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Emsley SA, Loughran RM, Shlafstein MD, Pfannmuller KM, De La Flor YT, Lein CG, Dove NC, Koyack MJ, Oline DK, Hanson TE, Videau P, Saw JH, Ushijima B. Fluctibacter corallii gen. nov., sp. nov., isolated from the coral Montipora capitata on a reef in Kāne'ohe Bay, O'ahu, Hawai'i, reclassification of Aestuariibacter halophilus as Fluctibacter halophilus comb. nov., and Paraglaciecola oceanifecundans as a later heterotypic synonym of Paraglaciecola agarilytica. Antonie Van Leeuwenhoek 2024; 117:45. [PMID: 38424217 DOI: 10.1007/s10482-024-01934-4] [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] [Received: 12/31/2023] [Accepted: 01/25/2024] [Indexed: 03/02/2024]
Abstract
Strain AA17T was isolated from an apparently healthy fragment of Montipora capitata coral from the reef surrounding Moku o Lo'e in Kāne'ohe Bay, O'ahu, Hawai'i, USA, and was taxonomically evaluated using a polyphasic approach. Comparison of a partial 16S rRNA gene sequence found that strain AA17T shared the greatest similarity with Aestuariibacter halophilus JC2043T (96.6%), and phylogenies based on 16S rRNA gene sequences grouped strain AA17T with members of the Aliiglaciecola, Aestuariibacter, Lacimicrobium, Marisediminitalea, Planctobacterium, and Saliniradius genera. To more precisely infer the taxonomy of strain AA17T, a phylogenomic analysis was conducted and indicated that strain AA17T formed a monophyletic clade with A. halophilus JC2043T, divergent from Aestuariibacter salexigens JC2042T and other related genera. As a result of monophyly and multiple genomic metrics of genus demarcation, strain AA17T and A. halophilus JC2043T comprise a distinct genus for which the name Fluctibacter gen. nov. is proposed. Based on a polyphasic characterisation and identifying differences in genomic and taxonomic data, strain AA17T represents a novel species, for which the name Fluctibacter corallii sp. nov. is proposed. The type strain is AA17T (= LMG 32603 T = NCTC 14664T). This work also supports the reclassification of A. halophilus as Fluctibacter halophilus comb. nov., which is the type species of the Fluctibacter genus. Genomic analyses also support the reclassification of Paraglaciecola oceanifecundans as a later heterotypic synonym of Paraglaciecola agarilytica.
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Affiliation(s)
- Sarah A Emsley
- Department of Biology, Southern Oregon University, Ashland, OR, USA
| | - Rachel M Loughran
- Microbiology Graduate Program, University of Delaware, Newark, DE, USA
| | | | | | - Yesmarie T De La Flor
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | | | | | - Marc J Koyack
- School of Arts and Sciences, Gwynedd Mercy University, Gwynedd Valley, PA, USA
| | - David K Oline
- Department of Biology, Southern Oregon University, Ashland, OR, USA
| | - Thomas E Hanson
- Microbiology Graduate Program, University of Delaware, Newark, DE, USA
- School of Marine Science and Policy and Delaware Biotechnology Institute, University of Delaware, Delaware, USA
| | - Patrick Videau
- Department of Biology, Southern Oregon University, Ashland, OR, USA
- AgBiome, Research Triangle Park, NC, USA
| | - Jimmy H Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, USA.
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA.
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Microbial Communities of Seawater and Coastal Soil of Russian Arctic Region and Their Potential for Bioremediation from Hydrocarbon Pollutants. Microorganisms 2022; 10:microorganisms10081490. [PMID: 35893548 PMCID: PMC9332119 DOI: 10.3390/microorganisms10081490] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022] Open
Abstract
The development of Arctic regions leads to pollution of marine and coastal environments with oil and petroleum products. The purpose of this work was to determine the diversity of microbial communities in seawater, as well as in littoral and coastal soil, and the potential ability of their members to degrade hydrocarbons degradation and to isolate oil-degrading bacteria. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, the dominance of bacteria in polar communities was shown, the proportion of archaea did not exceed 2% (of the total number of sequences in the libraries). Archaea inhabiting the seawater belonged to the genera Nitrosopumilus and Nitrosoarchaeum and to the Nitrososphaeraceae family. In the polluted samples, members of the Gammaproteobacteria, Alphaproteobacteria, and Actinomycetes classes predominated; bacteria of the classes Bacteroidia, Clostridia, Acidimicrobiia, Planctomycetia, and Deltaproteobacteria were less represented. Using the iVikodak program and KEGG database, the potential functional characteristics of the studied prokaryotic communities were predicted. Bacteria were potentially involved in nitrogen and sulfur cycles, in degradation of benzoate, terephthalate, fatty acids, and alkanes. A total of 19 strains of bacteria of the genera Pseudomonas, Aeromonas, Oceanisphaera, Shewanella, Paeniglutamicibacter, and Rhodococcus were isolated from the studied samples. Among them were psychrotolerant and psychrophilic bacteria growing in seawater and utilizing crude oil, diesel fuel, and motor oils. The data obtained suggest that the studied microbial communities could participate in the removal of hydrocarbons from arctic seawater and coastal soils and suggested the possibility of the application of the isolates for the bioaugmentation of oil-contaminated polar environments.
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Isolation, Diversity and Characterization of Ulvan-Degrading Bacteria Isolated from Marine Environments. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113420. [PMID: 35684358 PMCID: PMC9182395 DOI: 10.3390/molecules27113420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 05/24/2022] [Indexed: 11/29/2022]
Abstract
In this study, we aimed to isolate bacteria capable of degrading the polysaccharide ulvan from the green algae Ulva sp. (Chlorophyta, Ulvales, Ulvaceae) in marine environments. We isolated 13 ulvan-degrading bacteria and observed high diversity at the genus level. Further, the genera Paraglaciecola, Vibrio, Echinicola, and Algibacter, which can degrade ulvan, were successfully isolated for the first time from marine environments. Among the 13 isolates, only one isolate (Echinicola sp.) showed the ability not only to produce externally expressed ulvan lyase, but also to be periplasmic or on the cell surface. From the results of the full-genome analysis, lyase was presumed to be a member of the PL25 (BNR4) family of ulvan lyases, and the bacterium also contained the sequence for glycoside hydrolase (GH43, GH78 and GH88), which is characteristic of other ulvan-degrading bacteria. Notably, this bacterium has a unique ulvan lyase gene not previously reported.
