Bacterial Phylogenetic Groups Research Articles

Species abundance correlations carry limited information about microbial network interactions.

Unraveling the network of interactions in ecological communities is a daunting task. Common methods to infer interspecific interactions from cross-sectional data are based on co-occurrence measures. For instance, interactions in the human microbiome are often inferred from correlations between the abundances of bacterial phylogenetic groups across subjects. We tested whether such correlation-based methods are indeed reliable for inferring interaction networks. For this purpose, we simulated bacterial communities by means of the generalized Lotka-Volterra model, with variation in model parameters representing variability among hosts. Our results show that correlations can be indicative for presence of bacterial interactions, but only when measurement noise is low relative to the variation in interaction strengths between hosts. Indication of interaction was affected by type of interaction network, process noise and sampling under non-equilibrium conditions. The sign of a correlation mostly coincided with the nature of the strongest pairwise interaction, but this is not necessarily the case. For instance, under rare conditions of identical interaction strength, we found that competitive and exploitative interactions can result in positive as well as negative correlations. Thus, cross-sectional abundance data carry limited information on specific interaction types. Correlations in abundance may hint at interactions but require independent validation.

Murine response to the opportunistic bacterium Pseudomonas aeruginosa infection in gut dysbiosis caused by 5-fluorouracil chemotherapy-induced mucositis

Aims: This manuscript aims to explain the relationship between mucositis caused by 5-FU over gut bacterial species and susceptibility to opportunistic infection caused by P. aeruginosa. Main methods: BALB/c mice were intraperitoneally treated with PBS or 5-FU. Bodyweight and faecal consistency were checked daily. Mice faecal DNA was extracted, and bacterial phylogenetic groups were analysed using qPCR or high-throughput sequencing. Immunofluorescence was used to evaluate BMDM activation by mice-treated faecal content. Mice were challenged intratracheally with virulent P. aeruginosa, and the CFU and histology were analysed. Faecal microbiota were transplanted to evaluate the gut microbiota and resistance to pulmonary P. aeruginosa recovery. Key findings: The animals treated with 5-FU presented mucositis with great weight loss, altered faecal consistency, bacterial gut dysbiosis and histological changes in the intestinal mucosa. Mice under 5-FU treatment were more susceptible to lung infection by the bacteria P. aeruginosa and had more extensive tissue damage during their lung infection with greater pro-inflammatory gene expression. It was observed that the mucositis remained in the groups with 5-FU even with the FMT. The results caused by mucositis in animals that received allogeneic FMT were reversed, however, with a decrease in P. aeruginosa susceptibility in animals treated with 5-FU and allogeneic FMT compared to animals treated with 5-FU and autologous FMT. Significance: Treatment with 5-FU in a murine model makes it more susceptible to pulmonary infection by the bacterium P. aeruginosa, FMT offers an opportunity to protect against this susceptibility to infection.

Bacterial Morphotypes as Important Trait for Uropathogenic E. coli Diagnostic; a Virulence-Phenotype-Phylogeny Study

Urinary tract infections (UTIs) belong to the most common pathologies in Mexico and are mainly caused by Uropathogenic Escherichia coli (UPEC). UPEC possesses a wide diversity of virulence factors that allow it to carry out its pathogenesis mechanism in the urinary tract (UT). The development of morphotypes in UT represents an important feature of UPEC because it is associated with complications in diagnosis of UTI. The aim of this study was to determine the presence of bacterial morphotypes, virulence genes, virulence phenotypes, antibiotic resistant, and phylogenetic groups in clinical isolates of UPEC obtained from women in Sonora, Mexico. Forty UPEC isolates were obtained, and urine morphotypes were observed in 65% of the urine samples from where E. coli was isolated. Phylogenetic group B2 was the most prevalent. The most frequent virulence genes were fimH (100%), fliCD (90%), and sfaD/focC (72%). Biofilm formation (100%) and motility (98%) were the most prevalent phenotypes. Clinical isolates showed high resistance to aminoglycosides and β-lactams antibiotics. These data suggest that the search for morphotypes in urine sediment must be incorporated in the urinalysis procedure and also that clinical isolates of UPEC in this study can cause upper, lower, and recurrent UTI.

