiotic treatment in fish farms leads to increased concentrations of these compounds in water and sediments below the cages as well as in the fish stock produced.

As a result, there is a positive selection for antibiotic-resistant bacteria in water and sediments from fish cages, surrounding areas and among fish-associated bacteria Chelossi et al.

Often, the isolation of multiresistant bacteria i. bacteria resistant to several antibiotics is reported. This is in agreement with the simultaneous use of several types of antibiotics in fish farms Dang et al. Antibiotic-resistant bacteria isolated from fish-farm water and sediments are diverse.

Although most of them belong to the Gammaproteobacteria genera Vibrio , Photobacterium , Pseudomonas , Pseudoalteromonas , Alteromonas , Citrobacter , Salmonella , isolates from the Alphaproteobacteria , Firmicutes , Actinobacteria and Bacteroidetes have also been reported Furushita et al.

The presence of antibiotic-resistance genes in these isolates, as well as the ability of some of the isolates for transferring the resistance genes by conjugation to Escherichia coli recipient strains, have been demonstrated Rhodes et al.

Besides, closely related plasmids of the IncU group, carrying oxytetracycline-resistance determinants, have been found in isolates from hospitals in the UK and Germany and from fish-farm environments, demonstrating that plasmid transfer might occur between natural bacteria and potential human pathogens Rhodes et al.

Instead of isolating antibiotic-resistant bacteria, Hargrave et al. They measured profiles of resistance to the antibiotic oxytetracycline, widely used in aquaculture, in mixed bacterial communities from sediments around salmon aquaculture farms and in feed pellets which were proposed as the source of antibiotics.

Usually, numbers were higher in surface sediments but resistance levels were still high at intermediate depths, which mean that sediments around fish farms can constitute reservoirs for antibiotic-resistant bacteria in the marine environment Hargrave et al.

It is important to recognize that fish farms are not the only source of antibiotics in the marine environment. Thus, oxytetracycline-resistant bacteria are present in surface seawater and sediments receiving the input of sewage treatment plants, as demonstrated in Jiaozhou Bay in China and Halifax Harbour in Canada Dang et al.

The study conducted in the area of VH, where discharges of Anthropogenic use of coastal areas i. beaches also seems to have an effect on the natural abundance of antibiotic-resistant bacteria.

Studies performed in sand from beaches of the Southern Baltic Sea coast showed that bacteria isolated from a recreational beach had higher resistance to antibiotics from different chemical families than those in nonrecreational areas Mudryk, ; Mudryk et al. The level of multiresistance resistance to several antibiotics was also higher among isolates from the recreational beach.

The examples presented here provide evidence of the potential health risk derived from antibiotic contamination in the marine environment because they demonstrate the selection and enrichment of multiresistant bacteria. Some of them might be potential human pathogens i.

Vibrio , Pseudomonas , Salmonella or might potentially transfer genetic determinants of resistance to pathogenic bacteria. But none of these studies have addressed how antibiotics alter the composition and functionality of microbial communities in marine environments.

Given the magnitude and worldwide extension of the problem of antibiotic pollution, it is imperative to design carefully environmental and laboratory studies to address this issue, to determine which microbial groups are affected by the presence of antibiotics in the water and how antibiotics alter the functionality of microbial communities, both in water and in sediments.

Several of the uses of coastal resources have the risk of introducing potential human pathogenic bacteria, as shown in Table 1. The highest risk is derived from direct sewage discharges, which are a source of human faecal bacteria.

Therefore, sewage treatment and routine controls for faecal indicators coliforms, E. coli , enterococci in seawater in areas dedicated to bathing are usual procedures in developed countries Stewart et al. However, sewage discharge is not the only source of faecal bacteria in marine environments.

Other human-derived sources of potential pathogens are runoff from land urban and agricultural areas , leaking septic tanks, sewer overflows, discharges from boats, etc.

Stewart et al. Sources of faecal bacteria other than human i. birds, pets, wildlife, etc. should not be disregarded Choi et al. A recent publication has presented a novel and interesting approach to assess faecal pollution in coastal watersheds using community-based indicators Wu et al. Using PhyloChip, a phylogenetic microarray, these authors identified operational taxonomic units OTUs characteristic of faecal samples mainly belonging to the phyla Firmicutes , Proteobacteria , Bacteroidetes and Actinobacteria which were designated as faecal subsample associated OTUs FSAO.

