Habitat-Associated Phylogenetic Community Patterns of Microbial Ammonia Oxidizers.

9 páginas, 6 figuras.Microorganisms mediating ammonia oxidation play a fundamental role in the connection between biological nitrogen fixation and anaerobic nitrogen losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively) have colonized similar habitats worldwide. Ammonia oxidation is the rate-limiting step in nitrification, and the ammonia monooxygenase (Amo) is the key enzyme involved. The molecular ecology of this process has been extensively explored by surveying the gene of the subunit A of the Amo (amoA gene). In the present study, we explored the phylogenetic community ecology of AOB and AOA, analyzing 5776 amoA gene sequences from .300 isolation sources, and clustering habitats by environmental ontologies. As a whole, phylogenetic richness was larger in AOA than in AOB, and sediments contained the highest phylogenetic richness whereas marine plankton the lowest. We also observed that freshwater ammonia oxidizers were phylogenetically richer than their marine counterparts. AOA communities were more dissimilar to each other than those of AOB, and consistent monophyletic lineages were observed for sediments, soils, and marine plankton in AOA but not in AOB. The diversification patterns showed a more constant cladogenesis through time for AOB whereas AOA apparently experienced two fast diversification events separated by a long steady-state episode. The diversification rate (c statistic) for most of the habitats indicated cAOA . cAOB. Soil and sediment experienced earlier bursts of diversification whereas habitats usually eutrophic and rich in ammonium such as wastewater and sludge showed accelerated diversification rates towards the present. Overall, this work shows for the first time a global picture of the phylogenetic community structure of both AOB and AOA assemblages following the strictest analytical standards, and provides an ecological view on the differential evolutionary paths experienced by widespread ammonia-oxidizing microorganisms. The emerged picture of AOB and AOA distribution in different habitats provides a new view to understand the ecophysiology of ammonia oxidizers on Earth.This work was funded by grants PIRENA CGL2009-13318-CO2-01/BOS, and CONSOLIDER-INGENIO 2010 project GRACCIE CSD2007-00067 from the Spanish Ministerio de Ciencia e Innovacio´n (MICINN), and project GECA 2009SGR361 from Generalitat de Catalunya to JC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewe

High genetic diversity and high novelty in planktonic protists inhabiting inland and coastal high salinity water bodies

10 páginas, 5 figuras, 1 tabla.We analyzed the genetic diversity (18S rRNA gene) of planktonic microbial eukaryotes in 34 different coastal and inland saline ponds. A wide range of environmental conditions was covered with up to 30-fold differences in salinity concentrations (12.5–384 g L−1), and in situ temperatures (1.3–37.5 °C), and three orders of magnitude in the trophic status (i.e. chlorophyll a 50 mg L−1). Geographically distant sites were studied with contrasting salt origins, and different temporal patterns of wetting and drying. The genetic diversity was high, far beyond the few groups traditionally considered as high salinity-adapted, with sequences spread throughout eight high-rank taxonomic groups and 27 eukaryal classes. The novelty level was extremely high, with 10% of the whole dataset showing 6.5% salinity). Overall, this study shows important gaps in the current knowledge about protists inhabiting continental (hyper)saline water bodies, highlighting the need for future, more detailed investigations.This research was funded with the projects MONEGROS CGL2004-22780-E and DARKNESS CGL2012-32747 to E.O.C. from the Spanish Ministerio de Economia y Competitividad.Peer reviewe

Using network analysis to explore co-ocurrence patterns in soil microbial communities.

9 páginas, 1 tabla, 4 figuras.Exploring large environmental datasets generated by high-throughput DNA sequencing technologies requires new analytical approaches to move beyond the basic inventory descriptions of the composition and diversity of natural microbial communities. In order to investigate potential interactions between microbial taxa, network analysis of significant taxon co-occurrence patterns may help to decipher the structure of complex microbial communities across spatial or temporal gradients. Here, we calculated associations between microbial taxa and applied network analysis approaches to a 16S rRNA gene barcoded pyrosequencing dataset containing >160 000 bacterial and archaeal sequences from 151 soil samples from a broad range of ecosystem types. We described the topology of the resulting network and defined operational taxonomic unit categories based on abundance and occupancy (that is, habitat generalists and habitat specialists). Co-occurrence patterns were readily revealed, including general non-random association, common life history strategies at broad taxonomic levels and unexpected relationships between community members. Overall, we demonstrated the potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly.AB is supported by the Spanish FPU predoctoral scholarship program and EOC by grants PIRENA CGL2009-13318 and CONSOLIDER-INGENIO 2010 GRACCIE CSD2007-00067 from the Spanish Ministerio de Ciencia e Innovacio´n (MICINN).Peer reviewe

T-RFPred: a nucleotide sequence size prediction tool for microbial community description based on terminal-restriction fragment length polymorphism chromatograms