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Heins A, Amann RI, Harder J. Cultivation of particle-associated heterotrophic bacteria during a spring phytoplankton bloom in the North Sea. Syst Appl Microbiol 2021; 44:126232. [PMID: 34399113 DOI: 10.1016/j.syapm.2021.126232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
Seawater contains free-living and particle-attached bacteria. Only a small fraction is cultivable on plates. As free-living and particle-associated bacteria differ in their physiological traits, their cultivability on plates may coincide with particle association. Using filtration and Imhoff sedimentation cones, particles were collected during a spring phytoplankton bloom off Helgoland (North Sea) in order to obtain particle-associated bacteria as inocula. Direct dilution plating resulted in 526 strains from 3 µm filtration retentates and 597 strains from settled particles. Motile Gammaproteobacteria from the genera Pseudoalteromonas, Shewanella, Psychrobacter, Vibrio and Colwellia, as well as particle-attached Flavobacteriia affiliating with the genera Tenacibaculum and Gramella, were frequently isolated. As a result, a diverse collection comprised of 266 strains was deposited. Two strains were most likely to represent novel genera and 78 strains were probably novel species. Recently, a high-throughput cultivation study from the same site using seawater as an inoculum had retrieved 271 operational phylogenetic units (OPUs) that represented 88% of the 4136 characterized strains at the species level. A comparison of 16S rRNA gene sequences revealed that the collection obtained matched 104 of the 271 seawater OPUs at the species level and an additional 113 at the genus level. This large overlap indicated a significant contribution of particle-associated bacteria to the cultivable microbiome from seawater. The presence of 49 genera not identified in the larger seawater study suggested that sample fractionation was an efficient strategy to cultivate rare members of the planktonic microbiome. The diverse collection of heterotrophic bacteria retrieved in this study will be a rich source for future studies on the biology of particle-associated bacteria.
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Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Meng X, Chang YQ, Wang H, Du ZJ. Algibacillus agarilyticus gen. nov., sp. nov., isolated from the surface of the red algae Gelidium amansii. Int J Syst Evol Microbiol 2020; 71. [PMID: 33332262 DOI: 10.1099/ijsem.0.004558] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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, strictly aerobic, coccoid and agar-hydrolysing bacterium, designated RQJ05T, was isolated from the marine red algae Gelidium amansii collected from the coastal area of Rizhao, PR China. Cells of strain RQJ05T were approximately 0.8-1.0×1.3-3.0 µm in size and motile by means of a polar flagellum. Growth occurred at 4-33 °C (optimum, 25-30 °C), pH 7.0-8.5 (optimum, pH 7.5-8.0) and in the presence of 1.0-7.0 % (w/v) NaCl (optimum, 2.0-3.0 %). Strain RQJ05T showed oxidase-positive and catalase-negative activities. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain RQJ05T formed a phylogenetic lineage with members of the family Alteromonadaceae and exhibited 16S rRNA gene sequence similarities of 92.6, 91.3, 90.2 and 90.1 % to Catenovulum maritimum Q1T, Catenovulum agarivorans YM01T, Paraphotobacterium marinum NSCS20N07DT and Algicola sagamiensis B-10-31T, respectively. The major cellular fatty acids of strain RQJ05T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids of strain RQJ05T were phosphatidylethanolamine, phosphatidylglycerol and two aminophospholipids. Strain RQJ05T contained Q-8 as the major respiratory quinone. The genomic DNA G+C content was 39.0 mol%. On the basis of genotypic, phenotypic and phylogenetic evidence, strain RQJ05T is presented as a representative of a novel species in a new genus, for which the name Algibacillus agarilyticus gen. nov., sp. nov. is proposed. The type strain is RQJ05T (=KCTC 62846T=MCCC 1H00352T).
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Affiliation(s)
- Xue Meng
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ya-Qi Chang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Huan Wang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- State key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China.,Marine College, Shandong University, Weihai, Shandong, 264209, PR China
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Tisserand L, Dadaglio L, Intertaglia L, Catala P, Panagiotopoulos C, Obernosterer I, Joux F. Use of organic exudates from two polar diatoms by bacterial isolates from the Arctic Ocean. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190356. [PMID: 32862822 PMCID: PMC7481660 DOI: 10.1098/rsta.2019.0356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/12/2020] [Indexed: 05/12/2023]
Abstract
Global warming affects primary producers in the Arctic, with potential consequences for the bacterial community composition through the consumption of microalgae-derived dissolved organic matter (DOM). To determine the degree of specificity in the use of an exudate by bacterial taxa, we used simple microalgae-bacteria model systems. We isolated 92 bacterial strains from the sea ice bottom and the water column in spring-summer in the Baffin Bay (Arctic Ocean). The isolates were grouped into 42 species belonging to Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Forty strains were tested for their capacity to grow on the exudate from two Arctic diatoms. Most of the strains tested (78%) were able to grow on the exudate from the pelagic diatom Chaetoceros neogracilis, and 33% were able to use the exudate from the sea ice diatom Fragilariopsis cylindrus. 17.5% of the strains were not able to grow with any exudate, while 27.5% of the strains were able to use both types of exudates. All strains belonging to Flavobacteriia (n = 10) were able to use the DOM provided by C. neogracilis, and this exudate sustained a growth capacity of up to 100 times higher than diluted Marine Broth medium, of two Pseudomonas sp. strains and one Sulfitobacter strain. The variable bioavailability of exudates to bacterial strains highlights the potential role of microalgae in shaping the bacterial community composition. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.
