Emerging contaminants: A One Health perspective

Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.

Microbial defluorination of TFA, PFOA, and HFPO-DA by a native microbial consortium under anoxic conditions

In this study, the biodegradability of trifluoroacetate (TFA), perfluorooctanoic acid (PFOA), and perfluoro-2-methyl-3-oxahexanoic acid (HFPO-DA) by a native microbial community was evaluated over a 10-month incubation period. The observed microbial defluorination ratios and removal efficiency were 3.46 ( ± 2.73) % and 8.03 ( ± 3.03) %, 8.44 ( ± 1.88) % and 13.52 ( ± 4.96) %, 3.02 ( ± 0.62) % and 5.45 ( ± 2.99) % for TFA, PFOA and HFPO-DA, respectively. The biodegradation intermediate products, TFA and pentafluoropropionic acid (PFA), of PFOA and HFPO-DA were detected in their biodegradation treatment groups. Furthermore, the concentrations of the PFOA metabolites, perfluorohexanoic acid (PFHxA) and perfluoroheptanoic acid (PFHpA), in the aqueous solutions after incubation were quantified to be 0.21 and 4.14 µg/L. TFA, PFOA and HFPO-DA significantly reduced the microbial diversity and changed the structure of the community. The co-occurrence network analysis showed that low abundance species, such as Flexilinea flocculi, Bacteriovorax stolpii, and g_Sphingomonas, are positively correlated with the generation of fluoride ion, implying their potential collaborative functions contributing to the observed biodefluorination. The findings in this study can provide insights for the biodegradation of perfluoroalkyl carboxylic acids and their emerging alternatives by indigenous microorganisms in the environment.

Influence of shear stress on electroactive biofilm characteristics and performance in microbial fuel cells

This study has provided comprehensive insights into the intricate relationship between shear stress and the development, structure, and functionality of electroactive biofilms in Microbial Fuel Cells (MFCs). A multichannel microfluidic MFC reactors that created specific shear stress on the anode, were designed for the simultaneous study of multiple flow conditions using the same medium. Then, the evolution of the biofilm growth under different shear stress conditions (1, 5 and 10 mPa) were compared. The taxonomic and functional structure was studied by 16S rRNA gene and metagenomic sequencing and the physical biofilm characteristics were measured via fluorescence microscopy. The results demonstrate the pivotal role of shear stress in influencing the growth kinetics, electrical performance, and physical structure of anodic biofilms. Notably, the selection of specific EAB was observed to be shear stress-dependent, with a marked increase in specific EAB abundance as shear stress increased. The power density, while not directly correlated with the relative abundance of specific or nonspecific EAB, exhibited a strong linear relationship with biofilm coverage. This suggests that factors beyond the microbial composition, potentially including mass transport or electrochemical conditions, might be instrumental in determining electricity production. The functional metagenomic analysis further highlighted the complexities of extracellular electron transfer (EET) mechanisms in electroactive biofilm. While certain genes associated with EET in known species such as Geobacter and Shewanella were identified, the study also examined the limitations of solely relying on genetic markers to infer EET capabilities, emphasizing the need for complementary metaproteomic analyses. This study demonstrates the multifaceted impact of shear stress on electroactive biofilm and paves the way for future investigations aimed at harnessing the potential of electroactive biofilms in microbial fuel cell applications.

Influence of Hydrodynamic Forces on Electroactive Bacterial Adhesion in Microbial Fuel Cell Anodes

This investigation examined the role of shear stress on the dynamic development of microbial communities within anodic biofilms in single-chamber microbial fuel cells (MFCs). Bacterial attachment to surfaces, often regarded as a crucial step in biofilm formation, may significantly contribute to the selection of electroactive bacteria (EAB). It is well established that hydrodynamic forces, particularly shear forces, have a profound influence on bacterial adhesion. This study postulates that shear stress could select EAB on the anode during the adhesion phase by detaching non-EAB. To examine this hypothesis, MFC reactors equipped with a shear stress chamber were constructed, creating specific shear stress on the anode. The progression of adhesion under various shear stress conditions (1, 10, and 50 mPa) was compared with a control MFC lacking shear stress. The structure of the microbial community was assessed using 16S rRNA gene (rrs) sequencing, and the percentage of biofilm coverage was analyzed using fluorescence microscopy. The results indicate a significant impact of shear stress on the relative abundance of specific EAB, such as Geobacter, which was higher (up to 30%) under high shear stress than under low shear stress (1%). Furthermore, it was noted that shear stress decreased the percentage of biofilm coverage on the anodic surface, suggesting that the increase in the relative abundance of specific EAB occurs through the detachment of other bacteria. These results offer insights into bacterial competition during biofilm formation and propose that shear stress could be utilized to select specific EAB to enhance the electroactivity of anodic biofilms. However, additional investigations are warranted to further explore the effects of shear stress on mature biofilms.

Metaproteomic and Metagenomic-Coupled Approach to Investigate Microbial Response to Electrochemical Conditions in Microbial Fuel Cells

MFCs represent a promising sustainable biotechnology that enables the direct conversion of organic matter from wastewater into electricity using bacterial biofilms as biocatalysts. A crucial aspect of MFCs is how electroactive bacteria (EAB) behave and their associated mechanisms during extracellular electron transfer to the anode. A critical phase in the MFC start-up process is the initial colonization of the anode by EAB. Two MFCs were operated with an external resistance of 1000 ohms, one with an applied electrical voltage of 500 mV during the initial four days of biofilm formation and the other without any additional applied voltage. After stabilization of electricity production, total DNA and protein were extracted and sequenced from both setups. The combined metaproteomic/metagenomic analysis revealed that the application of voltage during the colonization step predominantly increased direct electron transfer via cytochrome c, mediated primarily by Geobacter sp. Conversely, the absence of applied voltage during colonization resulted in a broader diversity of bacteria, including Pseudomonas and Aeromonas, which participated in electricity production via mediated electron transfer involving flavin family members.

