Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during In Situ Uranium Reduction

Patterns of microbial distribution represent the integrated effects of historical and biological processes and are thus a central issue in ecology. However, there is still active debate on whether dispersal limitation contributes to microbial diversification in strongly connected systems. In this study, sediment samples were collected along a transect representing a variety of seawater pollution levels in the East China Sea. We investigated whether changes in sediment bacterial community structures would indicate the effects of the pollution gradient and of dispersal limitation. Our results showed consistent shifts in bacterial communities in response to pollution. More geographically distant sites had more dissimilar communities (r ‫؍‬ ؊0.886, P < 0.001) in this strongly connected sediment ecosystem. A variance analysis based on partitioning by principal coordinates of neighbor matrices (PCNM) showed that spatial distance (dispersal limitation) contributed more to bacterial community variation (8.2%) than any other factor, although the environmental factors explained more variance when combined (11.2%). In addition, potential indicator taxa (primarily affiliated with Deltaproteobacteria and Gammaproteobacteria) were identified; these taxa characterized the pollution gradient. This study provides direct evidence that dispersal limitation exists in a strongly connected marine sediment ecosystem and that candidate indicator taxa can be applied to evaluate coastal pollution levels.

Section: Discussionsupporting

confidence: 64%

Biogeography of the Sediment Bacterial Community Responds to a Nitrogen Pollution Gradient in the East China Sea

Xiong

Ye²,

Wang

et al. 2014

“…This discrepancy may be explained because the primary amplification microarray signals for Desulfotomaculum came from Desulfotomaculum carboxydivorans, D. putei, and D. thermobenzoicum, species that are not necessarily detected by targeted aps primers that also amplify the aps gene from members of the Desulfobacteraceae (see Table 2 in reference 28) or with the highly degenerate aps primers described in reference 29. Prior field experiments and observations at the Rifle site also show consistent stimulation of sulfate-reducing lineages in response to acetate amendment (1,8) and an increase in dsr gene abundance, as measured by the comprehensive GeoChip microarray that uses whole-genome amplification methods instead of broad-range, gene-specific primers (2). We therefore attribute the discrepancy in sulfate reducer signals between qPCR and amplification microarray platforms in the Super 8 field experiment to limitations in the design and use of broad-spectrum functional gene primers for the qPCR and not 16S rRNA gene amplification microarray bias or the absence of Desulfotomaculum or other sulfate-reducing microbial potential within the gallery.…”

Section: Resultsmentioning

confidence: 99%

Profiling In Situ Microbial Community Structure with an Amplification Microarray

Chandler

Knickerbocker

Bryant

et al. 2013

Self Cite

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO 3 ؊ ) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO 3 , but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications.

“…The effect could be particularly significant in U(VI)-contaminated groundwater like that at the Oak Ridge site, where electron donors and C sources are limited and multiple electron acceptors are present (6). Previous studies demonstrated that injection of fast-degrading, simple substrates (e.g., acetate or ethanol) stimulated distinct microbial communities (7,9,12,13). In this study, a slowly degrading, complex substrate, EVO, was used.…”

Section: Discussionmentioning

confidence: 99%

“…To remediate these sites, various fast-degrading substrates (e.g., acetate, ethanol, and lactate) have been used. The substrate injection stimulated microbial populations important to U(VI) reduction, resulting in distinct microbial communities whose functions were dependent upon the choice of substrate (6)(7)(8)(9)(10)(11)(12)(13). However, the use of these fast-degrading, simple substrates has several drawbacks.…”

mentioning

confidence: 99%

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

Zhang

Nostrand

et al. 2015

Self Cite

A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO 3 ؊ , Mn(IV), Fe(III), U(VI), and SO 4 2؊ significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO 3 ؊ , Mn(II), Fe(II), U(VI), and SO 4 2؊ . Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction. Mining, ore processing, and weapons and fuel production have left many sites around the world contaminated with uranium (U) (1). Groundwater contamination in particular is a critical public concern because the transport of highly soluble and toxic U(VI) within groundwater threatens drinking water resources. Bioreduction of U(VI) to insoluble U(IV) has been recognized as an effective approach to immobilize U in situ (2). However, while microorganisms capable of U(VI) reduction are present in aquifers, U(VI) still persists because of the lack of available electron donors and, in some cases, the presence of excess competing electron acceptors (e.g., NO 3 Ϫ ) (3). Injection of a substrate that would provide electron donors is essential to stimulate indigenous microbial communities toward U(VI) reduction (4, 5).Some U.S. Department of Energy (DOE) sites, for example, the Oak Ridge Integrated Field Research Challenge (ORIFRC) and the Old Rifle uranium mill tailing remedial action sites, are contaminated with U(VI). To remediate these sites, various fast-degrading substrates (e.g., acetate, ethanol, and lactate) have been used. The substrate injection stimulated microbial populations important to U(VI) reduction, resulting in distinct microbial co...