Phylogenetic diversity of bacterial communities in South China Sea mesoscale cyclonic eddy perturbations

Zhang, Yao; Jiao, Nianzhi; Sun, Zhenyu; Hu, Anyi; Zheng, Qiang

doi:10.1016/j.resmic.2010.12.006

Cited by 28 publications

(28 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To date, the South China Sea bacterial community distribution patterns remain unknown. Although a few surveys based on culture-dependent, denaturing gradient gel electrophoresis and constructed PCR product clone libraries methods analyzed the bacterial diversity, the obtained numbers of operational taxonomic units (OTUs) was lower than100 sequences for each sample [17–22]. These smaller datasets result in the underestimation of species richness and generally do not describe rare populations that might represent considerable diversity.…”

Section: Introductionmentioning

confidence: 99%

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

Zhu

Tanabe

Yang³

et al. 2013

PLoS ONE

View full text Add to dashboard Cite

BackgroundSubseafloor 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.Methodology/Principal FindingsPyrosequencing 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.ConclusionsThis 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.

show abstract

Section: Introductionmentioning

confidence: 99%

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

Zhu

Tanabe

Yang³

et al. 2013

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…Satellite altimetry and ADCP data documented the cold‐core cyclonic eddies occurring around CE1 and CE2. The isopycnals were elevated, and the subsurface waters hence exhibited higher nutrient concentrations (Table ), together with lower temperature, higher salinity, higher chlorophyll a concentration, and lower dissolved oxygen than SEATS (Zhang et al ., , ). The surface water of CE2 was probably influenced by the eastward jet off the coast of Vietnam with its relatively low salinity.…”

Section: Resultsmentioning

confidence: 99%

“…The water depths of the CE 1, CE 2, and SEATS sites were 2418, 2844, and 3839 m. CE 1 and CE 2 were located during sampling within two cyclonic eddies, delineated by dashed circles. For the real‐time sea‐surface height altimetry remote sensed images and the physical chemistry properties of these two eddy‐center sites, please refer to the references (Zhang et al ., , ).…”

Section: Introductionmentioning

confidence: 99%

Diversity and distribution of diazotrophic communities in the South China Sea deep basin with mesoscale cyclonic eddy perturbations

Zhang

Zhao

Sun

et al. 2011

FEMS Microbiol Ecol

Self Cite

View full text Add to dashboard Cite

The South China Sea (SCS) is an oligotrophic subtropical marginal ocean with a deep basin and a permanently stratified central gyre. Upwelling and nitrogen fixation provide new nitrogen for primary production in the SCS. This study was aimed at an investigation of phylogenetic diversity and quantification of the diazotroph community in the SCS deep basin, which is characterized by frequent mesoscale eddies. The diazotroph community had a relatively low diversity but a distinct spatial heterogeneity of diversity in the SCS deep basin. The potential for nitrogen fixation consistently occurred during cyclonic eddies, although upwelling of nutrient-replete deep water might have alleviated nitrogen limitation in the SCS. However, diazotrophic proteobacteria were dominant, but neither Trichodesmium nor heterocystous cyanobacterial diatom symbionts. Quantitative PCR analysis using probe-primer sets developed in this study revealed that the nif H gene of the two dominant alpha- and gammaproteobacterial groups was at the highest abundance (up to 10(4) to 10(5) copies L(-1) ). Trichodesmium thiebautii was detected with an average density of 10(2) trichomes L(-1) in the euphotic waters, while Richelia intracellularis was observed sporadically under the microscope. The unicellular cyanobacterial groups A and B were not detected in our libraries. Our results suggested that diazotrophic proteobacteria were significant components potentially contributing to nitrogen fixation in this oligotrophic marginal ocean ecosystem.

show abstract

“…This microorganism was classified as a Rhodospirillales with 100% similarity to bacteria associated with a marine sponge (AC JQ240926), the South China Sea (Zhang et al, 2011) and a shallow CH 4 seep (Wasmund et al, 2009). Redmond and Valentine (2012) reported that surface samples with a visible oil sheen collected during the Deepwater Horizon oil spill, were dominated by Rhodospirillales, other Alphaproteobacteria and Cyanobacteria.…”

Section: Euphotic Zone Bacterioplankton Structure and Diversitymentioning

confidence: 99%

Methane and microbial dynamics in the Gulf of Mexico water column

et al. 2015

View full text Add to dashboard Cite

In contrast to other oligotrophic water bodies the Gulf of Mexico (GOM) hosts an abundance of hydrocarbon seeps, which likely influences the microbial assemblages it hosts particularly regarding the availability of labile carbon in the aphotic GOM. The aphotic zone receives direct injection of seep methane (CH 4 ), but CH 4 from an unknown source has been reported at supersaturated concentrations relative to the atmosphere in the GOM photic zone. Here we used iTag sequencing of 16S rRNA genes to characterize GOM microbial communities and to relate changes in microbial community structure to the properties inherent to their oceanic province-seafloor to the photic zone, seep and non-seep. Along this trajectory water column communities were distinct in the euphotic zone compared to the mesopelagic and deep-sea. In the euphotic zone the relative abundance of a cyanobacterial species (Prochlorococcus) was significantly correlated with both CH 4 and chlorophyll a concentrations and was abundant in some deep-chlorophyll maximum (DCM) samples. The relative abundance of microorganisms related to known hydrocarbon degraders were also significantly correlated with CH 4 in the euphotic zone, but no canonical methanotrophs were observed. In the mesopelagic to the seafloor canonical methanotrophs were identified, but only a Marine Group II Euryarchaeota was significantly correlated with CH 4 . Overall, depth and the associated environmental conditions were the primary drivers in structuring microbial communities over the GOM water column. Further, CH 4 concentrations and relative microbial abundances covaried significantly from the seafloor to the photic zone in the GOM. The lack of a significant relationship between canonical methanotrophs and CH 4 in the aphotic zone, even when sampling at seep sites, may suggest methane-oxidation by unknown microorganisms. Similarly their absence in the CH 4 maximum and DCM suggested that CH 4 is either oxidized by unrecognized methanotrophs or escapes the CH 4 biofilter and fluxes to the atmosphere.

show abstract

Phylogenetic diversity of bacterial communities in South China Sea mesoscale cyclonic eddy perturbations

Cited by 28 publications

References 42 publications

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

Diversity and distribution of diazotrophic communities in the South China Sea deep basin with mesoscale cyclonic eddy perturbations

Methane and microbial dynamics in the Gulf of Mexico water column

Contact Info

Product

Resources

About