Snow Microorganisms Colonise Arctic Soils Following Snow Melt

Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.

Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.

Sub-inhibitory gentamicin pollution induces gentamicin resistance gene integration in class 1 integrons in the environment

Antibiotics at sub-inhibitory concentrations are often found in the environment. Here they could impose selective pressure on bacteria, leading to the selection and dissemination of antibiotic resistance, despite being under the inhibitory threshold. The goal of this study was to evaluate the effects of sub-inhibitory concentrations of gentamicin on environmental class 1 integron cassettes in natural river microbial communities. Gentamicin at sub-inhibitory concentrations promoted the integration and selection of gentamicin resistance genes (GmRG) in class 1 integrons after only a one-day exposure. Therefore, sub-inhibitory concentrations of gentamicin induced integron rearrangements, increasing the mobilization potential of gentamicin resistance genes and potentially increasing their dissemination in the environment. This study demonstrates the effects of antibiotics at sub-inhibitory concentrations in the environment and supports concerns about antibiotics as emerging pollutants.

Evolution and interaction of microbial communities in mangrove microbial fuel cells and first description of Shewanella fodinae as electroactive bacterium

Understanding exoelectrogenic bacteria mechanisms and their interactions in complex biofilm is critical for the development of microbial fuel cells (MFCs). In this article, assumptions concerning the benefits of the complex sediment microbial community for electricity production were explored with both the complex microbial community and isolates identified as Shewanella. Analysis of the microbial community revealed a strong influence of the sediment community on anodes and electrolytes compared to that of only water. Moreover, while Pelobacteraceae-related genera were dominant in our MFCs instead of Desulfuromonas and Geobacter as usually reported, the electroactive Shewanella algae and Shewanella fodinae were isolated and cultivated from the anodic biofilm. S. fodinae, described for the first time as an electroactive bacterium to the best of our knowledge, led to a maximal current density of 3.6 A/m² set as 0.3 V/SCE in a three-electrode set-up fed with lactate. S. algae, in a complex medium containing several available substrates, showed several preferential oxidative behaviors including a diauxic behavior. In pure culture and under our conditions, S. fodinae and S. algae were not able to use acetate as a sole electron donor. However, their presence in our acetate-fed MFCs and the adaptive behavior of S. algae hint a syntrophic interaction between the bacteria to optimize the use of the substrate in a complex environment.

Impact of in situ solar irradiation on snow bacterial communities and functional potential

Polar regions are increasingly exposed to ultraviolet light due to ozone depletion. Snowpacks contain photochemically-active particles that, when irradiated, can lead to the production and accumulation of reactive species that can induce oxidative stress on snow microorganisms. This could generate a selective pressure on snowpack bacteria. In this study, snow microcosms were buried in a snowpack at Ny-Ålesund (Svalbard), either exposed to solar irradiation or incubated in the dark for 10 days, and the bacterial response to solar irradiation was evaluated in situ using a metagenomics approach. Solar irradiation induced a significant decrease of bacterial abundance and richness. Genes involved in glutathione synthesis, sulfur metabolism and multidrug efflux were significantly enriched in the light, whereas genes related to cell wall assembly and nutrient uptake were more abundant in the dark. This is the first study demonstrating the response of snow bacterial communities to solar irradiation in situ and providing insights into the mechanisms involved. Our research shows that polar sun irradiation is sufficiently intense to impose a selective pressure on snow bacteria and supports the concern that increased ultraviolet exposure due to anthropogenic activities and climatic change could drive critical changes in the structure and functioning of snow bacterial communities.

Selection processes of Arctic seasonal glacier snowpack bacterial communities

BACKGROUND

Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.

METHODS

We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell's Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis.

RESULTS

While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers.

CONCLUSIONS

These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.

Environmental and Anthropogenic Factors Shape the Snow Microbiome and Antibiotic Resistome

Winter tourism can generate environmental pollution and affect microbial ecology in mountain ecosystems. This could stimulate the development of antibiotic resistance in snow and its dissemination through the atmosphere and through snow melting. Despite these potential impacts, the effect of winter tourism on the snow antibiotic resistome remains to be elucidated. In this study, snow samples subjected to different levels of anthropogenic activities and surrounding forest were obtained from the Sudety Mountains in Poland to evaluate the impact of winter tourism on snow bacteria using a metagenomic approach. Bacterial community composition was determined by the sequencing of the V3-V4 hypervariable region of the 16S rRNA gene and the composition of the antibiotic resistome was explored by metagenomic sequencing. Whereas environmental factors were the main drivers of bacterial community and antibiotic resistome composition in snow, winter tourism affected resistome composition in sites with similar environmental conditions. Several antibiotic resistance genes (ARGs) showed a higher abundance in sites subjected to human activities. This is the first study to show that anthropogenic activities may influence the antibiotic resistome in alpine snow. Our results highlight the need to survey antibiotic resistance development in anthropogenically polluted sites.

