Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic‐induced disease among exposed individuals. Human genetics is a known component, but it alone cannot account for the large inter‐individual variability in the presentation of arsenicosis symptoms. Each part of the gastrointestinal tract (GIT) may be considered as a unique environment with characteristic pH, oxygen concentration, and microbiome. Given the well‐established arsenic redox transformation activities of microorganisms, it is reasonable to imagine how the GIT microbiome composition variability among individuals could play a significant role in determining the fate, mobility and toxicity of arsenic, whether inhaled or ingested. This is a relatively new field of research that would benefit from early dialogue aimed at summarizing what is known and identifying reasonable research targets and concepts. Herein, we strive to initiate this dialogue by reviewing known aspects of microbe–arsenic interactions and placing it in the context of potential for influencing host exposure and health risks. We finish by considering future experimental approaches that might be of value.

It has been recently shown that magnetite nanoparticles (nanoFe3O4) can facilitate methanogenic syntrophy but the effect of magnetite on methanogenesis alone remains elusive. Here we show that aceticlastic methanogenesis by Methanosarcina mazei is accelerated by magnetite and is correlated with the redox cycling of structural Fe(II) and Fe(III) in the mineral. An enrichment and its closest pure culture relative, Ms. mazei zm‐15, both obtained from a natural wetland of the Tibetan plateau were tested in this experiment. The Fe(II) to Fe(III) ratios in magnetite, as measured by multiple approaches, show an initial increase in both the methanogenic cultures and the blank preparations containing no microbes. The Fe(II)/Fe(III) ratio then displays a distinct decline followed by an increase towards the end of incubation only in the enrichment and pure culture cultivations. This redox cycling of magnetite is in accordance with the stimulation of aceticlastic methanogenesis. Microscopic observation reveals the precipitation of nanoFe3O4 on methanogen cell surface. The genomic analysis predicts that in addition to electron transfer components essential for aceticlastic methanogenesis, Ms. mazei zm‐15 contains an outer‐surface multiheme c‐type cytochrome (MHC) and a few function‐unknown surface proteins that harbour monoheme motif. We hypothesize that the redox cycling of nanoFe3O4 delivers a positive influence via the MHC to the membrane electron transfer chain and hence promote the aceticlastic methanogenesis.

Rhizomicrobiome, the communities of microorganisms surrounding the root of the plant, plays a vital role in promoting plant growth and health. The composition of rhizomicrobiome is dynamic both temporally and spatially, and is influenced greatly by the plant host and environmental factors. One of the key influencing factors is rhizodeposits, composed of root‐released tissue cells, exudates, lysates, volatile compounds, etc. Rhizodeposits are rich in carbon and nitrogen elements, and able to select and fuel the growth of rhizomicrobiome. In this minireview, we overview the generation, composition and dynamics of rhizodeposits, and discuss recent work describing the general and specific impacts of rhizodeposits on rhizomicrobiome. We focus further on root exudates, the most dynamic component of rhizodeposits, and review recent progresses about the influence of specific root exudates in promoting bacterial root colonization, inducing biofilm development, acting as plant defence and shaping the rhizomicrobiome.

Euglenophyceae are unicellular algae with the majority of their diversity known from small freshwater reservoirs. Only two dozen species have been described to occur in marine habitats, but their abundance and diversity remain unexplored. Phylogenetic studies revealed marine prasinophyte green alga, Pyramimonas parkeae, as the closest extant relative of the euglenophytes' plastid, but similarly to euglenophytes, our knowledge about the diversity of Pyramimonadales is limited. Here we explored Euglenophyceae and Pyramimonadales phylogenetic diversity in marine environmental samples. We yielded 18S rDNA and plastid 16S rDNA sequences deposited in public repositories and reconstructed Euglenophyceae reference trees. We searched high‐throughput environmental sequences from the TARA Oceans expedition and Ocean Sampling Day initiative for 18S rDNA and 16S rDNA, placed them in the phylogenetic context and estimated their relative abundances. To avoid polymerase chain reaction (PCR) bias, we also exploited metagenomic data from the TARA Oceans expedition for the presence of rRNA sequences from these groups. Finally, we targeted these protists in coastal samples by specific PCR amplification of two parts of the plastid genome uniquely shared between euglenids and Pyramimonadales. All approaches revealed previously undetected, but relatively low‐abundant lineages of marine Euglenophyceae. Surprisingly, some of those lineages are branching within the freshwater or brackish genera.

Flagella are the well‐known structural appendages used by bacteria for motility. Although generally reported to be non‐motile, the enteropathogenic bacterial species Escherichia albertii produces flagella intermittently. We found that E. albertii expressed flagella under specific environmental conditions. After several generations (involving 4 to 12‐h incubations), six of the twelve strains we investigated displayed swimming motility in various aquatic environments, including pond water containing nutrients from pigeon droppings (10% suspension) as well as in 20 × −diluted tryptic soy broth. The most significant motility determinant was a temperature between 15 and 30 °C. At 20 °C in the 10% pigeon‐dropping suspension, microscopic observations revealed that some cells (1%–95% of six strains) showed swimming motility. Electron microscopy showed that the E. albertii cells expressed flagella. Lower concentrations of some substrates (including nutrients) may be of secondary importance for E. albertii flagella expression. Interestingly, the non‐motile strains (n = 6/12) contained pseudogenes corresponding to essential flagella structural proteins. After being released from its host into surface water, E. albertii may express flagella to move toward nutrient sources or new hosts.

To understand factors that influence the assembly of microbial communities, we inoculated Medicago sativa with a series of nested bacterial synthetic communities and grew plants in distinct nitrogen concentrations. Two isolates in our eight‐member synthetic community, Williamsia sp. R60 and Pantoea sp. R4, consistently dominate community structure across nitrogen regimes. While Pantoea sp. R4 consistently colonizes plants to a higher degree compared to the other six organisms across each community and each nutrient level, Williamsia sp. R60 exhibits nutrient specific colonization differences. Williamsia sp. R60 is more abundant in plants grown at higher nitrogen concentrations, but exhibits the opposite trend when no plant is present, indicating plant‐driven influence over colonization. Our research discovered unique, repeatable colonization phenotypes for individual microbes during plant microbiome assembly, and identified alterations caused by the host plant, microbes, and available nutrients.

Environmental cues that regulate motility are poorly understood, but specific carbon and nitrogen sources, such as casamino acids (CAA), are known to stimulate motility in model organisms. However, natural environments are commonly more nutrient‐limited than laboratory growth media, and the effect of energy‐rich CAA on the motility of oligotrophic microorganisms is unknown. In this study, an extreme oligocarbotroph, Variovorax paradoxus YC1, was isolated from weathered shale rock within a disused mine level in North Yorkshire, UK. The addition of 0.1% CAA to minimal media significantly reduced the motility of YC1 after 72 h and inhibited swimming motility resulting in enhanced surface growth. We propose this response to CAA is a physiological adaptation to oligotrophy, facilitating the colonization of nutrient‐rich environments.

