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Kashani M, Engle MA, Kent DB, Gregston T, Cozzarelli IM, Mumford AC, Varonka MS, Harris CR, Akob DM. Illegal dumping of oil and gas wastewater alters arid soil microbial communities. Appl Environ Microbiol 2024; 90:e0149023. [PMID: 38294246 PMCID: PMC10880632 DOI: 10.1128/aem.01490-23] [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: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024] Open
Abstract
The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.
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Affiliation(s)
- Mitra Kashani
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Mark A Engle
- Department of Earth, Environmental and Resource Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Douglas B Kent
- U.S. Geological Survey, Earth Systems Processes Division, Menlo Park, California, USA
| | | | - Isabelle M Cozzarelli
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Adam C Mumford
- U.S. Geological Survey, Maryland-Delaware-D.C. Water Science Center, Baltimore, Maryland, USA
| | - Matthew S Varonka
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Cassandra R Harris
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Denise M Akob
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
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van der Ent F, Skagseth S, Lund BA, Sǒan J, Griese JJ, Brandsdal BO, Åqvist J. Computational design of the temperature optimum of an enzyme reaction. SCIENCE ADVANCES 2023; 9:eadi0963. [PMID: 37379391 DOI: 10.1126/sciadv.adi0963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
Cold-adapted enzymes are characterized both by a higher catalytic activity at low temperatures and by having their temperature optimum down-shifted, compared to mesophilic orthologs. In several cases, the optimum does not coincide with the onset of protein melting but reflects some other type of inactivation. In the psychrophilic α-amylase from an Antarctic bacterium, the inactivation is thought to originate from a specific enzyme-substrate interaction that breaks around room temperature. Here, we report a computational redesign of this enzyme aimed at shifting its temperature optimum upward. A set of mutations designed to stabilize the enzyme-substrate interaction were predicted by computer simulations of the catalytic reaction at different temperatures. The predictions were verified by kinetic experiments and crystal structures of the redesigned α-amylase, showing that the temperature optimum is indeed markedly shifted upward and that the critical surface loop controlling the temperature dependence approaches the target conformation observed in a mesophilic ortholog.
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Affiliation(s)
- Florian van der Ent
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Susann Skagseth
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Bjarte A Lund
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Jaka Sǒan
- National Institute of Chemistry, SI-1001 Ljubljana, Slovenia
| | - Julia J Griese
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Bjørn O Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
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Dang YR, Zhang XY, Liu SS, Li PY, Ren XB, Qin QL. Genomic analysis of Marinimicrobium sp. C6131 reveals its genetic potential involved in chitin metabolism. Mar Genomics 2023; 67:101007. [PMID: 36682850 DOI: 10.1016/j.margen.2022.101007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Marinimicrobium sp. C6131, which had the ability to degrade chitin, was isolated from deep-sea sediment of the southwest Indian Ocean. Here, the genome of strain C6131 was sequenced and the chitin metabolic pathways were constructed. The genome contained a circular chromosome of 4,207,651 bp with a G + C content of 58.50%. A total of 3471 protein-coding sequences were predicted. Gene annotation and metabolic pathway reconstruction showed that strain C6131 possessed genes and two metabolic pathways involved in chitin catabolism: the hydrolytic chitin utilization pathway initiated by chitinases and the oxidative chitin utilization pathway initiated by lytic polysaccharide monooxygenases. Chitin is the most abundant polysaccharide in the ocean. Degradation and recycling of chitin driven by marine bacteria are crucial for biogeochemical cycles of carbon and nitrogen in the ocean. The genomic information of strain C6131 revealed its genetic potential involved in chitin metabolism. The strain C6131 could grow with colloidal chitin as the sole carbon source, indicating that these genes would have functions in chitin degradation and utilization. The genomic sequence of Marinimicrobium sp. C6131 could provide fundamental information for future studies on chitin degradation, and help to improve our understanding of the chitin degradation process in deep-sea environments.
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Affiliation(s)
- Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiao-Yu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Sha-Sha Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xue-Bing Ren
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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Li Y, Zhou M, Li C, Pan X, Lv N, Ye Z, Zhu G, Zhao Q, Cai G. Inoculating indoleacetic acid bacteria promotes the enrichment of halotolerant bacteria during secondary fermentation of composting. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:116021. [PMID: 36067675 DOI: 10.1016/j.jenvman.2022.116021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
The secondary fermentation stage is critical for stabilizing composting products and producing various secondary metabolites. However, the low metabolic rate of mesophilic bacteria is regarded as the rate-limiting stage in composting process. In present study, two indoleacetic acid (IAA)-producing bacteria (Bacillus safensis 33C and Corynebacterium stationis subsp. safensis 29B) were inoculated to strengthen the secondary fermentation stage to improve the plant-growth promoting potential of composting products. The results showed that the addition of IAA-producing bacteria promoted the assimilation of soluble salt, the condensation and aromatization of humus, and the accumulation of dissolved organic nitrogen (DON) and dissolved organic carbon (DOC). The bioaugmentation strategy also enabled faster microbial community succession during the medium-late phase of secondary fermentation. However, the colonization of Bacillus and Corynebacterium could not explain the disproportionate increase of IAA yield, which reached up to 5.6 times compared to the control group. Deeper analysis combined with physicochemical properties and microbial community structure suggested that IAA-producing bacteria might induce the increase of salinity, which enriched halotolerant bacteria capable of producing IAA, such as Halomonas, Brachybacterium and Flavobacterium. In addition, the results also proved that it was necessary to shorten secondary fermentation time to avoid IAA degradation without affecting composting maturity. In summary, enhancing secondary fermentation of composting via adding proper IAA-producing bacteria is an efficient strategy for upgrading the quality of organic fertilizer.
