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Garner CT, Sankaranarayanan K, Abin CA, Garner RM, Cai H, Lawson PA, Krumholz LR. Methylocystis suflitae sp. nov., a novel type II methanotrophic bacterium isolated from landfill cover soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38259170 DOI: 10.1099/ijsem.0.006239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
A bacterial strain, designated NLS-7T, was isolated through enrichment of landfill cover soil in methane-oxidizing conditions. Strain NLS-7T is a Gram-stain negative, non-motile rod, approximately 0.8 µm wide by 1.3 µm long. Phylogenetic analysis based on 16S rRNA gene sequencing places it within the genus Methylocystis, with its closest relatives being M. hirsuta, M. silviterrae and M. rosea, with 99.9, 99.7 and 99.6 % sequence similarity respectively. However, average nucleotide identity and average amino acid identity values below the 95 % threshold compared to all the close relatives and digital DNA-DNA hybridization values between 20.9 and 54.1 % demonstrate that strain NLS-7T represents a novel species. Genome sequencing generated 4.31 million reads and genome assembly resulted in the generation of 244 contigs with a total assembly length of 3 820 957 bp (N50, 37 735 bp; L50, 34). Genome completeness is 99.5 % with 3.98 % contamination. It is capable of growth on methane and methanol. It grows optimally at 30 °C between pH 6.5 and 7.0. Strain NLS-7T is capable of atmospheric dinitrogen fixation and can use ammonium (as NH4Cl), l-aspartate, l-arginine, yeast extract, nitrate, l-leucine, l-proline, l-methionine, l-lysine and l-alanine as nitrogen sources. The major fatty acids are C18:1 ω8c and C18:1 ω7c. Based upon this polyphasic taxonomic study, strain NLS-7T represents a novel species of the genus Methylocystis, for which the name Methylocystis suflitae sp. nov. is proposed. The type strain is NLS-7T (=ATCC TSD-256T=DSM 112294T). The 16S rRNA gene and genome sequences of strain NLS-7T have been deposited in GenBank under accession numbers ON715489 and GCA_024448135.1, respectively.
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Affiliation(s)
- Christopher T Garner
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK, 73019, USA
| | - Christopher A Abin
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK, 73019, USA
| | - Rosa M Garner
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Haiyuan Cai
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China. 73 East Beijing Road, Nanjing 210008, PR China
| | - Paul A Lawson
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Lee R Krumholz
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
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Honap TP, Monroe CR, Johnson SJ, Jacobson DK, Abin CA, Austin RM, Sandberg P, Levine M, Sankaranarayanan K, Lewis CM. Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era. Am J Biol Anthropol 2023; 182:542-556. [PMID: 37002784 DOI: 10.1002/ajpa.24735] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVES Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA. MATERIALS AND METHODS Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted. RESULTS Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains. DISCUSSION We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.
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Affiliation(s)
- Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cara R Monroe
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Center for the Ethics of Indigenous Genomics Research (CEIGR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Sarah J Johnson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Christopher A Abin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Rita M Austin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Paul Sandberg
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Marc Levine
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
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Abin CA, Hollibaugh JT. Transcriptional response of the obligate anaerobe Desulfuribacillus stibiiarsenatis MLFW-2 T to growth on antimonate and other terminal electron acceptors. Environ Microbiol 2019; 21:618-630. [PMID: 30548120 DOI: 10.1111/1462-2920.14503] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 11/29/2022]
Abstract
Enzymes of the dimethyl sulfoxide reductase (DMSOR) family catalyse two-electron redox reactions pivotal to the dissimilatory metabolism of a variety of organic and inorganic compounds. The draft genome of the obligately anaerobic bacterium Desulfuribacillus stibiiarsenatis MLFW-2T contains 14 genes that are predicted to encode catalytic subunits of DMSOR family enzymes. We quantified transcription of these genes during growth on antimonate, arsenate, nitrate and selenate, with the goal of identifying the respiratory antimonate reductase. Transcription of BHU72_10330, BHU72_03635 and BHU72_07355 was enhanced during growth on arsenate, nitrate and selenate, respectively, implicating these genes as encoding the catalytic subunits of a respiratory arsenate reductase (arrA), periplasmic nitrate reductase (napA) and membrane-bound selenate reductase (srdA) respectively. Transcription of BHU72_07145 increased markedly when MLFW-2T was grown on antimonate, suggesting that this gene encodes the catalytic subunit of a respiratory antimonate reductase, designated anrA. We also compared the transcriptomes of MLFW-2T during growth on antimonate and arsenate to examine the broader physiological response of the organism to growth on these substrates. Relative to arsenate, antimonate was found to induce transcription of genes involved in pathways for dealing with oxidative stress, including those involved in repairing damaged cellular biomolecules and scavenging reactive oxygen species.
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Affiliation(s)
- Christopher A Abin
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
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Abin CA, Hollibaugh JT. Desulfuribacillus stibiiarsenatis sp. nov., an obligately anaerobic, dissimilatory antimonate- and arsenate-reducing bacterium isolated from anoxic sediments, and emended description of the genus Desulfuribacillus. Int J Syst Evol Microbiol 2017; 67:1011-1017. [DOI: 10.1099/ijsem.0.001732] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abin CA, Hollibaugh JT. Dissimilatory antimonate reduction and production of antimony trioxide microcrystals by a novel microorganism. Environ Sci Technol 2013; 48:681-688. [PMID: 24319985 DOI: 10.1021/es404098z] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Antimony (Sb) is a metalloid that has been exploited by humans since the beginning of modern civilization. The importance of Sb to such diverse industries as nanotechnology and health is underscored by the fact that it is currently the ninth-most mined metal worldwide. Although its toxicity mirrors that of its Group 15 neighbor arsenic, its environmental chemistry is very different, and, unlike arsenic, relatively little is known about the fate and transport of Sb, especially with regard to biologically mediated redox reactions. To further our understanding of the interactions between microorganisms and Sb, we have isolated a bacterium that is capable of using antimonate [Sb(V)] as a terminal electron acceptor for anaerobic respiration, resulting in the precipitation of antimonite [Sb(III)] as microcrystals of antimony trioxide. The bacterium, designated strain MLFW-2, is a sporulating member of a deeply branching lineage within the order Bacillales (phylum Firmicutes). This report provides the first unequivocal evidence that a bacterium is capable of conserving energy for growth and reproduction from the reduction of antimonate. Moreover, microbiological antimonate reduction may serve as a novel route for the production of antimony trioxide microcrystals of commercial significance to the nanotechnology industry.
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Affiliation(s)
- Christopher A Abin
- Department of Microbiology, University of Georgia , Athens, Georgia 30602, United States
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