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Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea.
Syst Appl Microbiol. 2009 Feb; 32(1):17-26.SA

Abstract

This study is the first culture-independent report on the regional variability of bacterial diversity in oxic sediments from the unexplored southern Cretan margin (SCM). Three main deep basins (water column depths: 2670-3603m), located at the mouth of two submarine canyons (Samaria Gorge and Paximades Channel) and an adjacent slope system, as well as two shallow upper-slope stations (water column depths: 215 and 520m), were sampled. A total of 454 clones were sequenced and the bacterial richness, estimated through five clone libraries using rarefaction analysis, ranged from 71 to 296 unique phylotypes. The average sequence identity of the retrieved Cretan margin sequences compared to the >1,000,000 known rRNA sequences was only 93.5%. A diverse range of prokaryotes was found in the sediments, which were represented by 15 different taxonomic groups at the phylum level. The phylogenetic analysis revealed that these new sequences grouped with the phyla Acidobacteria, Planctomycetes, Actinobacteria, Gamma-, Alpha- and Delta-proteobacteria. Only a few bacterial clones were affiliated with Chloroflexi, Bacteroidetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Nitrospirae, Beta-proteobacteria, Lentisphaerae and Dictyoglomi. A large fraction of the retrieved sequences (12%) did not fall into any taxonomic division previously characterized by molecular criteria, whereas four novel division-level lineages, termed candidate division SCMs, were identified. Bacterial community composition demonstrated significant differences in comparison to previous phylogenetic studies. This divergence was mainly triggered by the dominance of Acidobacteria and Actinobacteria and reflected a bacterial community different from that currently known for oxic and pristine marine sediments.

Authors+Show Affiliations

Hellenic Centre for Marine Research, Institute of Marine Biology and Genetics, Gournes Pediados, P.O. Box 2214, GR-710 03 Heraklion, Crete, Greece. polymen@her.hcmr.grNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

19058941

Citation

Polymenakou, Paraskevi N., et al. "Phylogenetic Diversity of Sediment Bacteria From the Southern Cretan Margin, Eastern Mediterranean Sea." Systematic and Applied Microbiology, vol. 32, no. 1, 2009, pp. 17-26.
Polymenakou PN, Lampadariou N, Mandalakis M, et al. Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea. Syst Appl Microbiol. 2009;32(1):17-26.
Polymenakou, P. N., Lampadariou, N., Mandalakis, M., & Tselepides, A. (2009). Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea. Systematic and Applied Microbiology, 32(1), 17-26. https://doi.org/10.1016/j.syapm.2008.09.006
Polymenakou PN, et al. Phylogenetic Diversity of Sediment Bacteria From the Southern Cretan Margin, Eastern Mediterranean Sea. Syst Appl Microbiol. 2009;32(1):17-26. PubMed PMID: 19058941.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea. AU - Polymenakou,Paraskevi N, AU - Lampadariou,Nikolaos, AU - Mandalakis,Manolis, AU - Tselepides,Anastasios, Y1 - 2008/12/06/ PY - 2008/05/02/received PY - 2008/09/04/revised PY - 2008/09/05/accepted PY - 2008/12/9/pubmed PY - 2009/3/19/medline PY - 2008/12/9/entrez SP - 17 EP - 26 JF - Systematic and applied microbiology JO - Syst Appl Microbiol VL - 32 IS - 1 N2 - This study is the first culture-independent report on the regional variability of bacterial diversity in oxic sediments from the unexplored southern Cretan margin (SCM). Three main deep basins (water column depths: 2670-3603m), located at the mouth of two submarine canyons (Samaria Gorge and Paximades Channel) and an adjacent slope system, as well as two shallow upper-slope stations (water column depths: 215 and 520m), were sampled. A total of 454 clones were sequenced and the bacterial richness, estimated through five clone libraries using rarefaction analysis, ranged from 71 to 296 unique phylotypes. The average sequence identity of the retrieved Cretan margin sequences compared to the >1,000,000 known rRNA sequences was only 93.5%. A diverse range of prokaryotes was found in the sediments, which were represented by 15 different taxonomic groups at the phylum level. The phylogenetic analysis revealed that these new sequences grouped with the phyla Acidobacteria, Planctomycetes, Actinobacteria, Gamma-, Alpha- and Delta-proteobacteria. Only a few bacterial clones were affiliated with Chloroflexi, Bacteroidetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Nitrospirae, Beta-proteobacteria, Lentisphaerae and Dictyoglomi. A large fraction of the retrieved sequences (12%) did not fall into any taxonomic division previously characterized by molecular criteria, whereas four novel division-level lineages, termed candidate division SCMs, were identified. Bacterial community composition demonstrated significant differences in comparison to previous phylogenetic studies. This divergence was mainly triggered by the dominance of Acidobacteria and Actinobacteria and reflected a bacterial community different from that currently known for oxic and pristine marine sediments. SN - 0723-2020 UR - https://www.unboundmedicine.com/medline/citation/19058941/Phylogenetic_diversity_of_sediment_bacteria_from_the_southern_Cretan_margin_Eastern_Mediterranean_Sea_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0723-2020(08)00101-X DB - PRIME DP - Unbound Medicine ER -