Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing

Klindworth, Anna; Mann, Alexander J.; Huang, Sixing; Wichels, Antje; Quast, Christian; Waldmann, Jost; Teeling, Hanno; Glöckner, Frank Oliver

doi:10.1016/j.margen.2014.08.007

Cited by 80 publications

(75 citation statements)

References 51 publications

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“…We noted that different OTUs within Flavobacteriaceae, including Polaribacter , and Rhodobacteraceae peaked at different points during the phytoplankton bloom. This suggests niche specialization by different taxa within these groups, perhaps corresponding to different stages in the successive degradation of phytoplankton-derived organic compounds (Teeling et al, 2012; Klindworth et al, 2014). Polaribacter occurred in a cluster with only one other OTU ( Figures 3 and 4 ), suggesting a strong competitive advantage for Polaribacter early in the bloom, in support of the hypothesized role of this taxon (Williams et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula

et al. 2016

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The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.

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Section: Discussionmentioning

confidence: 99%

Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula

et al. 2016

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“…A recent metagenomic study showed that submerged insoluble polysaccharides such as cellulose are colonized by biofilm-forming marine bacterial communities, of which the Bacteroidetes are a major group that harbors an extensive repertoire of genes encoding glycoside hydrolases (803). Marine Bacteroidetes may also harbor TonB-dependent transport systems that can be used for the uptake of polysaccharides (804).…”

Section: Marine Bacteroidetesmentioning

confidence: 99%

Microbial Surface Colonization and Biofilm Development in Marine Environments

Dang

Lovell

2016

Microbiol Mol Biol Rev

837

636

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SUMMARYBiotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

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“…That observed in one region at a given time are the changes in the relative abundance of community members (Gibbons et al 2013). In addition to qualitative descriptions, studies have also addressed seasonal, interannual, and interseasonal variations (Hatosy et al 2013, Karl andChurch 2014), and considerable advances have been made in understanding the metabolic processes of the communities and their role in biogeochemical cycles (Hahnke et al 2013, Karl and Church 2014, Klindworth et al 2014, Logares et al 2014). …”

Section: Comunidades Microbianas Marinasmentioning

confidence: 99%

“…Más allá de una descripción cualitativa, los estudios han profundizado para determinar los niveles de fluctuación estacional, interanual e interestacional de estas comunidades (Hatosy et al 2013, Karl y Church 2014. Actualmente, se están realizando grandes avances en el conocimiento de los procesos metabólicos que desarrollan las comunidades y su papel en los ciclos biogeoquímicos (Hahnke et al 2013, Karl y Church 2014, Klindworth et al 2014, Logares et al 2014). …”

Section: S Rrnaunclassified

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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Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing

Cited by 80 publications

References 51 publications

Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula

Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula

Microbial Surface Colonization and Biofilm Development in Marine Environments

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

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