Recovery of novel bacterial diversity from a forested wetland impacted by reject coal

Brofft, Jennifer E.; McArthur, J. Vaun; Shimkets, Lawrence J.

doi:10.1046/j.1462-2920.2002.00337.x

Cited by 101 publications

(67 citation statements)

References 21 publications

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“…For example, the community of Sample LC exhibited low OTU diversity and greater dominance by fewer OTUs, which is similar to the pattern observed in low-carbon vadose zone sediments: some 1/D values of the saturated subsurface soil communities at low-carbon sites ranged from just 13 to 25, while others ranged from 70 to 27 331 (Zhou et al 2002). Some species of Actinobacteria, which were isolated from a forested wetland impacted by reject coal (Brofft et al 2002) and the AMD environments of Wheal Jane (Johnson et al 2002) and Iron Mountain (Nordstrom et al 2000), were also detected in samples from Sites LC and FS in Dabaoshan Mine, China. Acidobacteria is a genus of very important microbes in AMD ecology, which performs an indispensable function in the formation of AMD.…”

Section: Dbs-clone 46 Dq659221 (Jx Lc Fs)supporting

confidence: 64%

Bacterial diversity and community structure in acid mine drainage from Dabaoshan Mine, China

Yang¹,

Wan²,

Shi³

et al. 2007

Aquat. Microb. Ecol.

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Three samples of acid mine drainage (AMD) collected from Dabaoshan Mine (Guangdong Province, China) were studied. In addition to physico-chemical analyses, bacterial diversities and community structures of these samples were described at genetic level by amplified ribosomal DNA restriction analysis (ARDRA). A total of 60 different ARDRA patterns were obtained from 377 clones and were studied as operational taxonomic units (OTUs), which were re-amplified and sequenced. The sequence data and phylogenetic analysis showed that Acidithiobacillus ferrooxidans represented 88.0% of the bacterial population in Sample LC. However, Samples JX and FS contained more diverse colonies of bacteria, such as Leptospirillum ferrooxidans (JX: 16.9%, FS: 39.1%), Acidiphilum sp. (JX: 38.7%, FS: 25.8%) and A. ferrooxidans (JX: 12.1%, FS: 10.2%). These diversities were characterized by the reciprocal of Simpson's index (1/D) and correlated with the concentrations of ferrous iron and toxic ions in AMD.KEY WORDS: Bacterial diversity · Microbial community · Acid mine drainage · Amplified ribosomal DNA restriction analysis Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 47: [141][142][143][144][145][146][147][148][149][150][151] 2007 (e.g. Coram & Rawlings 2002, Kormas et al. 2006) have been conducted.New studies (since the 90s) on AMD from diverse geographical locations have revealed that many uncultured bacteria might be very important in the generation of acidic environments (Golyshina et al. 2000), and that AMD supports a diverse range of iron-and sulfuroxidizing chemolithotrophs as well as heterotrophic microorganisms (Johnson 1998). Community structure varies among diverse geographical locations, revealing that AMD niches and changes in dominant bacterial species are affected by geographical conditions.Studies of bacterial diversity and community structure in diverse AMD can help us to reveal principal bacterial species for mine dissolution in different geographical conditions, and the factors that affect such bacterial communities. To date, although there are many existing reports on bacterial ecology in AMD, to the best of our knowledge such studies in Chinese mines are rare. In this study, we investigated the bacterial and geochemical characteristics of 3 AMD sites in Dabaoshan Mine, Guangdong Province, China. The genomic DNA of the bacterial community at each site was extracted. Subsequently, Amplified Ribosomal DNA Restriction Analysis (ARDRA) was used to analyze the bacterial communities that occur at these sites, and the findings were correlated with the determined geochemistry and mineralogy of each site. MATERIALS AND METHODSStudy site, sample collection and physicochemical analyses. Dabaoshan Mine (24°31' 37'' N, 113°42' 49'' E) is located in the mountainous area of the northern part of Guangdong Province, China. It is a large, multi-metallic mineral deposit: the top of the main ore body appears to be a limonite body, while the lower body contains copper sulphur c...

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Section: Dbs-clone 46 Dq659221 (Jx Lc Fs)supporting

confidence: 64%

Bacterial diversity and community structure in acid mine drainage from Dabaoshan Mine, China

Yang¹,

Wan²,

Shi³

et al. 2007

Aquat. Microb. Ecol.

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“…The presence of Acidobacteria in the RT was detected previously by an oligonucleotide array experiment (Garrido et al, 2008), but here we report the actual sequences from acidobacteria new to the RT. The Deinococcus clones were related to sequences derived from a rejected coal pile (Brofft et al, 2002).…”

Section: Resultsmentioning

confidence: 99%

Microbial community structure across the tree of life in the extreme Río Tinto

et al. 2010

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Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidencebased methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.