Gentamicin at sub-inhibitory concentrations selects for antibiotic resistance in the environment

Antibiotics released into the environment at low (sub-inhibitory) concentrations could select for antibiotic resistance that might disseminate to the human microbiome. In this case, low-level anthropogenic sources of antibiotics would have a significant impact on human health risk. In order to provide data necessary for the evaluation of this risk, we implemented river water microcosms at both sub-inhibitory and inhibitory concentrations of gentamicin as determined previously based on bacterial growth in enriched media. Using metagenomic sequencing and qPCR/RT-qPCR, we assessed the effects of gentamicin on water bacterial communities and their resistome. A change in the composition of total and active communities, as well as a gentamicin resistance gene selection identified via mobile genetic elements, was observed during a two-day exposure. We demonstrated the effects of sub-inhibitory concentrations of gentamicin on bacterial communities and their associated resistome in microcosms (simulating in situ conditions). In addition, we established relationships between antibiotic dose and the magnitude of the community response in the environment. The scope of resistance selection under sub-inhibitory concentrations of antibiotics and the mechanisms underlying this process might provide the basis for understanding resistance dispersion and associated risks in relatively low impacted ecosystems.

Effect of Contact Area and Shape of Anode Current Collectors on Bacterial Community Structure in Microbial Fuel Cells

Low electrical conductivity of carbon materials is a source of potential loss for large carbonaceous electrode surfaces of MFCs due to the long distance traveled by electrons to the collector. In this paper, different configurations of titanium current collectors were used to connect large surfaces of carbon cloth anodes. The current collectors had different distances and contact areas to the anode. For the same anode surface (490 cm²), increasing the contact area from 28 cm² to 70 cm² enhanced power output from 58 mW·m^-2 to 107 mW·m^-2. For the same contact area (28 cm²), decreasing the maximal distance of current collectors to anodes from 16.5 cm to 7.75 cm slightly increased power output from 50 mW·m^-2 to 58 mW·m^-2. Molecular biology characterization (qPCR and 16S rRNA gene sequencing) of anodic bacterial communities indicated that the Geobacter number was not correlated with power. Moreover, Geobacter and Desulfuromonas abundance increased with the drop in potential on the anode and with the presence of fermentative microorganisms. Electrochemical impedance spectroscopy (EIS) showed that biofilm resistance decreased with the abundance of electroactive bacteria. All these results showed that the electrical gradient arising from collectors shapes microbial communities. Consequently, current collectors influence the performance of carbon-based anodes for full-scale MFC applications.

Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery

Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the soil microbiome and its ecosystem function. In this study, we compared the effects of DNA extraction and sequencing depth on bacterial richness discovery from two soil samples. Four DNA extraction methods were used, and sequencing duplicates were generated for each DNA sample. The V3–V4 region of the 16S rRNA gene was sequenced to determine the taxonomical richness measured by each method at the amplicon sequence variant (ASV) level. Both the overall functional richness and antibiotic resistance gene (ARG) richness were evaluated by metagenomics sequencing. Despite variable DNA extraction methods, sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Sequencing duplicates from the same sample provided access to different portions of bacterial richness, and this was related to differences in the sequencing depth. Thus, the sequencing depth introduced biases in the comparison of DNA extraction methods. An optimisation of the soil metagenomics workflow is needed in order to sequence at a sufficient and equal depth. This would improve the accuracy of metagenomic comparisons and soil microbiome profiles.

Functional trait relationships demonstrate life strategies in terrestrial prokaryotes

Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche.

Aminoglycosides analysis optimization using ion pairing liquid chromatography coupled to tandem mass spectrometry and application on wastewater samples

Aminoglycosides are mostly used as veterinary antibiotics. In France, their consumption accounts for about 10% of all prescribed animal medicine. Due to their high polarity nature (log Kow < -3), they require chromatographic separation by hydrophilic interaction liquid chromatography or ion-pairing chromatography. This study presents the development of an ion pairing liquid chromatography with alkanesulfonates coupled to tandem mass spectrometry for the analysis of 10 aminoglycosides (spectinomycin, streptomycin, dihydrostreptomycin, kanamycin, apramycin, gentamicin, neomycin and sisomicin) in wastewater samples. The novelty of this method lies in the addition of the ion paring salt directly and only into the sample vial and not in the mobile phase, lowering the amount of salt added and consequently reducing signal inhibition. The optimized method was validated and showed satisfactory resolution, performances suitable with the analysis of aminoglycosides in wastewater samples, with limits of quantifications less than 10 ng/mL for most of the compounds, low matrix effects, high accuracy (85%-115% recoveries) and reproducibility (2%-12%RSD). It was then applied successfully to raw and treated wastewater samples.

Gentamicin Adsorption onto Soil Particles Prevents Overall Short-Term Effects on the Soil Microbiome and Resistome

Antibiotics used in agriculture may reach the environment and stimulate the development and dissemination of antibiotic resistance in the soil microbiome. However, the scope of this phenomenon and the link to soil properties needs to be elucidated. This study compared the short-term effects of a range of gentamicin concentrations on the microbiome and resistome of bacterial enrichments and microcosms of an agricultural soil using a metagenomic approach. Gentamicin impact on bacterial biomass was roughly estimated by the number of 16SrRNA gene copies. In addition, the soil microbiome and resistome response to gentamicin pollution was evaluated by 16SrRNA gene and metagenomic sequencing, respectively. Finally, gentamicin bioavailability in soil was determined. While gentamicin pollution at the scale of µg/g strongly influenced the bacterial communities in soil enrichments, concentrations up to 1 mg/g were strongly adsorbed onto soil particles and did not cause significant changes in the microbiome and resistome of soil microcosms. This study demonstrates the differences between the response of bacterial communities to antibiotic pollution in enriched media and in their environmental matrix, and exposes the limitations of culture-based studies in antibiotic-resistance surveillance. Furthermore, establishing links between the effects of antibiotic pollution and soil properties is needed.

MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data

Niche is a fundamental concept in ecology. It integrates the sum of biotic and abiotic environmental requirements that determines a taxon's distribution. Microbiologists currently lack quantitative approaches to address niche-related hypotheses. We tested four approaches for the quantification of niche breadth and overlap of taxa in amplicon sequencing datasets, with the goal of determining generalists, specialists and environmental-dependent distributions of community members. We applied these indices to in silico training datasets first, and then to real human gut and desert biological soil crust (biocrust) case studies, assessing the agreement of the indices with previous findings. Implementation of each approach successfully identified a priori conditions within in silico training data, and we found that by including a limit of quantification based on species rank, one could identify taxa falsely classified as specialists because of their low, sparse counts. Analysis of the human gut study offered quantitative support for Bacilli, Gammaproteobacteria and Fusobacteria specialists enriched after bariatric surgery. We could quantitatively characterise differential niche distributions of cyanobacterial taxa with respect to precipitation gradients in biocrusts. We conclude that these approaches, made publicly available as an R package (MicroNiche), represent useful tools to assess microbial environment-taxon and taxon-taxon relationships in a quantitative manner.

Over Winter Microbial Processes in a Svalbard Snow Pack: An Experimental Approach

Snow packs cover large expanses of Earth’s land surface, making them integral components of the cryosphere in terms of past climate and atmospheric proxies, surface albedo regulators, insulators for other Arctic environments and habitats for diverse microbial communities such as algae, bacteria and fungi. Yet, most of our current understanding of snow pack environments, specifically microbial activity and community interaction, is limited to the main microbial growing season during spring ablation. At present, little is known about microbial activity and its influence on nutrient cycling during the subfreezing temperatures and 24-h darkness of the polar winter. Here, we examined microbial dynamics in a simulated cold (−5°C), dark snow pack to determine polar winter season microbial activity and its dependence on critical nutrients. Snow collected from Ny-Ålesund, Svalbard was incubated in the dark over a 5-week period with four different nutrient additions, including glacial mineral particles, dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP) and a combined treatment of DIN plus DIP. Data indicate a consumption of dissolved inorganic nutrients, particularly DIN, by heterotrophic communities, suggesting a potential nitrogen limitation, contradictory to phosphorus limitations found in most aquatic environments. 16S amplicon sequencing also reveal a clear difference in microbial community composition in the particulate mineral treatment compared to dissolved nutrient treatments and controls, suggesting that certain species of heterotrophs living within the snow pack are more likely to associate with particulates. Particulate phosphorus analyses indicate a potential ability of heterotrophic communities to access particulate sources of phosphorous, possibly explaining the lack of phosphorus limitation. These findings have importance for understanding microbial activity during the polar winter season and its potential influences on the abundance and bioavailability of nutrients released to surface ice and downstream environments during the ablation season.

Seasonal shift in airborne microbial communities

Microorganisms are ubiquitous in the atmosphere. Global investigations on the geographical and temporal distribution of airborne microbial communities are critical for identifying the sources and the factors shaping airborne communities. At mid-latitude sites, a seasonal shift in both the concentration and diversity of airborne microbial communities has been systematically observed in the planetary boundary layer. While the factors suspected of affecting this seasonal change were hypothesized (e.g., changes in the surface conditions, meteorological parameters and global air circulation), our understanding on how these factors influence the temporal variation of airborne microbial communities, especially at the microbial taxon level, remains limited. Here, we investigated the distribution of both airborne bacterial and fungal communities on a weekly basis over more than one year at the mid-latitude and continental site of puy de Dôme (France; +1465 m altitude above sea level). The seasonal shift in microbial community structure was likely correlated to the seasonal changes in the characteristics of puy de Dôme's landscape (croplands and natural vegetation). The airborne microbial taxa that were the most affected by seasonal changes trended differently throughout the seasons in relation with their trophic mode. In addition, the windy and variable local meteorological conditions found at puy de Dôme were likely responsible for the intraseasonal variability observed in the composition of airborne microbial communities.

Retrospective on microbial transformations of halogenated organics

Prior to the 1960s, knowledge of biological transformations of highly halogenated aliphatic compounds was limited, except in mammalian organisms where enzymatic transformations occurred to rid the body of ingested harmful chemicals. Limited abiotic transformation of such compounds had also been observed, with half-lives varying from days to centuries. Commonly believed was that aerobic transformation might occur by cometabolism rather than to conserve energy for respiration, while anaerobic transformations were in general thought not to occur. However, in the late 1960s anaerobic transformation of chlorinated pesticides was noted, and then in the early 1980s, partial microbial dehalogenation of chlorinated solvents such as tetrachlorethene, trichloroethene, trichlorethane, and carbon tetrachloride was also found to occur. With only partial dechlorination, complete detoxification was not achieved. And at the time, dehalogenation reactions were not believed to yield energy for growth to the degrading microorganisms. However, in the 1990s bacteria began to be found that obtain energy from anaerobic transformations, often enabling complete dechlorination and detoxification. Since then such ability has been found among several bacterial species, many of which use molecular hydrogen as a donor substrate and halogenated organics as electron acceptors, thus conserving energy through reductive dehalogenation. Growth of knowledge in this field has grown rapidly since the 1960s. Broad usages of such microorganisms are now underway to rid contaminated groundwater of hazardous halogenated chemicals.

Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow?

