Genome Sequence of the Facultative Anaerobic Arsenite-Oxidizing and Nitrate-Reducing Bacterium Acidovorax sp. Strain NO1

Huang, Yinyan; Li, Hang; Rensing, Christopher; Zhao, Kai Hong; Johnstone, Laurel; Wang, Gejiao

doi:10.1128/jb.06814-11

Cited by 53 publications

(24 citation statements)

References 16 publications

(15 reference statements)

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“…Therefore, the arsenic-related gene may have very early origins, especially the ars-like gene. This speculation was supported in part by recent literatures showing that bacterial arsenic resistance and transformation was an acquired trait via HGT, driven by adaptation to habitats containing arsenic [17], [19], [43]–[45]. However, we found that the arsenic-related genes were absent in ten of the 188 examined strains, which suggest that some microbes may lose their arsenic-related genes during adaption to arsenic-free niches.…”

Section: Discussionsupporting

confidence: 80%

Genomic Evidence Reveals the Extreme Diversity and Wide Distribution of the Arsenic-Related Genes in Burkholderiales

Zhang

Wang

2014

PLoS ONE

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So far, numerous genes have been found to associate with various strategies to resist and transform the toxic metalloid arsenic (here, we denote these genes as “arsenic-related genes”). However, our knowledge of the distribution, redundancies and organization of these genes in bacteria is still limited. In this study, we analyzed the 188 Burkholderiales genomes and found that 95% genomes harbored arsenic-related genes, with an average of 6.6 genes per genome. The results indicated: a) compared to a low frequency of distribution for aio (arsenite oxidase) (12 strains), arr (arsenate respiratory reductase) (1 strain) and arsM (arsenite methytransferase)-like genes (4 strains), the ars (arsenic resistance system)-like genes were identified in 174 strains including 1,051 genes; b) 2/3 ars-like genes were clustered as ars operon and displayed a high diversity of gene organizations (68 forms) which may suggest the rapid movement and evolution for ars-like genes in bacterial genomes; c) the arsenite efflux system was dominant with ACR3 form rather than ArsB in Burkholderiales; d) only a few numbers of arsM and arrAB are found indicating neither As III biomethylation nor AsV respiration is the primary mechanism in Burkholderiales members; (e) the aio-like gene is mostly flanked with ars-like genes and phosphate transport system, implying the close functional relatedness between arsenic and phosphorus metabolisms. On average, the number of arsenic-related genes per genome of strains isolated from arsenic-rich environments is more than four times higher than the strains from other environments. Compared with human, plant and animal pathogens, the environmental strains possess a larger average number of arsenic-related genes, which indicates that habitat is likely a key driver for bacterial arsenic resistance.

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Section: Discussionsupporting

confidence: 80%

Genomic Evidence Reveals the Extreme Diversity and Wide Distribution of the Arsenic-Related Genes in Burkholderiales

Zhang

Wang

2014

PLoS ONE

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“…The enrichment of Asticcacaulis in the family Caulobacteraceae might be caused by the attraction of the plant exudations, because these bacteria are adhesive and aerobic heterotrophs commonly found in freshwaters (30). Many members of Comamonadaceae, especially the genus Acidovorax (31)(32)(33), are frequently detected as denitrifiers coupled with the degradation of organic substrates in wastewater treatment plants (31,34). Species of Methylibium can also reduce nitrate into nitrite, and more importantly, they are capable of using methanol as a sole carbon source (35).…”

Section: Discussionmentioning

confidence: 99%

Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

Xie

Zhu

2015

Appl Environ Microbiol

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bThe phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and ␣-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments. Phyllosphere is a special niche harboring diverse species of microbes, especially bacteria (1, 2). There is a general consensus that phyllosphere microbial communities benefit the host plants profoundly and play an important role in the cycles of carbon and nitrogen (2, 3). However, the phyllosphere has gained much less attention for microbiological studies than other plant-related bacterial habitats, such as the rhizosphere (4). With the advent of culture-independent technologies, denaturing gradient gel electrophoresis (DGGE), and high-throughput sequencing, a considerable number of studies have provided insights into the diversities, structures, and even functions of the phyllosphere bacterial communities for terrestrial plants (3, 5-9). However, very limited studies have addressed the microbial diversity of the phyllosphere in aquatic/wetland environments.Aquatic ecosystems harbor diverse and large microbial populations which drive major biogeochemical processes (10). The surfaces of macrophytes in the water environments can support enormous communities of bacteria (11,12). Previous studies have focused mainly on the microbial communities of submerged plants with culture-dependent or culture-independent methods such as DGGE and fluorescent in situ hybridization (FISH) (11-13). Aquatic floating macrophytes, however, have received little attention regarding their phyllosphere bacterial communities. Wolffia, in the family Lemnaceae, is a rootless duckweed composed of fronds ...

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“…Within the Burkholderiales Order, two genera Polaromonas and Aquabacterium that were found in the BCR are frequently associated with hydrocarbon degradation in contaminated soils [43,44]. Another Burkholderiales genus present in the BCR, Acidovorax, includes species capable of arsenite oxidation [45]. Genera within the Rhizobiales Order (e.g., Rhizobium) were closely related to metal-tolerant species that might play a role in metal sequestration [45,46].…”

Section: Othersmentioning

confidence: 99%

“…Another Burkholderiales genus present in the BCR, Acidovorax, includes species capable of arsenite oxidation [45]. Genera within the Rhizobiales Order (e.g., Rhizobium) were closely related to metal-tolerant species that might play a role in metal sequestration [45,46]. Genera found within the Caulobacterales Order (Caulobacter and Brevundimonas) are ubiquitous in many different environments.…”

Section: Othersmentioning

confidence: 99%

Seasonal Microbial Population Shifts in a Bioremediation System Treating Metal and Sulfate-Rich Seepage

Baldwin¹,

Mattes²,

Rezadehbashi³

et al. 2016

Minerals

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Biochemical reactors (BCRs) using complex organics for bioremediation of mine-influenced water must operate successfully year round. In cold climates, where many mines in Canada are located, survival of the important microorganisms through the winter months is a concern. In this work, broad phylogenetic surveys, using metagenomics, of the microbial populations in pulp mill biosolids used to remediate metal leachate containing As, Zn, Cd and sulfate were performed to see if the types of microorganisms present changed over the seasons of one year (August 2008 to July 2009). Despite temperature variations between 0 and 17˝C the overall structure of the microbial population was fairly consistent. A cyclical pattern in relative abundance was detected in certain taxa. These included fermenter-related groups, which were out of phase with other taxa such as Desulfobulbus that represented potential consumers of fermentation byproducts. Sulfate-reducers in the BCR biosolids were closely related to psychrotolerant species. Temperature was not a factor that shaped the microbial population structure within the BCR biosolids. Kinetics of organic matter degradation by these microbes and the rate of supply of organic carbon to sulfate-reducers would likely affect the metal removal rates at different temperatures.

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Genome Sequence of the Facultative Anaerobic Arsenite-Oxidizing and Nitrate-Reducing Bacterium Acidovorax sp. Strain NO1

Cited by 53 publications

References 16 publications

Genomic Evidence Reveals the Extreme Diversity and Wide Distribution of the Arsenic-Related Genes in Burkholderiales

Genomic Evidence Reveals the Extreme Diversity and Wide Distribution of the Arsenic-Related Genes in Burkholderiales

Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

Seasonal Microbial Population Shifts in a Bioremediation System Treating Metal and Sulfate-Rich Seepage

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