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Affiliation(s)
- Lucas Tisserand
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | - Laëtitia Dadaglio
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | - Laurent Intertaglia
- Sorbonne Université, CNRS, FR3724, Observatoire Océanologique, 66650 Banyuls/Mer, France
| | - Philippe Catala
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | | | - Ingrid Obernosterer
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | - Fabien Joux
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
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Alterocin, an Antibiofilm Protein Secreted by Pseudoalteromonas sp. Strain 3J6. Appl Environ Microbiol 2020; 86:AEM.00893-20. [PMID: 32769182 DOI: 10.1128/aem.00893-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022] Open
Abstract
We sought to identify and study the antibiofilm protein secreted by the marine bacterium Pseudoalteromonas sp. strain 3J6. The latter is active against marine and terrestrial bacteria, including Pseudomonas aeruginosa clinical strains forming different biofilm types. Several amino acid sequences were obtained from the partially purified antibiofilm protein, named alterocin. The Pseudoalteromonas sp. 3J6 genome was sequenced, and a candidate alt gene was identified by comparing the genome-encoded proteins to the sequences from purified alterocin. Expressing the alt gene in another nonactive Pseudoalteromonas sp. strain, 3J3, demonstrated that it is responsible for the antibiofilm activity. Alterocin is a 139-residue protein that includes a predicted 20-residue signal sequence, which would be cleaved off upon export by the general secretion system. No sequence homology was found between alterocin and proteins of known functions. The alt gene is not part of an operon and adjacent genes do not seem related to alterocin production, immunity, or regulation, suggesting that these functions are not fulfilled by devoted proteins. During growth in liquid medium, the alt mRNA level peaked during the stationary phase. A single promoter was experimentally identified, and several inverted repeats could be binding sites for regulators. alt genes were found in about 30% of the Pseudoalteromonas genomes and in only a few instances of other marine bacteria of the Hahella and Paraglaciecola genera. Comparative genomics yielded the hypothesis that alt gene losses occurred within the Pseudoalteromonas genus. Overall, alterocin is a novel kind of antibiofilm protein of ecological and biotechnological interest.IMPORTANCE Biofilms are microbial communities that develop on solid surfaces or interfaces and are detrimental in a number of fields, including for example food industry, aquaculture, and medicine. In the latter, antibiotics are insufficient to clear biofilm infections, leading to chronic infections such as in the case of infection by Pseudomonas aeruginosa of the lungs of cystic fibrosis patients. Antibiofilm molecules are thus urgently needed to be used in conjunction with conventional antibiotics, as well as in other fields of application, especially if they are environmentally friendly molecules. Here, we describe alterocin, a novel antibiofilm protein secreted by a marine bacterium belonging to the Pseudoalteromonas genus, and its gene. Alterocin homologs were found in about 30% of Pseudoalteromonas strains, indicating that this new family of antibiofilm proteins likely plays an important albeit nonessential function in the biology of these bacteria. This study opens up the possibility of a variety of applications.
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Wang Y, Zhang Y, Liu T, Zhu X, Ma J, Su X, Kang J, Guo C. Paraglaciecola marina sp. nov., isolated from marine alga ( Sargassum natans (L.) Gaillon). Int J Syst Evol Microbiol 2020; 70:4451-4457. [PMID: 32687464 DOI: 10.1099/ijsem.0.004132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, straight or curved rod-shaped, non-spore-forming, strictly aerobic, motile bacterium with a single polar flagellum, designated D3211T, was isolated from marine alga collected at the seashore of Yantai, PR China. The organism grew optimally at 24 °C, pH 7.0 and in the presence of 2.0 % (w/v) NaCl. Strain D3211T contained ubiquinone 8 as the major respiratory quinone and C16 : 1 ω7c and/or C16 : 1 ω6c, C16 : 0, iso-C17 : 0 and anteiso-C17 : 1 B and/or iso-C17 : 1 I as the major fatty acids. The predominant polar lipids of strain D3211T were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain D3211T was 39.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Paraglaciecola arctica BSs20135T, Paraglaciecola aestuariivivens JDTF-33T, Paraglaciecola aquimarina KCTC 32108T, Paraglaciecola mesophila DSM 15026T, Paraglaciecola psychrophila JCM 13954T and Paraglaciecola polaris ARK 150T with 97.6, 97.6, 97.5, 97.4, 97.3 and 97.1 % sequence similarities, respectively. Calculated average nucleotide identity and DNA-DNAhybridization values between strain D3211T and its phylogenetically related Paraglaciecola species were in the range 70.2-73.4 % and 19.1-20.4 %, respectively. On the basis of polyphasic analyses, strain D3211T represents a novel species of the genus Paraglaciecola, for which the name Paraglaciecola marina sp. nov. is proposed. The type strain is D3211T (=KCTC 72122T=MCCC 1K03603T).
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Affiliation(s)
- Yan Wang
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Yao Zhang
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Tingwei Liu
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Xiang Zhu
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Jin Ma
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Xiaoman Su
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Jing Kang
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
| | - Changjiang Guo
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, 601 Jinsui Avenue, Xinxiang 453003, PR China
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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: 16] [Impact Index Per Article: 4.0] [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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Sisinthy S, Gundlapally SR. Mitsuaria chitinivorans sp. nov. a potential candidate for bioremediation: emended description of the genera Mitsuaria, Roseateles and Pelomonas. Arch Microbiol 2020; 202:1839-1848. [PMID: 32447433 DOI: 10.1007/s00203-020-01905-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 01/20/2023]
Abstract
As a part of studying the effect of deoxygenation, eutrophication and acidification on bacterial diversity, strain HWN-4T was isolated from tube well water and characterized. The draft genome sequencing of strain HWN-4T revealed a genome size of 5,774,764 bp and the annotation indicated 5102 coding sequences including 66 RNA genes. Strain HWN-4T is Gram negative, rod-shaped, motile in the log phase, catalase and oxidase positive, and the major fatty acids and respiratory quinone present are C10:0 3-OH, C14:0 3OH/C16:1 iso I, C16:1 ω7c/C16:1 ω6c, C16:0 and C17:0 cyclo and ubiquinone-8, respectively. The phylogenetic analyses, based on 16S rRNA gene sequence, indicated that strain HWN-4T is a member of the genus Mitsuaria. The average nucleotide identity (ANI) and genome-to-genome similarity between strain HWN-4T and all other species/strains of the genus Mitsuaria are less than (%) 95.0 and 70.0, respectively. This confirms the status of strain HWN-4T as a novel species. The species status is further confirmed by phenotypic differences exhibited by strain HWN-4T with other members of the same genus. Based on the collective differences exhibited by strain HWN-4T with other members of the genus Mitsuaria, the name Mitsuaria chitinivorans sp. nov. is proposed. Further, the diagnostic signature nucleotides were identified in the 16S rRNA gene sequences of members of the genera Mitsuaria, Pelomonas and Roseateles, that distinctly differentiate them and support an emendation of the genera. Besides, phylogenetic and structural characterization of chitinases from members of the genus Mitsuaria was performed. The type strain of Mitsuaria chitinivorans sp. nov. is HWN-4T = LMG 28685T = KTCC 42483T.