In recent years, there has been an increase in studies on the implications of gut microbiota (GM) on the behaviour of children with autism spectrum disorders (ASD) due to a dysbiosis in GM that can trigger onset, development or progression of ASD through the microbiota–gut–brain axis. The aim of this study is to carry out a systematic review of articles from the last 6 years that analyse GM in children with ASD compared to GM in control groups. Children with ASD showed a higher abundance of Roseburia and Candida genera, and lower abundance of Dialister, Bilophila, Veillonella, Streptococcus, Coprococcus and Prevotella genera. Those differences can be attributed to factors such as different nationalities, nature of control groups, place where the sample was taken, gastrointestinal (GI) problems or bacterial detection methods. It is still too early to define a specific GM profile of children with ASD, and future studies should focus on homogenizing the characteristics of samples and control groups. Furthermore, new multicentre studies should also focus on the impact of GM on GI physiology, neurophysiology and behaviour of children with ASD, and on performing psychometric analyses of the correlation between the severity of ASD behavioural symptoms and GM profiles.

Acetogenic bacteria are a group of strictly anaerobic bacteria that may have been first life forms on Earth since they employ an ancient pathway for CO2 fixation into acetyl‐CoA that is coupled to the synthesis of ATP, the Wood–Ljungdahl pathway. Electrons for CO2 reduction are derived from oxidation of H2 or CO and thus, these bacteria can grow lithotrophically on gases present on early Earth. Among the organic molecules present on early Earth is acetaldehyde, a highly volatile C2 compound. Here, we demonstrate that the acetogenic model bacterium Acetobacterium woodii grows on acetaldehyde. Acetaldehyde is dismutated to ethanol and acetyl‐CoA, most likely by the bifunctional alcohol dehydrogenase AdhE. Acetyl‐CoA is converted to acetate by two subsequent enzymes, phosphotransacetylase and acetate kinase, accompanied by the synthesis of ATP by substrate‐level phosphorylation. Apparently, growth on acetaldehyde does not employ the Wood–Ljungdahl pathway. Our finding opens the possibility of a simple and ancient metabolic pathway with only three enzymes that allows for biomass (acetyl‐CoA) and ATP formation on early Earth.

Cyclic diguanylate (c‐di‐GMP) is a broadly conserved bacterial signalling molecule that modulates diverse cellular processes, such as biofilm formation, colony morphology and swimming motility. The intracellular level of c‐di‐GMP is controlled by diguanylate cyclases (DGCs) with GGDEF domain and phosphodiesterases (PDEs) with either EAL or HD‐GYP domain. Pseudomonas putida KT2440 has a large group of genes on its genome encoding proteins with GGDEF/EAL/HD‐GYP domains. However, phenotypic–genotypic correlation and c‐di‐GMP metabolism of these genes were largely unknown. Herein, by systematically constructing deletion mutants/overexpression strains of the 42 predicted c‐di‐GMP metabolism–related genes and analysing the phenotypes, we preliminarily revealed the role of each gene in biofilm formation, colony morphology and swimming motility. Subsequent results from protein sequence alignments and cellular c‐di‐GMP assessment indicated that 25 out of the 42 genes were likely to encode DGCs, nine genes were predicted to encode PDEs, four genes encoded bifunctional enzymes and the other four genes encoded enzymatically inactive proteins. This study offers a basic understanding of the roles of these 42 genes and can serve as a toolkit for investigators to further elucidate the functions of these GGDEF and EAL/HD‐GYP domain‐containing proteins.

Plant‐ and alga‐associated bacterial communities are generally described via 16S rDNA metabarcoding using universal primers. As plastid genomes encode 16S rDNA related to cyanobacteria, these data sets frequently contain >90% plastidial sequences, and the bacterial diversity may be under‐sampled. To overcome this limitation we evaluated in silico the taxonomic coverage for four primer combinations targeting the 16S rDNA V3‐V4 region. They included a forward primer universal to Bacteria (S‐D‐Bact‐0341‐b‐S‐17) and four reverse primers designed to avoid plastid DNA amplification. The best primer combination (NOCHL) was compared to the universal primer set in the wet lab using a synthetic community and samples from three macroalgal species. The proportion of plastid sequences was reduced by 99%–100% with the NOCHL primers compared to the universal primers, irrespective of algal hosts, sample collection and extraction protocols. Additionally, the NOCHL primers yielded a higher richness while maintaining the community structure. As Planctomycetes, Verrucomicrobia and Cyanobacteria were underrepresented (70%–90%) compared to universal primers, combining the NOCHL set with taxon‐specific primers may be useful for a complete description of the alga‐associated bacterial diversity. The NOCHL primers represent an innovation to study algal holobionts without amplifying host plastid sequences and may further be applied to other photosynthetic hosts.

Electroactive type IV pili, or e‐pili, are used by some microbial species for extracellular electron transfer. Recent studies suggest that e‐pili may be more phylogenetically and structurally diverse than previously assumed. Here, we used updated aromatic density thresholds (≥9.8% aromatic amino acids, ≤22‐aa aromatic gaps and aromatic amino acids at residues 1, 24, 27, 50 and/or 51, and 32 and/or 57) to search for putative e‐pilin genes in metagenomes from diverse ecosystems with active microbial metal cycling. Environmental putative e‐pilins were diverse in length and phylogeny, and included truncated e‐pilins in Geobacter spp., as well as longer putative e‐pilins in Fe(II)‐oxidizing Betaproteobacteria and Zetaproteobacteria.

Multispecies biofilms are structured and spatially defined communities, where interspecies interactions impact assembly and functionality. Here, we compared the spatial organization and growth of bacterial cells in differently composed biofilm communities over time to determine links between interspecies interactions and selection for biofilm phenotypes of individual species. An established model community consisting of Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus was used. It was found that interspecies interactions led to varying levels of selection for a new colony phenotype of X. retroflexus, depending on the presence/absence of other species. When M. oxydans was absent, X. retroflexus was not able to establish in the top layers of the biofilm, which led to selection for a hyper‐matrix forming phenotype of X. retroflexus that successfully established in the biofilm top layers. No such phenotypic X. retroflexus variants were identified in the presence of M. oxydans. These findings indicate that interspecies interactions may lead to favourable localization of individual species in a multispecies biofilm and thereby reduce selection for competitive phenotypes.

We characterized ammonia‐oxidizing archaea (AOA) and bacteria (AOB) from salt marsh sediments in the Gulf of Mexico over 5 years to identify environmental drivers of nitrifying community patterns following the Deepwater Horizon oil spill. Samples were collected from oiled and unoiled sites in July of 2012–2016 from 12 marshes spanning three regions on the Louisiana coast. No consistent oil effect was detected for either AOA or AOB abundance or community composition. At the local scale, abundance was correlated with changes in marsh elevation, suggesting that oxygen may be an important driver. Regional differences in abundance were best explained by salinity and soil moisture, while interannual variation may be more linked to changes in climate and Mississippi River discharge. Variation of AOA communities was correlated with organic sediment nutrients, while AOB communities were correlated with soil extractable nutrients. AOA and AOB diversity and AOB abundance decreased in 2014 in all regions, suggesting that broad‐scale drivers, such as climate, may explain synchronous shifts throughout the coastal area. Our results provide insights about large‐scale disturbances on nitrifying microbes in the Gulf of Mexico, and suggest that nitrogen cycling may be controlled primarily by local factors, but large‐scale drivers might override these localized differences at times.

