Bacterial diversity in surface sediments from the Pacific Arctic Ocean

Li, Huirong; Yu, Yong; Luo, Wei; Zeng, Yangsu; Chen, Bin

doi:10.1007/s00792-009-0225-7

Cited by 83 publications

(47 citation statements)

References 59 publications

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“…Bacteria detected from the soil samples at a depth of 1 and 2 m were primarily affiliated with Chloroflexi, Gemmatimondetes, Acidobacteria, Actinobacterium and Rhodospirillaceae, which were commonly found in samples associated with marine and alkaline environments (Miller et al 2009;Li et al 2009;Pearson and Rusch 2009). Appearance of these bacteria matched the geographical position and the characteristics of the sampling sites where they inhabit.…”

Section: Discussionmentioning

confidence: 72%

Molecular biologic techniques applied to the microbial prospecting of oil and gas in the Ban 876 gas and oil field in China

Zhang

She

Zheng

et al. 2010

Appl Microbiol Biotechnol

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Currently, molecular biologic techniques achieve a great development in studies of soil samples. The objective of this research is to improve methods for microbial prospecting of oil and gas by applying cultureindependent techniques to soil sampled from above a known oil and gas field. Firstly, the community structure of soil bacteria above the Ban 876 Gas and Oil Field was analyzed based on 16S rRNA gene clone libraries. The soil bacteria communities were consistently different along the depth; however, Chloroflexi and Gemmatimonadetes were predominant and methanotrophs were minor in both bacteria libraries (DGS1 and DGS2). Secondly, the numbers of methane-oxidizing bacteria, quantified using a culture-dependent procedure and culture-independent group-specific real-time PCR (RT-PCR), respectively, were inconsistent with a quantify variance of one or two orders of magnitude. Special emphasis was given to the counting advantages of RT-PCR based on the methanotrophic pmoA gene. Finally, the diversity and distribution of methanotrophic communities in the soil samples were analyzed by constructing clone libraries of functional gene. All 508-bp inserts in clones phylogenetically belonged to the methanotrophic pmoA gene with similarities from 83% to 100%. However, most of the similarities were below 96%. Five clone libraries of methanotrophs clearly showed that the anomalous methanotrophs (Methylosinus and Methylocystis) occupy the studied area.

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Section: Discussionmentioning

confidence: 72%

Molecular biologic techniques applied to the microbial prospecting of oil and gas in the Ban 876 gas and oil field in China

Zhang

She

Zheng

et al. 2010

Appl Microbiol Biotechnol

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“…Seawater contains a large number of pathogenic bacteria, including vibrio bacteria and Enterobacteriaceae, especially Vibrionaceae (Ma et al, 2009). The rate of Streptococcus bacterial infection is highest after seawater immersion and is followed by Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, Proteus, Pseudomonas aeruginosa, seawater Vibrio and other bacteria (Li et al, 2009;Byard et al, 2011). Initially, the most reported pathogens in seawaterimmersed wounds were Pseudomonas aeruginosa and E. coli as well as Vibrio (Ma et al, 2009).…”

Section: Vac Affects Flora In Wounds and Reduces The Probability Of Imentioning

confidence: 99%

Application of vacuum-assisted closure in seawater-immersed wound treatment under different negative pressures

Cao¹,

Peng²,

Sun³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The therapeutic effect of vacuum-assisted closure (VAC) has been confirmed in many types of complex wounds, but there are few relevant reports regarding seawater-immersed wounds. The aim of this study was to determine the effect of VAC on seawater-immersed wound healing under different negative pressures and explore the optimal negative pressure value. Four purebred miniature pigs were used as the experimental animal models. Four acute, symmetrical wounds were made on each side of the spine and designated as the experimental group (wounds with 2 h of seawater immersion) and the control group (wounds without seawater immersion). Wounds were divided into a conventional dressing group and 3 further groups with different VAC therapies (negative pressure at either 120, 180, or 240 mmHg). The extent of wound healing, and speed of granulation growth and re-epithelialization were measured. Bacterial flora distribution in the wounds was observed, and fibronectin levels in the exudate of the wounds were tested. Results showed that seawater immersion aggravated (2015) wound injury and that VAC therapy with 180 mmHg negative pressure induced the fastest epidermis migration, obvious edema elimination, significant capillary proliferation, and the highest level of fibronectin, and that in wounds, the proportion of Gram-negative bacteria tended to decrease and that of Gram-positive bacteria tended to increase. Our results show that VAC promotes seawater-immersed wound healing and that 180 mmHg negative pressure may be optimal for wound healing.

