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

ABSTRACT 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, Sep 27, 2015
33 Reads
  • 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.
    Environmental Microbiology 06/2015; DOI:10.1111/1462-2920.12935 · 6.20 Impact Factor
  • Source
    • "Both the number of OTUs and sequences affiliated to the Class increased in abundance during periods of high sediment chlorophyll content. Flavobacteria are aerobic members of the phylum Bacteroidetes, considered to be specialist degraders of complex organic matter in the marine environment (Cottrell and Kirchman, 2000; Teeling et al., 2012; Williams et al., 2013), and are found in abundance in both open ocean (Schattenhofer et al., 2009) and coastal (Eilers et al., 2001; O&apos;Sullivan et al., 2004) waters, including L4 (O'Sullivan et al., 2004; Gilbert et al., 2009), and on marine snow (DeLong et al., 1993; Woebken et al., 2007) where their high abundance has been linked to phytoplankton blooms and areas with high levels of POC during upwelling events (e.g. Riemann et al., 2000; Fandino et al., 2005; Alonso-Sáez et al., 2007; Schattenhofer et al., 2009; Gómez-Pereira et al., 2010; Teeling et al., 2012). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The impact of the seasonal deposition of phytoplankton and phytodetritus on surface sediment bacterial abundance and community composition was investigated at the Western English Channel site L4. Sediment and water samples were collected from January to September in 2012, increasing in frequency during periods of high water column phytoplankton abundance. Compared to the past two decades, the spring bloom in 2012 was both unusually long in duration and contained higher than average biomass. Within spring months, the phytoplankton bloom was well mixed through the water column and showed accumulations near the sea bed, as evidenced by flow cytometry measurements of nanoeukaryotes, water column chlorophyll a and the appearance of pelagic phytoplankton at the sediment. Measurements of chlorophyll and chlorophyll degradation products indicated phytoplankton material was heavily degraded after it reached the sediment surface: the nature of the chlorophyll degradation products (predominantly pheophorbide, pyropheophorbide and hydroxychlorophyllone) was indicative of grazing activity. The abundance of bacterial 16S rRNA genes g-1 sediment (used as a proxy for bacterial biomass) increased markedly with the onset of the phytoplankton bloom, and correlated with measurements of chlorophyll at the surface sediment. Together, this suggests that bacteria may have responded to nutrients released via grazing activity. In depth sequencing of the 16S rRNA genes indicated that the composition of the bacterial community shifted rapidly through-out the prolonged spring bloom period. This was primarily due to an increase in the abundance of members of the Flavobacteria.
    Progress In Oceanography 05/2015; DOI:10.1016/j.pocean.2015.04.020 · 3.03 Impact Factor
  • Source
    • "Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments, which are often involved in variations of nutrient contents. Temperature and nutrient concentrations have been largely focused on the effect microbial communities in previous studies (Morris et al. 2005; Fuhrman et al. 2006; Gilbert et al. 2009). These are obvious candidates because of the strong effect of temperature on biological processes (Nedwell and Rutter 1994) and the fact that nutrient availability can drive niche structure through resource partitioning (Church 2008). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.
    Ecotoxicology 05/2015; DOI:10.1007/s10646-015-1472-2 · 2.71 Impact Factor
Show more