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Belykh E, Maystrenko T, Velegzhaninov I, Tavleeva M, Rasova E, Rybak A. Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review. Microorganisms 2024; 12:733. [PMID: 38674676 PMCID: PMC11051952 DOI: 10.3390/microorganisms12040733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.
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Affiliation(s)
- Elena Belykh
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Tatiana Maystrenko
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Ilya Velegzhaninov
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Marina Tavleeva
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
- Department of Biology, Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prospekt, Syktyvkar 167001, Russia
| | - Elena Rasova
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Anna Rybak
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
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Mashamaite L, Lebre PH, Varliero G, Maphosa S, Ortiz M, Hogg ID, Cowan DA. Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient. Front Microbiol 2023; 14:1203216. [PMID: 37555066 PMCID: PMC10406297 DOI: 10.3389/fmicb.2023.1203216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica. METHODS We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons. RESULTS AND DISCUSSION Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.
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Affiliation(s)
- Lefentse Mashamaite
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Silindile Maphosa
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Max Ortiz
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Clemson University Genomics & Bioinformatics Facility, Clemson University, Clemson, SC, United States
| | - Ian D. Hogg
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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Hou K, Cheng C, Shi B, Liu W, Du Z, Li B, Wang J, Wang J. New insights into the effects of chlorpyrifos on soil microbes: Carbon and nitrogen cycle related microbes in wheat/maize rotation agricultural field. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120908. [PMID: 36549448 DOI: 10.1016/j.envpol.2022.120908] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Chlorpyrifos, a broad-spectrum organophosphorus insecticide, has been widely detected worldwide and is a potential neurotoxin and endocrine disruptor. Besides, chlorpyrifos has been proven that have a negative effect on soil microbes. In the present study, chlorpyrifos formulation (LORSBAN®, 45% emulsifiable concentrate) was applied in an agricultural field at the recommended dose (R dose, 270.0 and 337.5 g a.i. ha-1 for wheat and maize respectively) and double recommended (DR) dose. Chlorpyrifos residue level and effect on soil microbes related to soil carbon and nitrogen cycle function were analyzed. Results showed that the half-lives of chlorpyrifos in wheat and maize field soil were 7.23-8.23 and 1.45-1.77 d, respectively. Application of chlorpyrifos at even DR dose did not result in unacceptable residual chlorpyrifos, where the final residual chlorpyrifos in wheat/maize (leaf, stem, and grain) was meet the requirement of the maximum residual limit (0.5 mg kg-1 for wheat and 0.05 mg kg-1 for maize) in China. Chlorpyrifos enhanced the activity of β-glucosidase by increasing the relative abundance of Sphingosinicella and promoted the carbon cycle in wheat field. The changes of cbbLR and cbbLG gene abundance also confirmed that chlorpyrifos could affect the import and export of soil carbon pool. The effect of chlorpyrifos on soil N cycle was determined by changes in the abundance of the bacterial genus Gemmatimonas, which is associated with denitrification. Further analysis of N-cycle functional genes and urease activity showed that chlorpyrifos inhibited nitrogen fixation in wheat field, but promoted nitrogen fixation in maize field. In general, bacterial abundance, urease, and AOA-amoA gene could be early warning markers of chlorpyrifos contamination. The results demonstrated the negative effects of chlorpyrifos on soil microbes especially on soil C and N cycle in actual agricultural field. It provides new insights about chlorpyrifos environmental pollution and its effect on soil ecosystems.
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Affiliation(s)
- Kaixuan Hou
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Chao Cheng
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Baihui Shi
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Wei Liu
- Experiment Management Centre, Dezhou University, No. 566 University West Road, Dezhou, 253023, PR China.
| | - Zhongkun Du
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Bing Li
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Jun Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
| | - Jinhua Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian, 271018, PR China.