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“…In Deltaproteobacteria, 11 OTUs (68.9% of bacterial clones) were affiliated with a recently proposed family Syntrophorhabdaceae (30), which was a clone cluster formerly known as "group TA" (44). Within Syntrophorhabdaceae, six OTUs (50.0%) were closely related to the clones retrieved from mesophilic terephthalate-and phenol-degrading consortia (9, 44) and a recent phenol-degrading isolate Syntrophorhabdus aromaticivorans (29,30), while the remaining five OTUs (PS-Ba2, PS-Ba90, PS-Ba101, PS-Ba151 and PS-Ba160; 18.9%) were affiliated with 16S rRNA clones mainly obtained from soil and contaminated aquifer (6,11). In addition, PS-Ba100 (2.8%) was very similar to the environmental clone WB03 retrieved from freshwater sediment with 99.9% sequence similarity, forming a cluster with Desulfonema magnum as a close neighbor.…”

Section: Microbial Compositions Asmentioning

confidence: 96%

Characterization of Active Microbes in a Full-Scale Anaerobic Fluidized Bed Reactor Treating Phenolic Wastewater

Chen

Tseng

et al. 2009

Microb. Environ.

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This study investigated the active microbial community in a full-scale granular activated carbon-anaerobic fluidized bed (GAC-AFB) reactor treating wastewater from the manufacturing of phenolic resin, using 16S rRNA-based molecular analyses. The results of cDNA from 16S rRNA revealed that Methanosaeta-related (83.9% of archaeal clones) and Syntrophorhabdaceae (formerly named Deltaproteobacteria group TA)-related (68.9% of bacterial clones) microorganisms were as the most predominant populations in the phenol-degrading GAC-AFB reactor. The high abundance of Syntrophorhabdaceae was supported by a terminal restriction fragment length polymorphism (T-RFLP) analysis, which showed that a Syntrophorhabdaceae-like fragment of 119 bp (~80% of total fragments) was the most predominant phylotype. Furthermore, fluorescence in situ hybridization (FISH) analyses suggested that Syntrophusand Chloroflexi-like cells were also in high abundance in the GAC biofilm. A non-layered structure of microorganisms was found in the GAC biofilm, where Methanosaeta (thick filamentous), Syntrophorhabdaceae (oval-shaped), Syntrophus (small rods) and Chloroflexi (thin-filamentous) were randomly distributed with high abundance. These findings greatly improve our understanding of the diversity and distribution of microbial populations in a full-scale mesophilic bioreactor treating an actual phenol-containing waste stream.Key words: phenol, anaerobic, microbial, phylogenetic, FISH Syntrophic association is an important process in anaerobic catabolism, whereby two or more microorganisms cooperate closely to completely degrade a substance neither can degrade alone. This process generally requires interaction between fermentative bacteria and methanogenic archaea (methanogens) to overcome the thermodynamic barrier in the initial step of degradation (e.g., fatty acids, solvents and aromatic substrates), and leads to the production of methane. Biodegradation of phenol under methanogenic conditions has been known for more than two decades (42, 48), and a number of different anaerobic processes (23,37,40,42) have been developed to successfully treat industrial waste streams containing phenol. A bottleneck to the starting up of these anaerobic processes was considered to be the cultivation/ acclimation of unique microbial specialists. A few reports have characterized these syntrophic phenol-degrading microorganisms. Fang and co-workers (16, 49) suggested that Desulfotomaculum, Clostridium and Syntrophus, together with Methanosaetaceae, Methanomicrobiales and Methanobacteriaceae, were the predominant microbial populations in a laboratory-scale upflow anaerobic sludge bed (UASB) reactor that degraded phenol under ambient temperature (26°C). Last year, we reported that Deltaproteobacteria group TA-and Pelotomaculum-related populations were the most important fermentative bacteria, in phenol-degrading enrichments under mesophilic (37°C) and thermophilic (55°C) conditions, respectively (9). More recently, a syntrophic phenol-degrading bacterium (Syntrophorhabd...

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Recovery of novel bacterial diversity from a forested wetland impacted by reject coal

Cited by 101 publications

References 21 publications

Bacterial diversity and community structure in acid mine drainage from Dabaoshan Mine, China

Bacterial diversity and community structure in acid mine drainage from Dabaoshan Mine, China

Microbial community structure across the tree of life in the extreme Río Tinto

Characterization of Active Microbes in a Full-Scale Anaerobic Fluidized Bed Reactor Treating Phenolic Wastewater

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