The Potential Role of Halothiobacillus spp. in Sulfur Oxidation and Acid Generation in Circum-Neutral Mine Tailings Reservoirs

Whaley-Martin, Kelly; Jessen, Gerdhard L; Nelson, Tara Colenbrander; Mori, Jiro F.; Apte, Simon C.; Jarolimek, Chad V.; Warren, Lesley A.

doi:10.3389/fmicb.2019.00297

Cited by 29 publications

(31 citation statements)

References 42 publications

(64 reference statements)

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“…In addition, some Halothiobacillus species isolated from hydrothermal vents are described as halotolerant and reclassified from the genus Thiobacillus [71]. However, recent investigation indicated that Halothiobacillus might be considered an important early indicator in acid mine drainage [72]. Some members of the genus Halothiobacillus might be adapted to play a role in t he sulfur cycle through sulfur oxidation metabolism in a metal mine environment.…”

Section: Discussionmentioning

confidence: 99%

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

Hur

Park

2019

Microorganisms

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Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.

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Section: Discussionmentioning

confidence: 99%

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

Hur

Park

2019

Microorganisms

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“…Genomic DNA was collected filtering approximately 1.5 l water through 0.22-µm Rapid-Flow sterile disposable filters (Thermo Fisher Scientific) and stored at −20 °C until DNA extraction. DNA was extracted from the filters as previously described 49 . The DNA samples were purified for library construction and sequenced on an Illumina HiSeq1500 platform with paired-end 150-bp kits.…”

Section: Methodsmentioning

confidence: 99%

Large freshwater phages with the potential to augment aerobic methane oxidation

et al. 2020

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There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host–phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.

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“…1.5 L water through 0.22-µm Rapid-Flow sterile disposable filters (Thermo Fisher Scientific) and stored at -20 ˚C until DNA extraction. DNA was extracted from the filters as previously described 46 . The DNA samples were purified for library construction and sequenced on an Illumina HiSeq1500 platform with paired-end (PE) 150 bp kits.…”

Section: Methodsmentioning

confidence: 99%

Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation

Chen

Méheust

Crits-Christoph

et al. 2020

Preprint

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There is growing evidence that phages with unusually large genomes are common across various natural and human microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. Here, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Twenty-two manually curated genomes (18 are complete) ranging from 159 to 527 kbp in length were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC show high similarity (> 90%) and affiliate phylogenetically with those of coexisting bacterial methanotrophs, and their abundance patterns correlate with the abundances of these bacteria, supporting host-phage relationships. We suggest that phage PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contribute to growth on methane. Transcriptomics data from one system showed that the phage-associated pmoC genes are actively expressed in situ . Augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this powerful greenhouse gas into the environment.

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The Potential Role of Halothiobacillus spp. in Sulfur Oxidation and Acid Generation in Circum-Neutral Mine Tailings Reservoirs

Cited by 29 publications

References 42 publications

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

Large freshwater phages with the potential to augment aerobic methane oxidation

Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation

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