By analysing the similarity of bacterial communities in several environmental samples from two watersheds in Santa Barbara CA to FSAO, they could identify the samples exposed to faecal sources.

The results obtained agree with traditional culture methods for the detection of faecal bacteria. In addition, they proposed a new community-based indicator to assess ecosystem health, based in the ratio of relative richness of three bacterial classes: Bacilli , Bacteroidetes and Clostridia to that of the Alphaproteobacteria BBC: A.

This ratio is higher in faecal and sewage samples and lower in samples not impacted by faecal material Wu et al. Approaches like this represent an important step forward in the analysis of faecal contamination in coastal areas because it is based in powerful molecular methods, and in the assessment of whole communities instead of using a few two or three indicator bacteria.

Faecal material is also a source of human pathogenic enteric viruses. Viruses from faecal origin belong to the families Adenoviridae adenovirus , Caliciviridae i. Norwalk virus , Picornaviridae i. poliovirus, hepatitis A and Reoviridae reoviruses and rotaviruses.

These viruses cause a variety of diseases in humans, either by direct exposure to water or after ingestion of contaminated seafood Griffin et al.

Viruses are shown to persist better in the environment than the bacterial indicators used for water quality monitoring Griffin et al. Apart from causing diseases in human and other marine mammals, epidemic viral infections can cause significant economic losses in aquaculture plants for commercial production of fish and shellfish Lang et al.

In addition to discharges of faecal material, other human activities such as bathing constitute a source of potential microbial contamination. For example, enterococci and Staphylococcus aureus are transferred directly from the skin of bathers in high loads into seawater 3—6 × 10 5 and 6.

These results highlight the importance of nonenteric bacteria as potential pathogens in the environment Stewart et al. Besides the health risk posed by allochthonous microorganisms from faecal or other origin, there are several potential human pathogenic species that are indigenous to marine and estuarine environments, such as Vibrio cholerae , Vibrio vulnificus and Vibrio parahaemolyticus Thompson et al.

The first two species, V. chlolerae and V. vulnificus , can cause severe, fatal diseases. In contrast, V. parahaemolyticus infections are usually not life-threatening but they are very common worldwide, mainly due to the consumption of contaminated seafood Collins et al.

These opportunistic pathogenic bacteria have a variety of virulence factors such as haemolysins V. vulnificus and V. parahaemolyticus , toxins cholera toxin , colonization factors, etc.

Thompson et al. The presence of pathogenicity-associated genes from V. cholerae and V. parahameolyticus has been proven in environmental isolates from different Vibrio spp.

In the marine environment, vibrios are usually associated to surfaces and establish symbiotic relationships with phyto- and zooplankton i. copepods , which might constitute vectors for disease transmission and for the development of disease outbreaks Lipp et al. Therefore, conditions favouring the development of phytoplankton blooms, such as in eutrophicated environments, might favour the development of vibrios.

In fact, as mentioned previously in this review, Vibrionaceae have been found in nutrient-rich environments Yakimov et al. In addition, vibrios proliferate at higher water temperatures and have a wide tolerance range to salinity, being able to survive well in low-salinity brackish water.

Therefore, their incidence is expected to increase in a scenario of global climate change. Different marine dinoflagellates Dinophysis spp. brevis and Gambierdiscus toxicus and a diatom Pseudonitzschia produce toxins with a variety of neurologic, gastrointestinal, respiratory and irritating effects.

Disease is usually caused by consumption of contaminated fish or shellfish, although aerosol inhalation and direct eye or skin exposure can also cause problems. Environmental perturbations derived from human activities that might have an effect in the increased incidence of harmful algal blooms are multiple and include: nutrient enrichment eutrophication , particularly in coastal waters; destruction of coastline due to coastal exploitation i.

Potential pathogens might be disseminated in the marine environment due to long-distance transport and discharge of ship ballast water used for ship stability and trim. For example, ballast water has been shown to contain epidemic-causing serotypes of V.

coli including strain O , Enterococcus spp. Concerns of the danger of ballast water discharges, not only for the spread of microbial pathogens but also of invasive species, have resulted in the establishment of guidelines for ballast water management and the promulgation of the International Convention for the Control and Management of Ship's Ballast Water and Sediments in by the International Maritime Organization.

