Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels

Waldron, P.J.; Wu, Liyou; Nostrand, Joy D. Van; Schadt, Christopher W.; He, Zhili; Watson, David B.; Jardine, Philip M.; Palumbo, Anthony V.; Hazen, Terry C.; Zhou, Jizhong

doi:10.1021/es803423p

Cited by 79 publications

(59 citation statements)

References 36 publications

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“…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.…”

Section: Discussionsupporting

confidence: 92%

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

Störmer

Wichels

Gerdts

2013

Marine Pollution Bulletin

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a b s t r a c tThe dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip 4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring.

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Section: Discussionsupporting

confidence: 92%

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

Störmer

Wichels

Gerdts

2013

Marine Pollution Bulletin

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“…The local groundwater in the vicinity of the site contains one of the most concentrated mobile, subsurface uranium plumes in the United States. Numerous SRM species (particularly from the Deltaproteobacteria and the Firmicutes) have been detected at various locations within the FRC site 97,108,113,[127][128][129][130][131][132][133][134][135][136][137][138][139][140][141] , suggesting that SRMs have successfully adapted to this environment.…”

Section: Metagenomics Of Srms In Heavy-metal-contaminated Sitesmentioning

confidence: 99%

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

et al. 2011

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| Sulphate-reducing microorganisms (SRMs) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. As SRMs have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. In this Review, we highlight recent applications of systems biology tools in studying the stress responses of SRMs, particularly Desulfovibrio spp., at the cell, population, community and ecosystem levels. The syntrophic lifestyle of SRMs is also discussed, with a focus on system-level analyses of adaptive mechanisms. Such information is important for understanding the microbiology of the global sulphur cycle and for developing biotechnological applications of SRMs for environmental remediation, energy production, biocorrosion control, wastewater treatment and mineral recovery.

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“…Currently, this technology has become a powerful and high-throughput tool for analyzing microbial communities and monitoring environmental processes and ecosystem functions (c.f., Wu et al, 2001Wu et al, , 2006Wu et al, , 2008Loy et al, 2002;TaroncherOldenburg et al, 2003;Bodrossy and Sessitsch, 2004;Rhee et al, 2004;Steward et al, 2004;Tiquia et al, 2004;Dix et al, 2006;Rodriguez-Martinez et al, 2006;He et al, 2007;Leigh et al, 2007;Yergeau et al, 2007;Zhou et al, 2008;Liang et al, 2009;Mason et al, 2009;Tas et al, 2009;Van Nostrand et al, 2009;Waldron et al, 2009;Wang et al, 2009). Especially, one of our previous functional gene arrays (FGAs), GeoChip 2.0, containing more than 24 000 probes and covering more than 10 000 gene sequences from B150 gene categories involved in key microbially mediated biogeochemical processes has been widely used to analyze microbial communities from different resources, such as soils (Yergeau et al, 2007;Zhou et al, 2008), waters Leigh et al, 2007;Tas et al, 2009;Van Nostrand et al, 2009;Waldron et al, 2009), oil fields (Liang et al, 2009), marine sediments (Wu et al, 2008), extreme environments (Mason et al, 2009;Wang et al, 2009), bioreactor systems (Rodriguez-Martinez et al, 2006) and other habitats (Kimes et al, 2010), to address a variety of questions related to biogeochemical cycles, bioremediati...…”

Section: Introductionmentioning

confidence: 99%

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

et al. 2010

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A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with ∼28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036–0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.

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Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels

Cited by 79 publications

References 36 publications

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

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

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

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