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Affiliation(s)
- Yanlin Li
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingdian Zhou
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxing Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Xiaofang Pan
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Nan Lv
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Zhilong Ye
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Gefu Zhu
- School of Environment and Nature Resources, Renmin University of China, Beijing, 100872, China; Key Laboratory of Energy Resource Utilization from Agriculture Residue, Ministry of Agriculture and Rural Affairs, China.
| | - Quanbao Zhao
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Guanjing Cai
- Biology Department and Institute of Marine Sciences, College of Science, And Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China.
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Liu J, Li J, Luo J, Li Y, Yang Z, Huang C, Sun F, Wang G. Sessilibacter corallicola gen. nov., sp. nov., a sessile bacterium isolated from coral Porites lutea. Int J Syst Evol Microbiol 2022; 72. [PMID: 35639595 DOI: 10.1099/ijsem.0.005401] [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: 03/02/2024] Open
Abstract
A Gram-stain-negative, non-spore-forming, motile, aerobic bacterium (strain C21T) was isolated from coral and identified using polyphasic identification approach. Global alignment of 16S rRNA gene sequences indicated that strain C21T shares 95.7 % sequence identity to its closest neighbour, Marinibactrum halimedae NBRC 110095T, followed by other type strains with identities of lower than 95 %. The average nucleotide identity and average amino acid identity values between strain C21T and M. halimedae NBRC 110095T were 69.6 and 64.8 %, respectively, indicating that strain C21T may represent a new species in a new genus. Phylogenetic analysis based on 16S rRNA gene and phylogenomic results indicated that strain C21T forms a distinct branch in the family Cellvibrionaceae. Cellular fatty acids and polar lipids could also readily distinguish strain C21T from closely related type strains. Therefore, strain C21T is suggested to represent a new species in a new genus, for which the name Sessilibacter corallicola gen. nov., sp. nov. is proposed. The type strain is C21T (=MCCC 1K03260T=KCTC 62317T).
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Affiliation(s)
- Jianfeng Liu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
| | - Jin Li
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Jixin Luo
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Yuanjin Li
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Zian Yang
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Chengli Huang
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Feilong Sun
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
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Extremophiles in Soil Communities of Former Copper Mining Sites of the East Harz Region (Germany) Reflected by Re-Analyzed 16S rRNA Data. Microorganisms 2021; 9:microorganisms9071422. [PMID: 34209398 PMCID: PMC8305195 DOI: 10.3390/microorganisms9071422] [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: 02/26/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining places and one sample from an industrial mine dump have been selected for investigation by 16S rRNA and compared with six samples from non-mining areas. Although most of the soil samples from the old mines show pH values around 7, RNA profiling reflects many operational taxonomical units (OTUs) belonging to acidophilic genera. For some of these OTUs, similarities were found with their abundances in the comparative samples, while others show significant differences. In addition to pH-dependent bacteria, thermophilic, psychrophilic, and halophilic types were observed. Among these OTUs, several DNA sequences are related to bacteria which are reported to show the ability to metabolize special substrates. Some OTUs absent in comparative samples from limestone substrates, among them Thaumarchaeota were present in the soil group from ancient mines with pH > 7. In contrast, acidophilic types have been found in a sample from a copper slag deposit, e.g., the polymer degrading bacterium Granulicella and Acidicaldus, which is thermophilic, too. Soil samples of the group of pre-industrial mines supplied some less abundant, interesting OTUs as the polymer-degrading Povalibacter and the halophilic Lewinella and Halobacteriovorax. A particularly high number of bacteria (OTUs) which had not been detected in other samples were found at an industrial copper mine dump, among them many halophilic and psychrophilic types. In summary, the results show that soil samples from the ancient copper mining places contain soil bacterial communities that could be a promising source in the search for microorganisms with valuable metabolic capabilities.
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Fotedar R, Caldwell ME, Sankaranarayanan K, Al-Zeyara A, Al-Malki A, Kaul R, Al Marri M, Al-Shamari HS, Lawson PA. Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf. Int J Syst Evol Microbiol 2020; 70:4130-4138. [PMID: 32614761 DOI: 10.1099/ijsem.0.004256] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain B66T was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 6.5-8) and with 0-6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66T was affiliated with the family Alteromonadaceae, sharing the highest sequence similarities to the genera Alteromonas (93.7-95.4 %), Aestuariibacter (94.0-95.1 %), Agaribacter (93.3-93.7 %), Glaciecola (92.0-93.7 %), Marisendiminitalea (93.2-93.3 %) and Planctobacterium (92.9 %). In the phylogenetic trees, strain B66T demonstrated the novel organism formed a distinct lineage closely associated with Aestuariibacter and Planctobacterium. Major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c/iso-C15 : 0 2-OH and iso-C15 : 0 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66T is considered to represent a novel species and genus for which the name Ningiella ruwaisensis gen. nov., sp. nov., is proposed. The type strain is B66T (=QCC B003/17T=LMG 30288 T=CCUG 70703T).
