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Yadav S, Koenen M, Bale NJ, Reitsma W, Engelmann JC, Stefanova K, Damsté JSS, Villanueva L. Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria. MICROBIOME 2024; 12:98. [PMID: 38797849 PMCID: PMC11129491 DOI: 10.1186/s40168-024-01816-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/15/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea. RESULTS We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1T and A2), Spirochaetota (strains M1T, M2, and S2), Bacteroidota (strains B1T, B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea. CONCLUSIONS This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract.
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Affiliation(s)
- Subhash Yadav
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Wietse Reitsma
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Julia C Engelmann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Kremena Stefanova
- Institute of Oceanology "Fridtjof Nansen", Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands.
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands.
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2
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Raut Y, Barr CR, Paris ER, Kapili BJ, Dekas AE, Capone DG. Autochthonous carbon loading of macroalgae stimulates benthic biological nitrogen fixation rates in shallow coastal marine sediments. Front Microbiol 2024; 14:1312843. [PMID: 38249476 PMCID: PMC10796445 DOI: 10.3389/fmicb.2023.1312843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
Macroalgae, commonly known as seaweed, are foundational species in coastal ecosystems and contribute significantly to coastal primary production globally. However, the impact of macroalgal decomposition on benthic biological nitrogen fixation (BNF) after deposition to the seafloor remains largely unexplored. In this study, we measure BNF rates at three different sites at the Big Fisherman's Cove on Santa Catalina Island, CA, USA, which is representative of globally distributed rocky bottom macroalgal habitats. Unamended BNF rates varied among sites (0.001-0.05 nmol N g-1 h -1) and were generally within the lower end of previously reported ranges. We hypothesized that the differences in BNF between sites were linked to the availability of organic matter. Indeed, additions of glucose, a labile carbon source, resulted in 2-3 orders of magnitude stimulation of BNF rates in bottle incubations of sediment from all sites. To assess the impact of complex, autochthonous organic matter, we simulated macroalgal deposition and remineralization with additions of brown (i.e., Macrocystis pyrifera and Dictyopteris), green (i.e., Codium fragile), and red (i.e., Asparagopsis taxiformis) macroalgae. While brown and green macroalgal amendments resulted in 53- to 520-fold stimulation of BNF rates-comparable to the labile carbon addition-red alga was found to significantly inhibit BNF rates. Finally, we employed nifH sequencing to characterize the diazotrophic community associated with macroalgal decomposition. We observed a distinct community shift in potential diazotrophs from primarily Gammaproteobacteria in the early stages of remineralization to a community dominated by Deltaproteobacteria (e.g., sulfate reducers), Bacteroidia, and Spirochaeta toward the latter phase of decomposition of brown, green, and red macroalgae. Notably, the nifH-containing community associated with red macroalgal detritus was distinct from that of brown and green macroalgae. Our study suggests coastal benthic diazotrophs are limited by organic carbon and demonstrates a significant and phylum-specific effect of macroalgal loading on benthic microbial communities.