<p>Abstract</p> <p>Background</p> <p>Terminal-Restriction Fragment Length Polymorphism (T-RFLP) is a technique used to analyze complex microbial communities. It allows for the quantification of unique or numerically dominant phylotypes in amplicon pools and it has been used primarily for comparisons between different communities. T-RFPred, Terminal-Restriction Fragment Prediction, was developed to identify and assign taxonomic information to chromatogram peaks of a T-RFLP fingerprint for a more comprehensive description of microbial communities. The program estimates the expected fragment size of representative 16S rRNA gene sequences (either from a complementary clone library or from public databases) for a given primer and restriction enzyme(s) and provides candidate taxonomic assignments.</p> <p>Results</p> <p>To show the accuracy of the program, T-RFLP profiles of a marine bacterial community were described using artificial bacterioplankton clone libraries of sequences obtained from public databases. For all valid chromatogram peaks, a phylogenetic group could be assigned.</p> <p>Conclusions</p> <p>T-RFPred offers enhanced functionality of T-RFLP profile analysis over current available programs. In particular, it circumvents the need for full-length 16S rRNA gene sequences during taxonomic assignments of T-RF peaks. Thus, large 16S rRNA gene datasets from environmental studies, including metagenomes, or public databases can be used as the reference set. Furthermore, T-RFPred is useful in experimental design for the selection of primers as well as the type and number of restriction enzymes that will yield informative chromatograms from natural microbial communities.</p

High bicarbonate assimilation in the dark by Arctic bacteria

10 páginas, 4 figuras, 1 tabla.Although both autotrophic and heterotrophic microorganisms incorporate CO2 in the dark through different metabolic pathways, this process has usually been disregarded in oxic marine environments. We studied the significance and mediators of dark bicarbonate assimilation in dilution cultures inoculated with winter Arctic seawater. At stationary phase, bicarbonate incorporation rates were high (0.5–2.5 μg C L−1 d−1) and correlated with rates of bacterial heterotrophic production, suggesting that most of the incorporation was due to heterotrophs. Accordingly, very few typically chemoautotrophic bacteria were detected by 16S rRNA gene cloning. The genetic analysis of the biotin carboxylase gene accC putatively involved in archaeal CO2 fixation did not yield any archaeal sequence, but amplified a variety of bacterial carboxylases involved in fatty acids biosynthesis, anaplerotic pathways and leucine catabolism. Gammaproteobacteria dominated the seawater cultures (40–70% of cell counts), followed by Betaproteobacteria and Flavobacteria as shown by catalyzed reporter deposition fluorescence in situ hybridization (CARDFISH). Both Beta- and Gammaproteobacteria were active in leucine and bicarbonate uptake, while Flavobacteria did not take up bicarbonate, as measured by microautoradiography combined with CARDFISH. Within Gammaproteobacteria, Pseudoalteromonas-Colwellia and Oleispira were very active in bicarbonate uptake (ca. 30 and 70% of active cells, respectively), while the group Arctic96B-16 did not take up bicarbonate. Our results suggest that, potentially, the incorporation of CO2 can be relevant for the metabolism of specific Arctic heterotrophic phylotypes, promoting the maintenance of their cell activity and/or longer survival under resource depleted conditions.This work is a contribution to the International Polar Year – Circumpolar Flaw Lead system study (IPY-CFL 2007/2008) lead by D. Barber (University of Manitoba) supported through grants from the Canadian IPY Federal Program Office, the National Sciences and Engineering Research Council, grant BOREAL (CLG2007-28872-E/ANT) from the Spanish Ministry of Science and Innovation to C.P.-A., and grants from the Swedish Research Council to S.B and L.A.S. L.A.S. was supported by a Marie Curie Intraeuropean Fellowship (CHEMOARC PIEF-GA-2008- 221121), E.O.C by the Spanish grant CGL2009-13318- BOS, and P. E. G by a Marie Curie grant (CRENARC MEIF-CT-2007-040247).Peer reviewe

Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes

12 páginas, 4 tablas, 3 figuras.Sharp boundaries in the physical environment are usually associated with abrupt shifts in organism abundance, activity ,and diversity. Aquatic surface microlayers (SML) from a steep gradient between two contrasted environments, the atmosphere and surface waters, where they regulate the gas exchange between both environments. They usually harbor an abundant and active microbial life: the neuston. Few ecosystems are subjected to such a high UVR regime as high altitude lakes during summer. Here, we measured bulk estimates of heterotrophic activity, community structure and single-cell physiological properties by flow cytometry in 19 high-altitude remote Pyrenean lakes and compared the biological processes in the SML with those in the underlying surface waters. Phototrophic picoplankton (PPP) populations, were generally present in high abundances and in those lakes containing PPP populations with phycoerythrin (PE), total PPP abundance was higher at the SML .Heterotrophic nanoflagellates (HNF) were also more abundant in the SML. Bacteria in the SML had lower leucine incorporation rates, lower percentages of “live” cells, and higher numbers of highly-respiring cells ,likely resulting in a lower growth efficiency. No simple and direct linea rrelationships could be found between microbial abundances or activities and environmental variables, but factor analysis revealed that, despite their physical proximity ,microbial life in SML and underlyingwaters was governed by different and independent processes. Overall, we demonstrate that piconeuston in high altitude lakes has specific features different from those of the picoplankton ,and that they are highly affected by potential stressful environmental factors, such as high UVR radiation.This work was supported by grants 2009SGR/1177 “Grup d’estructura i funcio de xarxes tròfiques microbianes planctòniques” and 2009SGR/361 “Grup d’Ecologia dels Canvis Ambientals, GECA” from Generalitat de Catalunya, AERBAC-2 178/2010 (to EOC) and EGALA 124/2010 (MF, LC) from the Ministerio de Medio Ambiente- Red de Parques Nacionales, and PIRENA CGL2009-13318 (EOC) and NITROPIR CGL2010-19373 (MF, LC) from MINECO. HS’s work was supported by CNPq and FAPESP (Process: 2014/ 14139-3).Peer reviewe