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Affiliation(s)
- Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Matthew E Caldwell
- Department of Microbiology and Plant Biology, University of Oklahoma, OK 73019, USA
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, OK 73019, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, OK 73019, USA
| | - Aisha Al-Zeyara
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Ameena Al-Malki
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Ridhima Kaul
- Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Masoud Al Marri
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Hamad S Al-Shamari
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, OK 73019, USA
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Yu H, Zhao S, Fan Y, Hu C, Lu W, Guo L. Cloning and heterologous expression of a novel halo/alkali-stable multi-domain xylanase (XylM18) from a marine bacterium Marinimicrobium sp. strain LS-A18. Appl Microbiol Biotechnol 2019; 103:8899-8909. [DOI: 10.1007/s00253-019-10140-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/06/2019] [Accepted: 09/12/2019] [Indexed: 10/25/2022]
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Furtado BU, Gołębiewski M, Skorupa M, Hulisz P, Hrynkiewicz K. Bacterial and Fungal Endophytic Microbiomes of Salicornia europaea. Appl Environ Microbiol 2019; 85:e00305-19. [PMID: 31003988 PMCID: PMC6581177 DOI: 10.1128/aem.00305-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/14/2019] [Indexed: 01/21/2023] Open
Abstract
We examined Salicornia europaea, a nonmycorrhizal halophyte associated with specific and unique endophytic bacteria and fungi. The microbial community structure was analyzed at two sites differing in salinization history (anthropogenic and naturally saline site), in contrasting seasons (spring and fall) and in two plant organs (shoots and roots) via 16S rRNA and internal transcribed spacer amplicon sequencing. We observed distinct communities at the two sites, and in shoots and roots, while the season was of no importance. The bacterial community was less diverse in shoot libraries than in roots, regardless of the site and season, whereas no significant differences were observed for the fungal community. Proteobacteria and Bacteroidetes dominated bacterial assemblages, and Ascomycetes were the most frequent fungi. A root core microbiome operational taxonomic unit belonging to the genus Marinimicrobium was identified. We detected a significant influence of the Salicornia bacterial community on the fungal one by means of cocorrespondence analysis. In addition, pathways and potential functions of the bacterial community in Salicornia europaea were inferred and discussed. We can conclude that bacterial and fungal microbiomes of S. europaea are determined by the origin of salinity at the sites. Bacterial communities seemed to influence fungal ones, but not the other way around, which takes us closer to understanding of interactions between the two microbial groups. In addition, the plant organs of the halophyte filter the microbial community composition.IMPORTANCE Endophytes are particularly fascinating because of their multifaceted lifestyle, i.e., they may exist as either free-living soil microbes or saprobic ones or pathogens. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. At the same time, they may contribute to the host's adaptation to adverse environmental conditions, which may be of importance in agriculture.
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Affiliation(s)
- Bliss Ursula Furtado
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Marcin Gołębiewski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Monika Skorupa
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Piotr Hulisz
- Department of Soil Science and Landscape Management, Faculty of Earth Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Toruń, Poland
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Song L, Liu H, Cai S, Zhou Y. Marinimicrobium alkaliphilum sp. nov., an alkaliphilic bacterium isolated from soil and emended description of the genus Marinimicrobium. Int J Syst Evol Microbiol 2018; 69:481-485. [PMID: 30566073 DOI: 10.1099/ijsem.0.003183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, rod-shaped bacterial strains, designated SW121T and W12, were isolated from a soil sample collected from Shanxi Province, China. The two strains were strictly aerobic, catalase-positive and oxidase-positive. Both strains grew at 6-42 °C (optimum, 30 °C), at pH 5.5-11.0 (optimum, pH 9.0) and in the presence of 0-15.0 % (w/v) NaCl (optimum, 2.0-3.0 %). The predominant cellular fatty acids of strain SW121T were C16 : 0, C18 : 1ω7c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). Strain SW121T contained ubiquinone-8 as the sole respiratory quinone. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were major polar lipids. The genomic DNA G+C content of strain SW121T was 58.5 mol%. Comparative analysis of 16S rRNA gene sequences revealed that strains SW121T and W12 showed the highest similarities to Marinimicrobium koreense DSM 16974T(95.7 and 95.5 %, respectively). On the basis of phylogenetic inference and phenotypic characteristics, it is proposed that the two strains represent a novel species of the genus Marinimicrobium, for which the name Marinimicrobiumalkaliphilum sp. nov. is proposed. The type strain is SW121T (=CGMCC 1.16166T=KCTC 62651T).