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Affiliation(s)
- Yubin Raut
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Casey R. Barr
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Emily R. Paris
- Earth System Science, Stanford University, Stanford, CA, United States
| | - Bennett J. Kapili
- Earth System Science, Stanford University, Stanford, CA, United States
| | - Anne E. Dekas
- Earth System Science, Stanford University, Stanford, CA, United States
| | - Douglas G. Capone
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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3
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Chen M, Zhang YQ, Krumholz LR, Zhao LY, Yan ZS, Yang YJ, Li ZH, Hayat F, Chen HB, Huang R. Black blooms-induced adaptive responses of sulfate reduction bacteria in a shallow freshwater lake. ENVIRONMENTAL RESEARCH 2022; 209:112732. [PMID: 35077715 DOI: 10.1016/j.envres.2022.112732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Decomposing cyanobacterial bloom-induced black blooms been seen as an issue in the management of freshwater ecosystems, but its effect on sulfate-reducing bacteria (SRB) in shallow freshwater lakes is not clear. The objective of this study is to present an in-depth investigation of black bloom effects on the activities and composition of SRB, as well as the interactions between SRB and other bacteria. Water and surface sediments samples were collected from a shallow freshwater lake during black and non-black blooms. Sulfate reduction rates (SRRs) in the water column were determined from the linear regression of sulfate depletion with time. Quantitative real-time polymerase chain reactions (qPCRs), targeting the dsrA gene and Illumina sequencing of 16S rDNA, were used to estimate the SRB population and SRB community structures, respectively. Our data indicate that although a higher abundance of SRB was responsible for the higher SRR in the bottom water (34.09 ± 2.37 nmol mL-1 day-1) than in the surface water (14.57 ± 2.91 nmol mL-1 day-1) during black blooms, cell-specific sulfate reduction rates (csSRRs) in the distinct water layers were not significantly different (P = 0.95), with the value of approximately 0.017 fmol cell-1 day-1. Additionally, Desulfomicrobium and Desulfovibrio were the two main genera of SRB in the water column during black bloom season, while Desulfobulbus, Desulfobacca and Desulfatiglans genera were identified in the sediments of both the black and non-black blooms in genera pools. Each SRB genus preferentially associated with bacteria for specific functions in the bacterial co-occurrence network, regardless of whether black booms occurred or not. These results extend our knowledge on the importance of SRB during black blooms and the adaptation of SRB to environmental changes in freshwater lakes.
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Affiliation(s)
- Mo Chen
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China.
| | - Ya-Qing Zhang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China
| | - Lee R Krumholz
- Department of Botany & Microbiology, University of Oklahoma, Norman, OK, USA
| | - Li-Ya Zhao
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Zai-Sheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yu-Jing Yang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Zhao-Hua Li
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Faisal Hayat
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China
| | - Hong-Bing Chen
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Ran Huang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China
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Nguyen TT, Paulsen JE, Landfald B. Seafloor deposition of water-based drill cuttings generates distinctive and lengthy sediment bacterial community changes. MARINE POLLUTION BULLETIN 2021; 164:111987. [PMID: 33515825 DOI: 10.1016/j.marpolbul.2021.111987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
The spatial extent and persistence of bacterial change caused by deposition of water-based drill cuttings on the seafloor were explored by a community-wide approach. Ten centimeter sediment cores were sampled along transects extending from ≤15 m to 250 m from three nearby drilling sites in the southern Barents Sea. Eight months, 8 years and 15 years, respectively, had passed since the completion of the drillings. At locations heavily affected by drill cuttings, the two most recent sites showed distinct, corresponding deviances from native Barents Sea bacterial community profiles. Otherwise marginal groups, including Mollicutes and Clostridia, showed significant increases in relative abundance. Beyond 100 m from the boreholes the microbiotas appeared undisturbed, as they did at any distance from the 15-years old borehole. The extent of the biological distortion, as indicated by the present microbial study, agreed with previously published macrofaunal surveys at the same drilling sites.
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Affiliation(s)
- Tan T Nguyen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, PO Box 6050 Langnes, 9037 Tromsø, Norway.
| | | | - Bjarne Landfald
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, PO Box 6050 Langnes, 9037 Tromsø, Norway.