Amino acids are vital components in cell metabolism. Leucine is a regulatory factor that generates significant impact on protein synthesis/turnover, modulates diverse cellular signalling pathways and participates in oxidative processes and immune responses. Here, we identified and characterized the functions of a leucine‐associated Zn2Cys6‐type transcription factor, MoLeu3. Disruption of MoLEU3 resulted in significantly reduced pathogenicity in barley and rice. Quantitative RT‐PCR showed that the expression levels of the putative leucine biosynthesis‐related genes, MoLEU1, MoLEU2 and MoLEU4 were downregulated in the ΔMoleu3 mutant. We used high‐throughput gene knockout method to generate the null mutants of MoLEU1, MoLEU2 and MoLEU4 respectively. The ΔMoleu1, ΔMoleu2 and ΔMoleu4 mutants are leucine auxotroph and showed similar phenotypic characterizations, including reduced conidiation, delayed mobilization and degradation of glycogen and lipid droplets, limited appressorium‐mediated penetration, and restricted invasive hyphae growth within host cells. Collectively, MoLEU1, MoLEU2, and MoLEU4 regulated by MoLEU3 play crucial roles in fungal development and infectious processes through modulation of leucine biosynthesis in Magnaporthe oryzae.

In recent years, whole shotgun metagenomics (WSM) of complex microbial communities has become an established technology to perform compositional analyses of complex microbial communities, an approach that is heavily reliant on bioinformatic pipelines to process and interpret the generated raw sequencing data. However, the use of such in silico pipelines for the microbial taxonomic classification of short sequences may lead to significant errors in the compositional outputs deduced from such sequencing data. To investigate the ability of such in silico pipelines, we employed two commonly applied bioinformatic tools, i.e., MetaPhlAn2 and Kraken2 together with two metagenomic data sets originating from human and animal faecal samples. By using these bioinformatic programs that taxonomically classify WSM data based on marker genes, we observed a trend to depict a lower complexity of the microbial communities. Here, we assess the limitations of the most commonly employed bioinformatic pipelines, i.e., MetaPhlAn2 and Kraken2, and based on our findings, we propose that such analyses should ideally be combined with experimentally based microbiological validations.

In silico and empirical quantification of viruses is paramount for obtaining information on viral populations that have a major impact on biogeochemical cycles. The uncultured Pelagibacter virus vSAG 37‐F6 discovered via single‐virus genomics is one of the most abundant and cosmopolitan marine viruses; however, little is understood about its temporal variation. Here, we estimated the absolute number of infecting 37‐F6 viruses in coastal bacterioplankton from the Mediterranean Sea by using a novel, feasible SYBR Green I chip‐based digital PCR (SYBR dPCR) technique, not implemented before for enumerating (uncultured) microbes. Quantitative SYBR dPCR estimated 450–3480 genome copies of virus 37‐F6 in cells/mL (i.e. infecting viruses) and a total of ≈10–400 putative infected cells/mL with a potential C release of 0.12–4.9 pg/ml in the analysed samples. Considering that virus 37‐F6 is ubiquitous and abundant in all Tara samples, an enormous amount of C could be transformed by this virus through the ‘viral shunt’. Thus, this SYBR dPCR technique has enabled the absolute quantification of an ecologically relevant uncultured virus in nature and the estimation of its potential contribution on biogeochemical cycles. Overall, our study also shows that this approach has a broad applicability for quantifying any other target loci in Microbiology and Virology.

During bloom events, Escherichia coli cell counts increase to between 10,000 and 100,000 cfu/100 ml of water. The strains responsible for bloom events belong to E. coli phylogenetic groups A and B1, and all have acquired a capsule from Klebsiella. A pan‐genome comparison of phylogroup A E. coli revealed that the ferric citrate uptake system (fecIRABCDE) was overrepresented in phylogroup A bloom strains compared with non‐bloom E. coli. A series of experiments were carried out to investigate if the capsule together with ferric citrate uptake system could confer a growth rate advantage on E. coli. Capsulated strains had a growth rate advantage regardless of the media composition and the presence/absence of the fec operon, and they had a shorter lag phase compared with capsule‐negative strains. The results suggest that the Klebsiella capsule may facilitate nutrient uptake or utilization by a strain. This, together with the protective roles played by the capsule and the shorter lag phase of capsule‐positive strains, may explain why it is only capsule‐positive strains that produce elevated counts in response to nutrient influx.

Nitrogen (N) deposition in many areas of the world is over an order of magnitude greater than it would be in absence of human activity. We ask how abiotic (N)and biotic (plant host and neighborhood) effects interact to influence root-associated bacterial (RAB)community assembly. Using 454 pyrosequencing, we examined RAB communities from two dominantal pine tundra plants, Geum rossii and Deschampsia cespitosa, under control, N addition and D. cespitosa removal treatments, implemented in a factorial design. We hypothesized that host would have the strongest effect on RAB assembly, followed by N,then neighbor effects.The most dominant phyla were Proteobacteria (mostly Gammaproteobacteria), Actinobacteria,Bacteroidetes and Acidobacteria. We found RAB communities were host specific, with only 17% overlap in operational taxonomic units. Host effects on composition were over twice as strong as Neffects. D. cespitosa RAB diversity declined with N, while G. rossii RAB did not. D. cespitosa removal did not influence G. rossii RAB community composition, but G. rossii RAB diversity declined with N only when D. cespitosa was absent. We conclude that RAB of both hosts are sensitive to N enrichment, and RAB response to N is influenced by host identity and plant neighborhood.

Semiarid environments are characterized by the uneven spread of rain throughout the year. This leads to the establishment of a biota that can go through long periods without rain. In order to understand the dynamics of rhizosphere microbial communities across these contrasting seasons in Caatinga, we used the Ion Torrent platform to sequence the metagenome of the rhizosphere of a native leguminous plant (Mimosa tenuiflora). The annotation indicated that most abundant groups detected were the Actinobacteria and Proteobacteria, and the dominant functional groups were carbohydrate and protein metabolisms, and that in the wet season, the communities carried carbohydrate and amino acid metabolisms.The major differences observed between seasons were higher abundance of genes related to carbohydrate and amino acid metabolisms in the rainy season, indicating that the populations present might be better adapted to a higher abundance of organic matter. Besides, no clear separation of samples was detected based on their taxonomic composition whereas the functional composition indicates that samples from the rain season are more related. Altogether, our results indicate that there is al arge functional stability in these communities mostly due to the selection of features that aid the biota to endure the dry season and blossom during rain.

Petroleum waste sludges are toxic and dangerous that is why environmental protection agencies have declared their treatment top priority. Physicochemical treatments are expensive and environmentally unfriendly, while alternative biological treatments are less costly but, in general, work at a slower pace. An in situ bioremediation and rhizoremediation field scale trial was performed in an area contaminated with oil refinery sludge under semiarid climate. The bioremediation and rhizoremediation treatments included the use of an artificial consortium made up of plant growth-promoting rhizobacteria and polycyclic aromatic hydrocarbon-degrading bacteria,and the combined use of the mentioned consortium along with pasture plants respectively. Rhizoremediation revealed that the development of vegetation favoured the evolution of indigenous microbiota with potential to remove petroleum wastes. This was inferred as the decline of total petroleum hydrocarbons 7 months after the biological treatment.