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Affiliation(s)
- Lei Song
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hongcan Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shichun Cai
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Ling SK, Xia J, Liu Y, Chen GJ, Du ZJ. Agarilytica rhodophyticola gen. nov., sp. nov., isolated from Gracilaria blodgettii. Int J Syst Evol Microbiol 2017; 67:3778-3783. [PMID: 28879838 DOI: 10.1099/ijsem.0.002193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, rod-shaped, non-spore-forming, aerobic, agarolytic bacterium, designated 017T, was isolated from Gracilaria blodgettii collected at the coast of Lingshui county, Hainan province, China. Optimal growth occurred at 28-33 °C (range 15-40 °C), with 3 % (w/v) NaCl (range 2-4 %) and at pH 8.0 (range pH 6.5-8.5). Cells of strain 017T were motile and formed yellow colonies on marine agar 2216. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 017T shared the highest similarity with Teredinibacter turnerae T7902T (94.4 %). The predominant polar lipids of the novel isolate consisted of phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and some other unknown lipids. Major cellular fatty acids (>10 %) were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH), and the sole respiratory lipoquinone was Q-8. The DNA G+C content of strain 017T was 40.2 mol%. Comparative analysis of 16S rRNA gene sequences and phenotypic characterization indicated that strain 017T represents a novel species in a new genus of the family Cellvibrionaceae, order Cellvibrionales, for which the name Agarilytica rhodophyticola gen. nov., sp. nov. is proposed. The type strain of Agarilytica rhodophyticola is 017T (=KCTC 42584T=MCCC 1H00123T).
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Affiliation(s)
- Si-Kai Ling
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Jun Xia
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Yan Liu
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Guan-Jun Chen
- College of Marine Science, Shandong University, Weihai 264209, PR China.,State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University, Weihai 264209, PR China.,State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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Guo LY, Li DQ, Sang J, Chen GJ, Du ZJ. Marinagarivorans algicola gen. nov., sp. nov., isolated from marine algae. Int J Syst Evol Microbiol 2016; 66:1593-1599. [DOI: 10.1099/ijsem.0.000925] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ling-Yun Guo
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Dong-Qi Li
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Jin Sang
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zong-Jun Du
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
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13
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Zhong ZP, Liu Y, Wang F, Zhou YG, Liu HC, Liu ZP. Lacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:422-429. [DOI: 10.1099/ijsem.0.000735] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100089, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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14
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Zhao JX, Liu QQ, Zhou YX, Chen GJ, Du ZJ. Alkalimarinus sediminis gen. nov., sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2015; 65:3511-3516. [DOI: 10.1099/ijsem.0.000446] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain FA028T, a beige-pigmented, facultatively anaerobic, heterotrophic, catalase-negative and oxidase-positive, Gram-stain-negative bacterium, was isolated from marine sediment of the coast of Weihai, China. Cells of strain FA028T were rod-shaped, 1–3 μm in length and 0.5 μm in width. The strain was able to grow at 13–37 °C, at pH 7.0–9.5 and in the presence of 1.0–4.0 % (w/v) NaCl. Optimal growth was observed at 28 °C, with 3.0 % NaCl and at pH 7.5–8.0. Nitrate was not reduced. The G+C content of the DNA was 43.4 mol%. The isoprenoid quinone was Q-9 and the main cellular fatty acids (>10 %) were C16 : 0, C16 : 1ω9c and iso-C15 : 0 2-OH/C16 : 1ω7c. The major polar lipids in strain FA028T were phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol; phospholipid was present in moderate to minor amounts in the polar lipid profile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FA028T was affiliated with the phylum Proteobacteria. 16S rRNA gene sequence comparisons showed that this isolate is unique, sharing < 93 % similarity with species of the families Alteromonadaceae and Oceanospirillaceae. On the basis of the phenotypic and phylogenetic data, strain FA028T should be classified as representing a novel species of a new genus within the family Alteromonadaceae, for which the name Alkalimarinus sediminis gen. nov., sp. nov. is proposed. The type strain of Alkalimarinus sediminis is FA028T ( = CICC 10906T = KCTC 42258T).
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Affiliation(s)
- Jin-Xin Zhao
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Qian-Qian Liu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Yan-Xia Zhou
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
- State key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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15
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Verma A, Mual P, Mayilraj S, Krishnamurthi S. Tamilnaduibacter salinus gen. nov., sp. nov., a halotolerant gammaproteobacterium within the family Alteromonadaceae, isolated from a salt pan in Tamilnadu, India. Int J Syst Evol Microbiol 2015; 65:3248-3255. [PMID: 26296662 DOI: 10.1099/ijsem.0.000401] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-negative, slow-growing, halotolerant strains with rod-shaped cells, designated as strains Mi-7T and Mi-8, which formed pin-point colonies on halophilic media were isolated during a study into the microbial diversity of a salt pan in the state of Tamilnadu, India. Both the strains had an obligate requirement for 1 % (w/v) NaCl for growth and were halotolerant, growing at NaCl concentrations of up to 20 % (w/v) in media. The strains, however, showed an inability to utilize the majority of substrates tested as sole carbon sources for growth and in fermentation reactions. Molecular phylogenetic analyses, based on 16S rRNA gene sequence revealed their closest phylogenetic neighbours to be members of the genus Marinobacter, with whom they showed the highest sequence similarity of 93.6 % and even less with the type strain of the type species, Marinobacter hydrocarbonoclasticus DSM 8798T (91.1 %). Similarities with other genera within the family Alteromonadaceae were below 91.0 %. However, the two strains were very closely related to each other with 99.9 % sequence similarity, and DNA–DNA hybridization analyses confirmed their placement in the same species. The DNA G+C content of both strains was 65 mol%. Using the polyphasic taxonomic data obtained from this study, strains Mi-7T and Mi-8 represent two strains of the same species of a novel genus for which the name Tamilnaduibacter salinus gen. nov., sp. nov., is proposed; the type strain of the novel species is Mi-7T ( = MTCC 12009T = DSM 28688T).