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Dubinina G, Leshcheva N, Mikheeva N, Spring S, Neumann-Schaal M, Shcherbakova V, Grabovich M. Description of Oceanispirochaeta crateris sp. nov. and reclassification of Spirochaeta perfilievii as Thiospirochaeta perfilievii gen. nov., comb. nov. Int J Syst Evol Microbiol 2020; 70:6373-6380. [DOI: 10.1099/ijsem.0.004544] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A novel obligately anaerobic spirochete strain K2T was isolated from bottom marine sediments at Crater Bay of Yankicha Island (Kuril Islands, Russia). Strain K2T had helical shape and Gram-negatively stained. The optimal growth conditions were as follows: the optimum temperature was 28–30 °C with range 5–34 °C; optimal pH at 7.0–7.5 with range of 6.8–8.5; NaCl optimum at 3–3.5 % (w/v) and range of 1–7 % (w/v). Strain K2T was catalase- and oxidase-negative. Glucose fermentation products were acetate, lactate, ethanol, CO2, H2. The major fatty acids were C14 : 0, iso-C13 : 0, iso-C15:0, C14 : 0 DMA, iso-C15 : 0 DMA. The G+C content of genomic DNA was 43.2 mol%. Phylogenetic analyses of 16S rRNA genes showed that strain K2T belonged to the genus
Oceanispirochaeta
of the family
Spirochaetaceae
. The 16S rRNA gene sequence similarity of strain K2T and
O. litoralis
DSM 2029T and
O. sediminicola
DSM 104770T was 96 and 94 %, respectively. Based on the results of our study, we propose the name Oceanispirochaeta crateris sp. nov.; type strain K2T (=DSM 16308T=VKM B-3266T). Also, the taxonomic status of Spirochaeta perfilevii was revised: 16S rRNA genes sequence showed less than 89 % similarity to nearest phylogenetic neighbours. Therefore, we proposed to separate this species into a novel genus Thiospirochaeta - T. perfilievii gen. nov., comb. nov.
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Affiliation(s)
- Galina Dubinina
- Federal State Institution Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Prospect 60-letiya Oktyabrya, 7/2, 117312 Moscow, Russia
| | - Natalia Leshcheva
- Federal State Institution Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Prospect 60-letiya Oktyabrya, 7/2, 117312 Moscow, Russia
| | - Natalia Mikheeva
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, Voronezh 394018, Russia
| | - Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Junior Research Group Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Viktoria Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, the Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, pr. Nauki 5, Pushchino Moscow region, 142290, Russia
| | - Margarita Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, Voronezh 394018, Russia
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6
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Yadav S, Villanueva L, Bale N, Koenen M, Hopmans EC, Damsté JSS. Physiological, chemotaxonomic and genomic characterization of two novel piezotolerant bacteria of the family Marinifilaceae isolated from sulfidic waters of the Black Sea. Syst Appl Microbiol 2020; 43:126122. [PMID: 32847788 DOI: 10.1016/j.syapm.2020.126122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 11/17/2022]
Abstract
Diversity analyses of microbial enrichments obtained from deep sulfidic water (2000 m) collected from the Black Sea indicated the presence of eleven novel putative lineages of bacteria affiliated to the family Marinifilaceae of the phylum Bacteroidetes. Pure cultures were obtained for four strains (i.e. M1PT, M3P, A4T and 44) of this family, which could be grouped into two different clades based on their 16S rRNA gene sequences. All four strains were Gram-negative, rod-shaped and facultative anaerobic bacteria. The genomes of all strains were sequenced and physiological analyses were performed. All strains utilized a wide range of carbon sources, which was supported by the presence of the pathways involved in carbon utilization encoded by their genomes. The strains were able to grow at elevated hydrostatic pressure (up to 50 MPa), which coincided with increased production of unsaturated and branched fatty acids, and a decrease in hydroxy fatty acids. Intact polar lipid analysis of all four strains showed the production of ornithine lipids, phosphatidylethanolamines and capnine lipids as major intact polar lipids (IPLs). Genes involved in hopanoid biosynthesis were also identified. However, bacteriohopanepolyols (BHPs) were not detected in the strains. Based on distinct physiological, chemotaxonomic, genotypic and phylogenetic differences compared to other members of the genera Ancylomarina and Labilibaculum, it was concluded that strains M1PT and A4T represented two novel species for which the names Ancylomarina euxinus sp. nov. and Labilibaculum euxinus sp. nov., respectively, are proposed.