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Affiliation(s)
- Shivaji Sisinthy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
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Jain A, Krishnan KP, Begum N, Singh A, Thomas FA, Gopinath A. Response of bacterial communities from Kongsfjorden (Svalbard, Arctic Ocean) to macroalgal polysaccharide amendments. MARINE ENVIRONMENTAL RESEARCH 2020; 155:104874. [PMID: 31975691 DOI: 10.1016/j.marenvres.2020.104874] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
Macroalgae are abundant in coastal Arctic habitats and contain a large amount of polysaccharides. Increased macroalgal productivity due to warmer temperatures and reduced sea-ice cover contribute a significant amount of polysaccharide-rich detritus in the region. To study bacterial degradation of macroalgal polysaccharides and their potential impact on biogeochemical processes we studied the response of bacterial communities from Kongsfjorden, Svalbard (Arctic Ocean) to alginate (AL) and agarose (AG) amendments, using an ex-situ microcosm experiment. Our results show that bacterial communities responded to the increased availability of macroalgal polysaccharides and community shift was congruent with a significant decline in nutrient concentrations. Initially-rare bacterial taxa affiliated with Gammaproteobacteria and Bacteroidia responded to the polysaccharide addition. Each polysaccharide addition incited the growth of certain distinct bacteria taxa. Compared to the un-amended control microcosms (CM), Polaribacter, Colwellia, Pseudoalteromonas, and unclassified Gammaproteobacteria responded to AL addition, whereas Paraglaciecola, Lentimonas, Colwellia, unclassified Gammaproteobacteria, unclassified Alteromonadales, and unclassified Alteromonadaceae responded to the AG addition. These results suggest that polysaccharides shift bacterial community composition towards copiotrophic bacterial taxa, with implications for carbon and nutrient cycling in coastal Svalbard.
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Affiliation(s)
- Anand Jain
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India.
| | | | - Nazira Begum
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India
| | - Archana Singh
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India
| | - Femi Anna Thomas
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India
| | - Anu Gopinath
- Department of Aquatic Environment Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
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12
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Zhang D, Gui J, Zheng S, Zhu X, Wu S, Tian Y, Lai Q, Xu H. Marisediminitalea mangrovi gen. nov., sp. nov., isolated from marine mangrove sediment, and reclassification of Aestuariibacter aggregatus as Marisediminitalea aggregata comb. nov. Int J Syst Evol Microbiol 2020; 70:457-464. [PMID: 31626587 DOI: 10.1099/ijsem.0.003773] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain GS-14T was isolated from a mangrove sediment sample collected at Beilun Estuary National Nature Reserve, Guangxi Province, PR China. Cells were Gram-stain-negative, strictly aerobic and rod-shaped with a polar flagellum. Optimal growth occurred in the presence of 3-6 % (w/v) NaCl, at pH 6-8 and at a temperature of 37 °C. The predominant polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 (Q-8) was the sole respiratory quinone. The major fatty acids (>10 % of the total fatty acids) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The DNA G+C content was 47.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain GS-14T had the highest sequence similarity to Aestuariibacter aggregatus WH169T (96.63 %), Aliiglaciecola coringensis AK49T (96.56 %) and Alteromonas lipolytica JW12T (96.22 %). In addition, the OrthoANIu value and dDDH values calculated from the genomes of strain GS-14T and A. aggregatus WH169T were 79.5 and 21.9 %, respectively. Based on the polyphasic taxonomic results, strain GS-14T is considered to represent a novel species in a new genus, for which the name Marisediminitalea mangrovi gen. nov., sp. nov. is proposed. The type strain of Marisediminitalea mangrovi is GS-14T (=KCTC 72401T=MCCC 1K03622T). Because Aestuariibacter aggregatus WH169T clustered with strain GS-14T in the phylogenetic trees and was clearly separated from the two species within the genus Aestuariibacter, it is reclassified as a member of the genus Marisediminitalea as Marisediminitalea aggregata comb. nov. (type strain WH169T=CGMCC 1.8995T=LMG 25283T). The type species of the genus Marisediminitalea is Marisediminitalea aggregata gen. nov., comb. nov.
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Affiliation(s)
- Danyang Zhang
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Jiali Gui
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Sisi Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Xiaoying Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Shiyin Wu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, 361005, PR China
| | - Hong Xu
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
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13
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Hira P, Singh P, Pinnaka AK, Korpole S, Lal R. Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade. Indian J Microbiol 2019; 60:54-61. [PMID: 32089574 DOI: 10.1007/s12088-019-00845-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/27/2019] [Indexed: 12/26/2022] Open
Abstract
Microbial taxonomy dealing with identification and characterization of prokaryotes like bacteria and archaea has always been a major area of research all over the world. Exploring diversity of microbes and description of novel species with different genes and secondary compounds is of utmost importance for better future and sustenance of life. India having an enormous range of ecosystems and diverse species inhabiting these niches is considered to be one of the richest biodiversity regions of the world. During the last decade, with newer methodologies and better technology, the prokaryotic taxonomy from India has extended our inventory of microbial communities in specific niches. However, there still exist some limitations in classifying the microbes from India as compared to that is done world-over. This review enlists the taxonomic description of novel taxa of prokaryotes from India in the past decade. A total of 378 new bacterial species have been classified from different habitats in India in the last ten years and no descriptions of archaeal species is documented till date.