The effect of nutrients on microbial interactions, including competition and collaboration, has mainly been studied in laboratories, but their potential application to complex ecosystems is unknown. Here, we examined the effect of changes in organic acids among other parameters on snow microbial communities in situ over 2 months. We compared snow bacterial communities from a low organic acid content period to that from a higher organic acid period. We hypothesized that an increase in organic acids would shift the dominant microbial interaction from collaboration to competition. To evaluate microbial interactions, we built taxonomic co-variance networks from OTUs obtained from 16S rRNA gene sequencing. In addition, we tracked marker genes of microbial cooperation (plasmid backbone genes) and competition (antibiotic resistance genes) across both sampling periods in metagenomes and metatranscriptomes. Our results showed a decrease in the average connectivity of the network during late spring compared to the early spring that we interpreted as a decrease of cooperation. This observation was strengthened by the significantly more abundant plasmid backbone genes in the metagenomes from the early spring. The modularity of the network from the late spring was also found to be higher than the one from the early spring, which is another possible indicator of increased competition. Antibiotic resistance genes were significantly more abundant in the late spring metagenomes. In addition, antibiotic resistance genes were also positively correlated to the organic acid concentration of the snow across both seasons. Snow organic acid content might be responsible for this change in bacterial interactions in the Arctic snow community.

Global airborne microbial communities controlled by surrounding landscapes and wind conditions

The atmosphere is an important route for transporting and disseminating microorganisms over short and long distances. Understanding how microorganisms are distributed in the atmosphere is critical due to their role in public health, meteorology and atmospheric chemistry. In order to determine the dominant processes that structure airborne microbial communities, we investigated the diversity and abundance of both bacteria and fungi from the PM10 particle size (particulate matter of 10 micrometers or less in diameter) as well as particulate matter chemistry and local meteorological characteristics over time at nine different meteorological stations around the world. The bacterial genera Bacillus and Sphingomonas as well as the fungal species Pseudotaeniolina globaosa and Cladophialophora proteae were the most abundant taxa of the dataset, although their relative abundances varied greatly based on sampling site. Bacterial and fungal concentration was the highest at the high-altitude and semi-arid plateau of Namco (China; 3.56 × 10⁶ ± 3.01 × 10⁶ cells/m³) and at the high-altitude and vegetated mountain peak Storm-Peak (Colorado, USA; 8.78 × 10⁴ ± 6.49 × 10⁴ cells/m³), respectively. Surrounding ecosystems, especially within a 50 km perimeter of our sampling stations, were the main contributors to the composition of airborne microbial communities. Temporal stability in the composition of airborne microbial communities was mainly explained by the diversity and evenness of the surrounding landscapes and the wind direction variability over time. Airborne microbial communities appear to be the result of large inputs from nearby sources with possible low and diluted inputs from distant sources.

Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima

Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.

Sources and selection of snow-specific microbial communities in a Greenlandic sea ice snow cover

Sea ice and its snow cover are critical for global processes including climate regulation and biogeochemical cycles. Despite an increase in studies focused on snow microorganisms, the ecology of snow inhabitants remains unclear. In this study, we investigated sources and selection of a snowpack-specific microbial community by comparing metagenomes from samples collected in a Greenlandic fjord within a vertical profile including atmosphere, snowpack with four distinct layers of snow, sea ice brine and seawater. Microbial communities in all snow layers derived from mixed sources, both marine and terrestrial, and were more similar to atmospheric communities than to sea ice or seawater communities. The surface snow metagenomes were characterized by the occurrence of genes involved in photochemical stress resistance, primary production and metabolism of diverse carbon sources. The basal saline snow layer that was in direct contact with the sea ice surface harbored a higher abundance of cells than the overlying snow layers, with a predominance of Alteromonadales and a higher relative abundance of marine representatives. However, the overall taxonomic structure of the saline layer was more similar to that of other snow layers and the atmosphere than to underlying sea ice and seawater. The expulsion of relatively nutrient-rich sea ice brine into basal snow might have stimulated the growth of copiotrophic psychro- and halotolerant snow members. Our study indicates that the size, composition and function of snowpack microbial communities over sea ice were influenced primarily by atmospheric deposition and inflow of sea ice brine and that they form a snow-specific assemblage reflecting the particular environmental conditions of the snowpack habitat.

Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH

Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide the complete sequence of the complex and plastic genome of the canonical chlorophenoxy herbicide-degrading Sphingobium herbicidovorans MH. The genome has an intricate organization of the chlorophenoxy-herbicide catabolic genes sdpA, rdpA, and cadABCD that encode the (R)- and (S)-enantiomer-specific 2,4-dichlorophenoxypropionate dioxygenases and four subunits of a Rieske non-heme iron oxygenase involved in 2-methyl-chlorophenoxyacetic acid degradation, respectively. Several major genomic rearrangements are proposed to help understand the evolution and mobility of these important genes and their genetic context. Single-strain mobilomic sequence analysis uncovered plasmids and insertion sequence-associated circular intermediates in this environmentally important bacterium and enabled the description of evolutionary models for pesticide degradation in strain MH and related organisms. The mobilome presented a complex mosaic of mobile genetic elements including four plasmids and several circular intermediate DNA molecules of insertion-sequence elements and transposons that are central to the evolution of xenobiotics degradation. Furthermore, two individual chromosomally integrated prophages were shown to excise and form free circular DNA molecules. This approach holds great potential for improving the understanding of genome plasticity, evolution, and microbial ecology.