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Affiliation(s)
- Subhash Yadav
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands.
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Nicole Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands
| | - Michel Koenen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands
| | - Ellen C Hopmans
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology, Biogeochemistry, Utrecht University, P.O. Box 59, 1797AB Den Burg, Texel, The Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
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7
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Effects of Italian Ryegrass (IRG) Supplementation on Animal Performance, Gut Microbial Compositions and Odor Emission from Manure in Growing Pigs. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10050647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fermentable carbohydrate (FC) is a promising material to reduce odor emission from pig manure. This study was conducted to investigate the impact of diets containing Italian ryegrass (IRG), as a FC, on animal performance, odorous chemical and bacterial composition of manure. Pigs were weighed and fed diets containing various levels of IRG powder (0%, 0.5%, 1.0% and 1.5%) for 28 days. At the end of the trial, manure was collected to analyze the chemical composition, odorous compounds and bacterial community structure. As dietary IRG levels increased, concentrations of phenols and indoles were decreased by 12% and 37% compared with control, respectively, without changes in growth performance. IRG treatment increased the relative abundances of genera belong to the family Lachnospiraceae, Ruminococcaceae, Veillonellaceae, Peptostreptococcaceae and Lactobacillaceae, in order Clostridiales of phylum Firmicutes, but decreased the relative abundances of genus Sphaerochaeta in phylum Spirochaetes and genus AB243818_g of family Porphyromonadaceae in phylum Bacteroidetes when compared with control. Results from the current study demonstrate that IRG supplemented diets had a beneficial effect of reducing the odorous compounds in manure, possibly by altering the bacterial community structure towards predominantly carbohydrate utilizing microorganisms in the large intestine.
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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9
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Brabec JL, Wright J, Ly T, Wong HT, McClimans CJ, Tokarev V, Lamendella R, Sherchand S, Shrestha D, Uprety S, Dangol B, Tandukar S, Sherchand JB, Sherchan SP. Arsenic disturbs the gut microbiome of individuals in a disadvantaged community in Nepal. Heliyon 2020; 6:e03313. [PMID: 32051876 PMCID: PMC7002857 DOI: 10.1016/j.heliyon.2020.e03313] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 12/18/2019] [Accepted: 01/24/2020] [Indexed: 01/15/2023] Open
Abstract
Arsenic is ubiquitous in nature, highly toxic, and is particularly abundant in Southern Asia. While many studies have focused on areas like Bangladesh and West Bengal, India, disadvantaged regions within Nepal have also suffered from arsenic contamination levels, with wells and other water sources possessing arsenic contamination over the recommended WHO and EPA limit of 10 μg/L, some wells reporting levels as high as 500 μg/L. Despite the region's pronounced arsenic concentrations within community water sources, few investigations have been conducted to understand the impact of arsenic contamination on host gut microbiota health. This study aims to examine differential arsenic exposure on the gut microbiome structure within two disadvantaged communities in southern Nepal. Fecal samples (n = 42) were collected from members of the Mahuawa (n = 20) and Ghanashyampur (n = 22) communities in southern Nepal. The 16S rRNA gene was amplified from fecal samples using Illumina-tag PCR and subject to high-throughput sequencing to generate the bacterial community structure of each sample. Bioinformatics analysis and multivariate statistics were conducted to identify if specific fecal bacterial assemblages and predicted functions were correlated with urine arsenic concentration. Our results revealed unique assemblages of arsenic volatilizing and pathogenic bacteria positively correlated with increased arsenic concentration in individuals within the two respective communities. Additionally, we observed that commensal gut bacteria negatively correlated with increased arsenic concentration in the two respective communities. Our study has revealed that arsenic poses a broader human health risk than was previously known. It is influential in shaping the gut microbiome through its enrichment of arsenic volatilizing and pathogenic bacteria and subsequent depletion of gut commensals. This aspect of arsenic has the potential to debilitate healthy humans by contributing to disorders like heart and liver cancers and diabetes, and it has already been shown to contribute to serious diseases and disorders, including skin lesions, gangrene and several types of skin, renal, lung, and liver cancers in disadvantaged areas of the world like Nepal.
