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Title: Bacterial Activity, Community Structure, and Centimeter-Scale Spatial Heterogeneity in Contaminated Soil

Authors:
; ; ; ;
Publication Date:
Research Org.:
Subsurface Biogeochemical Research (SBR)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1154142
Resource Type:
Journal Article
Resource Relation:
Journal Name: Microbial Ecology; Journal Volume: 51; Journal Issue: 2
Country of Publication:
United States
Language:
English

Citation Formats

Joanna M.,Becker, Tim,Parkin, Cindy H.,Nakatsu, Jayson D.,Wilbur, and Allan,Konopka. Bacterial Activity, Community Structure, and Centimeter-Scale Spatial Heterogeneity in Contaminated Soil. United States: N. p., 2006. Web. doi:10.1007/s00248-005-0002-9.
Joanna M.,Becker, Tim,Parkin, Cindy H.,Nakatsu, Jayson D.,Wilbur, & Allan,Konopka. Bacterial Activity, Community Structure, and Centimeter-Scale Spatial Heterogeneity in Contaminated Soil. United States. doi:10.1007/s00248-005-0002-9.
Joanna M.,Becker, Tim,Parkin, Cindy H.,Nakatsu, Jayson D.,Wilbur, and Allan,Konopka. Wed . "Bacterial Activity, Community Structure, and Centimeter-Scale Spatial Heterogeneity in Contaminated Soil". United States. doi:10.1007/s00248-005-0002-9.
@article{osti_1154142,
title = {Bacterial Activity, Community Structure, and Centimeter-Scale Spatial Heterogeneity in Contaminated Soil},
author = {Joanna M.,Becker and Tim,Parkin and Cindy H.,Nakatsu and Jayson D.,Wilbur and Allan,Konopka},
abstractNote = {},
doi = {10.1007/s00248-005-0002-9},
journal = {Microbial Ecology},
number = 2,
volume = 51,
place = {United States},
year = {Wed Feb 01 00:00:00 EST 2006},
month = {Wed Feb 01 00:00:00 EST 2006}
}
  • Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystemmore » scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.« less
  • The Office of Technology Assessment has estimated that there may be as many as 10,000 abandoned hazardous waste disposal sites across the United States, many of which have the potential to adversely impact drinking water supplies. Of the many options available for the remediation of these sites, the use of microorganisms to degrade organic chemicals offers many advantages in terms of speed, efficiency and cost. Bioremediation has been used with success to treat soils contaminated by kerosene and other hydrocarbon products. In these studies, the indigenous soil populations of the contaminated soils were effective in removing the spilled hydrocarbons andmore » returning the soil to productivity. The effectiveness of bioremediation for nonhydrocarbon compounds or the complex mixtures of chemicals likely to occur at abandoned hazardous waste sites has received less attention. The present study was designed to determine the activity of indigenous microbial populations at a hazardous waste site, their degree of adaptation to toxic chemicals present in the waste mixture, and their ability to degrade toxic organic compounds, using phenol as a model substrate.« less
  • The impact of ammonium availability on microbial community structure and the physiological status and activity of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by as much as two orders of magnitude (<4 to 400 {micro}M) across the study site. Analysis of 16S rRNA gene sequences suggested that ammonium influenced the composition of the microbial community prior to acetate addition with Rhodoferax species predominating over Geobacter species at the site with the highest ammonium, and Dechloromonas species dominating at sites with lowest ammonium. However, once acetate was added, and dissimilatory metal reduction was stimulated,more » Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to the concentration of acetate that was delivered to each location rather than the amount of ammonium available in the groundwater. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium importer gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during in situ uranium reduction, and that the abundance of amtB transcripts was inversely correlated to ammonium levels across all sites examined. These results suggest that nifD and amtB expression by subsurface Geobacter species are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB expression appears to be a useful approach for monitoring the nitrogen-related physiological status of Geobacter species in subsurface environments during bioremediation. This study also emphasizes the need for more detailed analysis of geochemical/physiological interactions at the field scale, in order to adequately model subsurface microbial processes.« less
  • The influence of ammonium availability on bacterial community structure and the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by two orders of magnitude (<4 to 400 μM) across the study site. Analysis of 16S rRNA sequences suggested that ammonium may have been one factor influencing the community composition prior to acetate amendment with Rhodoferax species predominating over Geobacter species with higher ammonium and Dechloromonas species dominating at the site with lowest ammonium. However, once acetate was added, and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms atmore » all locations. Rates of U(VI)-reduction appeared to be more related to acetate concentrations rather than ammonium levels. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium transporter gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during uranium reduction. The abundance of amtB was inversely correlated to ammonium levels whereas nifD transcript levels were similar across all sites examined. These results suggest that nifD and amtB expression are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB transcript expression appears to be a useful approach for monitoring the nitrogen-related physiological status of subsurface Geobacter species and. This study also emphasizes the need for more detailed analysis of geochemical/physiological interactions at the field scale, in order to adequately model subsurface microbial processes during bioremediation.« less
  • High concentrations of uranium, inorganic mercury [Hg(II)], and methylmercury (MeHg) have been detected in streams located in the Department of Energy reservation in Oak Ridge, TN. To determine the potential effects of the surface water contamination on the microbial community composition, surface stream sediments were collected 7 times during the year, from 5 contaminated locations and 1 control stream. Fifty-nine samples were analyzed for bacterial community composition and geochemistry. Community characterization was based on GS 454 FLX pyrosequencing with 235 Mb of 16S rRNA gene sequence targeting the V4 region. Sorting and filtering of the raw reads resulted in 588,699more » high-quality sequences with lengths of >200 bp. The bacterial community consisted of 23 phyla, including Proteobacteria (ranging from 22.9 to 58.5% per sample), Cyanobacteria (0.2 to 32.0%), Acidobacteria (1.6 to 30.6%), Verrucomicrobia (3.4 to 31.0%), and unclassified bacteria. Redundancy analysis indicated no significant differences in the bacterial community structure between midchannel and near-bank samples. Significant correlations were found between the bacterial community and seasonal as well as geochemical factors. Furthermore, several community members within the Proteobacteria group that includes sulfate-reducing bacteria and within the Verrucomicrobia group appeared to be associated positively with Hg and MeHg. This study is the first to indicate an influence of MeHg on the in situ microbial community and suggests possible roles of these bacteria in the Hg/MeHg cycle.« less