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Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Poonam Mual
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
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16
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Cheng H, Zhang S, Huo YY, Jiang XW, Zhang XQ, Pan J, Zhu XF, Wu M. Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus. Int J Syst Evol Microbiol 2014; 65:562-569. [PMID: 25392347 DOI: 10.1099/ijs.0.065078-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain YN3(T), which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0-10.0 and 4-32 °C in the presence of 0-9.0 % (w/v) NaCl. Strain YN3(T) was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3(T) should be assigned to the genus Gilvimarinus. 'Gilvimarinus agarilyticus' KCTC 23325 and Gilvimarinus chinensis QM42(T) had the closest phylogenetic relationship to strain YN3(T), and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA-DNA hybridization studies, we propose that strain YN3(T) represents a novel species of the genus Gilvimarinus, for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3(T) ( = KCTC 32438(T) = JCM 19198(T)). An emended description of the genus Gilvimarinus is also presented.
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Affiliation(s)
- Hong Cheng
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Shun Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Ying-Yi Huo
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xia-Wei Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, PR China
| | - Xin-Qi Zhang
- School of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Linan 311300, PR China
| | - Jie Pan
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xu-Fen Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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Genome Sequence of the Fructan-Degrading Organism
Marinimicrobium
sp. Strain LS-A18, Isolated from a Marine Solar Saltern. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00776-13. [PMID: 24092780 PMCID: PMC3790084 DOI: 10.1128/genomea.00776-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Marinimicrobium sp. strain LS-A18 is a fructan-degrading organism isolated from a brine sample from a marine solar saltern in Jiaozhou Bay, China. The draft genome sequence of this bacterium is 3,815,107 bp in length, with a G+C content of 59.03%. To our knowledge, this is the first genome announcement of a fructan-degrading strain of the genus Marinimicrobium.
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18
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Bacterial chitin utilisation at extremely haloalkaline conditions. Extremophiles 2012; 16:883-94. [PMID: 23007247 DOI: 10.1007/s00792-012-0484-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/09/2012] [Indexed: 10/27/2022]
Abstract
Chitin is produced in large amounts in hypersaline habitats with neutral pH due to the high biomass production of brine shrimp Artemia. Recently, a high abundance of Artemia was also noticed in hypersaline soda lakes in the Kulunda Steppe (Altai, Russia), which prompted us to survey the possibility of microbial chitin utilization at extremely haloalkaline conditions in soda brines. Most active chitin utilisation-supporting microbial growth was found at anaerobic conditions at pH 10 and up to 3.5 M total Na(+). At aerobic conditions, the degradation of chitin was slower, mostly incomplete and active at <2 M total Na(+), although very slow partial degradation was possible up to 4 M Na(+). Anaerobic enrichments at pH 10 yielded two different groups of obligately haloalkaliphilic fermentative anaerobes, exclusively specialized to utilise insoluble chitin as the only growth substrate. One group was represented by a single strain growing at moderate salinity, and another comprised multiple isolates growing up to 3.5 M Na(+). These groups represent two novel bacterial phyla not closely related to any other cultured bacteria. Aerobic enrichments from the lake sediments were dominated by several obligately haloalkaliphilic members of the genus Marinimicrobium in the Gammaproteobacteria. They were less specialised than the anaerobes and grew with chitin and its monomer and oligomers at a pH of 10 up to 2.5 M Na(+). Furthermore, several strains of haloalkaliphilic Gram-positive chitinolytics belonging to bacilli and actinobacteria were isolated from soda lake sediments and surrounding soda soils. In general, the results indicate the presence of an active and diverse haloalkaliphilic chitinolytic microbial community in hypersaline soda habitats.