Inhibition of Antimicrobial-Resistant Escherichia coli Using a Broad Host Range Phage Cocktail Targeting Various Bacterial Phylogenetic Groups.

Antimicrobial-resistant (AMR) commensal Escherichia coli is a major reservoir that disseminates antimicrobial resistance to humans through the consumption of contaminated foods, such as retail poultry products. This study aimed to control AMR E. coli on retail chicken using a broad host range phage cocktail. Five phages (JEP1, 4, 6, 7, and 8) were isolated and used to construct a phage cocktail after testing infectivity on 67 AMR E. coli strains isolated from retail chicken. Transmission electron microscopic analysis revealed that the five phages belong to the Myoviridae family. The phage genomes had various sizes ranging from 39 to 170 kb and did not possess any genes associated with antimicrobial resistance and virulence. Interestingly, each phage exhibited different levels of infection against AMR E. coli strains depending on the bacterial phylogenetic group. A phage cocktail consisting of the five phages was able to infect AMR E. coli in various phylogenetic groups and inhibited 91.0% (61/67) of AMR E. coli strains used in this study. Furthermore, the phage cocktail was effective in inhibiting E. coli on chicken at refrigeration temperatures. The treatment of artificially contaminated raw chicken skin with the phage cocktail rapidly reduced the viable counts of AMR E. coli by approximately 3 log units within 3 h, and the reduction was maintained throughout the experiment without developing resistance to phage infection. These results suggest that phages can be used as a biocontrol agent to inhibit AMR commensal E. coli on raw chicken.

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests.

Microbial communities in the immediate environment of socialized invertebrates can help to suppress pathogens, in part by synthesizing bioactive natural products. Here we characterized the core microbiomes of three termite species (genus Coptotermes) and their nest material to gain more insight into the diversity of termite-associated bacteria. Sampling a healthy termite colony over time implicated a consolidated and highly stable microbiome, pointing toward the fact that beneficial bacterial phyla play a major role in termite fitness. In contrast, there was a significant shift in the composition of the core microbiome in one nest during a fungal infection, affecting the abundance of well-characterized Streptomyces species (phylum Actinobacteria) as well as less-studied bacterial phyla such as Acidobacteria. High-throughput cultivation in microplates was implemented to isolate and identify these less-studied bacterial phylogenetic group. Amplicon sequencing confirmed that our method maintained the bacterial diversity of the environmental samples, enabling the isolation of novel Acidobacteriaceae and expanding the list of cultivated species to include two strains that may define new species within the genera Terracidiphilus and Acidobacterium.

Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria

Despite the development of several cultivation methods, the rate of discovery of microorganisms that are yet-to-be cultivated outpaces the rate of isolating and cultivating novel species in the laboratory. Furthermore, no current cultivation technique is capable of selectively isolating and cultivating specific bacterial taxa or phylogenetic groups independently of morphological or physiological properties. Here, we developed a new method to isolate living bacteria solely based on their 16S rRNA gene sequence. We showed that bacteria can survive a modified version of the standard fluorescence in situ hybridization (FISH) procedure, in which fixation is omitted and other factors, such as centrifugation and buffers, are optimized. We also demonstrated that labelled DNA probes can be introduced into living bacterial cells by means of chemical transformation and that specific hybridization occurs. This new method, which we call live-FISH, was then combined with fluorescence-activated cell sorting (FACS) to sort specific taxonomic groups of bacteria from a mock and natural bacterial communities and subsequently culture them. Live-FISH represents the first attempt to systematically optimize conditions known to affect cell viability during FISH and then to sort bacterial cells surviving the procedure. No sophisticated probe design is required, making live-FISH a straightforward method to be potentially used in combination with other single-cell techniques and for the isolation and cultivation of new microorganisms.

Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum

Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.

Abundance and Taxonomic Diversity of Bacteria Inhabiting the Sediment-Water Interface in a Marine Harbor Channel

The abundance of bacteria inhabiting the sediment-water interface and their taxonomic composition were determined with the fluorescence in situ hybridization (FISH) method in a marine harbor channel in Ustka. Among bacteria inhabiting the studied layer Gammaproteobacteria (1.4 cells 108·dm−3) and Cytophaga-Flavobacterium (1.1 cells 108·dm−3) dominated. Vibrio and Pseudomonas represented only a small fraction of the total cell counts. All taxonomic groups of studied bacteria show significant positive correlation between their abundance. The total bacterial number varied from 3.3 to 23.5 cells 108·dm−3 and their biomass oscillated from 39.4 to 282.4 μg C·dm−3. This parameter differed along horizontal profiles, while there were no significant differences in the abundance of the studied taxonomic groups among the study sites of the channel in Ustka. The total number of bacteria as well as the abundance of bacterial phylogenetic groups were subject to seasonal fluctuation in the studied water basin.

Microbial Community Diversity and Vertical Distribution in a Columnar Sediment of Maluku Strait

The sediment samples were collected from Maluku Strait at a depth of 1250 m, which is influenced by Mindanao Current and Indonesian Throughflow. Based on 16S rRNA clone libraries, the community structure and vertical distribution of archaea and bacteria were studied in a columnar sediment of 2m in length. From the surface sediment, 16S sequences were derived from fourteen bacterial phyla (Gammaproteobacteria, Planctomycetes, Alphaproteobacteria, Deltproteobacteria were dominant), but were limited to two groups of archaea: Crenarchaeota (99%) and Euryarchaeota (1%). Besides, 90% of the archaea clones were ammonia oxidation-related which indicated that the ammonia-oxidizing archaea might make a significant contribution to the chemosynthesis in the surface sediment. Contrastively in the bottom sediment, six bacterial phylogenetic groups were obtained (Gammaproteobacteria and Firmicutes were absolutely dominant), however no archaea 16S rRNA was detected. The microbial diversity of surface sediment was much higher than the bottom and seven unique bacterial phyla were obtained from two sediment respectively. The geochemical elements analysis revealed that the content of C, TOC and S in the surface sediment was much higher than the bottom, but the content of P is contrary. The microbial communities might be in response to the geochemical substance transfer and deposit influenced by the ocean current and it deserves further study compared with the other sediment samples in this area.

Testing the metabolic theory of ecology with marine bacteria: different temperature sensitivity of major phylogenetic groups during the spring phytoplankton bloom.

Although temperature is a key driver of bacterioplankton metabolism, the effect of ocean warming on different bacterial phylogenetic groups remains unclear. Here, we conducted monthly short-term incubations with natural coastal bacterial communities over an annual cycle to test the effect of experimental temperature on the growth rates and carrying capacities of four phylogenetic groups: SAR11, Rhodobacteraceae, Gammaproteobacteria and Bacteroidetes. SAR11 was the most abundant group year-round as analysed by CARD-FISH, with maximum abundances in summer, while the other taxa peaked in spring. All groups, including SAR11, showed high temperature-sensitivity of growth rates and/or carrying capacities in spring, under phytoplankton bloom or post-bloom conditions. In that season, Rhodobacteraceae showed the strongest temperature response in growth rates, estimated here as activation energy (E, 1.43 eV), suggesting an advantage to outcompete other groups under warmer conditions. In summer E values were in general lower than 0.65 eV, the value predicted by the Metabolic Theory of Ecology (MTE). Contrary to MTE predictions, carrying capacity tended to increase with warming for all bacterial groups. Our analysis confirms that resource availability is key when addressing the temperature response of heterotrophic bacterioplankton. We further show that even under nutrient-sufficient conditions, warming differentially affected distinct bacterioplankton taxa.

