Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing

Xie, Shuguang; Sun, Weimin; Luo, Chunling; Cupples, Alison M.

doi:10.1007/s10532-010-9377-5

Cited by 68 publications

(36 citation statements)

References 94 publications

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“…Aerobic degradation of these chemicals is generally rapid (39,56,62); however, in the saturated subsurface, anaerobic conditions typically exist. Therefore, understanding anaerobic biodegradation is also relevant to site cleanup.…”

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confidence: 99%

Diversity of Five Anaerobic Toluene-Degrading Microbial Communities Investigated Using Stable Isotope Probing

Sun

Cupples

2012

Appl Environ Microbiol

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Time-series DNA-stable isotope probing (SIP) was used to identify the microbes assimilating carbon from [ 13 C]toluene under nitrate-or sulfate-amended conditions in a range of inoculum sources, including uncontaminated and contaminated soil and wastewater treatment samples. In all, five different phylotypes were found to be responsible for toluene degradation, and these included previously identified toluene degraders as well as novel toluene-degrading microorganisms. In microcosms constructed from granular sludge and amended with nitrate, the putative toluene degraders were classified in the genus Thauera, whereas in nitrate-amended microcosms constructed from a different source (agricultural soil), microorganisms in the family Comamonadaceae (genus unclassified) were the key putative degraders. In one set of sulfate-amended microcosms (agricultural soil), the putative toluene degraders were identified as belonging to the class Clostridia (genus Desulfosporosinus), while in other sulfate-amended microcosms, the putative degraders were in the class Deltaproteobacteria, within the family Syntrophobacteraceae (digester sludge) or Desulfobulbaceae (contaminated soil) (genus unclassified for both). Partial benzylsuccinate synthase gene (bssA, the functional gene for anaerobic toluene degradation) sequences were obtained for some samples, and quantitative PCR targeting this gene, along with SIP, was further used to confirm anaerobic toluene degradation by the identified species. The study illustrates the diversity of toluene degraders across different environments and highlights the utility of ribosomal and functional gene-based SIP for linking function with identity in microbial communities.

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confidence: 99%

Diversity of Five Anaerobic Toluene-Degrading Microbial Communities Investigated Using Stable Isotope Probing

Sun

Cupples

2012

Appl Environ Microbiol

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“…Acidobacteriarelated bacteria have been proved in the degradation of petroleum [50], PAHs [33,50], and PCBs [32,50] in various habitats. To date, SIP has been successfully applied to investigate the ability of Acidobacterium to metabolize propionate [51], biocide [52], herbicide [53], and benzene [29]. Our recent SIP research also demonstrated that Acidobacteria-related bacteria were related to the degradation of PHE in forest soil [26].…”

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confidence: 94%

“…Clones with the predicted cut sites matching TRFLP cut sites of the corresponding TRFs were selected for phylogenetic analysis. Previous studies have shown that small differences (2-3 bases) often occur between the measured fragment lengths and those predicted using sequence data [29,30]. Clones with predicted cut sites matching 291-bp TRF (based on the analysis of the clone sequences, each with a predicted HaeIII cut site of 294 bp) accounted for the majority of microbes in the clone library.…”

Section: Microbial Structure Analysis Via Sip and Trflpmentioning

confidence: 93%

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Song

Jiang

Zhang

et al. 2016

Journal of Hazardous Materials

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h i g h l i g h t s• Investigate PAHs degraders in forest carbon-rich soils via DNA-SIP.• Rhodanobacter is identified to metabolite anthracene for the first time.• The first fluoranthene degrader belongs to Acidobacteria.• Different functions of PAHs degraders in forest soils from contaminated soils. a r t i c l e i n f o a b s t r a c tInformation on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually 13 C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene-and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter-and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three-and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

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“…Previously, SIP investigations of the metabolism of benzene, toluene, ethylbenzene, and xylene (BTEX) compounds largely focused on anaerobic benzene and toluene degradation, using PLFA and rRNA-based fingerprinting techniques to identify the active populations (32)(33)(34)(35). DNA-and RNA-based benzene SIP investigations have been conducted in coal tarcontaminated sediment, gasoline-contaminated water, and soil (31,36,37). However, the high diversities of habitat types and geochemical conditions where contaminants occur warrant additional SIP investigations.…”

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confidence: 99%

Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community

Posman

DeRito

Madsen

2017

Appl Environ Microbiol

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Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [13C]benzene enabled us to obtain 13C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities. IMPORTANCE Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation.

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Novel aerobic benzene degrading microorganisms identified in three soils by stable isotope probing

Cited by 68 publications

References 94 publications

Diversity of Five Anaerobic Toluene-Degrading Microbial Communities Investigated Using Stable Isotope Probing

Diversity of Five Anaerobic Toluene-Degrading Microbial Communities Investigated Using Stable Isotope Probing

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community

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