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Affiliation(s)
- Jeffrey L Brabec
- Department of Biology, Juniata College, Huntingdon, PA, 16652, USA
| | - Justin Wright
- Department of Biology, Juniata College, Huntingdon, PA, 16652, USA
| | - Truc Ly
- Department of Biology, Juniata College, Huntingdon, PA, 16652, USA
| | - Hoi Tong Wong
- Department of Biology, Juniata College, Huntingdon, PA, 16652, USA
| | | | - Vasily Tokarev
- Department of Biology, Juniata College, Huntingdon, PA, 16652, USA
| | | | - Shardulendra Sherchand
- Department of Microbiology, Immunology & Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, 70112, USA
| | | | - Sital Uprety
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Bipin Dangol
- Environment and Public Health Organization, Kathmandu, Nepal
| | - Sarmila Tandukar
- Public Health Research Laboratory, Tribhuvan University Teaching Hospital, 1524, Kathmandu, Nepal
| | - Jeevan B Sherchand
- Public Health Research Laboratory, Tribhuvan University Teaching Hospital, 1524, Kathmandu, Nepal
| | - Samendra P Sherchan
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, 70112, USA
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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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Shivani Y, Subhash Y, Sasikala C, Ramana CV. Characterisation of a newly isolated member of a candidatus lineage, Marispirochaeta aestuarii gen. nov., sp. nov. Int J Syst Evol Microbiol 2017; 67:3929-3936. [DOI: 10.1099/ijsem.0.002224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. Shivani
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Y. Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
- Present address: Department of Life Science, College of Natural Science, Kyonggi University, 94-6 Iui- 6 dong Yeongtong-gu, Suwon 443-760, Republic of Korea
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500 085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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Subhash Y, Lee SS. Description of Oceanispirochaeta sediminicola gen. nov., sp. nov., an obligately anaerobic bacterium isolated from coastal marine sediments, and reclassification of Spirochaeta litoralis as Oceanispirochaeta litoralis comb. nov. Int J Syst Evol Microbiol 2017; 67:3403-3409. [DOI: 10.1099/ijsem.0.002130] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
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13
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Shivani Y, Subhash Y, Sasikala C, Ramana CV. Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp. Int J Syst Evol Microbiol 2017; 67:87-93. [PMID: 27902290 DOI: 10.1099/ijsem.0.001574] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An antibiotic-producing, obligate anaerobic, Gram-stain-negative, catalase- and oxidase-negative strain (JC271T) was isolated from a marine habitat and identified, based on 16S rRNA gene sequence analysis, as a novel member of the family Desulfovibrionaceae. The closest phylogenetic relatives of strain JC271T were found to be Desulfovibrio marinisediminis C/L2T (99.2 %), Desulfovibrio acrylicus W218T (98.7 %), Desulfovibrio desulfuricans subsp. aestuarii (98.6 %), Desulfovibrio oceani subsp. oceani (98.0 %), Desulfovibrio oceani subsp. galatae (98.0 %) and other members of the genus Desulfovibrio (≤91.9 %). To resolve its full taxonomic position, the genomic sequence of strain JC271T was compared to available genomes of the most closely related phylogenetic members. Average Nucleotide Identity scores and DNA-DNA hybridization values confirmed that strain JC271T represents a novel genomic species. Iso-C17 : 0, iso-C17 : 1ω9c, and iso-C15 : 0 were found to be the major (comprising >10 % of the total present) fatty acids of strain JC271T. Phosphatidylglycerol, phosphatidylethanolamine and unidentified lipids (L1-8) were the polar lipids identified. The G+C content of strain JC271T was 46.2 mol%. Integrated genomic and phenotypic data supported the classification of strain JC271T as a representative of a novel genus, for which the name Halodesulfovibrio spirochaetisodalis gen. nov., sp. nov. is proposed. The type strain is JC271T (=KCTC 15474T=DSM 100016T). It is also proposed that Desulfovibrio acrylicus W218T is the latter heterotypic synonym of Desulfovibrio desulfuricans subsp. aestuarii Sylt 3T. Desulfovibrio desulfuricans subsp. aestuarii Sylt 3T should also be elevated as Halodesulfovibrio aestuarii comb. nov. and Desulfovibrio marinisediminisreclassified as Halodesulfovibrio marinisediminis comb. nov. Desulfovibrio oceani subsp. oceanishould be reclassified as Halodesulfovibrio oceani subsp. oceani comb. nov. and Desulfovibrio oceani subsp. galateae as Halodesulfovibrio oceani subsp. galateae comb. nov.