Metabolic in Vivo Labeling Highlights Differences of Metabolically Active Microbes from the Mucosal Gastrointestinal Microbiome between High-Fat and Normal Chow Diet.

The gastrointestinal microbiota in the gut interacts metabolically and immunologically with the host tissue in the contact zone of the mucus layer. For understanding the details of these interactions and especially their dynamics it is crucial to identify the metabolically active subset of the microbiome. This became possible by the development of stable isotope probing techniques, which have only sparsely been applied to microbiome research. We applied the in vivo stable isotope approach using 15N-labeled diet with subsequent identification of metabolically active bacterial species. Four-week old male Sprague-Dawley rats were randomly assigned to chow diet (CD, n =15) and high-fat diet (HFD, n =15). After 11 weeks, three animals from each group were sacrificed for baseline characterization of anthropometric and metabolic obesity. The remaining animals were exposed to either a 15N-labeled (n =9) or a 14N-unlabeled experimental diet (n =3). Three rats from each cohort (HFD and CD) were sacrificed at 12, 24, and 72 h. The remaining three animals from each cohort, which received the 14N-unlabeled diet, were sacrificed after 72 h. The colon was harvested and divided into three equal sections (proximal, medial, and distal), and the mucus layer of each specimen was sampled by scraping. We identified the active subset in an HFD model of obesity in comparison with lean controls rats using metaproteomics. In addition, all samples were investigated by 16S rRNA amplicon gene sequencing. The active microbiome of the HFD group showed an increase in bacterial taxa for Verrucomicrobia and Desulfovibrionaceae. In contrast with no significant changes in alpha diversity, time- and localization-dependent effects in beta-diversity were clearly observed. In terms of enzymatic functions the HFD group showed strong affected metabolic pathways such as energy production and carbohydrate metabolism. In vivo isotope labeling combined with metaproteomics provides a valuable method to distinguish the active from the non-active bacterial phylogenetic groups that are relevant for microbiota-host interaction. For morbid obesity such analysis may provide potentially new strategies for targeted pre- or probiotic treatments.

Bacterioplankton niche partitioning in the use of phytoplankton-derived dissolved organic carbon: quantity is more important than quality.

Some prokaryotes are known to be specialized in the use of phytoplankton-derived dissolved organic carbon (DOCp) originated by exudation or cell lysis; however, direct quantification measurements are extremely rare. Several studies have described bacterial selectivity based on DOCp quality, but very few have focused on the quantity of DOCp, and the relative importance of each of these variables (for example, quantity versus quality) on prokaryote responses. We applied an adapted version of the MAR-FISH (microautoradiography coupled with catalyzed reporter deposition fluorescence in situ hybridization) protocol using radiolabelled exudates from axenic algal cultures to calculate a specialization index (d') for large bacterioplankton phylogenetic groups using DOCp from different phytoplankton species and at different concentrations to elucidate to what extent the bacterial response to DOCp is driven by resource quantity (different DOCp concentrations) or by quality (DOCp from different phytoplankton species). All bacterial phylogenetic groups studied had lower d' at higher DOCp concentration, indicating more generalist behavior at higher resource availabilities. Indeed, at increasing resource concentrations, most bacterial groups incorporated DOCp indiscriminately, regardless of its origin (or quality). At low resource concentrations, only some specialists were able to actively incorporate the various types of organic matter effectively. The variability of bacterial responses to different treatments was systematically higher at varying concentrations than at varying DOCp types, suggesting that, at least for this range of concentrations (10-100 μM), DOCp quantity affects bacterial responses more than quality does. Therefore, resource quantity may be more relevant than resource quality in the bacterial responses to DOCp and affect how bacterioplankton use phytoplankton-derived carbon.