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Affiliation(s)
- Princy Hira
- 1Department of Zoology, Maitreyi College (University of Delhi), Chanakyapuri, New Delhi 110021 India
| | - Priya Singh
- 2Department of Zoology, Acharya Narendra Dev College (University of Delhi), Govindpuri, Kalkaji, New Delhi, 110019 India
| | - Anil Kumar Pinnaka
- 3CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Suresh Korpole
- 3CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Rup Lal
- The Energy and Resource Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
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14
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15
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Rossi A, Bellone A, Fokin SI, Boscaro V, Vannini C. Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study. MICROBIAL ECOLOGY 2019; 78:232-242. [PMID: 30411190 DOI: 10.1007/s00248-018-1279-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.
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Affiliation(s)
- Alessia Rossi
- Department of Biology, University of Pisa, Pisa, Italy
| | | | - Sergei I Fokin
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Invertebrate Zoology, St.-Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch of the S.I. Vavilov Institute of History of Science and Technology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vittorio Boscaro
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Botany, University of British Columbia, Vancouver, Canada
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16
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Luhtanen AM, Eronen-Rasimus E, Oksanen HM, Tison JL, Delille B, Dieckmann GS, Rintala JM, Bamford DH. The first known virus isolates from Antarctic sea ice have complex infection patterns. FEMS Microbiol Ecol 2019; 94:4898008. [PMID: 29481638 DOI: 10.1093/femsec/fiy028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/21/2018] [Indexed: 01/21/2023] Open
Abstract
Viruses are recognized as important actors in ocean ecology and biogeochemical cycles, but many details are not yet understood. We participated in a winter expedition to the Weddell Sea, Antarctica, to isolate viruses and to measure virus-like particle abundance (flow cytometry) in sea ice. We isolated 59 bacterial strains and the first four Antarctic sea-ice viruses known (PANV1, PANV2, OANV1 and OANV2), which grow in bacterial hosts belonging to the typical sea-ice genera Paraglaciecola and Octadecabacter. The viruses were specific for bacteria at the strain level, although OANV1 was able to infect strains from two different classes. Both PANV1 and PANV2 infected 11/15 isolated Paraglaciecola strains that had almost identical 16S rRNA gene sequences, but the plating efficiencies differed among the strains, whereas OANV1 infected 3/7 Octadecabacter and 1/15 Paraglaciecola strains and OANV2 1/7 Octadecabacter strains. All the phages were cold-active and able to infect their original host at 0°C and 4°C, but not at higher temperatures. The results showed that virus-host interactions can be very complex and that the viral community can also be dynamic in the winter-sea ice.
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Affiliation(s)
- Anne-Mari Luhtanen
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland.,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | | | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jean-Louis Tison
- Laboratoire de Glaciologie, DGES, Université Libre de Bruxelles, Belgium
| | - Bruno Delille
- Unité d'Océanographie Chimique, Université de Liège, Belgium
| | - Gerhard S Dieckmann
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Janne-Markus Rintala
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland.,Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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17
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Abstract
The streamlining hypothesis is usually used to explain the genomic reduction events in free-living bacteria like SAR11. However, we find that the genomic reduction phenomenon in the bacterial genus Idiomarina is different from that in SAR11. Therefore, we propose a new hypothesis to explain genomic reduction in this genus based on trophic specialization that could result in genomic reduction, which would be not uncommon in nature. Not only can the trophic specialization hypothesis explain the genomic reduction in the genus Idiomarina, but it also sheds new light on our understanding of the genomic reduction processes in other free-living bacterial lineages. The streamlining hypothesis is generally used to explain the genomic reduction events related to the small genome size of free-living bacteria like marine bacteria SAR11. However, our current understanding of the correlation between bacterial genome size and environmental adaptation relies on too few species. It is still unclear whether there are other paths leading to genomic reduction in free-living bacteria. The genome size of marine free-living bacteria of the genus Idiomarina belonging to the order Alteromonadales (Gammaproteobacteria) is much smaller than the size of related genomes from bacteria in the same order. Comparative genomic and physiological analyses showed that the genomic reduction pattern in this genus is different from that of the classical SAR11 lineage. Genomic reduction reconstruction and substrate utilization profile showed that Idiomarina spp. lost a large number of genes related to carbohydrate utilization, and instead they specialized on using proteinaceous resources. Here we propose a new hypothesis to explain genomic reduction in this genus; we propose that trophic specialization increasing the metabolic efficiency for using one kind of substrate but reducing the substrate utilization spectrum could result in bacterial genomic reduction, which would be not uncommon in nature. This hypothesis was further tested in another free-living genus, Kangiella, which also shows dramatic genomic reduction. These findings highlight that trophic specialization is potentially an important path leading to genomic reduction in some marine free-living bacteria, which is distinct from the classical lineages like SAR11.
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18
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Xiao YK, Yan ZF, Kim Y, Lee HM, Trinh H, Yang JE, Won KH, Yi TH, Kook M. Glaciecola amylolytica sp. nov., an amylase-producing bacterium isolated from seawater. Int J Syst Evol Microbiol 2019; 69:957-963. [PMID: 30608230 DOI: 10.1099/ijsem.0.003222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and coccus-shaped bacterium (THG-3.7T) was isolated from seawater. Growth occurred at 10-30 °C (optimum 25 °C), at pH 6-8 (optimum 7) and in the presence of 1-8 % (w/v) NaCl (optimum 4 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-3.7T were identified as Paraglaciecola mesophila DSM 15026T (95.3 % similarity), Glaciecola pallidula DSM 14239T (95.2 %), Paraglaciecola aquimarina KCTC 32108T (95.1 %), Paraglaciecola arctica KACC 14537T (94.9 %), Glaciecola nitratireducens KCTC 12276T (94.7 %) and Paraglaciecola psychrophila CGMCC 1.6130T (94.7 %). 16S rRNA gene sequence similarities among strain THG-3.7T and other species were lower than 94.7 %. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The quinone system was composed of Q-8. The major fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain THG-3.7T was 47.9 mol%. On the basis of the data presented, strain THG-3.7T represents a novel species of the genus Glaciecola, for which the name Glaciecola amylolytica sp. nov. is proposed. The type strain is THG-3.7T (=KACC 19478T=CCTCC AB 2017258T).