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Affiliation(s)
- Y Shivani
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Y Subhash
- Present address: Department of Life Science, College of Natural Science, Kyonggi University, 94-6 Iui- 6 dong Yeongtong-gu, Suwon 443-760, Republic of Korea.,Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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Shivani Y, Subhash Y, Sasikala C, Ramana CV. Description of 'Candidatus Marispirochaeta associata' and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica comb. nov. Int J Syst Evol Microbiol 2016; 66:5485-5492. [PMID: 27902269 DOI: 10.1099/ijsem.0.001545] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain JC231 was isolated from a coastal saline habitat of Gujarat and was identified based on 16S rRNA gene sequence analysis as a member belonging to the genus Spirochaeta and showed highest sequence similarity (<91 %) with Spirochaeta bajacaliforniensis DSM 16054T and other members of the family Spirochaetaceae. Intensive attempts to culture strain JC231 in pure culture have failed and were associated with only one species of a Desulfovibrio. However, presence of fosmidomycin inhibited the growth of Desulfovibrio sp. and strain JC231 was characterized in its presence. Strain JC231 was an obligate anaerobe, helical shaped and Gram-stain-negative with catalase and oxidase negative. Draft genome sequence analysis of strain JC231 indicated the full complement of genes for both 2-C-methyl-d-erythritol 4-phosphate and 3-hydroxy-3-methylglutaryl-CoA pathways of terpenogenesis. C14 : 0, iso-C15 : 0, C16 : 0, iso-C15 : 1H/C13 : 0 3OH and iso-C14 : 0 are the major (>5 %) fatty acids. Strain JC231 contains diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and six unidentified lipids (L1-L6). G+C content of strain JC231 was 55.7 mol%. Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC231 as a representative of a new genus and species in the family Spirochaetaceae, for which the name 'CandidatusMarispirochaeta associata' is proposed. Strain JC231 is deposited as a defined co-culture with Desulfovibrio sp. JC271 to DSMZ (DSM 29857) and KCTC (KCTC 15472). Based on phenotypic, genotypic and phylogenetic analyses, we also propose the reclassification of Spirochaeta bajacaliforniensis as Sediminispirochaeta bajacaliforniensis gen. nov., comb. nov., Spirochaeta smaragdinae as Sediminispirochaeta smaragdinae comb. nov. and Spirochaeta sinaica as Sediminispirochaeta sinaica comb. nov.
