GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent

Wang, Fengping; Zhou, Huaiyang; Meng, Jun; Peng, Xiaotong; Jiang, Lijing; Sun, Ping; Zhang, Chuanlun; Nostrand, Joy D. Van; Deng, Ye; He, Zhili; Wu, Liyou; Zhou, Jizhong; Xiao, Xiang

doi:10.1073/pnas.0810418106

Cited by 140 publications

(115 citation statements)

References 38 publications

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“…This prompted us to carry out a study to profile the overall functional genes; thus, a high-throughput tool based on functional gene markers is needed to this end. The GeoChip, a comprehensive functional gene array, is one of such tools, as it provides incomparable insight into many individual functional genes in the same sample sets (Wang et al 2009). …”

Section: Introductionmentioning

confidence: 99%

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors

Xia

Wang

Wen

et al. 2014

Appl Microbiol Biotechnol

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Understanding microbial community composition is thought to be crucial for improving process functioning and stabilities of full-scale activated sludge reactors in wastewater treatment plants (WWTPs). However, functional gene compositions of microbial communities within them have not been clearly elucidated. To gain a complete picture of microbial community, in this study, GeoChip 4.2 was used to profile the overall functional genes of three full-scale activated sludge bioreactors, the 16S rRNA gene diversities of which had been unveiled by 454-pyrosequencing in our previous investigation. Triplicate activated sludge samples from each system were analyzed, with the detection of 38,507 to 40,654 functional genes. A high similarity of 77.3-81.2 % shared functional genes was noted among the nine samples, verified by the high 16S rRNA gene similarity with shared operational taxonomic units (OTUs) constituting 66.4-70.0 % of the detected sequences in each system. Correlation analyses showed that the abundances of a wide array of functional genes were associated with system performances. For example, the abundances of carbon degradation genes were strongly correlated to chemical oxygen demand (COD) removal efficiencies (r=0.8697, P<0.01). Lastly, we found that sludge retention time (SRT), influent total nitrogen concentrations (TN inf), and dissolved oxygen (DO) concentrations were key environmental factors shaping the overall functional genes. Together, the results revealed vast functional gene diversity and some links between the functional gene compositions and microbe-mediated processes.

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Section: Introductionmentioning

confidence: 99%

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors

Xia

Wang

Wen

et al. 2014

Appl Microbiol Biotechnol

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“…has been extensively employed to analyze the functional gene structure of microbial communities in different environments (He et al, 2010b;Trivedi et al, 2012;Wang et al, 2009). It is, therefore, a suitable tool for examining the impact of antibiotic residues on microbial communities with regard to microbial functional gene structures as well as the occurrence of antibiotic resistance in biological antibiotic production wastewater treatment systems.…”

Section: Introductionmentioning

confidence: 99%

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems

et al. 2013

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a b s t r a c tIt is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a highthroughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase ( glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P < 0.05), showing that the fungal functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the envi- Available online at www.sciencedirect.com journal homepage: www.elsevier.com/locate /wa tres w a t e r r e s e a r c h 4 7 ( 2 0 1 3 ) 6 2 9 8 e6 3 0 8

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“…Microbial diversity surveys on the Juan de Fuca Ridge have focused at diffuse flow hydrothermal vents at Axial Seamount (e.g., Lynch, 2000; Alain et al, 2002;Pagé et al, 2004;Huber et al, 2006aHuber et al, , 2009Kaye et al, 2011;Meyer et al, 2013), high-temperature hydrothermal vents at Endeavor Segment (e.g., Wang et al, 2009aWang et al, , 2009bZhou et al, 2009;Anderson et al, 2013), a hydrothermal mound located at off-axis Cleft Segment (Davis et al, 2009), seafloor basalt (Mason et al, 2007(Mason et al, , 2009), sediment-buried basement fluid (Cowen et al, 2003;Huber et al, 2006b;Nakagawa et al, 2006;Jungbluth et al, 2013), and sediment-buried rock (Orcutt et al, 2011b;Smith et al, 2011;Lever et al, 2013). The limited number of microbiological studies focused on sediment of the Juan de Fuca Ridge have typically not incorporated phylogenetic marker-based surveys of community diversity such as small subunit ribosomal RNA (SSU rRNA) gene sequencing (e.g., Cragg et al, 2000;Mather and Parkes, 2000;Engelen et al, 2008); only studies focused on Cascadia margin methane hydrate-bearing sediment have incorporated such an approach (e.g., Bidle et al, 1999;Marchesi et al, 2001;Knittel et al, 2003;Inagaki et al, 2006;Nunoura et al, 2008;Briggs et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G

Jungbluth¹,

Johnson²,

Cowen³

et al. 2013

Proceedings of the IODP

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Microorganisms inhabiting sediment in close proximity to recharging basement outcrops are of interest because of the enhanced advective fluid flow in these locations, which is expected to exert unique selective pressures on the resident microbial communities. Here, Integrated Ocean Drilling Program (IODP) boreholes were used to access sediment microbial communities near Grizzly Bare recharge seamount on the Juan de Fuca Ridge eastern flank. The two locations examined in this study, Holes U1363G and U1363B, are 50 and 177 m away from the center of the outcrop, respectively. In general, small subunit ribosomal RNA gene clones from all three domains of life were detected; these groups were predominantly related to microorganisms known to reside in marine sediment. A large fraction of environmental gene clones recovered from Hole U1363B and U1363G sediment were related to uncultivated, candidate phyla of Bacteria such as BHI80-139, BRC1, JS1, OPB41, and TA06. Hole U1363B and U1363G sediment clone libraries were generally dominated by the domain Bacteria and particularly the phylum Chloroflexi, which comprised approximately one-quarter of the total gene clones identified. However, borehole sediment also contained several archaeal lineages that were phylogenetically affiliated with the Miscellanenous Crenarchaeotal Group. Eukaryotic fungi were only detected within the interstitial water sample from Hole U1363B. Finally, a minor portion of clones recovered from sediment in this study were also recovered from basement fluid samples previously characterized from Baby Bare discharge seamount and Ocean Drilling Program and IODP borehole Circulation Obviation Retrofit Kit Observatories (CORKs) in Holes 1026B and U1301A, which are ~50 km to the north-northeast.

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GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent

Cited by 140 publications

References 38 publications

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems

Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G

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