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Feng G, Yong J, Liu Q, Chen H, Mao P. Response of soil microbial communities to natural radionuclides along specific-activity gradients. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114156. [PMID: 36209527 DOI: 10.1016/j.ecoenv.2022.114156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/11/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Understanding the response of soil microbial community to abnormal natural radionuclides is important to maintain soil ecological function, but the underlying mechanism of tolerance and survival of microbes is poorly studied. The effects of natural radionuclides on the topsoil microbial communities in anomalous natural radiation area were investigated in this work, and it was found that microbial community composition was significantly influenced by the specific-activities of natural radionuclides. The results revealed that relative abundances of 10 major microbial phyla and genera displayed different patterns along specific-activity gradients, including decreasing, increasing, hump-shaped, U-shaped, and similar sinusoidal or cosine wave trends, which indicated that the natural radionuclides were the predominant driver for change of microbial community structure. At the phylum and genus level, microbial communities were divided into two special groups according to the tolerance to natural radionuclides, such as 238U and 232Th, including tolerant and sensitive groups. Taken together, our findings suggest that the high specific-activities of natural radionuclides can obviously drive changes in microbial communities, providing a possibility for future studies on the microbial tolerance genes and bioremediation strains.
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Affiliation(s)
- Guangwen Feng
- Research Center of Radiation Ecology and Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang 830017, PR China
| | - Jinlong Yong
- Research Center of Radiation Ecology and Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang 830017, PR China
| | - Qian Liu
- School of Statistics and Data Science, Xinjiang University of Finance & Economics, Urumqi, Xinjiang 830012, PR China.
| | - Henglei Chen
- Research Center of Radiation Ecology and Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang 830017, PR China
| | - Peihong Mao
- Research Center of Radiation Ecology and Ion Beam Biotechnology, College of Physics Science and Technology, Xinjiang University, Urumqi, Xinjiang 830017, PR China
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Kong X, Jin D, Jin S, Wang Z, Yin H, Xu M, Deng Y. Responses of bacterial community to dibutyl phthalate pollution in a soil-vegetable ecosystem. JOURNAL OF HAZARDOUS MATERIALS 2018; 353:142-150. [PMID: 29660700 DOI: 10.1016/j.jhazmat.2018.04.015] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 05/26/2023]
Abstract
Phthalate esters (PAEs) are a type of plasticizer that has aroused great concern due to their mutagenic, teratogenic, and carcinogenic effects, wherefore dibutyl phthalate (DBP) and other PAEs have been listed as priority pollutants. In this study, the impacts of DBP on a soil-vegetable ecosystem were investigated. The results showed that DBP could accumulate within vegetable tissues, and the accumulative effect was enhanced with higher levels of DBP contamination in soils. DBP accumulation also decreased vegetable quality in various ways, including decreased soluble protein content and increased nitrate content. The diversity of bacteria in soils gradually decreased with increasing DBP concentration, while no clear association with endophytic bacteria was observed. Also, the relative abundance, structure, and composition of soil bacterial communities underwent successional change during the DBP degradation period. The variation of bulk soil bacterial community was significantly associated with DBP concentration, while changes in the rhizosphere soil bacteria community were significantly associated with the properties of both soil and vegetables. The results indicated that DBP pollution could increase the health risk from vegetables and alter the biodiversity of indigenous bacteria in soil-vegetable ecosystems, which might further alter ecosystem functions in agricultural fields.
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Affiliation(s)
- Xiao Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shulan Jin
- School of History Geography and Tourism, Shangrao Normal University, Shangrao 334000, China
| | - Zhigang Wang
- Department of Biotechnology, Institute of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Adebo OA, Njobeh PB, Sidu S, Adebiyi JA, Mavumengwana V. Aflatoxin B1 degradation by culture and lysate of a Pontibacter specie. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.04.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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VanMensel D, Chaganti SR, Boudens R, Reid T, Ciborowski J, Weisener C. Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective. MICROBIAL ECOLOGY 2017; 74:362-372. [PMID: 28246922 DOI: 10.1007/s00248-017-0953-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/15/2017] [Indexed: 06/06/2023]
Abstract
Open-pit mining of the Athabasca oil sands has generated large volumes of waste termed fluid fine tailings (FFT), stored in tailings ponds. Accumulation of toxic organic substances in the tailings ponds is one of the biggest concerns. Gamma irradiation (GI) treatment could accelerate the biodegradation of toxic organic substances. Hence, this research investigates the response of the microbial consortia in GI-treated FFT materials with an emphasis on changes in diversity and organism-related stimuli. FFT materials from aged and fresh ponds were used in the study under aerobic and anaerobic conditions. Variations in the microbial diversity in GI-treated FFT materials were monitored for 52 weeks and significant stimuli (p < 0.05) were observed. Chemoorganotrophic organisms dominated in fresh and aged ponds and showed increased relative abundance resulting from GI treatment. GI-treated anaerobic FFTaged reported stimulus of organisms with biodegradation potential (e.g., Pseudomonas, Enterobacter) and methylotrophic capabilities (e.g., Syntrophus, Smithella). In comparison, GI-treated anaerobic FFTfresh stimulated Desulfuromonas as the principle genus at 52 weeks. Under aerobic conditions, GI-treated FFTaged showed stimulation of organisms capable of sulfur and iron cycling (e.g., Geobacter). However, GI-treated aerobic FFTfresh showed no stimulus at 52 weeks. This research provides an enhanced understanding of oil sands tailings biogeochemistry and the impacts of GI treatment on microorganisms as an effect for targeting toxic organics. The outcomes of this study highlight the potential for this approach to accelerate stabilization and reclamation end points. Graphical Abstract.