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19
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Zhao K, Guo LZ, Lu WD. Extracellular Production of Novel Halotolerant, Thermostable, and Alkali-Stable Carboxymethyl Cellulase by Marine Bacterium Marinimicrobium sp. LS-A18. Appl Biochem Biotechnol 2012; 168:550-67. [DOI: 10.1007/s12010-012-9796-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Accepted: 07/03/2012] [Indexed: 01/25/2023]
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Kim BC, Poo H, Lee KH, Kim MN, Park DS, Oh HW, Lee JM, Shin KS. Simiduia areninigrae sp. nov., an agarolytic bacterium isolated from sea sand. Int J Syst Evol Microbiol 2012; 62:906-911. [DOI: 10.1099/ijs.0.031153-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study intended to screen for agar-degrading bacteria, strain M2-5T was isolated from black sand off the shore of Jeju Island, Republic of Korea. Strain M2-5T exhibited agarase activity; the β-agarase gene of the isolate had 62 % amino acid sequence identity to the β-agarase gene of
Microbulbifer thermotolerans
JAMB A94T. The isolate was closely related to members of the genus
Simiduia
but was clearly discernible from reported
Simiduia
species, based on a polyphasic analysis. Cells of strain M2-5T were Gram-negative, catalase- and oxidase-positive, motile rods. The DNA G+C content was 53.3 mol%. The predominant isoprenoid quinone was Q-8. The major cellular fatty acids were C17 : 1ω8c (25.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 17.2 %) and C17 : 0 (15.0 %). Phylogenetic analysis using 16S rRNA gene sequences showed that strain M2-5T had 96.6 % gene sequence similarity to
Simiduia agarivorans
SA1T, the most closely related type strain of the genus
Simiduia
. These results suggest that strain M2-5T represents a novel species in the genus
Simiduia
, for which the name
Simiduia
areninigrae sp. nov. is proposed; the type strain is M2-5T ( = KCTC 23293T = NCAIM B 02424T).
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Affiliation(s)
- Byung-Chun Kim
- Microbiological Resources Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Haryoung Poo
- Bionanotechnology Research Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Kang Hyun Lee
- Microbiological Resources Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Mi Na Kim
- Microbiological Resources Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Doo-Sang Park
- Microbiological Resources Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Hyun Woo Oh
- Industrial Biomaterials Research Center, KRIBB Daejeon 305-806, Republic of Korea
| | - Jin Man Lee
- Department of Food and Biotechnology, Hoseo University, Asan 336-795, Republic of Korea
| | - Kee-Sun Shin
- Microbiological Resources Center, KRIBB, Daejeon 305-806, Republic of Korea
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Li AX, Guo LZ, Lu WD. Alkaline inulinase production by a newly isolated bacterium Marinimicrobium sp. LS–A18 and inulin hydrolysis by the enzyme. World J Microbiol Biotechnol 2011; 28:81-9. [DOI: 10.1007/s11274-011-0794-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 05/18/2011] [Indexed: 10/18/2022]
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Du ZJ, Lv GQ, Rooney AP, Miao TT, Xu QQ, Chen GJ. Agarivorans gilvus sp. nov. isolated from seaweed. Int J Syst Evol Microbiol 2011; 61:493-496. [DOI: 10.1099/ijs.0.019810-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel agarase-producing, non-endospore-forming marine bacterium, WH0801T, was isolated from a fresh seaweed sample collected from the coast of Weihai, China. Preliminary characterization based on 16S rRNA gene sequence analysis showed that WH0801T shared 96.1 % similarity with Agarivorans albus MKT 106T, the type species of the genus Agarivorans. A polyphasic taxonomic study was conducted and confirmed the phylogenetic affiliation of strain WH0801T to the genus Agarivorans. Isolate WH0801T produces light-yellow-pigmented colonies; cells are Gram-stain-negative, straight or curved rods, which are motile with a single polar flagellum. Strain WH0801T grew in 0.5–5 % NaCl, with optimum growth at 3 % NaCl, and its optimal pH and cultivation temperature were 8.4–8.6 and 28–32 °C, respectively. Data from biochemical tests, whole-cell fatty acid profiling, 16S rRNA gene sequence studies and DNA–DNA hybridization clearly indicated that isolate WH0801T represented a novel species within the genus Agarivorans, for which the name Agarivorans gilvus sp. nov. is proposed. The type strain of Agarivorans gilvus sp. nov. is WH0801T (=NRRL B-59247T =CGMCC 1.10131T).
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Affiliation(s)
- Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guo-Qiang Lv
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Alejandro P. Rooney
- National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, 1815 North University Street, Peoria, IL 61604, USA
| | - Ting-Ting Miao
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Qing-Qiang Xu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
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Kharroub K, Aguilera M, Jiménez-Pranteda ML, González-Paredes A, Ramos-Cormenzana A, Monteoliva-Sánchez M. Marinobacter oulmenensis sp. nov., a moderately halophilic bacterium isolated from brine of a salt concentrator. Int J Syst Evol Microbiol 2010; 61:2210-2214. [PMID: 20935087 DOI: 10.1099/ijs.0.027284-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, moderately halophilic bacterium, designated Set74(T), was isolated from brine of a salt concentrator at Ain Oulmene, Algeria. The strain grew optimally at 37-40 °C, at pH 6.5-7.0 and with 5-7.5 % (w/v) NaCl and used various organic compounds as sole carbon, nitrogen and energy sources. Ubiquinone 9 (Q-9) was the major lipoquinone. The main cellular fatty acids were C₁₆:₀, C₁₈:₁ω9c, summed feature 7 (ECL 18.846; C₁₉:₀ cyclo ω10c and/or C₁₉:₁ω6c), C₁₂:₀ 3-OH, C₁₆:₁ω9c, C₁₈:₀ and C₁₂:₀. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 57.4 mol%. The 16S rRNA gene sequence analysis indicated that strain Set74(T) was a member of the genus Marinobacter. The closest relatives of strain Set74(T) were Marinobacter santoriniensis NKSG1(T) (97.5 % 16S rRNA gene sequence similarity) and Marinobacter koreensis DD-M3(T) (97.4 %). DNA-DNA relatedness between strain Set74(T) and M. santoriniensis DSM 21262(T) and M. koreensis DSM 17924(T) was 45 and 37 %, respectively. On the basis of the phenotypic, chemotaxonomic and phylogenetic features, a novel species, Marinobacter oulmenensis sp. nov., is proposed. The type strain is Set74(T) ( = CECT 7499(T) = DSM 22359(T)).
