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

Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp. Strain MED134

González, José M. ... et al.-- 12 pages, 8 figures, 1 table, supplemental material http://aem.asm.org/content/77/24/8676/suppl/DC1Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine bacteria. However, the genetic features contributing to the success of proteorhodopsin-containing bacteria remain largely unknown. We investigated the genome of Dokdonia sp. strain MED134 (Bacteroidetes) for features potentially explaining its ability to grow better in light than darkness. MED134 has a relatively high number of peptidases, suggesting that amino acids are the main carbon and nitrogen sources. In addition, MED134 shares with other environmental genomes a reduction in gene copies at the expense of important ones, like membrane transporters, which might be compensated by the presence of the proteorhodopsin gene. The genome analyses suggest Dokdonia sp. MED134 is able to respond to light at least partly due to the presence of a strong flavobacterial consensus promoter sequence for the proteorhodopsin gene. Moreover, Dokdonia sp. MED134 has a complete set of anaplerotic enzymes likely to play a role in the adaptation of the carbon anabolism to the different sources of energy it can use, including light or various organic matter compounds. In addition to promoting growth, proteorhodopsin phototrophy could provide energy for the degradation of complex or recalcitrant organic matter, survival during periods of low nutrients, or uptake of amino acids and peptides at low concentrations. Our analysis suggests that the ability to harness light potentially makes MED134 less dependent on the amount and quality of organic matter or other nutrients. The genomic features reported here may well be among the keys to a successful photoheterotrophic lifestyleJ.M.G. and C.P.-A. were supported by grant CTM2010-11060-E from the Spanish Ministry of Science and Innovation, J.P. was supported by the Swedish Research Council and FORMAS, and P.P. was supported by the intramural funds of the U.S. Department of Health and Human Services (National Library of Medicine, National Institutes of Health)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

Data from: Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers

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 (γ statistic) for most of the habitats indicated γ_AOA > γ_AOB. 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

Pheromone Evolution, Reproductive Genes, and Comparative Transcriptomics in Mediterranean Earthworms (Annelida, Oligochaeta, Hormogastridae)

16 páginas, 5 tablas, 8 figurasAnimals inhabiting cryptic environments are often subjected to morphological stasis due to the lack of obvious agents driving selection, and hence chemical cues may be important drivers of sexual selection and individual recognition. Here, we provide a comparative analysis of de novo-assembled transcriptomes in two Mediterranean earthworm species with the objective to detect pheromone proteins and other reproductive genes that could be involved in cryptic speciation processes, as recently characterized in other earthworm species. cDNA libraries of unspecific tissue of Hormogaster samnitica and three different tissues of H. elisae were sequenced in an Illumina Genome Analyzer II or Hi-Seq. Two pheromones, Attractin and Temptin were detected in all tissue samples and both species. Attractin resulted in a reliable marker for phylogenetic inference. Temptin contained multiple paralogs and was slightly overexpressed in the digestive tissue, suggesting that these pheromones could be released with the casts. Genes involved in sexual determination and fertilization were highly expressed in reproductive tissue. This is thus the first detailed analysis of the molecular machinery of sexual reproduction in earthworms.This research was funded by internal funds from the Museum of Comparative Zoology and the Faculty of Arts and Sciences to G.G.Peer reviewe

Alignment files and trees

The file contains all bacterial and archaeal amoA aligned sequences, gblocks trimmed alignments and resulting tree files from doi:10.1371/journal.pone.004733

Level of <i>amoA</i> gene sequence divergence detected in each habitat for bacterial (left panel) and archaeal (right panel) ammonia oxidizers.

<p>The boxplot represents all-against-all pairwise alignment identities for the gene sequences compiled from each habitat and for each domain.</p

Scatter-plot comparing the AOB vs. AOA.

<p>A) phylogenetic diversity (PD), B) phylogenetic species variability (PSV) and C) diversification rates (γ-statistic) for the different shared habitats. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047330#pone.0047330.s001" target="_blank">Table S1</a> for data.</p

Graphical representation of AOB and AOA Unifrac distance matrices.

<p>A thicker line represents phylogenetically more similar communities. Phylogenetic diversity (PD) represented as node size, large nodes have larger PD values. Phylogenetic species variability (PSV) represented as node color, darker nodes have larger PSV values. The length of the edges does not contain information.</p

Dynamics of the cladogenesis events versus relative time using log-lineage through time plots (LTT) for the inferred phylogenies using the whole dataset of AOA and AOB. Time 0, the present.

<p>Dynamics of the cladogenesis events versus relative time using log-lineage through time plots (LTT) for the inferred phylogenies using the whole dataset of AOA and AOB. Time 0, the present.</p