Dissolved organic carbon bioreactivity and DOC:DIN stoichiometry control ammonium uptake in an intermittent Mediterranean stream

1. Heterotrophic organisms in streams use dissolved organic carbon (DOC) and dissolved inorganic nitrogen (DIN) from the water column to meet their growth and energy requirements. However, the role of DOC availability in driving DIN uptake in headwater streams is still poorly understood. In this study, we focus on how DOC:DIN stoichiometry and DOC bioreactivity control ammonium (NH$_4$$^+$) uptake and heterotrophic aerobic respiration, and how this influence varies among seasons in a forested Mediterranean headwater stream. 2. We estimated in-stream NH$_4$$^+$ uptake rates seasonally by conducting whole-reach constant-rate additions of NH$_4$$^+$ with and without amendments of either lignin (recalcitrant DOC) or acetate (labile DOC). During each addition, we characterised microbial community composition by molecular analyses, stream metabolism with the single-station method, and heterotrophic aerobic respiration by adding a metabolic tracer (resazurin). 3. The stream was heterotrophic (net ecosystem production 800% higher during the co-additions of acetate than when adding NH$_4$$^+$ either alone or with lignin. 4. Our results indicate that in-stream NH$_4$$^+$ uptake was largely controlled by heterotrophic bacteria, and that the stoichiometric balance between organic resources and nutrients was key to explaining the variability of in-stream NH$_4$$^+$ uptake and heterotrophic aerobic respiration. Moreover, the observed increase in NH$_4$$^+$ uptake during acetate additions suggests that heterotrophic activity was limited by labile DOC availability. 5. Our study highlights that both DOC:DIN stoichiometry and DOC bioreactivity are relevant factors driving the seasonal pattern of in-stream N processing in this forested Mediterranean headwater stream

Climate mediates continental scale patterns of stream microbial functional diversity

Background Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China. Results We find that alpha diversity declines towards high elevations and assemblage composition shows increasing turnover with greater elevational distances. These elevational patterns are highly consistent across mountains, kingdoms and functional categories and exhibit the strongest trends in China due to its largest environmental gradients. Across mountains, functional gene assemblages differ in alpha diversity and composition between the mountains in Europe and Asia. Climate, such as mean temperature of the warmest quarter or mean precipitation of the coldest quarter, is the best predictor of alpha diversity and assemblage composition at both mountain and continental scales, with local non-climatic predictors gaining more importance at mountain scale. Under future climate, we project substantial variations in alpha diversity and assemblage composition across the Eurasian river network, primarily occurring in northern and central regions, respectively. Conclusions We conclude that climate controls microbial functional gene diversity in streams at large spatial scales; therefore, the underlying ecosystem processes are highly sensitive to climate variations, especially at high latitudes. This biogeographical framework for microbial functional diversity serves as a baseline to anticipate ecosystem responses and biogeochemical feedback to ongoing climate change.Peer reviewe

Ecology of marine Bacteroidetes: a comparative genomics approach

5th Congress of European Microbiologists (FEMS 2013), 21-25 july 2013, Leipzig, Germany.-- 1 pagePeer Reviewe

Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes

Sharp boundaries in the physical environment are usually associated with abrupt shifts in organism abundance, activity, and diversity. Aquatic surface microlayers (SML) form a steep gradient between two contrasted environments, the atmosphere and surface waters, where they regulate the gas exchange between both environments. They usually harbor an abundant and active microbial life: the neuston. Few ecosystems are subjected to such a high UVR regime as high altitude lakes during summer. Here, we measured bulk estimates of heterotrophic activity, community structure and single-cell physiological properties by flow cytometry in 19 high-altitude remote Pyrenean lakes and compared the biological processes in the SML with those in the underlying surface waters. Phototrophic picoplankton (PPP) populations, were generally present in high abundances and in those lakes containing PPP populations with phycoerythrin (PE), total PPP abundance was higher at the SML. Heterotrophic nanoflagellates (HNF) were also more abundant in the SML. Bacteria in the SML had lower leucine incorporation rates, lower percentages of "live" cells, and higher numbers of highly-respiring cells, likely resulting in a lower growth efficiency. No simple and direct linear relationships could be found between microbial abundances or activities and environmental variables, but factor analysis revealed that, despite their physical proximity, microbial life in SML and underlying waters was governed by different and independent processes. Overall, we demonstrate that piconeuston in high altitude lakes has specific features different from those of the picoplankton, and that they are highly affected by potential stressful environmental factors, such as high UVR radiation