scholarly journals Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

2010 ◽  
Vol 5 (3) ◽  
pp. 403-413 ◽  
Author(s):  
Yuting Liang ◽  
Joy D Van Nostrand ◽  
Ye Deng ◽  
Zhili He ◽  
Liyou Wu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Gene Diversity ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Soil Microbial ◽  
Functional Gene Diversity

scholarly journals Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities

2014 ◽  
Vol 23 (12) ◽  
pp. 2988-2999 ◽  
Author(s):  
Fabiana S. Paula ◽  
Jorge L. M. Rodrigues ◽  
Jizhong Zhou ◽  
Liyou Wu ◽  
Rebecca C. Mueller ◽  
...  
Keyword(s):  
Land Use ◽  
Land Use Change ◽  
Microbial Communities ◽  
Forest Soil ◽  
Gene Diversity ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Amazon Forest ◽  
Soil Microbial ◽  
Functional Gene Diversity

scholarly journals GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage

2010 ◽  
Vol 77 (3) ◽  
pp. 991-999 ◽  
Author(s):  
Jianping Xie ◽  
Zhili He ◽  
Xinxing Liu ◽  
Xueduan Liu ◽  
Joy D. Van Nostrand ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Gene Diversity ◽  
Organic Contaminant ◽  
Functional Gene ◽  
Metabolic Potential ◽  
Methane Generation ◽  
Contaminant Degradation ◽  
Functional Gene Diversity

ABSTRACTAcid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g.,narGandnorB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P< 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems.

Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil

Chemosphere ◽  
2009 ◽  
Vol 75 (2) ◽  
pp. 193-199 ◽  
Author(s):  
Yuting Liang ◽  
Joy D. Van Nostrand ◽  
Jian Wang ◽  
Xu Zhang ◽  
Jizhong Zhou ◽  
...  
Keyword(s):  
Crude Oil ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Gene Analysis ◽  
Soil Microbial ◽  
Functional Gene Analysis

scholarly journals Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

2012 ◽  
Vol 79 (4) ◽  
pp. 1284-1292 ◽  
Author(s):  
Kai Xue ◽  
Liyou Wu ◽  
Ye Deng ◽  
Zhili He ◽  
Joy Van Nostrand ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Agricultural Research ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Functional Genes ◽  
N Availability ◽  
Low Input ◽  
Soil Microbial ◽  
Denitrification Genes

ABSTRACTVarious agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO3−, NH4+, available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO3−concentration and denitrification genes, NH4+concentration and ammonification genes, and N2O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.

scholarly journals Development of an Environmental Functional Gene Microarray for Soil Microbial Communities

2010 ◽  
Vol 76 (21) ◽  
pp. 7161-7170 ◽  
Author(s):  
Ken C. McGrath ◽  
Rhiannon Mondav ◽  
Regina Sintrajaya ◽  
Bill Slattery ◽  
Susanne Schmidt ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Environmental Samples ◽  
Agricultural Soils ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Gene Microarray ◽  
Independent Manner ◽  
Soil Microbial ◽  
Functional Attributes ◽  
Culture Independent

ABSTRACT Functional attributes of microbial communities are difficult to study, and most current techniques rely on DNA- and rRNA-based profiling of taxa and genes, including microarrays containing sequences of known microorganisms. To quantify gene expression in environmental samples in a culture-independent manner, we constructed an environmental functional gene microarray (E-FGA) consisting of 13,056 mRNA-enriched anonymous microbial clones from diverse microbial communities to profile microbial gene transcripts. A new normalization method using internal spot standards was devised to overcome spotting and hybridization bias, enabling direct comparisons of microarrays. To evaluate potential applications of this metatranscriptomic approach for studying microbes in environmental samples, we tested the E-FGA by profiling the microbial activity of agricultural soils with a low or high flux of N2O. A total of 109 genes displayed expression that differed significantly between soils with low and high N2O emissions. We conclude that mRNA-based approaches such as the one presented here may complement existing techniques for assessing functional attributes of microbial communities.

scholarly journals Long-Term Effects of Soil Remediation with Willow Short Rotation Coppice on Biogeographic Pattern of Microbial Functional Genes

2022 ◽  
Vol 10 (1) ◽  
pp. 140
Author(s):  
Wenjing Liu ◽  
Kai Xue ◽  
Runpeng Hu ◽  
Jizhong Zhou ◽  
Joy D. Van Nostrand ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Gene Diversity ◽  
Soil Microbial Communities ◽  
Short Rotation Coppice ◽  
Functional Genes ◽  
Long Term Effects ◽  
Soil Microbial ◽  
Biogeographic Pattern ◽  
Short Rotation

Short rotation coppice (SRC) is increasingly being adopted for bioenergy production, pollution remediation and land restoration. However, its long-term effects on soil microbial communities are poorly characterized. Here, we studied soil microbial functional genes and their biogeographic pattern under SRC with willow trees as compared to those under permanent grassland (C). GeoChip analysis showed a lower functional gene diversity in SRC than in C soil, whereas microbial ATP and respiration did not change. The SRC soil had lower relative abundances of microbial genes encoding for metal(-oid) resistance, antibiotic resistance and stress-related proteins. This indicates a more benign habitat under SRC for microbial communities after relieving heavy metal stress, consistent with the lower phytoavailability of some metals (i.e., As, Cd, Ni and Zn) and higher total organic carbon, NO3−-N and P concentrations. The microbial taxa–area relationship was valid in both soils, but the space turnover rate was higher under SRC within 0.125 m2, which was possibly linked to a more benign environment under SRC, whereas similar values were reached beyond thisarea. Overall, we concluded that SRC management can be considered as a phytotechnology that ameliorates the habitat for soil microorganisms, owing to TOC and nutrient enrichment on the long-term.

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