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Affiliation(s)
- Yong-Kun Xiao
- College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Zheng-Fei Yan
- College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Yoosung Kim
- College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Hyun-Myung Lee
- College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Huan Trinh
- College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Jung-Eun Yang
- SDBiotechnologies Co., Ltd., Seoul Hightech Venture Center, 29, Gonghang-daero 61-gil, Gangseo-gu, Seoul 07563, Republic of Korea
| | - Kyung-Hwa Won
- SDBiotechnologies Co., Ltd., Seoul Hightech Venture Center, 29, Gonghang-daero 61-gil, Gangseo-gu, Seoul 07563, Republic of Korea
| | - Tae-Hoo Yi
- College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Moochang Kook
- Department of Food Nutrition, Baewha Women's University, Seoul 03039, Republic of Korea
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19
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Liu X, Lai Q, Du Y, Zhang X, Liu Z, Sun F, Shao Z. Neptunicella marina gen. nov., sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2018. [PMID: 29533174 DOI: 10.1099/ijsem.0.002660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, short rod-shaped bacterium with a single polar flagellum, designated strain S27-2T, was isolated from surface seawater from the Indian Ocean. Growth was observed in 0-12.0 % (w/v) NaCl with an optimum of 0.5-2.0 % (w/v) NaCl, pH 6.0-9.0 with an optimum of pH 7.0, and growth temperature of 10-41 °C with an optimum of 25-37 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S27-2T belonged to the family Alteromonadaceae and formed a distinct lineage with the type strain of Pseudobowmanella zhangzhouensis. Levels of 16S rRNA gene sequence similarity between strain S27-2T and members of related genera included in the trees ranged from 86.7 to 93.8 %. Strain S27-2T contained Q-8 as the predominant ubiquinone. The principal fatty acids (>10 %) were C16 : 0 (22.1 %), C16 : 1ω7c/ω6c (22.7 %) and C18 : 1ω7c/ω6c (20.1 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and two unknown lipids. The G+C content of strain S27-2T was 43.7 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, strain S27-2T should be classified as a novel species in a new genus within the family Alteromonadaceae, for which the name Neptunicella marina gen. nov., sp. nov. is proposed, with the type strain S27-2T (= KCTC52335T=MCCC 1A02149T).
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Affiliation(s)
- Xiupian Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China.,Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen 361005, PR China
| | - Qiliang Lai
- Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
| | - Yaping Du
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen 361005, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
| | - Xiaorong Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen 361005, PR China
| | - Zhen Liu
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China.,Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China.,Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zongze Shao
- Fujian Collaborative Innovation Center of Marine Biological Resources, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
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20
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Pu W, Cui C, Guo C, Wu ZL. Characterization of two styrene monooxygenases from marine microbes. Enzyme Microb Technol 2018; 112:29-34. [PMID: 29499777 DOI: 10.1016/j.enzmictec.2018.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/29/2018] [Accepted: 02/01/2018] [Indexed: 12/16/2022]
Abstract
Styrene monooxygenases (SMOs) are highly stereoselective enzymes that catalyze the formation of chiral epoxides as versatile building blocks. To expand the enzyme toolbox, two bacterial SMOs were identified from the genome of marine microbes Paraglaciecola agarilytica NO2 and Marinobacterium litorale DSM 23545, and heterologously expressed in Escherichia coli in soluble form. Both of the resulting whole-cell biocatalysts exhibited maximal activity at 30 °C and pH 8.0. They catalyzed the sulfoxidation reactions, and the epoxidation of both conjugated and unconjugated styrene derivatives with up to >99%ee. MlSMO displayed higher activity toward most substrates tested. Compared to an established SMO from Pseudomonas species (PsSMO), MlSMO achieved 3.0-, 3.4- and 2.6-fold conversions for substrates styrene, cinnamyl alcohol and 4-vinyl-2, 3-dihydrobenzofuran, respectively.
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Affiliation(s)
- Wei Pu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Can Cui
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Guo
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Zhong-Liu Wu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
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21
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Park S, Choi SJ, Choi J, Yoon JH. Paraglaciecola aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2017; 67:4754-4759. [DOI: 10.1099/ijsem.0.002370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Su Jung Choi
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jeehyun Choi
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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22
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Bech PK, Schultz-Johansen M, Glaring MA, Barbeyron T, Czjzek M, Stougaard P. Paraglaciecola hydrolytica sp. nov., a bacterium with hydrolytic activity against multiple seaweed-derived polysaccharides. Int J Syst Evol Microbiol 2017; 67:2242-2247. [PMID: 28671532 DOI: 10.1099/ijsem.0.001933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, S66T, was isolated from eelgrass collected on the coastline of Zealand, Denmark. Polyphasic analyses involving phenotypic, phylogenetic and genomic methods were used to characterize strain S66T. The strain was Gram-reaction-negative, rod-shaped, aerobic, and displayed growth at 10-25 °C (optimum 20-25 °C) and at pH 7-9 (optimum pH 7.5). Furthermore, strain S66T grew on seaweed polysaccharides agar, agarose, porphyran, κ-carrageenan, alginate and laminarin as sole carbon sources. Major fatty acids were C16 : 0, C16 : 1ω7c and C18 : 1ω7c. The respiratory quinone was determined to be Q-8, and major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was determined to be 42.2 mol%. Phylogenetic analyses based on the 16S rRNA gene and GyrB sequence comparisons showed that the bacterium was affiliated with the genus Paraglaciecola within the family Alteromonadaceae of the class Gammaproteobacteria. The percentage similarity between the 16S rRNA gene and GyrB sequences of strain S66T and other members of the genus Paraglaciecola were 94-95 % and 84-85 %, respectively. Based on the genome sequence of S66T, the average nucleotide identity (ANI) between strain S66T and other members of the genus Paraglaciecola was 77-80 %, and DNA-DNA hybridization prediction showed values of less than 24 % relatedness, respectively, between S66T and other species of the genus Paraglaciecola. The phenotypic, phylogenetic and genomic analyses support the hypothesis that strain S66T represents a novel species of the genus Paraglaciecola, for which the name Paraglaciecola hydrolytica sp. nov. is proposed. The type strain is S66T (=LMG 29457T=NCIMB 15060T=DSM 102834T).