We previously showed the isolation of biofilmpersistent Pseudomonas putida mutants that fail to undergo biofilm dispersal upon entry in stationary phase. Two such mutants were found to bear insertions in PP0914, encoding a GGDEF/EAL domain protein with high similarity to Pseudomon asaeruginosa BifA. Here we show the phenotypic characterization of a ΔbifA mutant in P. putida KT2442.This mutant displayed increased biofilm and pellicle formation, cell aggregation in liquid medium and decreased starvation-induced biofilm dispersal relative to the wild type. Unlike its P. aeruginosa counterpart, P. putida BifA did not affect swarming motility. The hyperadherent phenotype of the ΔbifA mutant correlates with a general increase in cyclic diguanylate (c-di-GMP) levels, Congo Red-binding exopolyaccharide production and transcription of the adhesin-encoding lapA gene. Integrity of the EAL motif and a modified GGDEF motif (altered to GGDQF)were crucial for BifA activity, and c-di-GMP depletion by overexpression of a heterologous c-di-GMP phosphodiesterase in the ΔbifA mutant restored wild-type biofilm dispersal and lapA expression.Our results indicate that BifA is a phosphodiesterase involved in the regulation of the c-di-GMP pool and required for the generation of the low c-di-GMP signal that triggers starvation-induced biofilm dispersal.

An isolate, designated strain SD-1, was obtained from a biofilm dominated by Geobacter sulfurreducens in a microbial fuel cell. The electrochemical activity of strain SD-1 was compared with type strains, G. sulfurreducens PCA and Geobacter metallireducens GS-15, and a mixed culture in microbial electrolysis cells. SD-1 produced a maximum current density of 290 ± 29 A m−3 in a high-concentration phosphate buffer solution (PBS-H, 200 mM). This current density was significantly higher than that produced by the mixed culture (189 ± 44 A m−3) or the type strains (< 70 A m−3). In a highly saline water (SW; 50 mM PBS and 650 mM NaCl), current by SD-1 (158 ± 4 A m−3) was reduced by 28% compared with 50 mM PBS (220 ± 4 A m−3), but it was still higher than that of the mixed culture (147 ± 19 A m−3), and strains PCA and GS-15 did not produce any current. Electrochemical tests showed that the improved performance of SD-1 was due to its lower charge transfer resistance and more negative potentials produced at higher current densities. These results show that the electrochemical activity of SD-1 was significantly different than other Geobacter strains and mixed cultures in terms of its salt tolerance.

Ammonium-oxidizing chemoautotrophic members of Thaumarchaea are proposed to be the key players in the assimilation of bicarbonate in the dark (ABD). However, this process may also involve heterotrophic metabolic pathways, such as fixation of carbon dioxide (CO2) via various anaplerotic reactions. We collected samples from the depth of 4900 m at the Matapan-Vavilov Deep (MVD) station (Hellenic Trench, Eastern Mediterranean) and used the multiphasic approach to study the ABD mediators in this deep-sea ecosystem. At this depth, our analysis indicated the occurrence of actively CO2-fixing heterotrophic microbial assemblages dominated by Gammaproteobacteria with virtually no Thaumarchaea present. [14C]-bicarbonate incorporation experiments combined with shotgun [14C]-proteomic analysis identified a series of proteins of gammaproteobacterial origin. More than quarter of them were closely related with Alteromonas macleodii ‘deep ecotype’ AltDE, the predominant organism in the microbial community of MVD. The present study demonstrated that in the aphotic/hadal zone of the Mediterranean Sea, the assimilation of bicarbonate is associated with both chemolithoauto- and heterotrophic ABD. In some deep-sea areas, the latter may predominantly contribute to the de novo synthesis of organic carbon which points at the important and yet underestimated role heterotrophic bacterial populations can play the in global carbon cycle/sink in the ocean interior.

Methicillin-resistant Staphylococcus aureus (MRSA) is a public health concern due to limited treatment options. The recent description of a mecA homologue, mecC in human and cattle, led to studies to detect this new variant in human and other animal species. Detection of mecC in wild boar and fallow deer in a Spanish game estate led us to further investigate the presence of mecC-MRSA at this location. Samples from cattle, wild animals, workers and river water were tested. A further three mecC-MRSA isolates were obtained from river water. Molecular characterization (multilocus sequence typing and spa typing) and antimicrobial susceptibility testing (broth microdilution) showed that isolates were similar to those detected in wild animals. Whole genome sequencing confirmed that the isolates from the river water and wild animals in the same geographic area were all closely related isolates of ST425 mecC-MRSA. The presence of mecC-MRSA in the river water highlights the potential role of water in the dissemination of mecC-MRSA.

We study the metaproteome of the GF/F-prefiltered fraction of a microbial community from Shantou coast summer surface waters using a shotgun proteomic approach. Spectra attributed to the marine Roseobacter clade (MRC), the oligotrophic marine Gammaproteobacteria (OMG) group and Flavobacteria dominated in the microbial community, accounting for 21.0%, 23.2% and 12.7% of all of the detected spectra, respectively, whereas the SAR 92 clade accounted for 50% of the OMG group. The abundance of TonB-dependent receptors (TBDRs) was detected and the majority of TBDRs were attributed to the OMG, whereas a large number of ABC transporters matched to the MRC, which suggests niche separation in the microbial community. Expression of proteorhodopsin and RagB/SusD from Flavobacteria facilitates their attachment and growth on algal-derived organic matter. Taurine and glycine betaine appear to be an important source of carbon and nitrogen for the Rhodobacteraceae and SAR11 cluster. The detection of carbon monoxide dehydrogenase, formate dehydrogenase, O-acetylhomoserine sulfhydrylase and sulfur oxidation protein from the MRC demonstrated that members of the MRC play important roles in coastal ocean biogeochemical cycles. This study provides the first insight into functional processes occurring in microbial communities in coastal waters in the South China Sea.

Viruses attract increasing interest from environmental microbiologists seeking to understand their function and role in coral health. However, little is known about their main ecological traits within the coral holobiont. In this study, a quantitative and qualitative characterization of viral and bacterial communities was conducted on the mucus of seven different coral species of the Van Phong Bay (Vietnam). On average, the concentrations of viruses and bacteria were, respectively, 17- and twofold higher in the mucus than in the surrounding water. The examination of bacterial community composition also showed remarkable differences between mucus and water samples. The percentage of active respiring cells was nearly threefold higher in mucus (m = 24.8%) than in water (m = 8.6%). Interestingly, a positive and highly significant correlation was observed between the proportion of active cells and viral abundance in the mucus, suggesting that the metabolism of the bacterial associates is probably a strong determinant of the distribution of viruses within the coral holobiont. Overall, coral mucus, given its unique physicochemical characteristics and sticking properties, can be regarded as a highly selective biotope for abundant, diversified and specialized symbiotic microbial and viral organisms.

The shallow submarine hydrothermal field of the Prony Bay (New Caledonia) discharges hydrogen- and methane-rich fluids with low salinity, temperature (< 40°C) and high pH (11) produced by the serpentinization reactions of the ultramafic basement into the lagoon seawater. They are responsible for the formation of carbonate chimneys at the lagoon seafloor. Capillary electrophoresis single-strand conformation polymorphism fingerprinting, quantitative polymerase chain reaction and sequence analysis of 16S rRNA genes revealed changes in microbial community structure, abundance and diversity depending on the location, water depth, and structure of the carbonate chimneys. The low archaeal diversity was dominated by few uncultured Methanosarcinales similar to those found in other serpentinization-driven submarine and subterrestrial ecosystems (e.g. Lost City, The Cedars). The most abundant and diverse bacterial communities were mainly composed of Chloroflexi, Deinococcus-Thermus, Firmicutes and Proteobacteria. Functional gene analysis revealed similar abundance and diversity of both Methanosarcinales methanoarchaea, and Desulfovibrionales and Desulfobacterales sulfate-reducers in the studied sites. Molecular studies suggest that redox reactions involving hydrogen, methane and sulfur compounds (e.g. sulfate) are the energy driving forces of the microbial communities inhabiting the Prony hydrothermal system.