Combined iron and sulfate reduction biostimulation as a novel approach to enhance BTEX and PAH source-zone biodegradation in biodiesel blend-contaminated groundwater

The use of biodiesel as a transportation fuel and its growing mandatory blending percentage in diesel increase the likelihood of contaminating groundwater with diesel/biodiesel blends. A 100L-field experiment with B20 (20% biodiesel and 80% diesel, v/v) was conducted to assess the potential for the combined biostimulation of iron and sulfate reducing bacteria to enhance BTEX and PAH biodegradation in a diesel/biodiesel blend-contaminated groundwater. A B20 field experiment under monitored natural attenuation (MNA) was used as a baseline control. Ammonium acetate and a low-cost and sustainable product recovered from acid mine drainage treatment were used to stimulate iron and sulfate-reducing conditions. As a result, benzene and naphthalene concentrations (maximum concentrations were 28.1μgL^-1 and 10.0μgL^-1, respectively) remained lower than the MNA experiment (maximum concentrations were 974.7μgL^-1 and 121.3μgL^-1, respectively) over the whole experiment. Geochemical changes were chronologically consistent with the temporal change of the predominance of Geobacter and GOUTA19 which might be the key players responsible for the rapid attenuation of benzene and naphthalene. To the best of our knowledge, this is the first field experiment to demonstrate the potential for the combined iron and sulfate biostimulation to enhance B20 source-zone biodegradation.

A Modified Approach for in Situ Chemical Oxidation Coupled to Biodegradation Enhances Light Nonaqueous Phase Liquid Source-Zone Remediation

Field and batch experiments were conducted to assess whether a modified approach for in situ chemical oxidation (ISCO) (with MgO₂ and Fe₂O₃ particles recovered from acid mine drainage treatment) can enhance LNAPL (light nonaqueous phase liquid) dissolution and produce bioavailable soluble compounds. This modified ISCO approach was coupled to biodegradation to further remove residual compounds by microbially mediated processes. Pure palm biodiesel (B100) was chosen to represent a poorly water-soluble compound that behaves like LNAPLs, and 100 L was released to a 2 m² area excavated down to the water table. A past adjacent B100-field experiment under natural attenuation was conducted as a baseline control. Results demonstrated the enhancement of organic compound dissolution and production of soluble compounds due to the modified in situ chemical oxidation. The slow release of H₂O₂ by MgO₂ decomposition (termed partial chemical oxidation) and production of soluble compounds allowed the stimulation of microbial growth and promoted a beneficial response in microbial communities involved in oxidized biodiesel compound biodegradation. This is the first field experiment to demonstrate that this modified ISCO approach coupled to biodegradation could be a feasible strategy for the removal of poorly water-soluble compounds (e.g., biodiesel) and prevent the long-term effects generally posed in source zones.

Microbial fuel cell anodic microbial population dynamics during MFC start-up

In order to optimize energy production in MFCs, a better understanding of anodic communities is essential. Our objective was to determine the taxonomic structure of the bacterial communities present at the surface of the anode during the formation and development of electro-active biofilms in MFCs inoculated with fresh primary clarifier overflow. Quantitative microbial community dynamics were evaluated as a function of time and electrical performance using 16S rRNA gene-based phylogenetic microarrays and flow cytometry. Results show that the bacterial community stabilized partially but not completely when voltage output was stable. Geobacter appeared to be the predominant genus, whose growth was associated with voltage, while some other genus still developed or declined after the voltage stabilization. Flow cytometry revealed that some genus showing a decreasing proportional fluorescence intensity over time were still actively respiring bacteria, and thus, active albeit minor members of the biofilm. Finally, this study shows that anodic biofilm selection and maturation is still occurring after more than 20 days of operation and over ten days after voltage is stabilized.

Biodiesel presence in the source zone hinders aromatic hydrocarbons attenuation in a B20-contaminated groundwater

The behavior of biodiesel blend spills have received limited attention in spite of the increasing and widespread introduction of biodiesel to the transportation fuel matrix. In this work, a controlled field release of biodiesel B20 (100L of 20:80 v/v soybean biodiesel and diesel) was monitored over 6.2years to assess the behavior and natural attenuation of constituents of major concern (e.g., BTEX (benzene, toluene, ethyl-benzene and xylenes) and PAHs (polycyclic aromatic hydrocarbons)) in a sandy aquifer material. Biodiesel was preferentially biodegraded compared to diesel aromatic compounds with a concomitant increase in acetate, methane (near saturation limit (≈22mgL^-1)) and dissolved BTEX and PAH concentrations in the source zone during the first 1.5 to 2.0years after the release. Benzene and benzo(a)pyrene concentrations remained above regulatory limits in the source zone until the end of the experiment (6.2years after the release). Compared to a previous adjacent 100-L release of ethanol-amended gasoline, biodiesel/diesel blend release resulted in a shorter BTEX plume, but with higher residual dissolved hydrocarbon concentrations near the source zone. This was attributed to greater persistence of viscous (and less mobile) biodiesel than the highly-soluble and mobile ethanol in the source zone. This persistence of biodiesel/diesel NAPL at the source zone slowed BTEX and PAH biodegradation (by the establishment of an anaerobic zone) but reduced the plume length by reducing mobility. This is the first field study to assess biodiesel/diesel blend (B20) behavior in groundwater and its effects on the biodegradation and plume length of priority groundwater pollutants.

Snow and ice ecosystems: not so extreme

Snow and ice environments cover up to 21% of the Earth's surface. They have been regarded as extreme environments because of their low temperatures, high UV irradiation, low nutrients and low water availability, and thus, their microbial activity has not been considered relevant from a global microbial ecology viewpoint. In this review, we focus on why snow and ice habitats might not be extreme from a microbiological perspective. Microorganisms interact closely with the abiotic conditions imposed by snow and ice habitats by having diverse adaptations, that include genetic resistance mechanisms, to different types of stresses in addition to inhabiting various niches where these potential stresses might be reduced. The microbial communities inhabiting snow and ice are not only abundant and taxonomically diverse, but complex in terms of their interactions. Altogether, snow and ice seem to be true ecosystems with a role in global biogeochemical cycles that has likely been underestimated. Future work should expand past resistance studies to understanding the function of these ecosystems.

