GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity

He, Zi

doi:10.2172/986221

Cited by 76 publications

(143 citation statements)

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“…GeoChip 4.0 analysis was performed as described previously (He et al, 2010;Tu et al, 2014). Briefly, DNA samples were labelled with the fluorescent dye Cy-5 by a random priming method (Tu et al, 2014;Su et al, 2015), followed by purification with a QIA Quick Purification Kit (Qiagen, Valencia, CA, USA).…”

Section: Molecular Analysismentioning

confidence: 99%

“…Thereafter, DNA was hybridized with GeoChip 4.0 at 42°C for 16 h in a MAUI hybridization station (BioMicro, Salt-Lake City, UT, USA) and scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm, using 100% and 75% laser power and photomultiplier tube gain, respectively. Data processing was performed as previously described (He et al, 2010) using Microarray Data Manager (http:/ieg.ou.edu/microarray/).…”

Section: Molecular Analysismentioning

confidence: 99%

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Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

et al. 2016

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A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R 2 40.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.

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Section: Molecular Analysismentioning

confidence: 99%

Section: Molecular Analysismentioning

confidence: 99%

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

et al. 2016

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“…According to the GeoChip 3.0 analysis result, a total of 6133 functional genes from all of the nine functional gene categories targeted by the chip were detected (Table S4 in Supporting Information), including antibiotic resistance, carbon cycling (mainly carbon degradation), nitrogen cycling, sulphur cycling, phosphorus cycling, metal resistance and energy processes (He et al, 2010a), showing the presence of diverse functional genes in these systems. A total of 4520 genes were detected among the four sludge samples, while 3945 were detected in the eight wastewater samples.…”

Section: 2mentioning

confidence: 99%

“…The rapid development of high throughput metagenomic approaches like GeoChip (He et al, 2010a) has made it possible to easily examine microbial functional diversity, composition and structure in a rapid fashion. GeoChip 3.0, which contains more than 57,000 gene variants from 292 functional gene families, including antibiotic resistance genes (He et al, 2010a),…”

Section: Introductionmentioning

confidence: 99%

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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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A long‐term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure

Sun

Wang

Jiang

et al. 2014

Ecology and Evolution

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The spatial patterns of microbial communities are largely determined by the combined effects of historical contingencies and contemporary environmental disturbances, but their relative importance remains poorly understood. Empirical biogeographic data currently available are mostly based on the traditional method of observational survey, which typically involves comparing indigenous microbial communities across spatial scales. Here, we report a long-term soil transplantation experiment, whereby the same two soils (red Acrisol and purple Cambisol from Yingtan) were placed into two geographic locations of ∼1000 km apart (i.e., Yingtan in the mid-subtropical region and Fengqiu in warm-temperate region; both located in China). Twenty years after the transplantation, the resulting soil microbial communities were subject to high-throughput 454 pyrosequencing analysis of 16S and 18S rRNA genes. Additionally, bacteria and archaea involved in nitrogen cycling were estimated using clone library analysis of four genes: archaeal amoA, bacterial amoA,nirK, and nifH. Data of subsequent phylogenetic analysis show that bacteria, fungi, and other microbial eukaryotes, as well as the nitrogen cycling genes, are grouped primarily by the factor of geographic location rather than soil type. Moreover, a shift of microbial communities toward those in local soil (i.e., Chao soil in Fengqiu) has been observed. The results thus suggest that the historical effects persistent in the soil microbial communities can be largely erased by contemporary disturbance within a short period of 20 years, implicating weak effects of historical contingencies on the structure and composition of microbial communities in the soil.

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GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity

Cited by 76 publications

References 0 publications

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

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

A long‐term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure

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