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Affiliation(s)
- Pernille Kjersgaard Bech
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Mikkel Schultz-Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Mikkel Andreas Glaring
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Tristan Barbeyron
- UPMC University Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France
| | - Mirjam Czjzek
- UPMC University Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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23
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Foran E, Buravenkov V, Kopel M, Mizrahi N, Shoshani S, Helbert W, Banin E. Functional characterization of a novel “ulvan utilization loci” found in Alteromonas sp. LOR genome. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.04.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Sisinthy S, Chakraborty D, Adicherla H, Gundlapally SR. Emended description of the family Chromatiaceae, phylogenetic analyses of the genera Alishewanella, Rheinheimera and Arsukibacterium, transfer of Rheinheimera longhuensis LH2-2 T to the genus Alishewanella and description of Alishewanella alkalitolerans sp. nov. from Lonar Lake, India. Antonie van Leeuwenhoek 2017; 110:1227-1241. [PMID: 28612170 DOI: 10.1007/s10482-017-0896-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/31/2017] [Indexed: 11/30/2022]
Abstract
Phylogenetic analyses were performed for members of the family Chromatiaceae, signature nucleotides deduced and the genus Alishewanella transferred to Chromatiaceae. Phylogenetic analyses were executed for the genera Alishewanella, Arsukibacterium and Rheinheimera and the genus Rheinheimera is proposed to be split, with the creation of the Pararheinheimera gen. nov. Furthermore, the species Rheinheimera longhuensis, is transferred to the genus Alishewanella as Alishewanella longhuensis comb. nov. Besides, the genera Alishewanella and Rheinheimera are also emended. Strain LNK-7.1T was isolated from a water sample from the Lonar Lake, India. Cells were Gram-negative, motile rods, positive for catalase, oxidase, phosphatase, contained C16:0, C17:1ω8c, summed feature3 (C16:1ω6c and/or C16:1ω7c) and summed feature 8 (C18:1ω7c) as major fatty acids, PE and PG as the major lipids and Q-8 as the sole respiratory quinone. Phylogenetic analyses using NJ, ME, ML and Maximum parsimony, based on 16S rRNA gene sequences, identified Alishewanella tabrizica RCRI4T as the closely related species of strain LNK-7.1T with a 16S rRNA gene sequence similarity of 98.13%. The DNA-DNA similarity between LNK-7.1T and the closely related species (A. tabrizica) was only 12.0% and, therefore, strain LNK-7.1T was identified as a novel species of the genus Alishewanella with the proposed name Alishewanella alkalitolerans sp. nov. In addition phenotypic characteristics confirmed the species status to strain LNK-7.1T. The type strain of A. alkalitolerans is LNK-7.1T (LMG 29592T = KCTC 52279T), isolated from a water sample collected from the Lonar lake, India.
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Affiliation(s)
- Shivaji Sisinthy
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Dwaipayan Chakraborty
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Harikrishna Adicherla
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Sathyanarayana Reddy Gundlapally
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
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25
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von Scheibner M, Sommer U, Jürgens K. Tight Coupling of Glaciecola spp. and Diatoms during Cold-Water Phytoplankton Spring Blooms. Front Microbiol 2017; 8:27. [PMID: 28154558 PMCID: PMC5243806 DOI: 10.3389/fmicb.2017.00027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/05/2017] [Indexed: 11/15/2022] Open
Abstract
Early spring phytoplankton blooms can occur at very low water temperatures but they are often decoupled from bacterial growth, which is assumed to be often temperature controlled. In a previous mesocosm study with Baltic Sea plankton communities, an early diatom bloom was associated with a high relative abundance of Glaciecola sequences (Gammaproteobacteria), at both low (2°C) and elevated (8°C) temperatures, suggesting an important role for this genus in phytoplankton-bacteria coupling. In this study, the temperature-dependent dynamics of free-living Glaciecola spp. during the bloom were analyzed by catalyzed reporter deposition fluorescence in situ hybridization using a newly developed probe. The analysis revealed the appearance of Glaciecola spp. in this and in previous spring mesocosm experiments as the dominating bacterial clade during diatom blooms, with a close coupling between the population dynamics of Glaciecola and phytoplankton development. Although elevated temperature resulted in a higher abundance and a higher net growth rate of Glaciecola spp. (Q10 ∼ 2.2), their growth was, in contrast to that of the bulk bacterial assemblages, not suppressed at 2°C and showed a similar pattern at 8°C. Independent of temperature, the highest abundance of Glaciecola spp. (24.0 ± 10.0% of total cell number) occurred during the peak of the phytoplankton bloom. Together with the slightly larger cell size of Glaciecola, this resulted in a ∼30% contribution of Glaciecola to total bacterial biomass. Overall, the results of this and previous studies suggest that Glaciecola has an ecological niche during early diatom blooms at low temperatures, when it becomes a dominant consumer of phytoplankton-derived dissolved organic matter.
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Affiliation(s)
| | | | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research WarnemündeRostock, Germany
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26
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Sheu DS, Sheu SY, Lin KR, Chen YLL, Chen WM. Planctobacterium marinum gen. nov., sp. nov., a new member of the family Alteromonadaceae isolated from seawater. Int J Syst Evol Microbiol 2016; 67:974-980. [PMID: 27959781 DOI: 10.1099/ijsem.0.001726] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated K7T was isolated from the South China Sea and characterized using a polyphasic taxonomic approach. Cells of strain K7T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore forming rods surrounded by a thick capsule and forming yellow colonies. Growth occurred at 4-35 °C (optimum, 25-30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and with 0.5-10 % (w/v) NaCl [optimum, 1-4 % (w/v)]. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8 and the DNA G+C content was 46.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, one uncharacterized phospholipid, two uncharacterized aminophospholipids and five uncharacterized lipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain K7T formed a distinct lineage with respect to closely related genera in the family Alteromonadaceae. Strain K7T was most closely related to Aestuariibacter, Aliiglaciecola, Paraglaciecola and Glaciecola, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 95 %. On the basis of the genotypic and phenotypic data, strain K7T represents a novel species of a new genus of the family Alteromonadaceae, for which the name Planctobacterium marinum gen. nov., sp. nov. is proposed. The type strain of Planctobacterium marinum is K7T (=BCRC 80901T=LMG 28835T=KCTC 42657T).
