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Saikh SR, Mushtaque MA, Pramanick A, Prasad JK, Roy D, Saha S, Das SK. Fog caused distinct diversity of airborne bacterial communities enriched with pathogens over central Indo-Gangetic plain in India. Heliyon 2024; 10:e26370. [PMID: 38420377 PMCID: PMC10901028 DOI: 10.1016/j.heliyon.2024.e26370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/30/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Fog causes enhancement of bacterial loading in the atmosphere. Current study represents the impact of occurrences of fog on the alteration of diversity of airborne bacteria and their network computed from metagenomic data of airborne samples collected at Arthauli (25.95°N, 85.10°E) situated at central Indo-Gangetic Plain (IGP) during 1-14 January 2021. A distinct bacterial diversity with a complex network is identified in foggy condition due to the enrichment of unique types of bacteria. Present investigation highlights a statistically significant enrichment of airborne pathogenic bacteria found in a unique ecosystem within air evolved due to the occurrences of fog over central IGP. In the foggy network, Cutibacterium, an opportunistic pathogen, is identified to be interacting maximum (21 edges) with other bacteria with statistically significant copresence relation, which are responsible for various infections for human beings. A 40-60% increase (p < 0.01) in the abundance of pathogenic bacteria for respiratory and skin diseases is noticed in fog period. Among the fog-enriched bacteria, Cutibacterium, Herbaspirillum, Paenibacillus, and Tsukamurella are examples of opportunistic bacteria causing various respiratory diseases, while Paenibacillus can even cause skin cancer and acute lymphoblastic leukemia.
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Affiliation(s)
- Shahina Raushan Saikh
- Department of Physical Sciences, Bose Institute, Kolkata, India
- Department of Life Science & Bio-technology, Jadavpur University, Kolkata, India
| | | | | | | | - Dibakar Roy
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Sudipto Saha
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Sanat Kumar Das
- Department of Physical Sciences, Bose Institute, Kolkata, India
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Zhu X, Deng Y, Liu Y. Methylocystis dominates methane oxidation in glacier foreland soil at elevated temperature. FEMS Microbiol Lett 2024; 371:fnae011. [PMID: 38366911 DOI: 10.1093/femsle/fnae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Methane-oxidizing bacteria (methanotrophs) play an important role in mitigating methane emissions in various ecological environments, including cold regions. However, the response of methanotrophs in these cold environments to extreme temperatures above the in-situ temperature has not been thoroughly explored. Therefore, this study collected soil samples from Longxiazailongba (LXZ) and Qiangyong (QY) glacier forelands and incubated them with 13CH4 at 35°C under different soil water conditions. The active methanotroph populations were identified using DNA stable isotope probing (DNA-SIP) and high throughput sequencing techniques. The results showed that the methane oxidation potential in LXZ and QY glacier foreland soils was significantly enhanced at an unusually high temperature of 35°C during microcosm incubations, where abundant substrate (methane and oxygen) was provided. Moreover, the influence of soil water conditions on this potential was observed. Interestingly, Methylocystis, a type II and mesophilic methanotroph, was detected in the unincubated in-situ soil samples and became the active and dominant methanotroph in methane oxidation at 35°C. This suggests that Methylocystis can survive at low temperatures for a prolonged period and thrive under suitable growth conditions. Furthermore, the presence of mesophilic methanotrophs in cold habitats could have potential implications for reducing greenhouse gas emissions in warming glacial environments.