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Affiliation(s)
- Karima Kharroub
- Institut de Nutrition de l'Alimentation et des Technologies Agro-Alimentaires, Université Mentouri, Constantine, Algeria.,Departamento de Microbiología, Facultad de Farmacia Campus de Cartuja s/n, 18071 Granada, Spain
| | - Margarita Aguilera
- Departamento de Microbiología, Facultad de Farmacia Campus de Cartuja s/n, 18071 Granada, Spain
| | | | - Ana González-Paredes
- Departamento de Microbiología, Facultad de Farmacia Campus de Cartuja s/n, 18071 Granada, Spain
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Møller MF, Kjeldsen KU, Ingvorsen K. Marinimicrobium haloxylanilyticum sp. nov., a new moderately halophilic, polysaccharide-degrading bacterium isolated from Great Salt Lake, Utah. Antonie van Leeuwenhoek 2010; 98:553-65. [PMID: 20574646 DOI: 10.1007/s10482-010-9472-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 06/09/2010] [Indexed: 11/29/2022]
Abstract
A new moderately halophilic, strictly aerobic, Gram-negative bacterium, strain SX15(T), was isolated from hypersaline surface sediment of the southern arm of Great Salt Lake (Utah, USA). The strain grew on a number of carbohydrates and carbohydrate polymers such as xylan, starch, carboxymethyl cellulose and galactomannan. The strain grew at salinities ranging from 2 to 22% NaCl (w/v). Optimal growth occurred in the presence of 7-11% NaCl (w/v) at a temperature of 35°C and a pH of 6.7-8.2. Major whole-cell fatty acids were C16:0 (30.5%), C18:0 (14.8%), C18:1ω7c (13.1%) and C12:0 (7.8%). The G+C content of the DNA was 60 ± 0.5 mol%. By 16S rRNA gene sequence analysis, strain SX15(T) was shown to be affiliated to members of the gammaproteobacterial genus Marinimicrobium with pair wise identity values of 92.9-94.6%. The pheno- and genotypic properties suggest that strain SX15(T) represents a novel species of the genus Marinimicrobium for which the name Marinimicrobium haloxylanilyticum is proposed. The type strain is SX15(T) (= DSM 23100(T) = CCUG 59572(T)).
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Oh HM, Kim H, Kim KM, Min GS, Cho JC. Porticoccus litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from the Yellow Sea. Int J Syst Evol Microbiol 2010; 60:727-732. [DOI: 10.1099/ijs.0.013938-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A marine bacterium, designated IMCC2115T, was isolated from coastal seawater (Yellow Sea, Korea) using a high throughput cultivation method based on dilution-to-extinction, and taxonomically investigated. Cells of the strain formed tiny, beige to off-white colonies and were Gram-stain-negative, obligately aerobic, chemoheterotrophic, non-motile cocci. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to the genera Marinimicrobium (92.0–92.4 %) and Microbulbifer (91.6–92.8 %), but phylogenetic trees showed that the strain formed a distinct phyletic line in the class Gammaproteobacteria adjacent to the OM60 and SAR92 clades. The DNA G+C content of the strain was 47.8 mol% and the predominant cellular fatty acids were anteiso-C15 : 0 (67.6 %), anteiso-C17 : 0 (14.4 %) and C16 : 0 (6.9 %). The 16S rRNA gene sequence analyses and phenotypic and chemotaxonomic tests allowed the differentiation of IMCC2115T from other related genera in the class Gammaproteobacteria. Therefore, strain IMCC2115T (=KCCM 42369T =NBRC 102686T) is proposed as the representative of a new genus and species, for which the name Porticoccus litoralis gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Hyun-Myung Oh
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Hana Kim
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Kyung-Mi Kim
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Gi-Sik Min
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Jang-Cheon Cho
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
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Mormile MR, Hong BY, Benison KC. Molecular analysis of the microbial communities of Mars analog lakes in Western Australia. ASTROBIOLOGY 2009; 9:919-30. [PMID: 20041745 DOI: 10.1089/ast.2008.0293] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Unique, shallow interdune lakes and groundwaters with extremely low pH and high salinity exist in Australia, along with nearby lakes that possess higher pH values. These acidic hypersaline environments are possibly the best modern terrestrial analogues for past martian environments. However, no previous microbiological analyses of these lakes have been conducted. During the Australian winter of 2005, water samples were taken from several hypersaline lakes located in southern Western Australia that possessed acidic to slightly alkaline pH. These samples were subjected to molecular analysis to identify bacterial communities. DNA extraction and polymerase chain reaction (PCR) amplification of the 16S rRNA gene sequences, by using universal bacterial primers, were also performed on the samples. Extracted DNA was amplified with 1070 forward and 1392 GC-clamped reverse primers and analyzed by using denaturant gradient gel electrophoresis (DGGE). In addition, libraries were developed from DNA retrieved from four lakes, including a marginal marine neutral lake, an inland neutral lake, and two inland acid lakes, and selected clones with distinct operational taxonomic units were sequenced. The DGGE profiles and clone sequence data indicate that there are distinct, abundant, and diverse microbial populations in these Australian hypersaline environments, especially the acidic ones. These results are significant for two reasons: (1) they provide the first microbiological survey of natural acid saline lakes and (2) they hint at the possibility that there could have been a diverse microbial population in acidic hypersaline environments on Mars.