Shifts in a bacterial community composition of a mesotrophic peatland after wildfire

The structural changes in the bacterial community composition of the Galitskii Mokh mesotrophic peatland (Tver oblast) after the 2010 wildfire were analyzed. Burned sites demonstrated an increase in peat water pH and mineralization, with elevated nitrate and sulfate concentrations, which resulted in doubling of the numbers of culturable sulfate reducers. Although the rate of methane oxidation by peat samples from burned sites decreased, methane emission did not increase. Enumeration of bacterial phylogenetic groups by fluorescent in situ hybridization revealed doubling of the numbers of Alphaproteobacteria and Bacteroidetes in burned areas compared to an undamaged site, while a reverse pattern was observed for Deltaproteobacteria and Planctomycetes. Comparative analysis of the 16S rRNA clone libraries revealed shifts in the bacterial community composition in the peat from burned sites. Slowly growing bacteria of the phyla Verrucomicrobia and Planctomycetes were replaced by fast-growing colonizers from the Proteobacteria. The originally diverse Actinobacterial community was replaced by the one dominated by the phylotypes related to thermophilic Aciditerrimonas ferrireducens. In the Acidobacteria, a typical group of peat-inhabiting bacteria, the subgroups 3, 6, and 17 were replaced by subgroups 7 and 10. These changes in the structure of peatland microbial communities could result in disturbances of some biospheric functions of these ecosystems.

Geosphere-biosphere interactions in bio-activity volcanic lakes: evidences from Hule and Rìo Cuarto (Costa Rica).

Hule and Río Cuarto are maar lakes located 11 and 18 km N of Poás volcano along a 27 km long fracture zone, in the Central Volcanic Range of Costa Rica. Both lakes are characterized by a stable thermic and chemical stratification and recently they were affected by fish killing events likely related to the uprising of deep anoxic waters to the surface caused by rollover phenomena. The vertical profiles of temperature, pH, redox potential, chemical and isotopic compositions of water and dissolved gases, as well as prokaryotic diversity estimated by DNA fingerprinting and massive 16S rRNA pyrosequencing along the water column of the two lakes, have highlighted that different bio-geochemical processes occur in these meromictic lakes. Although the two lakes host different bacterial and archaeal phylogenetic groups, water and gas chemistry in both lakes is controlled by the same prokaryotic functions, especially regarding the CO2-CH4 cycle. Addition of hydrothermal CO2 through the bottom of the lakes plays a fundamental priming role in developing a stable water stratification and fuelling anoxic bacterial and archaeal populations. Methanogens and methane oxidizers as well as autotrophic and heterotrophic aerobic bacteria responsible of organic carbon recycling resulted to be stratified with depth and strictly related to the chemical-physical conditions and availability of free oxygen, affecting both the CO2 and CH4 chemical concentrations and their isotopic compositions along the water column. Hule and Río Cuarto lakes were demonstrated to contain a CO2 (CH4, N2)-rich gas reservoir mainly controlled by the interactions occurring between geosphere and biosphere. Thus, we introduced the term of bio-activity volcanic lakes to distinguish these lakes, which have analogues worldwide (e.g. Kivu: D.R.C.-Rwanda; Albano, Monticchio and Averno: Italy; Pavin: France) from volcanic lakes only characterized by geogenic CO2 reservoir such as Nyos and Monoun (Cameroon).

Effect of East Asian aerosol enrichment on microbial community composition in the South China Sea

East Asian aerosol has been regarded as an increasingly important nutrient source in the Northwest Pacific region due to intensifying human activities in the last decades. However, its effects on bacterial communities, an important component of the marine microbial food web and biogeochemical cycles, have been little studied. In our study, two types of aerosol enrichment microcosm experiments were conducted in the oligotrophic South China Sea by adding the aerosol initially or daily. Our results showed that the potential stimulus of bacteria by aerosol enrichment was likely masked by a more intense grazing pressure in these treatments. Distinct responses of various bacterial phylogenetic groups, including Actinobacteria, Cyanobacteria, Alphaproteobacteria and Gammaproteobacteria, were revealed by denaturing gradient gel electrophoresis analysis. High aerosol addition resulted in a decrease in autotrophic picocyanobacteria abundance, but no significant composition change was observed. Such responses of microbial abundance and composition could be directly triggered by the input of aerosol-derived organic or inorganic components and further shaped by the changes in the phytoplankton community structure or differentiated mortality loss caused by enhanced protist grazing, which may have implications for oceanic carbon dynamics under future scenarios of increasing atmospheric deposition.