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Affiliation(s)
- Danielle VanMensel
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
| | - Subba Rao Chaganti
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Ryan Boudens
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Thomas Reid
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Jan Ciborowski
- Department of Biology, University of Windsor, Windsor, Ontario, Canada
| | - Christopher Weisener
- Great Lakes Institute of Environmental Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
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Roiko M, May M, Relich RF. Characterization of Pontibacter altruii, sp. nov., isolated from a human blood culture. New Microbes New Infect 2017; 19:71-77. [PMID: 28725439 PMCID: PMC5502793 DOI: 10.1016/j.nmni.2017.05.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/23/2017] [Indexed: 01/25/2023] Open
Abstract
The genus Pontibacter is a recent addition to the family Cytophagaceae, phylum Bacteroidetes. Previous reports of its cultivation and molecular detection are from a variety of environmental sources, including marine and desert habitats. We report the first description of a Pontibacter sp., which was initially identified as Elizabethkingia meningoseptica, isolated from a human clinical specimen. On the basis of 16S rRNA gene sequence, unique mass spectral profile and phenotypic characterization, this isolate represents a novel species within the genus Pontibacter that has been named Pontibacter altruii, sp. nov., strain Grand Forks.
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Affiliation(s)
- M Roiko
- Altru Health System, Department of Pathology and Laboratory Services, Grand Forks, ND, USA
| | - M May
- University of New England College of Osteopathic Medicine, Department of Biomedical Sciences, Biddeford, ME, USA
| | - R F Relich
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy TBK, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Göker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati A. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. Stand Genomic Sci 2015; 10:8. [PMID: 26203325 PMCID: PMC4511580 DOI: 10.1186/1944-3277-10-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/24/2014] [Indexed: 12/21/2022] Open
Abstract
Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1(T) along with its complete genome sequence and annotation from a culture of DSM 17521(T). The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.
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Affiliation(s)
| | - Alla Lapidus
- T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | | | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefan Spring
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Brian J Tindall
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
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Draft Genome Sequence of the Extremely Halophilic Bacterium Halomonas salina Strain CIFRI1, Isolated from the East Coast of India. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01321-14. [PMID: 25573926 PMCID: PMC4290979 DOI: 10.1128/genomea.01321-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Halomonas salina strain CIFRI1 is an extremely salt-stress-tolerant bacterium isolated from the salt crystals of the east coast of India. Here we report the annotated 3.45-Mb draft genome sequence of strain CIFRI1 having 86 contigs with 3,139 protein coding loci, including 62 RNA genes.
