A Global Census of Marine Microbes

Amaral‐Zettler, Linda; Artigas, Luis Felipe; Baross, John A.; LokaBharathi, P.A.; Boetius, Antje; Chandramohan, D.; Herndl, Gerhard J.; Kogure, Kazuhiro; Neal, Phillip R.; Pedrós-Alió, Carlos; Ramette, Alban; Schouten, Stefan; Stal, Lucas J.; Thessen, Anne E.; Leeuw, Johannes de; Sogin, Mitchell L.

doi:10.1002/9781444325508.ch12

Cited by 109 publications

(75 citation statements)

References 68 publications

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“…In Fig. 1 we analyze microbial communities sampled from the human gut and skin microbiomes (24), phyllosphere communities sampled on Barro Colorado Island (25), and marine environments at various latitudes drawn from the International Census of Marine Microbes (26). We choose these habitats to provide a broad range of community similarities, so that we can compare communities from two human-associated habitats, nonhuman host-associated communities and a set of non-hostassociated communities.…”

Section: Documenting Patterns Of Phylogenetic Diversitymentioning

confidence: 99%

Backbones of evolutionary history test biodiversity theory for microbes

O’Dwyer

Kembel

Sharpton

2015

Proc. Natl. Acad. Sci. U.S.A.

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Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities.

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Section: Documenting Patterns Of Phylogenetic Diversitymentioning

confidence: 99%

Backbones of evolutionary history test biodiversity theory for microbes

O’Dwyer

Kembel

Sharpton

2015

Proc. Natl. Acad. Sci. U.S.A.

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“…Members of the phylum Bacteroidetes are the most abundant group of bacteria in the ocean after Proteobacteria and Cyanobacteria (Glö ckner et al, 1999;Kirchman, 2002;Amaral-Zettler et al, 2010). They account for a significant fraction of marine bacterioplankton especially in coastal areas, where they represent between 10% and 30% of the total bacterial counts (Alonso-Sáez and Gasol, 2007).…”

Section: Introductionmentioning

confidence: 99%

Ecology of marine Bacteroidetes: a comparative genomics approach

et al. 2013

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Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO 2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface.

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“…El International Census of Marine Microbes (ICoMM), uno de los 14 censos de la vida marina apoyado por diferentes laboratorios de investigación, tiene como finalidad determinar la distribución y los rangos de diversidad genética de diferentes microorganismos en los océanos. Comprende 356 bases de datos de secuencias de la región V6 del gen rRNA 16S bacteriano recabados de estudios de 40 biomas diferentes, desde regiones pelágicas y bentónicas hasta manglares y comunidades bacterianas asociadas a esponjas (Amaral-Zettler et al 2010, Karsenti et al 2011, Zinger et al 2012. Con base en estudios de muestras de recolectadas de 210 sitios oceánicos distintos y a profundidades de hasta 2000 m, el consorcio multinacional Tara Oceans ha generado un catálogo de genes de referencia (Ocean Microbial Reference Gene Catalog) de 35,650 microbios oceánicos taxonómicamente diferentes (Karsenti et al 2011, Logares et al 2014, Sunagawa et al 2015.…”

Section: Comunidades Microbianas Marinasunclassified

“…The International Census of Marine Microbes (ICoMM), one of 14 censuses of marine life supported by several research laboratories, aims to determine the range of genetic diversity and distribution of different microorganisms in the oceans. It comprises 356 datasets of sequences from the V6 region of the bacterial 16S rRNA gene obtained from studies of 40 different biomes, from pelagic and benthic regions to mangrove forests and sponge-associated bacteria (Amaral-Zettler et al 2010, Karsenti et al 2011, Zinger et al 2012. Based on studies of samples collected at 210 diverse oceanic sites and depths of 2000 m, the multinational consortium Tara Oceans has generated the Ocean Microbial Reference Gene Catalog comprising 35,650 taxonomically different organisms (Karsenti et al 2011, Logares et al 2014, Sunagawa et al 2015.…”

Section: Marine Microbial Communitiesmentioning

confidence: 99%

The 16S rRNA gene in the study of marine microbial communities

et al. 2015

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ABSTRACT. New sequencing technologies and analytical capabilities have stimulated the study of microbial communities from specific environments, enabling researchers to understand the complexity of those systems. The 16S rRNA gene has proved very useful in describing the diversity and characterization of marine microbial communities, particularly of uncultivated organisms. The development of new sequencing techniques has contributed to the exponential increase in the number of reported 16S rRNA sequences as barcodes for microorganisms, forcing a review of concepts and methods for the taxonomic classification of these organisms. Manipulation and analysis of large amounts of genetic information have prompted the development of specific databases, specialized algorithms, and computational tools to compare thousands of such sequences and make a taxonomic assignment. Complete 16S rRNA sequences are thus needed for accurate and reproducible taxonomy assignment in the study of marine bacterial communities.Key words: metagenomics, marine microbial communities, 16S rRNA databases. RESUMEN. Las nuevas tecnologías de secuenciación y capacidades analíticas han estimulado el estudio de las comunidades microbianas deambientes específicos, lo cual ha permitido conocer la complejidad de estos sistemas. El gen ARNr 16S ha demostrado ser de gran utilidad para describir y caracterizar las comunidades microbianas marinas, especialmente los organismos no cultivados. Las nuevas técnicas de secuenciación han contribuido al incremento exponencial de registro de secuencias, aunque parciales, del ARNr 16S como elemento de código de barras para microorganismos. Consecuentemente, ha sido necesaria una revisión de conceptos y métodos de clasificación taxonómica para estos organismos. El manejo y análisis de una gran cantidad de información génica han impulsado el desarrollo de bases de datos específicas, algoritmos y herramientas computacionales especializadas para comparar miles de secuencias semejantes y hacer la asignación taxonómica. Por lo tanto, las secuencias completas del ARNr 16S son necesarias para una asignación taxonómica certera y reproducible en los estudios de comunidades microbianas marinas.Palabras clave: metagenómica, comunidades microbianas marinas, bases de datos ARNr 16S.

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A Global Census of Marine Microbes

Cited by 109 publications

References 68 publications

Backbones of evolutionary history test biodiversity theory for microbes

Backbones of evolutionary history test biodiversity theory for microbes

Ecology of marine Bacteroidetes: a comparative genomics approach

The 16S rRNA gene in the study of marine microbial communities

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