Molecular Characterization of Bacterial Phylogenetic and Functional Groups at Terrebonne Bay along the Coastline of the Gulf of Mexico

The detection and quantification of bacterial phylogenetic and functional groups as well as community diversity at the site of the Deepwater Horizon oil spill in Terrebonne Bay along the Gulf of Mexico were carried out using nucleic acid staining, Fluorescence in situ Hybridization (FISH) and 16S rRNA gene cloning and sequencing approaches. Results from the 16S rRNA gene clone library analysis revealed high occurrences of bacterial members belonging to the Cyanobacteria (28%), β- Proteobacteria (21%), Bacteroidetes (17%), Actinobacteria (12%) and the α- Proteobacteria (10%). Particularly, bacterial members identified within the clone library as belonging to the β- Proteobacteria subclass were mostly hydrocarbon degraders, including Methylibium petroleiphilum, Burkholderia cepacia, Hydrogenophaga taeniospiralis and Methylobacillus flagellates. Simultaneous analyses of both planktonic and benthic bacterial communities by FISH revealed the numerical dominance of members of the type I Methanotrophic Bacteria (MB) over the type II populations. The results from the study clearly reveal a shift in the bacterial community structure and composition in response to the tragic methane and crude oil discharges from the Deepwater Horizon rig along the Gulf of Mexico.

Molecular characterization of ancient algal mats from the McMurdo Dry Valleys, Antarctica

AbstractThe McMurdo Dry Valleys possess a cold and dry climate which favours biomolecular preservation, and present the possibility for preservation of biological materials over long timescales. We examined patterns of bacterial DNA abundance and diversity in algal mats from 8–26 539 years of age. Bacterial DNA abundance was inferred from extractable DNA quantity and quantitative polymerase chain reaction targeting the bacterial 16S rRNA gene. Because damage to bacterial DNA could limit its availability for polymerase chain reaction, the efficacy of DNA repair by a commercially available kit was also examined. Polymerase chain reaction amplicons of the bacterial 16S rRNA gene were obtained from seven of eight samples. Bulk DNA abundance and bacterial 16S rRNA gene copy number of template DNA declined with increasing sample age consistent with expectations of accumulation of DNA damage in ancient materials. Clone libraries revealed age related patterns of abundance for some bacterial phylogenetic groups. For example, Firmicutes and several other lineages were abundant in ancient samples, but Cyanobacteria were absent. This points to a biased persistence of bacterial lineages that change over time since photosynthesis was active.

Jellyfish blooms result in a major microbial respiratory sink of carbon in marine systems

Jellyfish blooms occur in many estuarine and coastal regions and may be increasing in their magnitude and extent worldwide. Voracious jellyfish predation impacts food webs by converting large quantities of carbon (C), fixed by primary producers and consumed by secondary producers, into gelatinous biomass, which restricts C transfer to higher trophic levels because jellyfish are not readily consumed by other predators. In addition, jellyfish release colloidal and dissolved organic matter (jelly-DOM), and could further influence the functioning of coastal systems by altering microbial nutrient and DOM pathways, yet the links between jellyfish and bacterioplankton metabolism and community structure are unknown. Here we report that jellyfish released substantial quantities of extremely labile C-rich DOM, relative to nitrogen (25.6 ± 31.6 C:1N), which was quickly metabolized by bacterioplankton at uptake rates two to six times that of bulk DOM pools. When jelly-DOM was consumed it was shunted toward bacterial respiration rather than production, significantly reducing bacterial growth efficiencies by 10% to 15%. Jelly-DOM also favored the rapid growth and dominance of specific bacterial phylogenetic groups (primarily γ-proteobacteria) that were rare in ambient waters, implying that jelly-DOM was channeled through a small component of the in situ microbial assemblage and thus induced large changes in community composition. Our findings suggest major shifts in microbial structure and function associated with jellyfish blooms, and a large detour of C toward bacterial CO(2) production and away from higher trophic levels. These results further suggest fundamental transformations in the biogeochemical functioning and biological structure of food webs associated with jellyfish blooms.