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Xu L, Zeng XC, Nie Y, Luo X, Zhou E, Zhou L, Pan Y, Li W. Pontibacter diazotrophicus sp. nov., a novel nitrogen-fixing bacterium of the family Cytophagaceae. PLoS One 2014; 9:e92294. [PMID: 24647674 PMCID: PMC3960232 DOI: 10.1371/journal.pone.0092294] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 02/20/2014] [Indexed: 11/18/2022] Open
Abstract
Few diazotrophs have been found to belong to the family Cytophagaceae so far. In the present study, a Gram-negative, rod-shaped bacterium that forms red colonies, was isolated from sands of the Takalamakan desert. It was designated H4XT. Phylogenetic and biochemical analysis indicated that the isolate is a new species of the genus Pontibacter. The 16S rRNA gene of H4XT displays 94.2–96.8% sequence similarities to those of other strains in Pontibacter. The major respiratory quinone is menaquinone-7 (MK-7). The DNA G+C content is 46.6 mol%. The major cellular fatty acids are iso-C15∶0, C16∶1ω5c, summed feature 3 (containing C16∶1ω6c and/or C16∶1ω7c) and summed feature 4 (comprising anteiso-C17∶1B and/or iso-C17∶1I). The major polar lipids are phosphatidylethanolamine (PE), one aminophospholipid (APL) and some unknown phospholipids (PLs). It is interesting to see that this bacterium can grow very well in a nitrogen-free medium. PCR amplification suggested that the bacterium possesses at least one type of nitrogenase gene. Acetylene reduction assay showed that H4XT actually possesses nitrogen-fixing activity. Therefore, it can be concluded that H4XT is a new diazotroph. We thus referred it to as Pontibacter diazotrophicus sp. nov. The type strain is H4XT ( = CCTCC AB 2013049T = NRRL B-59974T).
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Affiliation(s)
- Linghua Xu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
- School of Chemical and Material Engineering, Hubei Polytechnic University, Huangshi, China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
- * E-mail: (XCZ); (XL)
| | - Yao Nie
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- * E-mail: (XCZ); (XL)
| | - Enmin Zhou
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Lingli Zhou
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Yunfan Pan
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Wenjun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
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Cao H, Nie Y, Zeng XC, Xu L, He Z, Luo X, Wu R. Pontibacter yuliensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:968-972. [PMID: 24425811 DOI: 10.1099/ijs.0.055004-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, rod-shaped and pink bacterium was isolated from the soil of a Populus euphratica forest in the Taklamakan desert, Xinjiang, China. It was designated strain H9X(T). A 16S rRNA gene sequence homology search indicated that the isolate was most closely related to the family Cytophagaceae. The 16S rRNA gene of strain H9X(T) displayed 94.2-96.3 % sequence identities to those of type strains of other species of the genus Pontibacter. It only possessed menaquinone-7. The major cellular fatty acids of the novel isolate were iso-C15 : 0, C16 : 1ω5c summed feature 3 (containing C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 4 (comprising anteiso-C17 : 1 B and/or iso-C17 : 1 I). The major polar lipids were phosphatidylethanolamine, one unknown aminophospholipid, one unknown glycophospholipid and several unknown phospholipids. The DNA G+C content of this bacterium was 55.2 mol%. Based on the phenotypic and genotypic data presented, it can be concluded that this isolate represents a novel species of the genus Pontibacter, for which the name Pontibacter yuliensis sp. nov. is proposed. The type strain is H9X(T) ( = CCTCC AB 2013047(T) = KCTC 32396(T)).
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Affiliation(s)
- Hanjun Cao
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Yao Nie
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Linghua Xu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Zancan He
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Xuesong Luo
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Rina Wu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome. PLoS One 2013; 8:e82985. [PMID: 24349412 PMCID: PMC3861447 DOI: 10.1371/journal.pone.0082985] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/29/2013] [Indexed: 12/27/2022] Open
Abstract
Functional environmental screening of metagenomic libraries is a powerful means to identify and assign function to novel genes and their encoded proteins without any prior sequence knowledge. In the current study we describe the identification and subsequent analysis of a salt-tolerant clone from a human gut metagenomic library. Following transposon mutagenesis we identified an unknown gene (stlA, for “salt tolerance locus A”) with no current known homologues in the databases. Subsequent cloning and expression in Escherichia coli MKH13 revealed that stlA confers a salt tolerance phenotype in its surrogate host. Furthermore, a detailed in silico analysis was also conducted to gain additional information on the properties of the encoded StlA protein. The stlA gene is rare when searched against human metagenome datasets such as MetaHit and the Human Microbiome Project and represents a novel and unique salt tolerance determinant which appears to be found exclusively in the human gut environment.
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Affiliation(s)
- Eamonn P. Culligan
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Roy D. Sleator
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
- * E-mail: (RS); (JM); (CH)
| | - Julian R. Marchesi
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- Department of Hepatology and Gastroenterology, Imperial College London, London, United Kingdom
- * E-mail: (RS); (JM); (CH)
| | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- * E-mail: (RS); (JM); (CH)
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