The seasonal structure of microbial communities in the Western English Channel. Environ Microbiol

Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK.
Environmental Microbiology (Impact Factor: 6.2). 08/2009; 11(12):3132-9. DOI: 10.1111/j.1462-2920.2009.02017.x
Source: PubMed


Very few marine microbial communities are well characterized even with the weight of research effort presently devoted to it. Only a small proportion of this effort has been aimed at investigating temporal community structure. Here we present the first report of the application of high-throughput pyrosequencing to investigate intra-annual bacterial community structure. Microbial diversity was determined for 12 time points at the surface of the L4 sampling site in the Western English Channel. This was performed over 11 months during 2007. A total of 182 560 sequences from the V6 hyper-variable region of the small-subunit ribosomal RNA gene (16S rRNA) were obtained; there were between 11 327 and 17 339 reads per sample. Approximately 7000 genera were identified, with one in every 25 reads being attributed to a new genus; yet this level of sampling far from exhausted the total diversity present at any one time point. The total data set contained 17 673 unique sequences. Only 93 (0.5%) were found at all time points, yet these few lineages comprised 50% of the total reads sequenced. The most abundant phylum was Proteobacteria (50% of all sequenced reads), while the SAR11 clade comprised 21% of the ubiquitous reads and approximately 12% of the total sequenced reads. In contrast, 78% of all operational taxonomic units were only found at one time point and 67% were only found once, evidence of a large and transient rare assemblage. This time series shows evidence of seasonally structured community diversity. There is also evidence for seasonal succession, primarily reflecting changes among dominant taxa. These changes in structure were significantly correlated to a combination of temperature, phosphate and silicate concentrations.

Download full-text


Available from: Lindsay Newbold
  • Source
    • "They hold high capability to acquire genetic diversity mainly by lateral gene transfer and other mechanisms for gene expansion favoring their functional diversity and, therefore, a widespread diversification of metabolic pathways (Whitman et al., 1998; Doolittle and Papke, 2006). This implies a competitive advantage allowing them to be adapted to the surrounding conditions (Giovannoni and Stingl, 2005; Massana and Logares, 2013), which largely explains the changes in heterotrophic bacterioplankton composition recorded along different spatio-temporal gradients (Giovannoni et al., 1996; Morris et al., 2005; Pommier et al., 2007; Gilbert et al., 2009). Therefore, bacterial taxonomic and functional versatility have been the main variables used to explain changes in bacterioplankton metabolism. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Prokaryotic planktonic organisms are small in size but largely relevant in marine biogeochemical cycles. Due to their reduced size range (0.2 to 1 μm in diameter), the effects of cell size on their metabolism have been hardly considered and are usually not examined in field studies. Here, we show the results of size-fractionated experiments of marine microbial respiration rate along a latitudinal transect in the Atlantic Ocean. The scaling exponents obtained from the power relationship between respiration rate and size were significantly higher than one. This superlinearity was ubiquitous across the latitudinal transect but its value was not universal revealing a strong albeit heterogeneous effect of cell size on microbial metabolism. Our results suggest that the latitudinal differences observed are the combined result of changes in cell size and composition between functional groups within prokaryotes. Communities where the largest size fraction was dominated by prokaryotic cyanobacteria, especially Prochlorococcus, have lower allometric exponents. We hypothesize that these larger, more complex prokaryotes fall close to the evolutionary transition between prokaryotes and protists, in a range where surface area starts to constrain metabolism and, hence, are expected to follow a scaling closer to linearity.The ISME Journal advance online publication, 4 December 2015; doi:10.1038/ismej.2015.203.
    Full-text · Article · Dec 2015 · The ISME Journal
  • Source
    • "To this end, the availability of molecular techniques such as ribosomal gene sequencing has enabled tremendous upgrades to the knowledge of environmental microbes by allowing comprehensive description of natural communities (Lane et al., 1985; Weisburg et al., 1991; Hugenholtz and Pace, 1996). Further advances in molecular methods have shed light on the immense diversity of complex bacterial communities (Sogin et al., 2006) and have allowed the detailed description of geographic and temporal patterns created by microbial populations (Lauber et al., 2009; Gilbert et al., 2009, 2011). High-throughput molecular methods are thus ideal to study intricate microbial communities such as those found in marine sediments (Nealson, 1997; Lozupone and Knight, 2007; Baker et al., 2015). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Coastal areas are critical in mitigating the impact of nutrient runoffs and downstream eutrophication of aquatic ecosystems. In the Gulf of Finland, the easternmost sub-basin of the Baltic Sea, seasonal and long-term oxygen depletion at the surface of the sediment feeds back the eutrophication loop by promoting the release of nutrients locked in the sediment matrix. In order to understand how the bacterial community responds to the seasonal variations, we sequenced ribosomal gene fragments from the top sediment layer at two coastal sites in southern Finland in spring, summer and late autumn during two consecutive years. Analysis of the samples collected at a shallow (11 m) and deep site (33 m) revealed that the overall community composition was rather constant over time with an extensive collection of shared operational taxonomic units (OTU) between sites. The dominant taxa were related to organoheterotrophs and sulfate reducers and the variation in community structure was linked to the availability of organic matter in the surface sediment. Proteobacteria formed the most abundant and diverse group. The taxa characteristic of spring samples belonged primarily to Actinobacteria, possibly of fresh water origin and linked to humic carbon. Summer communities were characterized by an increase in the number of reads associated with heterotrophic bacteria such as Bacteroidetes which feed on labile organic matter from spring bloom. Taxa typical of autumn samples were linked to Cyanobacteria and other bloom-forming bacteria from the overlying water and to bacteria feeding on organic matter drifting from the phytal zone.
    Full-text · Article · Sep 2015 · Estuarine Coastal and Shelf Science
  • Source
    • "Formosa, 15%) (Fig. 1A). These results agree with previous studies carried out at station L4 where Alphaproteobacteria 16S rRNA gene sequences, particularly those belonging to the SAR11 clade (Pelagibacteraceae), predominated (Gilbert et al., 2009; 2012; Sargeant, 2013). Potential methanol utilizers, such as Methylophaga, Ruegeria and Roseovarius, represented < 0.5% of the total 16S rRNA gene sequences analyzed (included in 'Others' in Fig. 1A). "
    [Show abstract] [Hide abstract]
    ABSTRACT: A variety of culture-independent techniques have been developed that can be used in conjunction with culture-dependent physiological and metabolic studies of key microbial organisms, in order to better understand how the activity of natural populations influences and regulates all major biogeochemical cycles. In this study, we combined DNA-stable isotope probing with metagenomics and metaproteomics to characterize an as yet uncultivated marine methylotroph that actively incorporated carbon from (13) C-labeled methanol into biomass. By metagenomic sequencing of the heavy DNA, we retrieved virtually the whole genome of this bacterium and determined its metabolic potential. Through protein-stable isotope probing, the RuMP cycle was established as the main carbon assimilation pathway, and the classical methanol dehydrogenase-encoding gene mxaF, as well as three out of four identified xoxF homologues were found to be expressed. This proof-of-concept study is the first in which theculture-independent techniques of DNA- and protein-stable isotope probing have been used to characterize the metabolism of a naturally-ocurring Methylophaga-like bacterium in the marine environment (i.e. M. thiooxydans L4) and thus provides a powerful approach to access the genome and proteome of uncultivated microbes involved in key processes in the environment. This article is protected by copyright. All rights reserved.
    Full-text · Article · Jun 2015 · Environmental Microbiology
Show more