These numbers are highly variable and depend on many factors such as the source region of the boat, season of the year and ballast-water management, i. whether or not there had been open-ocean exchange of water Drake et al. The changes in the microbial component of ballast water during a transoceanic voyage in tanks with and without open-ocean exchange have been studied by quantifying bacterial and viral numbers Drake et al.

The results showed that containment of ballast water in boat tanks led to a decrease in the bacterial and viral load in comparison with the initial water, irrespective of performing open-ocean exchange or not Drake et al. Bacterial communities in ballast water initially resemble those of the source seawater, which is usually from a coastal location Tomaru et al.

This ballast water is replaced in the open ocean at some point during the voyage to reduce the risk of discharging invasive species in the reception port. The open-ocean water filling the tanks has a significantly different microbial composition Tomaru et al.

This means that allochthonous microorganisms from coastal regions are routinely discharged into the open ocean, and vice versa, open-ocean microorganisms are discharged into coastal regions. However, the microbial assemblages discharged in each case are different from those in the source water because there is a change in composition during the voyage within the time frame of days Tomaru et al.

A recent study analysed bacterial diversity in ballast water in a ship anchored in Xiamen Port, and compared it with that of the receiving harbour seawater Ma et al. The source of the ballast water was Singapore and it had been partially replaced with water from the South China Sea.

The analysis of the corresponding 16S rRNA gene clone libraries revealed that ballast water contained a less diverse bacterial community, with representatives of only two classes, Alpha - and Gammaproteobacteria.

There was no evidence of the presence of pathogenic bacteria. Within these two groups, the phylotypes retrieved in ballast water were different from those in Xiamen Harbour seawater Ma et al. Thus, wherever it is done, the discharge of ballast water might potentially alter, at least transiently, the autochthonous microbial composition of the discharge site.

Whether this is significant or not has not been determined. If an open-ocean exchange is performed, we can expect that most of the coastal microorganisms will not be able to compete with the autochthonous bacteria in the more oligotrophic open ocean, and the opposite, i.

oligotrophic bacteria from the open ocean will not survive in coastal regions. Results from metagenomic studies show that microbial communities with dissimilar genomic composition i. genetic repertoire develop in different marine locations or at different depths DeLong et al.

Therefore, the success of an invasive microorganism, potentially dangerous such as a pathogen, would depend on the size of the inoculum, its capability to survive in the new environment and its competitive ability in facing a microbial community adapted to the conditions at the site of discharge.

As reported by Halpern et al. Thus, the interest in studying the effect of processes such as increase of seawater temperature and ocean acidification is increasing rapidly in the last years. No particular studies have been done targeting the microbial compartment but the information gathered so far provides clues on how microbial communities could be affected.

Anthropogenic activities such as the burning of fossil fuels, deforestation, industrialization and cement production are causing increased levels of atmospheric carbon dioxide CO 2 and, consequently, an increase in dissolved CO 2 in the oceans.

The acidification of the oceans will be detrimental for calcifying organisms and will cause changes in species distribution and abundance, as well as in food-web dynamics and structure. The increase in dissolved CO 2 has an effect in the carbon cycle of the oceans but also in the cycles of the major nutrient elements: nitrogen, phosphorus, silicon and iron for a review, see Hutchings et al.

The information available indicates that three important processes in the nitrogen cycle might be affected. For example, nitrogen fixation is predicted to increase in a high-CO 2 ocean, based on the results of experiments done with nitrogen-fixing Trichodesmium and unicellular Cyanobacteria.

In contrast, a decrease in pH seems to reduce nitrification rates and the abundance of bacterial and archaeal nitrifiers in seawater Hutchings et al. Consequently, the fluxes of oxidized nitrogen species, such as nitrate, will be affected.

This in turn would have a negative effect on denitrification rates, although there can also be positive effects over this process due to the expansion of suboxic zones in the oceans.

An increase in the relative proportions of ammonium to nitrate due to decreased nitrification will cause a shift in the composition of primary producers, by favouring microbial components such as picocyanobacteria and nanoflagellates Hutchings et al.

On the other hand, global warming will lead to an increase in seawater temperatures and cause a stronger stratification of the oceans.

