Phylogenetic diversity of sediment bacteria from the deep Northeastern Pacific Ocean: A comparison with the deep Eastern Mediterranean Sea

Department of Chemistry, University of Crete, Heraklion, Crete, Greece.
International Microbiology (Impact Factor: 1.34). 09/2010; 13(3):143-50. DOI: 10.2436/20.1501.01.119
Source: PubMed

ABSTRACT The variability of bacterial community composition and diversity was studied by comparative analysis of five 16S rRNA gene clone libraries from deep-sea sediments (water column depth: 4000 m) of the Northeastern Pacific Ocean and Eastern Mediterranean Sea. This is the first comparison of the bacterial communities living in these deep-sea ecosystems. The estimated chlorophyll a, organic carbon, and C/N ratio provided evidence of significant differences in the trophic state of the sediments between the Northeastern Pacific Ocean and the much warmer Eastern Mediterranean Sea. A diverse range of 16S rRNA gene phylotypes was found in the sediments of both regions. These were represented by 11 different taxonomic groups, with Gammaproteobacteria predominating in the Northeastern Pacific Ocean sediments and Acidobacteria in the Eastern Mediterranean microbial community. In addition, several 16S rRNA gene phylotypes only distantly related to any of the previously identified sequences (non-affiliated rRNA genes) represented a significant fraction of the total sequences. The potential diversity at the two sites differs but remains largely unexplored and remains of continuing scientific interest.

Download full-text


Available from: Manolis Mandalakis, Jul 08, 2015
  • Source
    • "The observation of Acidobacteria, Bacteroidetes, and Nitrospira in all four Lake Erie regions may reflect the metabolic versatility of these groups. Acidobacteria are often prevalent constituents in freshwater sediments (Kouridaki et al., 2010; Zeglin et al., 2011), while also being observed in diverse environments such as hot springs (Barns et al., 1996), as well as sewage sludge (Layton et al., 2000) and a wastewater treatment plant (LaPara et al., 2000). Bacteroidetes metabolize a wide range of high-weight carbohydrates and proteins in aquatic sediments (Teske et al., 2011), while Nitrospira is one of the most highly diverse groups of nitrite-oxidizing bacteria that contributes substantially to nitrification in freshwater systems (Lücker et al., 2010). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Lake Erie is a large freshwater ecosystem with three distinct basins that exhibit an east-to-west gradient of increasing productivity, as well as allochthonous inputs of nutrients and xenobiotics. To evaluate microbial community composition throughout this ecosystem, 435 16S rDNA environmental clones were sequenced from 11 sediment samples throughout the Western, Central, and Eastern basins, as well as the hypoxic “dead zone” of Lake Erie in the hypolimnetic region of the Central basin. Rank abundance distributions of bacterial taxa within each location revealed that Gamma- and Betaproteobacteria, microbes capable of metabolizing a wide range of organic matter pools, comprised a greater fraction of the microbial community within inshore sites of the Central and Western basins compared to the Eastern basin. While geophysical characteristics of the three major basins and the dead zone did not drive significant differences in species diversity, Fast UniFrac analyses revealed microbial community spatial structuring, with the Central basin showing higher phylogenetic uniqueness of bacterial lineages. Principal component analyses based on phylogenetic distances consistently grouped the dead zone with the Central basin and highlighted the distinctiveness of microbial communities from the Eastern basin. Results from this study provide evidence for the local adaptation of microbial communities and the potential role of riverine inputs in modulating taxonomic composition of lacustrine bacterial communities. These results are consistent with previous functional studies on microbial metabolism, which showed that differences in geochemistry across the three basins of Lake Erie play an important role in the local adaptation of microbial communities.
    Journal of Great Lakes Research 06/2013; 39(2):344-351. DOI:10.1016/j.jglr.2013.03.003 · 1.77 Impact Factor
  • Source
    • "Moreover, most dominant OTUs were equally present in both Mediterranean sampling areas and the Cape Basin (Figure 2; Shah Salani, 2009), supporting the hypothesis that some marine protists are indeed cosmopolitan despite geographic barriers and different ecological parameters. Kouridaki et al. (2010) even reported of communities of prokaryotes from the same depth layer (4000 m) of the North-East Pacific and the Eastern Mediterranean having different trophic states and temperature conditions, but which did not show substantial differences in community composition. Wide dispersal ranges, however, of microbes may be a general characteristic of, at least, marine ecosystems. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Knowledge of the spatial scales of diversity is necessary to evaluate the mechanisms driving biodiversity and biogeography in the vast but poorly understood deep sea. The community structure of kinetoplastids, an important group of microbial eukaryotes belonging to the Euglenozoa, from all abyssal plains of the South Atlantic and two areas of the eastern Mediterranean was studied using partial small subunit ribosomal DNA gene clone libraries. A total of 1364 clones from 10 different regions were retrieved. The analysis revealed statistically not distinguishable communities from both the South-East Atlantic (Angola and Guinea Basin) and the South-West Atlantic (Angola and Brazil Basin) at spatial scales of 1000-3000 km, whereas all other communities were significantly differentiated from one another. It seems likely that multiple processes operate at the same time to shape communities of deep-sea kinetoplastids. Nevertheless, constant and homogenous environmental conditions over large spatial scales at abyssal depths, together with high dispersal capabilities of microbial eukaryotes, maintain best the results of statistically indistinguishable communities at larger spatial scales.
    The ISME Journal 11/2011; 6(4):713-23. DOI:10.1038/ismej.2011.138 · 9.27 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The composition of the microbial community inhabiting the anoxic coastal sediments of the Bay of Cádiz (southern Spain) was investigated using a molecular approach consisting of PCR cloning and denaturing gradient gel electrophoresis (DGGE), based on 16S rRNA sequences. The total cell count was 1-5 × 10⁸ cells/g sediment and, as determined by catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH), the proportion of Bacteria to Archaea was about 70:30. The analysis of 16S-rRNA gene sequences revealed a wide spectrum of microorganisms, which could be grouped into 111 operational taxonomic units (OTUs). Many of the OTUs showed high phylogenetic similarity to microorganisms living in marine sediments of diverse geographic origin. The phylogenetic groups that were predominantly detected were Firmicutes, Deltaproteobacteria, and Gammaproteobacteria, accounting for 23, 15, and 14% of the clones, respectively. Diversity in the domain Archaea was significantly lower than in the domain Bacteria. The majority of the archaeal OTUs belonged to the Crenarchaeota phylum. Since most of the sequences could not be identified precisely at the genus/species level, the functional roles of the microorganisms in the ecosystem could not be inferred. However, seven OTUs affiliated with the Delta- and Epsilonproteobacteria were identified down to the genus level, with all of the identified genera known to occur in sulfate-rich marine environments.
    International Microbiology 09/2011; 14(3):143-54. · 1.34 Impact Factor