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

Abstract

Acid 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., narG and norB) 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.When sulfide ores are exposed to air, water, and microbes (autotrophic and heterotrophic archaea and bacteria) during the exploration of coals and metal deposits, acid mine drainage (AMD), which usually has low pH and high concentrations of sulfate and metals, is formed (5,8,34,52). AMD is a prevalent, international environmental problem that threatens aquatic life and surrounding ecosystems (11,15,21,24,26,33,43,44), although it also has been regarded as an excellent model to investigate linkages between microbial communities and geochemistry because of its relatively simple microbial community composition and structure (5,6,8). A better understanding of the microbial community diversity and ecology in AMD would provide a scientific foundation not only for the bioremediation of AMD-contaminated environments but also for potential applications for the energy-efficient recovery of valuable metals from mine waste and the removal of sulfur from coal (6, 23).The phylogenetic diversity of AMD microbial communities has been well studied by 16S rRNA-based approaches, including PCR cloning (36,54,55,57), denaturing gradient gel electrophoresis (DGGE) (10,20,21), fluorescence in situ hybridization (9,29,40), and oligonucleotide microarrays (14, 56). For instance, the DNA sequencing of a natural acidophilic biofilm (pH 0.80)...

Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment

“…In the present study, the distLM approach was used to calculate the significant influence of DDX compounds on the bacterial community structure, suggesting that the biogeochemical conditions at the dumping site influence the functional diversity of the bacterial community. The significant influence of environmental factors on the functional diversity of bacterial communities was previously reported in similar studies investigating the relationships between the diversity of functional genes and environmental factors (Waldron et al, 2009;Xie et al, 2011). Waldron and co-workers observed lower gene diversity in highly contaminated samples and the significant influence of contaminants on the functional structure of the bacterial communities, consistent with the results presented herein.…”

“…Molecular approaches, such as functional gene arrays, facilitate a relatively easy assessment of the information in the microbenthic community, including community structure and function (Lu et al, 2012). Various studies have demonstrated the capacity of functional gene arrays to detect microbial community responses to environmental stressors Liu et al, 2010;Wang et al, 2009;Ward et al, 2007;Wu et al, 2008;Yergeau et al, 2007;Zhou, 2003), including heavily contaminated habitats (Lu et al, 2012;Neufeld et al, 2006;Van Nostrand et al, 2009;Xie et al, 2011). The results of these studies and other approaches evaluating the response of bacterial communities on environmental perturbation (chemically or physically) have demonstrated changes in the respective community structure and function (dos Santos et al, 2011;Findlay et al, 1990;Suarez-Suarez et al, 2011), thereby forming the basis for our hypothesis.…”

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

“…Wastewater and sludge properties (Table S2 and Table S3) were standardized to have comparability prior to further analysis using the formula, z ¼ ðx i À xÞ=s, where x i is the sample value, x is the mean of all samples, and s is the standard deviation on (Freeman, 1994;Xie et al, 2011). Diversity indices including Shannon-Weaver H and Simpson were calculated using R 2.9.1 (http://www.r-project.org/) with the vegan package to evaluate the microbial functional diversity.…”

A microarray for assessing transcription from pelagic marine microbial taxa

“…The most comprehensive microbial functional microarray to date, the GeoChip 4.0, targets 410 000 sequences represented by 150 genes mainly from soil microbial communities and reductionoxidation processes (He et al, , 2010; Bai et al, 2013;Zhou et al, 2013). In addition to contaminated soils, acid mine drainage sites and Antarctic soils (Yergeau et al, 2007;Mason et al, 2010;Xie et al, 2011), the GeoChip has been applied to detect microbial DNA and RNA in the marine environment (Lu et al, 2012;Wawrik et al, 2012). Aside from the PhyloChip, which targets 16S rRNA genes (Brodie et al, 2006), existing microarrays target a specific genus (Rinta-Kanto et al, 2011), a particular process (Tiquia et al, 2004;Moisander et al, 2006Moisander et al, , 2007Ward et al, 2007;Bulow et al, 2008;Wu et al, 2008;Bouskill et al, 2011;Abell et al, 2012) or ecosystem (Rich et al, 2008;Smith et al, 2010;Rich et al, 2011).…”