Associations between bacteria from the γ-Proteobacterial order Oceanospirillales and marine invertebrates are quite common. Members of the Oceanospirillales exhibit a diversity of interactions with their various hosts, ranging from the catabolism of complex compounds that benefit host growth to attacking and bursting host nuclei. Here, we describe the association between a novel Oceanospirillales phylotype and the hydrothermal vent snail Alviniconcha. Alviniconcha typically harbour chemoautotrophic γ- or ε-Proteobacterial symbionts inside their gill cells. Via fluorescence in situ hybridization and transmission electron microscopy, we observed an Oceanospirillales phylotype (named AOP for ‘Alviniconcha Oceanospirillales phylotype’) in membrane-bound vacuoles that were separate from the known γ- or ε-Proteobacterial symbionts. Using quantitative polymerase chain reaction, we surveyed 181 Alviniconcha hosting γ-Proteobacterial symbionts and 102 hosting ε-Proteobacterial symbionts, and found that the population size of AOP was always minor relative to the canonical symbionts (median 0.53% of the total quantified 16S rRNA genes). Additionally, we detected AOP more frequently in Alviniconcha hosting γ-Proteobacterial symbionts than in those hosting ε-Proteobacterial symbionts (96% and 5% of individuals respectively). The high incidence of AOP in γ-Proteobacteria hosting Alviniconcha implies that it could play a significant ecological role either as a host parasite or as an additional symbiont with unknown physiological capacities.

Metatranscriptomics of environmental samples enables the identification of community activities without a priori knowledge of taxonomic or functional composition. However, several technical challenges associated with the RNA preparation protocols can affect the relative representation of transcripts and data interpretation. Here, seven replicate metatranscriptomes from planktonic freshwater samples (Lake Lanier, USA) were sequenced to evaluate technical and biological reproducibility of different RNA extraction protocols. Organic versus bead-beating extraction showed significant enrichment for low versus high G + C% mRNA populations respectively. The sequencing data were best modelled by a negative binomial distribution to account for the large technical and biological variation observed. Despite the variation, the transcriptional activities of populations that persisted in year-round metagenomes from the same site consistently showed distinct expression patterns, reflecting different ecologic strategies and allowing us to test prevailing models on the contribution of both rare biosphere and abundant members to community activity. For instance, abundant members of the Verrucomicrobia phylum systematically showed low transcriptional activity compared with other abundant taxa. Our results provide a practical guide to the analysis of metatranscriptomes and advance understanding of the activity and ecology of abundant and rare members of temperate freshwater microbial communities.

We present a method for the physical isolation of endospores from environmental samples allowing the specific targeting of endospore-forming bacteria for sequencing (endospore-enriched community). The efficiency of the method was tested on lake sediment samples. After 16S rRNA gene amplicon sequencing, the composition in the endospore-enriched community was compared with the community from untreated control samples (whole community). In the whole community, Firmicutes had a relative abundance of 8% and 19% in the two different lake sediments. In contrast, in the endospore-enriched community, Firmicutes abundance increased to 90.6% and 83.9%, respectively, confirming the efficiency of the endospore enrichment. The relative abundance of other microbial groups that form spore-like resisting states (i.e. actinobacteria, cyanobacteria and myxococcales) was below 2% in the endospore-enriched community, indicating that the method is adapted to true endospores. Representatives from two out of the three known classes of Firmicutes (Bacilli and Clostridia) were detected and supposedly asporogenic groups (e.g. Ethanoligenes and Trichococcus) could be detected. The method presented here is a leap forward for ecological studies of endospore-forming Firmicutes. It can be applied to other types of samples in order to reveal the diversity and metabolic potential of this bacterial group in the environment.

The diversity of airborne microorganisms that potentially reach aquatic ecosystems during rain events is poorly explored. Here, we used a culture-independent approach to characterize bacterial assemblages during rain events with and without Saharan dust influence arriving to a high mountain lake in the Austrian Alps. Bacterial assemblage composition differed significantly between samples with and without Saharan dust influence. Although alpha diversity indices were within the same range in both sample categories, rain events with Atlantic or continental origins were dominated by Betaproteobacteria, whereas those with Saharan dust intrusions were dominated by Gammaproteobacteria. The high diversity and evenness observed in all samples suggests that different sources of bacteria contributed to the airborne assemblage collected at the lake shore. During experiments with bacterial assemblages collected during rain events with Saharan dust influence, cell numbers rapidly increased in sterile lake water from initially ∼3 × 103 cell ml-1 to 3.6-11.1 x105 cells ml-1 within 4-5 days, and initially, rare taxa dominated at the end of the experiment. Our study documents the dispersal of viable bacteria associated to Saharan dust intrusions travelling northwards as far as 47° latitude.

A recent pyrosequencing study along the whole Baltic Sea salinity transect identified members of the Verrucomicrobia class Spartobacteria as an important component of Baltic Sea bacterioplankton. In this study, catalysed reporter deposition-fluorescence in situ hybridization was used for cellular quantification. The published probes VER47 and SPA714 were optimized for samples from the Baltic Sea and a new, specific probe (SPA476) was used to quantify the dominant spartobacterial lineage ‘LD29’. The results confirmed that in the brackish surface waters of the Baltic Sea Spartobacteria comprise an important component, constituting up to 12% of all bacteria. The positive correlation and physical association of Spartobacteria with phytoplankton suggest their involvement in the utilization of phytoplankton-derived organic matter in the Baltic Sea.

The FISH probe TM7-305 is thought to target the filamentous Eikelboom morphotype 0041 as a member of the Candidatus ‘Saccharibacteria’ (formerly TM7) phylum. However, with activated sludge samples in both Japan and Australia, this probe hybridized consistently with filamentous bacteria fitting the description of the morphotype 1851, which also responded positively to the CHL1851 FISH probe designed to target Chloroflexi members of this morphotype. 16S rRNA clone libraries from samples containing type 1851 TM7-305-positive filaments yielded Chloroflexi clones with high sequence similarity to Kouleothrix aurantiaca. These contained a variant TM7-305 probe target site possessing weakly destabilizing mismatches insufficient to prevent probe hybridization. Furthermore, the TM7-905 FISH probe, designed to target members of the entire Candidatus ‘Saccharibacteria’ phylum, also hybridized with the filament morphotypes 0041/0675, which responded also to the phylum level Chloroflexi probes. Many Chloroflexi sequences have only a single base mismatch to the TM7-905 probe target sequence. When competitor probes for both the TM7-305 and TM7-905 Chloroflexi non-target sites were applied, no fluorescent signal was seen in any of the filamentous organisms also hybridizing with the aforementioned Chloroflexi probes. These data indicate that these competitor probes must be included in hybridizations when both the TM7-905 and TM7-305 FISH probes are applied, to minimize potential false positive FISH results.

