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Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat

Liu, Zhenfeng; Klatt, Christian G; Wood, Jason M; Rusch, Douglas B; Ludwig, Marcus; Wittekindt, Nicola; Tomsho, Lynn P; Schuster, Stephan C; Ward, David M; Bryant, Donald A
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
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The phototrophic microbial mat community of Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, was studied by metatranscriptomic methods. RNA was extracted from mat specimens collected at four timepoints during light-to-dark and dark-to-light transitions in one diel cycle, and these RNA samples were analyzed by both pyrosequencing and SOLiD technologies. Pyrosequencing was used to assess the community composition, which showed that ∼84% of the rRNA was derived from members of four kingdoms Cyanobacteria, Chloroflexi, Chlorobi and Acidobacteria. Transcription of photosynthesis-related genes conclusively demonstrated the phototrophic nature of two newly discovered populations; these organisms, which were discovered through metagenomics, are currently uncultured and previously undescribed members of Chloroflexi and Chlorobi. Data sets produced by SOLiD sequencing of complementary DNA provided >100-fold greater sequence coverage. The much greater sequencing depth allowed transcripts to be detected from ∼15 000 genes and could be used to demonstrate statistically significant differential transcription of thousands of genes. Temporal differences for in situ transcription patterns of photosynthesis-related genes suggested that the six types of chlorophototrophs in the mats may use different strategies for maximizing their solar-energy capture...

Phylogenetic community structure: temporal variation in fish assemblage

Santorelli, Sergio; Magnusson, William; Ferreira, Efrem; Caramaschi, Erica; Zuanon, Jansen; Amadio, Sidnéia
Fonte: Blackwell Publishing Ltd Publicador: Blackwell Publishing Ltd
Tipo: Artigo de Revista Científica
Português
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Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales (grouped at three temporal scales). Phylogenetic distance was measured as the mean pairwise distances (MPD) and as mean nearest-neighbor distance (MNTD). Both distances were based on counts of nodes. We compared the observed values of MPD and MNTD with values that were generated randomly using null model independent swap. A serial runs test was used to assess the temporal independence of indices over time. The phylogenetic pattern in the whole assemblage and the functional groups varied widely over time. Conclusions about phylogenetic clustering or dispersion depended on the temporal scales. Conclusions about the frequency with which biotic processes and environmental filters affect the local assembly do not depend only on taxonomic grouping and spatial scales. While these analyzes allow the assertion that all proposed patterns apply to the fish assemblages in the floodplain...

Locally Controlled Scholarly Publishing via the Internet: The Guild Model

Kling, Rob; Spector, Lisa; McKim, Geoff
Fonte: Rob Kling Center for Social Informatics Publicador: Rob Kling Center for Social Informatics
Tipo: Trabalho em Andamento Formato: 64029 bytes; 10176 bytes; text/html; image/jpeg
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Many librarians and scholars believe that the Internet can be used to dramatically improve scholarly communication. During the last decade there has been substantial discussion of five major publishing models where readers could access articles without a fee: electronic journals, hybrid paper-electronic journals, authors' self-posting on web sites, free online access to all peer reviewed literature, and disciplinary repositories where authors post their own unrefereed articles. There have been numerous projects within each of these models, as well as extensive discussions about their strengths and limitations. While some of these projects have become important scholarly resources in specific disciplines; none of them has become commonplace across numerous disciplines. There is a sixth model that has been quietly adopted and developed in a number of disciplines -- the research publication series called working papers or technical reports that are sponsored by academic departments or research institutes. Many of these manuscript series are available to readers, online, and free of charge. This model -- which we call Guild Publishing -- has a distinct set of advantages and limitations when compared with the other five publishing models. This article explains the Guild Publishing Model...

Loss in microbial diversity affects nitrogen cycling in soil

Philippot, Laurent; Spor, Aymé; Hénault, Catherine; Bru, David; Bizouard, Florian; Jones, Christopher M; Sarr, Amadou; Maron, Pierre-Alain
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Português
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Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 sequencing. As expected, the diversity metrics indicated a decrease in diversity in the 1/103 and 1/105 dilution treatments compared with the undiluted one. However, the extent of dilution and the corresponding reduction in diversity were not commensurate, as a dilution of five orders of magnitude resulted in a 75% decrease in estimated richness. This reduction in denitrifier diversity resulted in a significantly lower potential denitrification activity in soil of up to 4–5 folds. Addition of wheat residues significantly increased differences in potential denitrification between diversity levels...