Phylogenetic diversity of sediment bacteria in the northern Bering Sea

Zeng, Yangsu; Zou, Yang; Chen, Bin; Grebmeier, Jacqueline M.; Li, Huirong; Yu, Yong; Zheng, Tao

doi:10.1007/s00300-010-0947-0

Cited by 33 publications

(22 citation statements)

References 67 publications

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“…In this study, no significant differences in the coverage percentage of different subclasses of the Proteobacteria phylum were observed among the five sites; this agrees with other studies in which different libraries of marine sediments collected in different sites showed similar bacterial compositions [35]. The Bacteroidetes phylum is the only further phylum with an appreciable presence in all sites, and the percentages of abundance are comparable to those found by other authors [35, 38]. This result can mean that bacteria belonging to these groups play the main role in nutrient recycling in the harbor seabed ecosystem.…”

Section: Discussionsupporting

confidence: 92%

“…There are no significant differences among the coverage percentages of different subclasses of the Proteobacteria phylum among the two libraries and the 5 sites; these data are in agreement with previously published studies, where PCR-based techniques on marine sediment samples revealed a dominance of bacteria related to Proteobacteria phylum [35, 37] or to Firmicutes , Delta- , and Gammaproteobacteria [40, 41]. In other papers, the analysis of marine sediment showed a dominance of Actinobacteria [38].…”

Section: Discussionsupporting

confidence: 92%

“…The molecular approach is commonly used in the recent literature for the study of bacterial communities in marine sediments [35–38] and to study the influence of bacterial communities in removing pollutants from marine sediments [39]. The two libraries highlighted a substantial similarity concerning the abundance and diversity of the sequences represented in the two different sites, even though the chemical composition was different [13].…”

Section: Discussionmentioning

confidence: 99%

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Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

Chiellini

Iannelli

Verni

et al. 2013

The Scientific World Journal

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Seabed sediments of commercial ports are often characterized by high pollution levels. Differences in number and distribution of bacteria in such areas can be related to distribution of pollutants in the port and to sediment conditions. In this study, the bacterial communities of five sites from Leghorn Harbor seabed were characterized, and the main bacterial groups were identified. T-RFLP was used for all samples; two 16S rRNA libraries and in silico digestion of clones were used to identify fingerprint profiles. Library data, phylogenetic analysis, and T-RFLP coupled with in silico digestion of the obtained sequences evidenced the dominance of Proteobacteria and the high percentage of Bacteroidetes in all sites. The approach highlighted similar bacterial communities between samples coming from the five sites, suggesting a modest differentiation among bacterial communities of different harbor seabed sediments and hence the capacity of bacterial communities to adapt to different levels and types of pollution.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

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Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

Chiellini

Iannelli

Verni

et al. 2013

The Scientific World Journal

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“…The dominance of this taxonomic group of bacteria in water basins has been reported by Cottrell and Kirchman (2000), Simanato et al (2010) in water and by Xia et al (2014), Galand et al (2016) in sediment. A large number of Gammaproteobacteria in the sediment-water interface in the channel in Ustka most probably is due to the fact that those bacteria as a group are involved in many biodegradation processes, suggesting their importance in organic matter decomposition in SWI (Tanase et al 2009;Zeng et al 2011). Many bacteria from this taxonomic subclass have particular gene generating high proteolytic activity (Zhou et al 2009;Alonso et al 2010).…”

Section: Discussionmentioning

confidence: 99%

Abundance and Taxonomic Diversity of Bacteria Inhabiting the Sediment-Water Interface in a Marine Harbor Channel

2019

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The abundance of bacteria inhabiting the sedimentwater interface and their taxonomic composition were determined with the fluorescence in situ hybridization (FISH) method in a marine harbor channel in Ustka. Among bacteria inhabiting the studied layer Gammaproteobacteria (1.4 cells 10 8 •dm-3) and Cytophaga-Flavobacterium (1.1 cells 10 8 •dm-3) dominated. Vibrio and Pseudomonas represented only a small fraction of the total cell counts. All taxonomic groups of studied bacteria show significant positive correlation between their abundance. The total bacterial number varied from 3.3 to 23.5 cells 10 8 •dm-3 and their biomass oscillated from 39.4 to 282.4 µg C•dm-3. This parameter differed along horizontal profiles, while there were no significant differences in the abundance of the studied taxonomic groups among the study sites of the channel in Ustka. The total number of bacteria as well as the abundance of bacterial phylogenetic groups were subject to seasonal fluctuation in the studied water basin.

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“…Current estimates indicate that we are able to culture less than 1% of soil bacteria (Amann, Ludwig, and Schleifer 1995;Zeng et al 2011). This means that a strictly culturedependent approach to the determination of microbial diversity will vastly underestimate the true diversity of an environmental sample.…”

Section: Introductionmentioning

confidence: 96%

Diversity of The Chlorite Dismutase Gene in Low and High Organic Carbon Rhizosphere Soil Colonized by Perchlorate-Reducing Bacteria

Struckhoff¹,

Livermore²,

Parkin³

2013

International Journal of Phytoremediation

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Chlorite dismutase (cld) is an essential enzyme in the biodegradation of perchlorate. The objective of this study was to determine the change in sequence diversity of the cld gene, and universal bacterial 16S rRNA genes, in soil samples under varying conditions of organic carbon, bioaugmentation, and plant influence. The cld gene diversity was not different between high organic carbon (HOC) and low organic carbon (LOC) soil. Combining results from HOC and LOC soil, diversity of the cld gene was decreased in soil that had been bioaugmented or planted. However, with both bioaugmentation and planting the cld diversity was not decreased. These observations were repeated when focusing on LOC soil. However, in HOC soil the cld diversity was not affected by reactor treatment. General bacterial diversity as measured with 16S rRNA was significantly greater in HOC soil than in LOC soil, but no significant difference was observed between reference soil and planted or bioaugmented soil. Different sequences of the cld gene occur in different species of microorganisms. In LOC soil, combining bioaugmentation and planting results in a highly diverse population of perchlorate degraders. This diverse population will be more resilient and is desirable where perchlorate reduction is a critical remediation process. Supplemental materials are available for this article. Go to the publisher's online edition of International Journal of Phytoremediation to view the supplemental file.

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Phylogenetic diversity of sediment bacteria in the northern Bering Sea

Cited by 33 publications

References 67 publications

Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

Abundance and Taxonomic Diversity of Bacteria Inhabiting the Sediment-Water Interface in a Marine Harbor Channel

Diversity of The Chlorite Dismutase Gene in Low and High Organic Carbon Rhizosphere Soil Colonized by Perchlorate-Reducing Bacteria

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