Group-specific effects on coastal bacterioplankton of polyunsaturated aldehydes produced by diatoms

Polyunsaturated aldehydes (PUAs), produced as secondary metabolites by diatoms, have been shown to induce toxic effects on a variety of organisms, including copepods and phyto- and bacterioplankton. However, the nature of and the players in this interaction remain poorly under- stood. We tested the effect of 3 PUAs commonly produced by marine diatoms—2E,4E/Z-heptadienal (HEPTA), 2E,4E/Z-octadienal (OCTA), 2E,4E/Z-decadienal (DECA) and a mix of HEPTA and OCTA (MIX)—on a natural bacterial community from a coastal area of the NW Mediterranean Sea (Blanes Bay, Spain). Little effect on total or relative cell abundance or bulk bacterial production was observed after 6 or 24 h exposure to 7.5 nM of the 3 different PUAs for the different bacterial phylogenetic groups (Gammaproteobacteria, Bacteroidetes, Rhodobacteraceae and SAR11), assessed by catalysed reporter deposition (CARD)-fluorescence in situ hybridisation (FISH). Metabolic activity, i.e. single- cell activity as determined by microautoradiography combined with CARD-FISH (MAR-CARD- FISH), was least affected by the addition of single PUAs in Gammaproteobacteria, markedly in Bac- teroidetes and most markedly in Rhodobacteraceae, leading to a decrease in Rhodobacteraceae abundance by 21% (by 38% of the active cells assessed by leucine uptake) compared to the control. Bacteroidetes, although markedly affected in single-cell activity, were the most abundant group (54% of total cell counts). The addition of a mixture of OCTA and HEPTA produced a more pro- nounced decrease in the metabolic activity of all groups than the incubation with the single PUAs, suggesting a synergistic effect. Our results demonstrate that PUAs have a differential effect on the single-cell activity of distinct bacterial groups in natural communities. PUAs may therefore play an important role in shaping bacterial community composition by conferring a competitive advantage to PUA-resistant groups, allowing them to preferentially use the organic matter released by diatoms.

Anaerobic Oxidation of Methane at a Marine Methane Seep in a Forearc Sediment Basin off Sumatra, Indian Ocean

A cold methane seep was discovered in a forearc sediment basin off the island Sumatra, exhibiting a methane-seep adapted microbial community. A defined seep center of activity, like in mud volcanoes, was not discovered. The seep area was rather characterized by a patchy distribution of active spots. The relevance of anaerobic oxidation of methane (AOM) was reflected by 13C-depleted isotopic signatures of dissolved inorganic carbon. The anaerobic conversion of methane to CO2 was confirmed in a 13C-labeling experiment. Methane fueled a vital microbial community with cell numbers of up to 4 × 109 cells cm−3 sediment. The microbial community was analyzed by total cell counting, catalyzed reporter deposition–fluorescence in situ hybridization (CARD–FISH), quantitative real-time PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). CARD–FISH cell counts and qPCR measurements showed the presence of Bacteria and Archaea, but only small numbers of Eukarya. The archaeal community comprised largely members of ANME-1 and ANME-2. Furthermore, members of the Crenarchaeota were frequently detected in the DGGE analysis. Three major bacterial phylogenetic groups (δ-Proteobacteria, candidate division OP9, and Anaerolineaceae) were abundant across the study area. Several of these sequences were closely related to the genus Desulfococcus of the family Desulfobacteraceae, which is in good agreement with previously described AOM sites. In conclusion, the majority of the microbial community at the seep consisted of AOM-related microorganisms, while the relevance of higher hydrocarbons as microbial substrates was negligible.