Marine microbial community dynamics and their ecological interpretation

Fuhrman, Jed A.; Cram, Jacob A.; Needham, David M.

doi:10.1038/nrmicro3417

Cited by 669 publications

(616 citation statements)

References 135 publications

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“…Time scale appears to be an important determinant of organismal associations. We previously reported that members of the SAR11 cluster were correlated on a daily time scale but not monthly (Fuhrman and Steele, 2008;Steele et al, 2011;Needham et al, 2013;Fuhrman et al, 2015), reflecting patterns of temporal variability in network structure seen in other systems (Alarcón et al, 2008). A common feature of networks is the presence of modules, that is, highly interconnected groups of nodes (Newman, 2006;Olesen et al, 2007;Ings et al, 2009) and microbial networks are no exception Chow et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

“…Microbial communities throughout the water column show long-term, seasonal and short-term dynamics that relate to various biological, chemical and physical environmental parameters (Gilbert et al, 2012;Giovannoni and Vergin, 2012;Chow et al, 2013;Hatosy et al, 2013;Needham et al, 2013;Cram et al, 2014a;Fuhrman et al, 2015). Microbial interactions have been observed experimentally (Jurgens et al, 1999;Miller and Bassler, 2001;Jürgens and Matz, 2002;Bonilla-Findji et al, 2009) through physical attachment ) and inferred through genomic and physiological information (for example, Bothe et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes

et al. 2015

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Interactions among microbes and stratification across depths are both believed to be important drivers of microbial communities, though little is known about how microbial associations differ between and across depths. We have monitored the free-living microbial community at the San Pedro Ocean Time-series station, monthly, for a decade, at five different depths: 5 m, the deep chlorophyll maximum layer, 150 m, 500 m and 890 m (just above the sea floor). Here, we introduce microbial association networks that combine data from multiple ocean depths to investigate both within-and between-depth relationships, sometimes time-lagged, among microbes and environmental parameters. The euphotic zone, deep chlorophyll maximum and 890 m depth each contain two negatively correlated 'modules' (groups of many inter-correlated bacteria and environmental conditions) suggesting regular transitions between two contrasting environmental states. Two-thirds of pairwise correlations of bacterial taxa between depths lagged such that changes in the abundance of deeper organisms followed changes in shallower organisms. Taken in conjunction with previous observations of seasonality at 890 m, these trends suggest that planktonic microbial communities throughout the water column are linked to environmental conditions and/or microbial communities in overlying waters. Poorly understood groups including Marine Group A, Nitrospina and AEGEAN-169 clades contained taxa that showed diverse association patterns, suggesting these groups contain multiple ecological species, each shaped by different factors, which we have started to delineate. These observations build upon previous work at this location, lending further credence to the hypothesis that sinking particles and vertically migrating animals transport materials that significantly shape the time-varying patterns of microbial community composition.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes

et al. 2015

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“…So far, studies of marine mycoplankton diversity have been largely based on samples collected from one-off sampling campaigns that have provided important and insightful 'snap shots' of diversity, but with limited temporal resolution (Bass et al, 2007;Gao et al, 2010;Richards et al, 2012;Manohar and Raghukumar, 2013;. Time series assessments of other plankton groups have proven invaluable in developing our understanding of their biology and ecology (Karl and Church, 2014;Fuhrman et al, 2015). Spatially defined and reoccurring assessments of plankton diversity and abundance that are aligned with co-occurring environmental variables (temperature, nutrients and so on) have been used to identify the key controlling environmental drivers that influence planktonic organisms, and to form the basis of establishing the underpinning principles of their ecologies and ecosystem functional roles.…”

Section: Introductionmentioning

confidence: 99%

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

2016

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Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services.

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“…Los océanos son los ambientes de mayor extensión en el planeta y los microorganismos son la parte dominante tanto en biomasa como en actividad metabólica, por lo que el estudio de la composición y dinámica de las poblaciones microbianas marinas es muy importante (Fuhrman et al 2015). En el océano, los microorganismos son los que capturan y traducen la energía solar, catalizan las transformaciones biogeoquímicas clave de los nutrientes y elementos traza que soportan la productividad oceánica, participan en la regulación de los gases de efecto invernadero y representan una gran reserva de variabilidad genética (Karl 2007, Karl y Church 2014.…”

Section: Marine Microbial Communitiesunclassified

“…The study of the composition and dynamics of marine microbial communities is therefore of the utmost importance (Fuhrman et al 2015). In oceans, microorganisms capture and convert solar energy, catalyze key biogeochemical transformations of nutrients and trace elements that support productivity, participate in the regulation of greenhouse gases, and represent a vast reservoir of genetic diversity (Karl 2007, Karl andChurch 2014).…”

Section: Introductionmentioning

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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Marine microbial community dynamics and their ecological interpretation

Cited by 669 publications

References 135 publications

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

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

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