Escherichia coli can be divided into several distinct phylogenetic groups that differ in their capacity to cause disease. However, what drives the relative abundance of these different phylogenetic groups in the commensal intestinal community of humans is poorly understood. This study investigated how host age and sex influences E. coli community structure in humans. Faecal samples were collected from 205 outpatients in Australia. Different strains within each sample were identified using rep-PCR profiles and their phylogenetic group membership was determined by quadruplex PCR. Female individuals carrying a dominant B2 strain were found to possess fewer strains than those carrying dominant A or B1 strains. Additionally, strains from the same phylogenetic group were more likely to co-occur in females. By contrast, strain diversity and phylogenetic group associations did not differ significantly from random in males. Host age was found to have a significant effect on the phylogenetic group of the dominant strain. Together these findings indicate that the distribution of the different phylogenetic groups within the human intestinal tract may be mediated by a complex interaction between the host environment and the competitive interactions between strains.

Anaerobic ammonium oxidizers contribute to the removal of fixed nitrogen in oxygen-deficient marine ecosystems such as oxygen minimum zones (OMZ). Here we surveyed for the first time the occurrence and diversity of anammox bacteria in the Colombian Pacific, a transition area between the prominent South and North Pacific OMZs. Anammox bacteria were detected in the coastal and oceanic areas of the Colombian Pacific in low oxygen (< 22 μM), high nitrate (25–35 μM) and low nitrite (< 0.07 μM), and ammonium (< 1 μM) waters. In these waters, anammox bacteria were rich [∼ 7 operational taxonomic units (OTUs), 98% cut-off) and microdiverse (Shannon index H′ < 1.24), in comparison with the observed at the prominent OMZ of the Eastern Tropical South Pacific, Arabian Sea and Black Sea. Anammox bacteria-like sequences from the Colombian Pacific were grouped together with sequences retrieved from the distinct OMZ's marine subclusters (Peru, Northern Chile and Arabian Sea) within Candidatus ‘Scalindua spp’. Moreover, some anammox bacteria OTUs shared a low similarity with environmental phylotypes (86–94%). Our results indicated that a microdiverse anammox community inhabits the Colombian Pacific, generating new questions about the ecological and biogeochemical differences influencing its community structure.

Cyanophages are abundant in the oceanic environment and directly impact cyanobacterial distributions, physiological processes and evolution. Two samples collected from coastal Maine in July and September 2009 were enriched for Synechococcus cells using flow cytometry and examined through metagenomic sequencing. Homology-based sequence prediction indicated cyanophages, largely myoviruses, accounted for almost half the reads and provided insights into environmental infection events. T4-phage core-gene phylogenetic reconstruction revealed unique diversity among uncultured cyanophages and reference isolates resulting in identification of a new phylogenetic cluster. Genomic comparison of reference cyanophage strains S-SM2 and Syn1 with putative homologous contigs recovered from metagenomes provided evidence that gene insertion, deletion and recombination have occurred among, and are likely important for diversification of, natural populations. Identification of putative genetic exchange between cyanophage and non-cyanophage viruses, i.e. Micromonas virus and Pelagibacter phage, supports hypotheses related to a significant role for viruses in mediating transfer of genetic material between taxonomically diverse organisms with overlapping ecological niches.

It is well established that the release of anthropogenic-derived CO2 into the atmosphere will be mainly absorbed by the oceans, with a concomitant drop in pH, a process termed ocean acidification. As such, there is considerable interest in how changes in increased CO2 and lower pH will affect marine biota, such as bacteria, which play central roles in oceanic biogeochemical processes. Set within an ecological framework, we investigated the direct effects of elevated CO2, contrasted with ambient conditions on the resistance and resilience of marine bacterial communities in a replicated temporal seawater mesocosm experiment. The results of the study strongly indicate that marine bacterial communities are highly resistant to the elevated CO2 and lower pH conditions imposed, as demonstrated from measures of turnover using taxa–time relationships and distance–decay relationships. In addition, no significant differences in community abundance, structure or composition were observed. Our results suggest that there are no direct effects on marine bacterial communities and that the bacterial fraction of microbial plankton holds enough flexibility and evolutionary capacity to withstand predicted future changes from elevated CO2 and subsequent ocean acidification.

Aerobic nitrite oxidation in marine environments plays a key role in the nitrification process. Marine bacteria involved in this nitrate-producing process have however been seldom studied compared with the ammonia-oxidizing community. Here, we report for the first time the community structure of aerobic nitrite-oxidizing bacteria (NOB) in the seasonal upwelling and oxygen-deficient area off Central Chile. Analysis of 16S rRNA by tag pyrosequencing was combined with specific quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR in summer and wintertime. Nitrospina-like bacteria were the only known NOB detected by means of pyrosequencing between 30 and 80 m depth, accounting for up to 5% of total bacteria. This guild was represented by 11 and 7 operational taxonomic units (97% cut-off) in winter and summertime respectively. Nitrospina-like bacteria were phylogenetically related to sequences retrieved from coastal upwelling, oxygen minimum zones and deep-sea environments. This group was also detected by qPCR with abundances that increased with depth throughout the water column. Importantly, Nitrospina from surface layers showed low abundances but high 16S rRNA : rDNA ratios and mainly in summertime. Overall, our results highlight the seasonal variability between the structure and physiological state of this community and suggest a significant role of Nitrospina in the nitrogen cycle of seasonal upwelling areas.

We investigated H2S attenuation by dissimilatory perchlorate-reducing bacteria (DPRB). All DPRB tested oxidized H2S coupled to (per)chlorate reduction without sustaining growth. H2S was preferentially utilized over organic electron donors resulting in an enriched (34S)-elemental sulfur product. Electron microscopy revealed elemental sulfur production in the cytoplasm and on the cell surface of the DPRB Azospira suillum. Based on our results, we propose a novel hybrid enzymatic-abiotic mechanism for H2S oxidation similar to that recently proposed for nitrate-dependent Fe(II) oxidation. The results of this study have implications for the control of biosouring and biocorrosion in a range of industrial environments.

Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome-wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria.

Little is known about endophytic microbes in cold climate plants and how their communities are formed.We compared culturable putative endophytic bacteria and fungi in the ecologically important circumpolargrass, Deschampsia flexuosa growing in two successional stages of subarctic sand dune (68°29′N).Sequence analyses of partial 16S rRNA and internal transcribed spacer (ITS) sequences of culturable endophytes showed that diverse bacteria and fungi inhabit different tissues of D. flexuosa. A total of 178 bacterial isolates representing seven taxonomic divisions, Alpha, Beta and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Acidobacteria, and 30 fungal isolates representing the phylum Ascomycota were identified. Several endophytes were affiliated with specific plant tissues or successional stages. This first report of bacterial endophytes in D. flexuosa revealed that the genus Pseudomonas is tightly associated with D. flexuosa, and encompassed 39% of the bacterial isolates, and 58% of seed isolates. Based on 16S rRNA and ITS sequence data, most of the D. flexuosa endophytes were closely related to microbes from other cold environments. The majority of seed endophytic bacterial isolates were able to solubilize organic form of phosphate suggesting that these endophytes could play a role in resource mobilization in germinating seeds in nutrient-poor habitat.