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Affiliation(s)
- Y Shivani
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Y Subhash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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15
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Rhodobacter sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:2965-2970. [DOI: 10.1099/ijsem.0.001130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Zhou X, Jiang X, Yang C, Ma B, Lei C, Xu C, Zhang A, Yang X, Xiong Q, Zhang P, Men S, Xiang R, Wang H. Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing. Microbiologyopen 2016; 5:753-762. [PMID: 27139888 PMCID: PMC5061713 DOI: 10.1002/mbo3.367] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/11/2016] [Accepted: 03/23/2016] [Indexed: 12/22/2022] Open
Abstract
Tibetan Chickens should have unique gastrointestinal microbiota because of their particular habitats. Thus, the aim of this study was to investigate the cecal microbiota of Tibetan Chickens from five typical high-altitude regions of China. Lohmann egg-laying hens (LMs) and Daheng broiler chickens (DHs) were chosen as controls. The cecal bacterial populations of Tibetan Chickens were surveyed by high-throughput sequencing (HTS) of the bacterial 16S rRNA hypervariable region V3-V4 (16S rRNAV3-V4) combined with community-fingerprinting analysis of the 16S rRNA gene based on polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The results revealed that the majority of cecal microbiota differed between the Tibetan Chicken and LM/DH. The microbial communities in the cecum were composed of 16 phyla, 28 classes, 36 orders, 57 families, 101 genera, and 189 species. Represented phyla were Bacteroidetes (>47%), Firmicutes (>18.8%), Spirochaetae (>0.3%), and Proteobacteria (>0.4%). Bacteroides and the RC9 gut group were the two most abundant genera. There were relatively more Christensenellaceae, Subdoligranulum, Spirochaeta, and Treponema in Tibetan Chickens, whereas there were more Phascolarctobacterium, Faecalibacterium, Megamonas, and Desulfovibrio in LMs and DHs. The cecal microbiota of Tibetan Chicken have slightly diverged due to exposure to different geographic environments. Differences in the intestinal bacterial communities of Tibetan Chicken and LM/DH were noted.
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Affiliation(s)
- Xueyan Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaosong Jiang
- Institute of Poultry Science, Academy of Sichuan Animal Husbandry Research, Chengdu, China
| | - Chaowu Yang
- Institute of Poultry Science, Academy of Sichuan Animal Husbandry Research, Chengdu, China
| | - Bingcun Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Changwen Xu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xin Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Qi Xiong
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Peng Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shuai Men
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Rong Xiang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern China, College of Life Sciences, Sichuan University, Chengdu, China.
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Sravanthi T, Tushar L, Sasikala C, Ramana CV. Alkalispirochaeta cellulosivorans gen. nov., sp. nov., a cellulose-hydrolysing, alkaliphilic, halotolerant bacterium isolated from the gut of a wood-eating cockroach (Cryptocercus punctulatus), and reclassification of four species of Spirochaeta as new combinations within Alkalispirochaeta gen. nov. Int J Syst Evol Microbiol 2016; 66:1612-1619. [DOI: 10.1099/ijsem.0.000865] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- T. Sravanthi
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - L. Tushar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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Sasi Jyothsna TS, Tushar L, Sasikala C, Ramana CV. Paraclostridium benzoelyticum gen. nov., sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii. Int J Syst Evol Microbiol 2016; 66:1268-1274. [DOI: 10.1099/ijsem.0.000874] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- T. S. Sasi Jyothsna
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad,P.O. Central University, Hyderabad 500 046,India
| | - L. Tushar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad,P.O. Central University, Hyderabad 500 046,India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad,Kukatpally, Hyderabad 500 085,India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad,P.O. Central University, Hyderabad 500 046,India
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Oren A, Garrity GM. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2015. [DOI: 10.1099/ijs.0.000286] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2015. [DOI: 10.1099/ijs.0.000317] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Draft Genome Sequence of Spirochaeta sp. Strain JC202, an Endosymbiont of the Termite (Isoptera) Gut. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01481-14. [PMID: 25614577 PMCID: PMC4319587 DOI: 10.1128/genomea.01481-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
We announce here the draft genome sequence of Spirochaeta sp. strain JC202 isolated from gut of a termite (Isoptera). The genome suggests that Spirochaeta sp. JC202 has the capability for natural conjugation with the help of fimbriae and pili. Experimental evidence and the genome sequence suggest that strain JC202 is capable of producing colicin V and a bacteriocin group of peptides in a specific interaction.
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