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Affiliation(s)
- Melanie R Mormile
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, Missouri 65409-1120, USA.
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Yoon JH, Kang SJ, Jung YT, Oh TK. Marinimicrobium locisalis sp. nov., isolated from a marine solar saltern, and emended description of the genus Marinimicrobium. Int J Syst Evol Microbiol 2009; 59:2260-3. [PMID: 19620360 DOI: 10.1099/ijs.0.008458-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, motile and rod-shaped bacterial strain, designated ISL-43T, was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain ISL-43T grew optimally at pH 7.0-8.0 and 30 degrees C and in the presence of approximately 2% NaCl. It contained Q-8 as the predominant ubiquinone and C16:0, C19:0omega8c, C16:1omega7c and/or iso-C15:0 2-OH, and C18:1omega7c as the major fatty acids. The DNA G+C content was 58.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ISL-43T fell within the genus Marinimicrobium, clustering with Marinimicrobium agarilyticum M18T with a bootstrap value of 100%. Strain ISL-43T exhibited 16S rRNA gene sequence similarity values of 98.1 and 95.5% to M. agarilyticum M18T and Marinimicrobium koreense M9T, respectively. Strain ISL-43T exhibited DNA-DNA relatedness values of 17 and 10% to M. agarilyticum KCTC 12357T and M. koreense KCTC 12356T, respectively. On the basis of phenotypic, phylogenetic and genetic data, strain ISL-43T represents a novel species within the genus Marinimicrobium, for which the name Marinimicrobium locisalis sp. nov. is proposed. The type strain is ISL-43T (=KCTC 22484T=CCUG 56757T).
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea.
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Aestuariicola saemankumensis gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from tidal flat sediment. Int J Syst Evol Microbiol 2008; 58:2126-31. [DOI: 10.1099/ijs.0.65717-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Jung SY, Kim HS, Song JJ, Lee SG, Oh TK, Yoon JH. Aestuariimicrobium kwangyangense gen. nov., sp. nov., an ll-diaminopimelic acid-containing bacterium isolated from tidal flat sediment. Int J Syst Evol Microbiol 2007; 57:2114-2118. [PMID: 17766882 DOI: 10.1099/ijs.0.64917-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Gram-positive, catalase-positive, short rod- or coccoid-shaped bacterial strains, R27T, R44, R45 and R47, were isolated from an enrichment culture with diesel oil-degradation activity and their taxonomic positions were investigated using a polyphasic approach. Phenotypic, phylogenetic and genetic similarities indicated that strains R27T, R44, R45 and R47 belong to the same species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four strains form a distinct evolutionary lineage within the family Propionibacteriaceae. The novel four strains had cell-wall peptidoglycan based on ll-diaminopimelic acid, MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0 as the major cellular fatty acid. The DNA G+C contents were 68.8–69.2 mol%. These chemotaxonomic properties, together with phylogenetic distinctiveness, distinguish the four novel strains from recognized members of the family Propionibacteriaceae. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strains R27T, R44, R45 and R47 are classified as representatives of a new genus and novel species, Aestuariimicrobium kwangyangense gen. nov., sp. nov., within the family Propionibacteriaceae. The type strain of Aestuariimicrobium kwangyangense sp. nov. is R27T (=KCTC 19182T=JCM 14204T).
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- Catalase/biosynthesis
- Cell Wall/chemistry
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Diaminopimelic Acid/analysis
- Fatty Acids/analysis
- Gasoline
- Genes, rRNA
- Geologic Sediments/microbiology
- Hydrocarbons/metabolism
- Korea
- Molecular Sequence Data
- Peptidoglycan/chemistry
- Phylogeny
- Propionibacteriaceae/chemistry
- Propionibacteriaceae/classification
- Propionibacteriaceae/genetics
- Propionibacteriaceae/isolation & purification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Vitamin K 2/analysis
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Affiliation(s)
- Seo-Youn Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Hee-Sik Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Jae Jun Song
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Seung-Goo Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
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