This will limit the fluxes of nutrients from sediments and the deep sea i. phosphorus, iron , and potentially intensify problems of hypoxia and anoxia. Changes in the climate system can also cause alterations in the abundance and global distribution i. spread from tropical areas to lower latitudes of pathogens such as Vibrio spp.

The abundance of V. cholerae , the causative agent of cholera epidemics, is already shown to follow climatic patterns Lipp et al. Higher water temperatures, together with increased nutrient levels, would also increase the frequency and severity of harmful algal blooms Moore et al.

Environmental changes due to anthropogenic activities seawater warming or increased CO 2 and nutrient supply are also suspected of being involved in the expansion of coral diseases worldwide, diseases in which microorganisms are important Sokolov et al.

In addition, strong rainfall events and flooding due to sea-level changes, both expected under a global change scenario, would result in an increase of estuarine and brackish low-salinity environments, which again would favour the growth of Vibrio spp.

Lipp et al. Moreover, floods may also cause problems of inefficient water sanitation and increase runoff from land, with the consequent increase in the risk of faecal bacterial and viral , nutrient and chemical contamination of the marine environment Kite-Powell et al.

The possibility of generating phytoplankton blooms by ocean fertilization with the aim of increasing the flux of organic matter towards the deep ocean causing carbon burial and alleviating problems of increasing CO 2 concentrations is catching the attention of companies for commercial exploitation.

This represents a new anthropogenic use of the marine environment. Several scientific experiments involving iron and phosphorous fertilization have been performed in order to test the premise that these nutrients were limiting primary production in different oceanic regions Thingstad et al.

However, based on the experience gathered on the functioning of marine ecosystems and the interplay of biogeochemical cycles, there is strong scientific criticism of the usefulness of ocean fertilization to sequester carbon, as well as concerns about the risks associated Secretariat of the Convention on Biological Diversity, In particular, the plans of the Australian company Ocean Nourishing Corporation to discharge urea in nitrogen-deficient areas of the ocean have been criticized on scientific grounds Glibert et al.

In this scenario, there will not be an increase in CO 2 sequestration and carbon burial, and in addition, undesired gases will be released into the atmosphere, aggravating the problem instead of alleviating it.

Worldwide marine ecosystems suffer from the impact caused by human activities. In view of the development of our societies and the increase in human population, the stress posed by humans to the marine environment will continue to increase. The microbial component of marine ecosystems has been neglected in many studies of anthropogenic impact.

Therefore, our knowledge on microbial communities of anthropogenically impacted environments lags far behind those involving higher organisms. Many studies report changes in prokaryotic numbers and a few have included measurements of microbial activity.

Changes in diversity have also been analysed, although in many cases, this has been done only by electrophoretic profiling methods.

As a result, we have a partial view on the composition of microbial communities in stressed environments. Therefore, there is a need for a better cataloguing of microbial diversity in anthropogenically stressed environments.

New technologies such as remote ocean-observing systems, metagenomics, metatranscriptomics and massive tag sequencing can help us to gain more information on these communities.

Thanks to the use of comparative studies of impacted and reference sites, we know that human impact causes significant changes in microbial community composition.

However, we are still unable to make predictions on how important this could be for the functioning of the ecosystems, particularly in the long term, especially if the stressor does not disappear or it is likely to increase.

For example, we know already that certain microbial groups are favoured in conditions of nutrient enrichment or chemical pollution, but most of this information is provided for broad phylogenetic groups i.

division, class and not for particular species or ecotypes. phylum, class, genera, species, etc. There is also a need for relating the changes in diversity to the metabolic processes, which are important for the functioning of the ecosystem.

Because of the complexity of marine ecosystems, these goals would need the combination of environmental observations as well as carefully designed microcosms or mesocosms experiments. In the context of global climate change, for which human activities can be blamed, microbial communities of human-stressed environments are of paramount importance, and therefore the study of their composition, dynamics and functioning is of the utmost relevance for the development of less destructive human practices or for alleviating problems already present in our environment.

The authors wish to thank Margarita Gomila for her comments on the manuscript. and J. are supported by PhD fellowships of MICINN. Ager D Evans S Li H Lilley AK van der Gast CJ Anthropogenic disturbance affects the structure of bacterial communities.

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Citation: Mylonakis E Frontiers in bacteriology: Challenges and opportunities. Received: 28 July ; Accepted: 22 August ; Published: 10 February Copyright © Mylonakis.

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