Kouridaki I, Polymenakou PN, Tselepides A, Mandalakis M, Smith Jr KL.. Phylogenetic diversity of sediment bacteria from the deep Northeastern Pacific Ocean: a comparison with the deep Eastern Mediterranean Sea. Int Microbiol 13: 143-150

Department of Chemistry, University of Crete, Heraklion, Crete, Greece.
International Microbiology (Impact Factor: 1.33). 09/2010; 13(3):143-50. DOI: 10.2436/20.1501.01.119
Source: PubMed


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.

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    • "However, Alphaproteobacteria and Betaproteobacteria were the second and the third most dominant classes in the deep-sea sediment samples (Figure 3B). Gammaproteobacteria, the predominant bacterial group, prevailed over other taxa identified in several deep-sea investigations, including the Eastern Mediterranean Sea [24] and Northeastern Pacific Ocean [25]. Sequences affiliated with Desulfobacterales, Myxococcales, and Sh765B-TzT-29, dominated the Deltaproteobacteria and their common role is to regulate the sulfur cycle. "
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    ABSTRACT: Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.
    PLoS ONE 11/2013; 8(10):e78501. DOI:10.1371/journal.pone.0078501 · 3.23 Impact Factor
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    • "Prokaryotes are key players in all ecosystems, and in the deep-sea they have a crucial role in recycling particulate and dissolved organic matter that sinks down from the photic zone [8]. Despite their importance, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments [9,10], as most of the scientific literature has focused on the water column [11–14]. "
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    ABSTRACT: The deep-sea represents a substantial portion of the biosphere and has a major influence on carbon cycling and global biogeochemistry. Benthic deep-sea prokaryotes have crucial roles in this ecosystem, with their recycling of organic matter from the photic zone. Despite this, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments. To assess the influence of environmental and trophic variables on the large-scale distribution of prokaryotes, we investigated the prokaryotic assemblage composition (Bacteria to Archaea and Euryarchaeota to Crenarchaeota ratio) and activity in the surface deep-sea sediments of the Mediterranean Sea and the adjacent North Atlantic Ocean. Prokaryotic abundance and biomass did not vary significantly across the Mediterranean Sea; however, there were depth-related trends in all areas. The abundance of prokaryotes was positively correlated with the sedimentary concentration of protein, an indicator of the quality and bioavailability of organic matter. Moving eastwards, the Bacteria contribution to the total prokaryotes decreased, which appears to be linked to the more oligotrophic conditions of the Eastern Mediterranean basins. Despite the increased importance of Archaea, the contributions of Crenarchaeota Marine Group I to the total pool was relatively constant across the investigated stations, with the exception of Matapan-Vavilov Deep, in which Euryarchaeota Marine Group II dominated. Overall, our data suggest that deeper areas of the Mediterranean Sea share more similar communities with each other than with shallower sites. Freshness and quality of sedimentary organic matter were identified through Generalized Additive Model analysis as the major factors for describing the variation in the prokaryotic community structure and activity in the surface deep-sea sediments. Longitude was also important in explaining the observed variability, which suggests that the overlying water masses might have a critical role in shaping the benthic communities.
    PLoS ONE 08/2013; 8(8):e72996. DOI:10.1371/journal.pone.0072996 · 3.23 Impact Factor
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    • "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). "
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    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 · 1.75 Impact Factor
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