Bacterial Rieske-type aromatic ring-hydroxylating oxygenases (RHOs) constitute a large family of enzymes, primarily involved in bioremediation of diverse aromatic compounds in the environment. In the present study, we have designed a manually curated database, Ring-Hydroxylating Oxygenase database (RHObase), which provides comprehensive information on all biochemically characterized bacterial RHOs. It consists of ∼ 1000 entries including 196 oxygenase α-subunits, 153 oxygenase β-subunits, 92 ferredoxins and 110 reductases, distributed among 131 different bacterial strains implementing a total of 318 oxygenation reactions. For each protein, users can get detailed information about its structure and conserved domain(s) with motif signature. RHObase allows users to search a query, based on organism, oxygenase, substrate, or protein structure. In addition, this resource provides analysis tools to perform blast search against RHObase for prediction of putative substrate(s) for the query oxygenase and its phylogenetic affiliation. Furthermore, there is an integrated cheminformatics tool to search for structurally similar compound(s) in the database vis-a-vis RHO(s) capable of transforming those compound(s). Resources in the RHObase and multiple search/display options therein are intended to provide oxygenase-related requisite information to researchers, especially working in the field of environmental microbiology and biocatalysis to attain difficult chemistry of biotechnological importance.

Nickel (Ni)-tolerant ectomycorrhizal Pisolithus albus was isolated from extreme ultramafic soils that are naturally rich in heavy metals. This study aimed to identify the specific molecular mechanisms associated with the response of P. albus to nickel. In presence of high concentration of nickel, P. albus Ni-tolerant isolate showed a low basal accumulation of nickel in its fungal tissues and was able to perform a metal efflux mechanism. Three genes putatively involved in metal efflux were identified from the P. albus transcriptome, and their overexpression was confirmed in the mycelium that was cultivated in vitro in the presence of nickel and in fungal tissues that were sampled in situ. Cloning these genes in yeast provided significant advantages in terms of nickel tolerance (+ 31% Ni EC50) and growth (+ 83% μ) compared with controls. Furthermore, nickel efflux was also detected in the transformed yeast cells. Protein sequence analysis indicated that the genes encoded a P-type-ATPase, an ABC transporter and a major facilitator superfamily permease (MFS). This study sheds light on a global mechanism of metal efflux by P. albus cells that supports nickel tolerance. These specific responses to nickel might contribute to the fungal adaptation in ultramafic soil.

Manganese (Mn) is an essential nutrient and precipitates as minerals with technological and environmental relevance. To gain a proteomic understanding of how bacteria respond to Mn(II) and its connection to oxidation, a comparative examination of the proteomic response of Mn(II)-oxidizing (Roseobacter sp. AzwK-3b) and non-oxidizing (Ruegeria sp. TM1040) alphaproteobacteria was conducted. Both bacteria show an operative Mn(II) transport system. In the absence of Mn(II), both bacteria have higher expression of proteins that were homologous to SitA and SitB, known proteins in the Mn(II) transport system of other alphaproteobacteria. Overall, each bacterium demonstrated a varied response to Mn(II). Ru. TM1040 had a greater number of proteins differentially expressed in response to Mn(II) and also had a group of proteins related to chemotaxis at higher concentrations of Mn(II), suggesting a potential stress response. While both bacteria are able to generate extracellular superoxide and Mn(II) is a known antioxidant, the presence of Mn(II) did not significantly alter the expression of proteins related to antioxidant activity. Heme peroxidases, previously connected to Mn(II) oxidation, were found in the soluble protein extract of R. AzwK-3b, but only minor differential expression was observed as a function of Mn(II), indicating that their expression was not induced by Mn(II).

Soluble Mn(III) represents an important yet overlooked oxidant in marine and freshwater systems. The molecular mechanism of microbial Mn(III) reduction, however, has yet to be elucidated. Extracellular reduction of insoluble Mn(IV) and Fe(III) oxides by the metal-reducing γ-proteobacterium Shewanella oneidensis involves inner (CymA) and outer (OmcA) membrane-associated c-type cytochromes, the extracellular electron conduit MtrCAB, and GspD, the secretin of type II protein secretion. CymA, MtrCAB and GspD mutants were unable to reduce Mn(III) and Mn(IV) with lactate, H2, or formate as electron donor. The OmcA mutant reduced Mn(III) and Mn(IV) at near wild-type rates with lactate and formate as electron donor. With H2 as electron donor, however, the OmcA mutant was unable to reduce Mn(III) but reduced Mn(IV) at wild-type rates. Analogous Fe(III) reduction rate analyses indicated that other electron carriers compensated for the absence of OmcA, CymA, MtrCAB and GspD during Fe(III) reduction in an electron donor-dependent fashion. Results of the present study demonstrate that the S. oneidensis electron transport and protein secretion components involved in extracellular electron transfer to external Mn(IV) and Fe(III) oxides are also required for electron transfer to Mn(III) and that OmcA may function as a dedicated component of an H2 oxidation-linked Mn(III) reduction system.

The chromosome of Pseudomonas putida KT2440 carries two clusters of genes, denoted ars1 and ars2, that are annotated as putative arsenic resistance operons. In this work, we present evidence that both operons encode functional arsenic-response regulatory genes as well as arsenic extrusion systems that confer resistance to both arsenite [As(III)] and arsenate [As(V)]. Transcriptional fusions of P(ars1) and P(ars2) to lacZ revealed that expression of both operons was induced by arsenite and arsenate. We generated single mutants in ars1 and ars2, which showed lower resistance to arsenic than the wild-type strain. A double ars1/ars2 was found to be highly sensitive to arsenic. Minimum inhibitory concentrations (MICs) for single mutants decreased two- to fourfold with respect to the parental strain, while in the double mutant the MIC decreased 128-fold for arsenite and 32-fold for arsenate. Bioinformatic analysis revealed that the ars2 resistance operon is part of the core genome of P. putida, while the ars1 operon appears to only occur in the KT2440 strain, suggesting that ars1 was acquired by horizontal gene transfer. The presence of ars1 in KT2440 may explain why it exhibits higher resistance to arsenic than other P. putida strains, which bear only the ars2 operon.

Microbial arsenic transformation pathways associated with a saline lake located in northern Mongolia were examined using molecular biological and culturing approaches. Bacterial 16S rRNA gene sequences recovered from saline lake sediments and soils were affiliated with haloalkaliphiles, including Bacillus and Halomonas spp. Diverse sequences of arsenate respiratory reductase (arrA) and a new group of arsenite oxidase (arxA) genes were also identified. Pure cultures of arsenate-reducing Nitrincola strain and anaerobic arsenite-oxidizing Halomonas strain were isolated. The chemoorganotrophic Halomonas strain contains arxA gene similar to that of a chemoautotrophic arsenite-oxidizing Alkalilimnicola ehrlichii strain MLHE-1. These results revealed the diversity of arsenic transformation pathways associated with a geographically distinct saline system and the potential contribution of arx-dependent arsenite oxidation by heterotrophic bacteria.

The cyanobacterial phylum includes oxygenic photosynthetic prokaryotes of a wide variety of morphologies, metabolisms and ecologies. Their adaptation to their various ecological niches is mainly achieved by sophisticated regulatory mechanisms and depends on a fine cross-talk between them. We assessed the global transcriptomic response of the filamentous cyanobacterium Nostoc PCC 7120 to iron starvation and oxidative stress. More than 20% of the differentially expressed genes in response to iron stress were also responsive to oxidative stress. These transcripts include antioxidant proteins-encoding genes that confirms that iron depletion leads to reactive oxygen accumulation. The activity of the Fe-superoxide dismutase was not significantly decreased under iron starvation, indicating that the oxidative stress generated under iron deficiency is not a consequence of (SOD) deficiency. The transcriptional data indicate that the adaptation of Nostoc to iron-depleted conditions displays important differences with what has been shown in unicellular cyanobacteria. While the FurA protein that regulates the response to iron deprivation has been well characterized in Nostoc, the regulators in charge of the oxidative stress response are unknown. Our study indicates that the alr0957 (perR) gene encodes the master regulator of the peroxide stress. PerR is a peroxide-sensor repressor that senses peroxide by metal-catalysed oxidation.