Functional Basis of Microorganism Classification

Correctly identifying nearest “neighbors” of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with phylogenetic descent.

Taxonomic classification of microorganisms according to similarity is important for industrial and clinical applications where close relationships imply similar uses and/or treatments. Current microbial taxonomy is phylogeny-guided, i.e., the organisms are grouped based on their evolutionary relationships, defined by vertical inheritance of genetic information from mother to daughter cells. Microbes, however, are capable of horizontal gene transfer (HGT). Thus, the current taxonomic assignments cannot guarantee genome-encoded molecular functional similarity; i.e. two microbes of the same taxonomic group inhabiting different environments may be very different—just as your cousin may be more different from you than your unrelated best friend. Our work establishes a computational framework for comparison of microorganisms based on their molecular functionality. In our functional-repertoire similarity-based organism network (FuSiON; flattened to fusion) representation, organisms can be consistently assigned to groups based on a quantitative measure of their functional similarities. Our approach highlights the specific environmental factor(s) that explain the functional differences between groups of microorganism. Fusion is a more practical choice for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment.

Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics

Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.

Linking environmental prokaryotic viruses and their host through CRISPRs

The ecological pressure that viruses place on microbial communities is not only based on predation, but also on gene transfer. In order to determine the potential impact of viruses and transduction, we need a better understanding of the dynamics of interactions between viruses and their hosts in the environment. Data on environmental viruses are scarce, and methods for tracking their interactions with prokaryotes are needed. Clustered regularly interspaced short palindromic repeats (CRISPRs), which contain viral sequences in bacterial genomes, might help document the history of virus-host interactions in the environment. In this study, a bioinformatics network linking viruses and their hosts using CRISPR sequences obtained from metagenomic data was developed and applied to metagenomes from Arctic glacial ice and soil. The application of our network approach showed that putative interactions were more commonly detected in the ice samples than the soil which would be consistent with the ice viral-bacterial interactions being more dynamic than those in soil. Further analysis of the viral sequences in the CRISPRs indicated that Ralstonia phages might be agents of transduction in the Arctic glacial ice.

Ethyl tert-butyl ether (ETBE)-degrading microbial communities in enrichments from polluted environments

The ethyl tert-butyl ether (ETBE) degradation capacity and phylogenetic composition of five aerobic enrichment cultures with ETBE as the sole carbon and energy source were studied. In all cases, ETBE was entirely degraded to biomass and CO2. Clone libraries of the 16S rRNA gene were prepared from each enrichment. The analyses of the DNA sequences obtained showed different taxonomic compositions with a majority of Proteobacteria in three cases. The two other enrichments have different microbiota with an abundance of Acidobacteria in one case, whereas the microbiota in the second was more diverse (majority of Actinobacteria, Chlorobi and Gemmatimonadetes). Actinobacteria were detected in all five enrichments. Several bacterial strains were isolated from the enrichments and five were capable of degrading ETBE and/or tert-butyl alcohol (TBA), a degradation intermediate. The five included three Rhodococcus sp. (IFP 2040, IFP 2041, IFP 2043), one Betaproteobacteria (IFP 2047) belonging to the Rubrivivax/Leptothrix/Ideonella branch, and one Pseudonocardia sp. (IFP 2050). Quantification of these five strains and two other strains, Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP2049, which had been previously isolated from one of the enrichments was carried out on the different enrichments based on quantitative PCR with specific 16S rRNA gene primers and the results were consistent with the hypothesized role of Actinobacteria and Betaproteobacteria in the degradation of ETBE and the possible role of Bradyrhizobium strains in the degradation of TBA.

Potential drivers of microbial community structure and function in Arctic spring snow

The Arctic seasonal snowpack can extend at times over a third of the Earth’s land surface. This chemically dynamic environment interacts constantly with different environmental compartments such as atmosphere, soil and meltwater, and thus, strongly influences the entire biosphere. However, the microbial community associated with this habitat remains poorly understood. Our objective was to investigate the functional capacities, diversity and dynamics of the microorganisms in snow and to test the hypothesis that their functional signature reflects the snow environment. We applied a metagenomic approach to nine snow samples taken over 2 months during the spring season. Fungi, Bacteroidetes, and Proteobacteria were predominant in metagenomic datasets and changes in community structure were apparent throughout the field season. Functional data that strongly correlated with chemical parameters like mercury or nitrogen species supported that this variation could be explained by fluctuations in environmental conditions. Through inter-environmental comparisons we examined potential drivers of snowpack microbial community functioning. Known cold adaptations were detected in all compared environments without any apparent differences in their relative abundance, implying that adaptive mechanisms related to environmental factors other than temperature may play a role in defining the snow microbial community. Photochemical reactions and oxidative stress seem to be decisive parameters in structuring microbial communities inside Arctic snowpacks.

Large-scale metagenomic-based study of antibiotic resistance in the environment

Antibiotic resistance, including multiresistance acquisition and dissemination by pathogens, is a critical healthcare issue threatening our management of infectious diseases [1-3]. Rapid accumulation of resistance phenotypes implies a reservoir of transferable antibiotic resistance gene determinants (ARGDs) selected in response to inhibition of antibiotic concentrations, as found in hospitals [1, 3-5]. Antibiotic resistance genes were found in environmental isolates, soil DNA [4-6], secluded caves [6, 7], and permafrost DNA [7, 8]. Antibiotics target essential and ubiquitous cell functions, and resistance is a common characteristic of environmental bacteria [8-11]. Environmental ARGDs are an abundant reservoir of potentially transferable resistance for pathogens [9-12]. Using metagenomic sequences, we show that ARGDs can be detected in all (n=71) environments analyzed. Soil metagenomes had the most diverse pool of ARGDs. The most common types of resistances found in environmental metagenomes were efflux pumps and genes conferring resistance to vancomycin, tetracycline, or β-lactam antibiotics used in veterinary and human healthcare. Our study describes the diverse and abundant antibiotic resistance genes in nonclinical environments and shows that these genes are not randomly distributed among different environments (e.g., soil, oceans or human feces).

Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library

A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.

Microbial ecology of chlorinated solvent biodegradation

This study focused on the microbial ecology of tetrachloroethene (PCE) degradation to trichloroethene, cis-1,2-dichloroethene and vinyl chloride to evaluate the relationship between the microbial community and the potential accumulation or degradation of these toxic metabolites. Multiple soil microcosms supplied with different organic substrates were artificially contaminated with PCE. A thymidine analogue, bromodeoxyuridine (BrdU), was added to the microcosms and incorporated into the DNA of actively replicating cells. We compared the total and active bacterial communities during the 50-day incubations by using phylogenic microarrays and 454 pyrosequencing to identify microorganisms and functional genes associated with PCE degradation to ethene. By use of this integrative approach, both the key community members and the ecological functions concomitant with complete PCE degradation could be determined, including the presence and activity of microbial community members responsible for producing hydrogen and acetate, which are critical for Dehalococcoides-mediated PCE degradation. In addition, by correlation of chemical data and phylogenic microarray data, we identified several bacteria that could potentially oxidize hydrogen. These results demonstrate that PCE degradation is dependent on some microbial community members for production of appropriate metabolites, while other members of the community compete for hydrogen in soil at low redox potentials.

Interactions between snow chemistry, mercury inputs and microbial population dynamics in an Arctic snowpack

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79 °N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes.

Soil bacterial community shifts after chitin enrichment: an integrative metagenomic approach

Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome.

Selective occurrence of Rhizobiales in frost flowers on the surface of young sea ice near Barrow, Alaska and distribution in the polar marine rare biosphere

Frost flowers are highly saline ice structures that grow on the surface of young sea ice, a spatially extensive environment of increasing importance in the Arctic Ocean. In a previous study, we reported organic components of frost flowers in the form of elevated levels of bacteria and exopolymers relative to underlying ice. Here, DNA was extracted from frost flowers and young sea ice, collected in springtime from a frozen lead offshore of Barrow, Alaska, to identify bacteria in these understudied environments. Evaluation of the distribution of 16S rRNA genes via four methods (microarray analysis, T-RFLP, clone library and shotgun metagenomic sequencing) indicated distinctive bacterial assemblages between the two environments, with frost flowers appearing to select for Rhizobiales. A phylogenetic placement approach, used to evaluate the distribution of similar Rhizobiales sequences in other polar marine studies, indicated that some of the observed strains represent widely distributed members of the marine rare biosphere in both the Arctic and Antarctic.

Life on human surfaces: skin metagenomics

The human skin microbiome could provide another example, after the gut, of the strong positive or negative impact that human colonizing bacteria can have on health. Deciphering functional diversity and dynamics within human skin microbial communities is critical for understanding their involvement and for developing the appropriate substances for improving or correcting their action. We present a direct PCR-free high throughput sequencing approach to unravel the human skin microbiota specificities through metagenomic dataset analysis and inter-environmental comparison. The approach provided access to the functions carried out by dominant skin colonizing taxa, including Corynebacterium, Staphylococcus and Propionibacterium, revealing their specific capabilities to interact with and exploit compounds from the human skin. These functions, which clearly illustrate the unique life style of the skin microbial communities, stand as invaluable investigation targets for understanding and potentially modifying bacterial interactions with the human host with the objective of increasing health and well being.

The dynamic arctic snow pack: an unexplored environment for microbial diversity and activity

The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of process rates and shifts in the structure of microbial communities. Biodiversity may increase as the Arctic warms and population shifts occur as psychrophilic/psychrotolerant species disappear in favor of more mesophylic ones. In order to predict how ecological processes will evolve as a function of global change, it is essential to identify which populations participate in each process, how they vary physiologically, and how the relative abundance, activity and community structure will change under altered environmental conditions. This review covers aspects of the importance and implication of snowpack in microbial ecology emphasizing the diversity and activity of these critical members of cold zone ecosystems.

In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes

The bioremediation of chloroethene contaminants in groundwater polluted systems is still a serious environmental challenge. Many previous studies have shown that cooperation of several dechlorinators is crucial for complete dechlorination of trichloroethene to ethene. In the present study, we used an explorative functional DNA microarray (DechloArray) to examine the composition of specific functional genes in groundwater samples in which chloroethene bioremediation was enhanced by delivery of hydrogen‐releasing compounds. Our results demonstrate for the first time that complete biodegradation occurs through spatial and temporal variations of a wide diversity of dehalorespiring populations involving both Sulfurospirillum, Dehalobacter, Desulfitobacterium, Geobacter and Dehalococcoides genera. Sulfurospirillum appears to be the most active in the highly contaminated source zone, while Geobacter was only detected in the slightly contaminated downstream zone. The concomitant detection of both bvcA and vcrA genes suggests that at least two different Dehalococcoides species are probably responsible for the dechlorination of dichloroethenes and vinyl chloride to ethene. These species were not detected on sites where cis‐dichloroethene accumulation was observed. These results support the notion that monitoring dechlorinators by the presence of specific functional biomarkers using a powerful tool such as DechloArray will be useful for surveying the efficiency of bioremediation strategies.