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“…Members of "Candidatus Endobugula" and related species that belong to a bacterial symbiont group affiliated with the OMG clade have gained attention because these microbial symbionts have the bryostatin polyketide synthase gene cluster (7,9). Other close relatives included uncultured gammaproteobacterial clone H102, isolated from seahorses (Hippocampus guttulatus) (FM878644; 96.3%) (2), and surface sediment clone B78-56, retrieved from the Arctic Ocean (EU287020; 95.0%) (8).…”

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confidence: 99%

Genome Sequence of Strain IMCC1989, a Novel Member of the Marine Gammaproteobacteria

Jang

Kim

et al. 2011

Journal of Bacteriology

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Strain IMCC1989 is a novel member of the oligotrophic marine Gammaproteobacteria (OMG) group and is closely related with a symbiont group of the genera Teredinibacter and "Candidatus Endobugula." Here we present the genome sequence of strain IMCC1989, which was isolated from the Yellow Sea by using dilutionto-extinction culturing.A marine bacterium designated strain IMCC1989 was isolated from a surface seawater sample collected off the coast near Deokjeok Island, in the Yellow Sea, by using highthroughput culturing techniques based on dilution-to-extinction culturing (6). The extinction culture of strain IMCC1989 was originally cultivated in a low-nutrient heterotrophic medium that was prepared with 0.2-m-filtered and autoclaved natural seawater. The initial extinction culture was successfully subcultured on marine 1/10 R2A medium as tiny colonies, which were subsequently maintained on marine agar 2216 (BD Difco).Phylogenetic analysis of 16S rRNA gene sequences positioned strain IMCC1989 in a phylogenetic clade affiliated with the oligotrophic marine Gammaproteobacteria (OMG) group (5). The OMG group includes five distinct bacterial clades (BD1-7, Kl89A, OM60, OM182, SAR92), together with several oligotrophic marine bacterial clades, such as a bacterial symbiont group represented by Teredinibacter and "Candidatus Endobugula." The described species that is most closely related to strain IMCC1989 was Eionea nigra 17X/A02/237 T (96.6% 16S rRNA gene sequence similarity), isolated from the Mediterranean Sea (10). Strain IMCC1989 was also closely related to "Candidatus Endobugula sertula" (95.0%) (7, 9) and Pseudoteredinibacter isoporae SW-11 T (94.2%) (4). Members of "Candidatus Endobugula" and related species that belong to a bacterial symbiont group affiliated with the OMG clade have gained attention because these microbial symbionts have the bryostatin polyketide synthase gene cluster (7, 9). Other close relatives included uncultured gammaproteobacterial clone H102, isolated from seahorses (Hippocampus guttulatus) (FM878644; 96.3%) (2), and surface sediment clone B78-56, retrieved from the Arctic Ocean (EU287020; 95.0%) (8).Genomic DNA of strain IMCC1989 was prepared using the DNeasy blood and tissue genomic DNA kit (Qiagen Korea Ltd., Seoul, South Korea). Tagged genomic library generation and whole-genome shotgun sequencing based on Solexa paired-end sequencing technology (3) were performed by Macrogen, Inc. (Seoul, South Korea). About 8.5 million short reads, totaling 647,001,680 bp, were initially obtained for the genome library tagged for strain IMCC1989. After quality filtering and trimming, 3,028,681 reads were assembled into 455 contigs (AEVK01000001 to AEVK01000455) using Velvet (11), with a depth of 112-fold genome coverage for the unclosed draft genome of strain IMCC1989. The IMCC1989 genome has 3,939,451 bp, with a mean GϩC content of 42.06%.Annotation of the open reading frames (ORFs) and noncoding RNAs were performed using the RAST (rapid annotations using subsystem technology) server (1). Predicted O...

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Bacterial diversity in surface sediments from the Pacific Arctic Ocean

Cited by 83 publications

References 59 publications

Molecular biologic techniques applied to the microbial prospecting of oil and gas in the Ban 876 gas and oil field in China

Molecular biologic techniques applied to the microbial prospecting of oil and gas in the Ban 876 gas and oil field in China

Application of vacuum-assisted closure in seawater-immersed wound treatment under different negative pressures

Genome Sequence of Strain IMCC1989, a Novel Member of the Marine Gammaproteobacteria

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