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Affiliation(s)
- Der-Shyan Sheu
- Department of Marine Biotechnology, National KaohsiungMarine University, No. 142, Hai-ChuanRd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National KaohsiungMarine University, No. 142, Hai-ChuanRd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC
| | - Kai-Rou Lin
- Laboratoryof Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC
| | - Yuh-Ling Lee Chen
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung 80424, Taiwan ROC
| | - Wen-Ming Chen
- Laboratoryof Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC
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27
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Hauptmann AL, Markussen TN, Stibal M, Olsen NS, Elberling B, Bælum J, Sicheritz-Pontén T, Jacobsen CS. Upstream Freshwater and Terrestrial Sources Are Differentially Reflected in the Bacterial Community Structure along a Small Arctic River and Its Estuary. Front Microbiol 2016; 7:1474. [PMID: 27708629 PMCID: PMC5030300 DOI: 10.3389/fmicb.2016.01474] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/05/2016] [Indexed: 12/02/2022] Open
Abstract
Glacier melting and altered precipitation patterns influence Arctic freshwater and coastal ecosystems. Arctic rivers are central to Arctic water ecosystems by linking glacier meltwaters and precipitation with the ocean through transport of particulate matter and microorganisms. However, the impact of different water sources on the microbial communities in Arctic rivers and estuaries remains unknown. In this study we used 16S rRNA gene amplicon sequencing to assess a small river and its estuary on the Disko Island, West Greenland (69°N). Samples were taken in August when there is maximum precipitation and temperatures are high in the Disko Bay area. We describe the bacterial community through a river into the estuary, including communities originating in a glacier and a proglacial lake. Our results show that water from the glacier and lake transports distinct communities into the river in terms of diversity and community composition. Bacteria of terrestrial origin were among the dominating OTUs in the main river, while the glacier and lake supplied the river with water containing fewer terrestrial organisms. Also, more psychrophilic taxa were found in the community supplied by the lake. At the river mouth, the presence of dominant bacterial taxa from the lake and glacier was unnoticeable, but these taxa increased their abundances again further into the estuary. On average 23% of the estuary community consisted of indicator OTUs from different sites along the river. Environmental variables showed only weak correlations with community composition, suggesting that hydrology largely influences the observed patterns.
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Affiliation(s)
- Aviaja L Hauptmann
- Center for Biosustainability, Technical University of DenmarkHoersholm, Denmark; DTU Bioinformatics, Technical University of DenmarkKgs. Lyngby, Denmark; Center for Permafrost, University of CopenhagenCopenhagen, Denmark
| | - Thor N Markussen
- Center for Permafrost, University of Copenhagen Copenhagen, Denmark
| | - Marek Stibal
- Center for Permafrost, University of CopenhagenCopenhagen, Denmark; Department of Ecology, Faculty of Science, Charles UniversityPrague, Czech Republic
| | - Nikoline S Olsen
- Center for Permafrost, University of Copenhagen Copenhagen, Denmark
| | - Bo Elberling
- Center for Permafrost, University of Copenhagen Copenhagen, Denmark
| | | | | | - Carsten S Jacobsen
- Center for Permafrost, University of CopenhagenCopenhagen, Denmark; Department of Environmental Science, Aarhus UniversityRoskilde, Denmark
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Mantri S, Chinthalagiri MR, Gundlapally SR. Description of Hydrogenophaga laconesensis sp. nov. isolated from tube well water. Arch Microbiol 2016; 198:637-44. [DOI: 10.1007/s00203-016-1224-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/30/2016] [Accepted: 04/11/2016] [Indexed: 11/28/2022]
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Draft Genome Sequence of a Novel Marine Bacterium, Paraglaciecola sp. Strain S66, with Hydrolytic Activity against Seaweed Polysaccharides. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00304-16. [PMID: 27103729 PMCID: PMC4841144 DOI: 10.1128/genomea.00304-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A novel agarolytic gammaproteobacterium, Paraglaciecola sp. S66, was isolated from marine samples of eelgrass (Zostera sp.) and sequenced. The draft genome contains a large number of enzyme-encoding genes with predicted function against several complex polysaccharides found in the cell walls of algae.
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30
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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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31
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Jin HM, Jeong HI, Jeon CO. Aliiglaciecola aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Aliiglaciecola Jean et al. 2013. Int J Syst Evol Microbiol 2015; 65:1550-1555. [DOI: 10.1099/ijs.0.000133] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative heterotrophic bacterium, designated GSD6T, capable of growth on aliphatic hydrocarbons as a sole carbon and energy source, was isolated from sea-tidal flat sediment of the Yellow Sea, South Korea. Cells were facultatively aerobic, catalase- and oxidase-positive, motile rods with a single polar flagellum. Growth of strain GSD6T was observed at 4–37 °C (optimum 30 °C), at pH 5.5–9.0 (optimum pH 6.5–7.5) and in the presence of 1–9 % (w/v) NaCl (optimum 2 %). Strain GSD6T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C17 : 0 10-methyl and C17 : 1ω8c as the major fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSD6T formed a phylogenetic lineage with members of the genus
Aliiglaciecola
. Strain GSD6T was most closely related to
Aliiglaciecola lipolytica
E3T with a 16S rRNA gene sequence similarity of 97.4 %, but their DNA–DNA hybridization value was 39.1±7.1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain GSD6T represents a novel species of the genus
Aliiglaciecola
, for which the name Aliiglaciecola aliphaticivorans sp. nov. is proposed. The type strain is GSD6T ( = KACC 18129T = JCM 30133T). An emended description of the genus
Aliiglaciecola
is also proposed.
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Affiliation(s)
- Hyun Mi Jin
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Hye Im Jeong
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
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Description of Thalassospira lohafexi sp. nov., isolated from Southern Ocean, Antarctica. Arch Microbiol 2015; 197:627-37. [DOI: 10.1007/s00203-015-1092-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
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