Effects of long‐term benzene pollution on bacterial diversity and community structure in groundwater

Fahy, Anne; Lethbridge, G.; Earle, Richard; Ball, Andrew S.; Timmis, Kenneth N.; McGenity, Terry J.

doi:10.1111/j.1462-2920.2005.00799.x

Cited by 57 publications

(56 citation statements)

References 29 publications

(27 reference statements)

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“…A majority of the studies dealing with these questions involve experimental amendment of contaminants followed by assessment of microbial responses measured over periods ranging from days to few years. Depending on the level of pollution, however, the time required to observe ecologically relevant responses towards pollution might rather be in the order of few decades (Lindstrom et al, 1999;Davis et al, 2004;Fahy et al, 2005;Oorts et al, 2006). In addition, in the restoration of polluted sites, aged contamination is one of the most important concerns.…”

Section: Introductionmentioning

confidence: 99%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

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Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.

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Section: Introductionmentioning

confidence: 99%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

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“…Multivariate statistical analyses indicated a correlation between the decrease in microbial diversity and anoxia. Rather than the toxic effect of benzene itself, anoxia caused by the microbial degradation of benzene and the decrease of available redox species were the major factors explaining the decline of microbial diversity (Fahy et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Archaeal and bacterial community composition of a pristine coastal aquifer in Doñana National Park, Spain

López-Archilla

Moreira²,

Velasco³

et al. 2007

Aquat. Microb. Ecol.

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We studied the biological activity and prokaryotic diversity associated with 2 samples of different physico-chemical characteristics in a pristine coastal aquifer at Doñana National Park, south-western Spain. Sulphate reduction, denitrification and iron-metabolising activities were detected in the aquifer, as well as different enzymatic activities related to the degradation of labile and complex pools of organic matter. Prokaryotic diversity was assessed by environmental 16S rRNA gene amplification, cloning and sequencing. Bacterial diversity was greater in the shallower aquifer sample (49S1, 15 m depth), including members of the Proteobacteria, Acidobacteria, Planctomycetes, Nitrospirae, some divergent lineages and the candidate divisions SPAM, OP3, OP11, 'Endomicrobia' or Termite Group 1 and a novel division-level group including denitrifying bacteria associated to anaerobic methane-oxidising archaea, whereas only Proteobacteria and Firmicutes were detected in the deeper sample (56S, 80 m depth). By contrast, archaea seemed much more diverse in the deeper aquifer sample, with members of the Methanomicrobiales, ANME2-related Methanosarcinales and other divergent lineages, whereas only Group I Crenarchaeota were detected in the shallower sample. Betaproteobacteria were the most abundant and diverse group in both sample libraries, together with the Gammaproteobacteria in the deeper and more saline 56S sample. We detected microorganisms potentially involved in carbon, sulphur and nitrogen cycling. Interestingly, members of both aerobic (Alpha-and Gammaproteobacteria) and anaerobic methane oxidisers (ANME2 archaea) were found in the same aquifer sample.

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“…To date, skim milk has been widely employed as an additive for the extraction of DNA from diverse environmental samples including oil-contaminated soil 29) , chemically polluted soil 46) , coral reef sediments 10) , groundwater 7) , woody tissues 24) and stone samples 37) . Moreover, the DNA obtained using methodologies that employ skim milk as an additive has been used in a series of studies for the detection of specific organisms 6,9,24,25,28,33,36,37,43,45) and genes 29,38) in a variety of environments.…”

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confidence: 99%

Evaluation of the Effects of Different Additives in Improving the DNA Extraction Yield and Quality from Andosol

et al. 2008

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A series of additives were evaluated for their effects on improving the yield and quality of DNA extracted from recalcitrant soils. Levels of possible DNA contaminants in these supplements were also assessed. Three of the additives (skim milk, casein, and RNA) were shown to be effective in improving the stable extraction of DNA from recalcitrant samples of Andosol. However, whereas skim milk appeared to be the most effective additive for this purpose, our data indicated that this commercially sourced product contained considerable amounts of contaminant DNA (30 to 40 µg/g skim milk). A ribosomal intergenic spacer analysis (RISA) revealed the consistent contamination of different batches of this product with DNA of several species of both eukaryotes (cattle and protists) and prokaryotes. In particular, thermophilic bacteria such as Geobacillus and Anoxybacillus were identified in the sequenced PCR amplicons from skim milk. The results of the RISA clearly also indicated that the impact of contaminated DNA on the analysis of a microbial community could be significant when skim milk is used for extracting DNA from a recalcitrant soil. In contrast, only a trace amount of contaminating DNA was evident in casein and none was detected in the RNA examined in the present study.

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Effects of long‐term benzene pollution on bacterial diversity and community structure in groundwater

Cited by 57 publications

References 29 publications

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Archaeal and bacterial community composition of a pristine coastal aquifer in Doñana National Park, Spain

Evaluation of the Effects of Different Additives in Improving the DNA Extraction Yield and Quality from Andosol

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