Siderophores are organic chelators produced by microorganisms to fulfil their iron requirements. Siderophore-promoted dissolution of iron-bearing minerals has been clearly documented for some siderophores, but few studies have addressed metabolizing siderophore-producing bacteria. We investigated iron acquisition from clays by fluorescent Pseudomonads, bacteria that are ubiquitous in the environment. We focused on the interactions between smectite and Pseudomonas aeruginosa, a bacterium producing two structurally different siderophores: pyoverdine and pyochelin. The presence of smectite in iron-limited growth media promoted planktonic growth of P. aeruginosa and biofilm surrounding the smectite aggregates. Chemical analysis of the culture media indicated increases in the dissolved silicon, iron and aluminium concentrations following smectite supplementation. The use of P. aeruginosa mutants unable to produce either one or both of the two siderophores indicated that pyoverdine, the siderophore with the higher affinity for iron, was involved in iron and aluminium solubilization by the wild-type strain. However, in the absence of pyoverdine, pyochelin was also able to solubilize iron but with a twofold lower efficiency. In conclusion, pyoverdine and pyochelin, two structurally different siderophores, can solubilize structural iron from smectite and thereby make it available for bacterial growth.

Currently, little is known about the impact of silver nanoparticles (AgNPs) on ecologically important microorganisms such as ammonia-oxidizing bacteria (AOB). We performed a multi-analytical approach to demonstrate the effects of uncapped nanosilver (uAgNP), capped nanosilver (cAgNP) and Ag2SO4 on the activities of the AOB: Nitrosomonas europaea, Nitrosospira multiformis and Nitrosococcus oceani, and the growth of Escherichia coli and Bacillus subtilis as model bacterial systems in relation to AgNP type and concentration. All Ag treatments caused significant inhibition to the nitrification potential rates (NPRs) of Nitrosomonas europaea (decreased from 34 to < 16.7 μM NH4+ oxidized day−1), Nitrosospira multiformis (decreased from 46 to < 24.8 μM NH4+ oxidized day−1) and Nitrosococcus oceani (decreased from 26 to < 18.4 μM NH4+ oxidized day−1). Escherichia coli-Ag interactions revealed that the percentage of damaged E. coli cells was 45% greater with Ag2SO4, 39% with cAgNPs and 33% with uAgNPs compared with controls. Generally, the inhibitory effect on AOB NPRs and E. coli/B. subtilis growth was in the following order Ag2SO4 > cAgNP > uAgNP. In conclusion, AgNPs (especially cAgNPs) and Ag2SO4 adversely affected AOB activities and thus have the potential to severely impact key microbially driven processes such as nitrification in the environment.

The corrinoid protein, HgcA has been shown to be essential for Hg methylation in anaerobic bacteria. We investigated the diversity of hgcA from temperate and tropical wetland soils where Hg methylation is demonstrated. Sequences obtained from both environments clustered with those from the δ-Proteobacteria, Chloroflexi and Methanomicrobia with significant overlap in hgcA phylogeny between libraries. Clear differences in hgcA distribution were observed between two highly contrasting sites within a tropical wetland in Everglades National Park, USA. hgcA sequences obtained from the northern site clustered primarily with those of methanogens, while sequences from the estuarine site clustered primarily with sulphate-reducing bacteria and syntrophs in the δ-Proteobacteria. Libraries obtained from soils collected from a temperate swamp in Sweden were dominated by hgcA sequences within the δ-Proteobacteria with hgcA sequences clustering primarily with iron reducers in the upstream portion of the swamp and with sulphate reducers in the downstream portion of the swamp. Interestingly, enrichments prepared from the lower portion of this temperate wetland contained a high abundance of hgcA sequences clustering with methanogens. This first report on hgcA diversity in environmental samples suggests a role in Hg methylation for various phenotypic groups in different portions of wetlands.

Pectate lyases are enzymes involved in plant cell wall degradation. They cleave pectin using a β-elimination mechanism, specific for acidic polysaccharides. They are mainly produced by plant pathogens and plant-associated organisms, and only rarely by animals. Pectate lyases are also commonly produced in the bacterial world, either by bacteria living in close proximity with plants or by gut bacteria that find plant material in the digestive tract of their hosts. The role of pectate lyases is essential for plant pathogens, such as Dickeya dadantii, that use a set of pectate lyases as their main virulence factor. Symbiotic bacteria produce their own pectate lyases, but they also induce plant pectate lyases to initiate the symbiosis. Pectin degradation products may act as signals affecting the plant–bacteria interactions. Bacterial pectate lyases are also essential for using the pectin of dead or living plants as a carbon source for growth. In the animal gut, Bacteroides pectate lyases degrade the pectin of ingested food, and this is particularly important for herbivores that depend on their microflora for the digestion of pectin. Some human pathogens, such as Yersinia enterocolitica, produce a few intracellular pectate lyases that can facilitate their growth in the presence of highly pectinolytic bacteria, at the plant surface, in the soil or in the animal gut.

Pseudomonads are a diverse and ecologically successful group of γ-proteobacteria present in many environments (terrestrial, freshwater and marine), either free living or associated with plants or animals. Their success is at least partly based on their ability to grow over a wide range of temperatures, their capacity to withstand different kinds of stress and their great metabolic versatility. Although the optimal growth temperature of pseudomonads is usually close to 25–30°C, many strains can also grow between 5°C and 10°C, and some of them even close to 0°C. Such low temperatures strongly affect the physicochemical properties of macromolecules, forcing cells to evolve traits that optimize growth and help them withstand cold-induced stresses such as increased levels of reactive oxygen species, reduced membrane fluidity and enzyme activity, cold-induced protein denaturation and the greater stability of DNA and RNA secondary structures. This review gathers the information available on the strategies used by pseudomonads to adapt to low temperature growth, and briefly describes some of the biotechnological applications that might benefit from cold-adapted bacterial strains and enzymes, e.g., biotransformation or bioremediation processes to be performed at low temperatures.

Removal of selenium from groundwater was documented during injection of acetate into a uranium-contaminated aquifer near Rifle, Colorado (USA). Bioreduction of aqueous selenium to its elemental form (Se0) concentrated it within mineralized biofilms affixed to tubing used to circulate acetate-amended groundwater. Scanning and transmission electron microscopy revealed close association between Se0 precipitates and cell surfaces, with Se0 aggregates having a diameter of 50-60 nm. Accumulation of Se0 within biofilms occurred over a three-week interval at a rate of c. 9 mg Se0 m(-2) tubing day(-1). Removal was inferred to result from the activity of a mixed microbial community within the biofilms capable of coupling acetate oxidation to the reduction of oxygen, nitrate and selenate. Phylogenetic analysis of the biofilm revealed a community dominated by strains of Dechloromonas sp. and Thauera sp., with isolates exhibiting genetic similarity to the latter known to reduce selenate to Se0. Enrichment cultures of selenate-respiring microorganisms were readily established using Rifle site groundwater and acetate, with cultures dominated by strains closely related to D. aromatica (96-99% similarity). Predominance of Dechloromonas sp. in recovered biofilms and enrichments suggests this microorganism may play a role in the removal of selenium oxyanions present in Se-impacted groundwaters and sediments.