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Affiliation(s)
- Xinshu Zhu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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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] [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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Kaise H, Sawadogo JB, Alam MS, Ueno C, Dianou D, Shinjo R, Asakawa S. Methylocystis iwaonis sp. nov., a type II methane-oxidizing bacterium from surface soil of a rice paddy field in Japan, and emended description of the genus Methylocystis ( ex Whittenbury et al. 1970) Bowman et al. 1993. Int J Syst Evol Microbiol 2023; 73. [PMID: 37279153 DOI: 10.1099/ijsem.0.005925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
A novel methane-oxidizing bacterial strain SS37A-ReT was isolated from surface soil of a rice paddy field in Japan. Cells were Gram-stain-negative, motile rods with single polar flagellum and type II intracytoplasmic membrane arrangement. The strain grew on methane or methanol as the sole carbon and energy source. It grew at 15–37 °C (optimum 25–30 °C), pH 6.0–9.0 (optimum 7.0–8.0) and with 0–0.1 % (w/w) NaCl (no growth at 0.5 % or above). Cells formed cysts, but not exospores. The results of sequence analysis of the 16S rRNA gene indicated that SS37A-ReT represented a member of the family
Methylocystaceae
, with the highest similarity (98.9 %) to Methylocystis parva corrig. OBBPT. Phylogenetic analysis of pmoA and mxaF genes and core genes in the genome indicated that the strain was closely related to the members of the genus
Methylocystis
, while the analysis of the mmoX gene indicated the close relationships with the genus
Methylosinus
. The values of genome relatedness between SS37A-ReT and species of the genera
Methylocystis
and
Methylosinus
were 78.6–82.5% and 21.7–24.9 % estimated by the average nucleotide identity and digital DNA–DNA hybridisation, respectively, showing the highest values with
Methylocystis echinoides
LMG 27198T. The DNA G+C content was 63.2 mol% (genome). The major quinone and fatty acids were Q-8 and, C18 : 1 (C18 : 1ω8t and C18 : 1ω8c) and C18 : 2, respectively. On the basis of the phenotypic and phylogenetic features, the strain represents a novel species of the genus
Methylocystis
, for which the name Methylocystis iwaonis sp. nov. is proposed. The type strain is SS37A-ReT (=JCM 34278T =NBRC 114996T=KCTC 82710T).
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Affiliation(s)
- Hirotaka Kaise
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Joseph Benewindé Sawadogo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Université Nazi BONI, Bobo-Dioulasso, 01 BP 1091 Bobo-Dioulasso 01, Burkina Faso
| | - Mohammad Saiful Alam
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur 1706, Bangladesh
| | - Chihoko Ueno
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Dayéri Dianou
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Centre National de la Recherche Scientifique et Technologique, Ouagadougou, 03 BP 7047 Ouagadougou 03, Burkina Faso
| | - Rina Shinjo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Susumu Asakawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
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Methylocystis sp. Strain SC2 Acclimatizes to Increasing NH 4+ Levels by a Precise Rebalancing of Enzymes and Osmolyte Composition. mSystems 2022; 7:e0040322. [PMID: 36154142 PMCID: PMC9600857 DOI: 10.1128/msystems.00403-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A high NH4+ load is known to inhibit bacterial methane oxidation. This is due to a competition between CH4 and NH3 for the active site of particulate methane monooxygenase (pMMO), which converts CH4 to CH3OH. Here, we combined global proteomics with amino acid profiling and nitrogen oxides measurements to elucidate the cellular acclimatization response of Methylocystis sp. strain SC2 to high NH4+ levels. Relative to 1 mM NH4+, a high (50 mM and 75 mM) NH4+ load under CH4-replete conditions significantly increased the lag phase duration required for proteome adjustment. The number of differentially regulated proteins was highly significantly correlated with an increasing NH4+ load. The cellular responses to increasing ionic and osmotic stress involved a significant upregulation of stress-responsive proteins, the K+ "salt-in" strategy, the synthesis of compatible solutes (glutamate and proline), and the induction of the glutathione metabolism pathway. A significant increase in the apparent Km value for CH4 oxidation during the growth phase was indicative of increased pMMO-based oxidation of NH3 to toxic hydroxylamine. The detoxifying activity of hydroxlyamine oxidoreductase (HAO) led to a significant accumulation of NO2- and, upon decreasing O2 tension, N2O. Nitric oxide reductase and hybrid cluster proteins (Hcps) were the candidate enzymes for the production of N2O. In summary, strain SC2 has the capacity to precisely rebalance enzymes and osmolyte composition in response to increasing NH4+ exposure, but the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH4+. IMPORTANCE In addition to reducing CH4 emissions from wetlands and landfills, the activity of alphaproteobacterial methane oxidizers of the genus Methylocystis contributes to the sink capacity of forest and grassland soils for atmospheric methane. The methane-oxidizing activity of Methylocystis spp. is, however, sensitive to high NH4+ concentrations. This is due to the competition of CH4 and NH3 for the active site of particulate methane monooxygenase, thereby resulting in the production of toxic hydroxylamine with an increasing NH4+ load. An understanding of the physiological and molecular response mechanisms of Methylocystis spp. is therefore of great importance. Here, we combined global proteomics with amino acid profiling and NOx measurements to disentangle the cellular mechanisms underlying the acclimatization of Methylocystis sp. strain SC2 to an increasing NH4+ load.
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