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Huang Z, Huang Y, Lai Q, Oren A, Wang W. Paracrocinitomix mangrovi gen. nov., sp. nov., isolated from a mangrove sediment: proposal of two new families, Phaeocystidibacteraceae fam. nov. and Owenweeksiaceae fam. nov., and emended description of the family Schleiferiaceae. Antonie Van Leeuwenhoek 2023; 116:171-184. [PMID: 36346556 DOI: 10.1007/s10482-022-01790-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
A Gram-stain-negative and short rod-shaped bacterial strain designated GM2-3-6-6T was obtained from a mangrove sediment. Cells were light yellow-pigmented, catalase-positive and oxidase-positive. Carotenoid pigment was produced. Phylogeny of the 16S rRNA gene showed that strain GM2-3-6-6T was affiliated to the family Crocinitomicaceae, sharing maximum sequence similarities with Crocinitomix algicola 0182T, C. catalasitica IFO 15977T, and Putridiphycobacter roseus SM1701T of 93.8%, 93.6%, and 92.5%, respectively. The average nucleotide identity values, digital DNA-DNA hybridization estimates and average amino acid identity values between strain GM2-3-6-6T and the three close relatives were 68.6-68.8%, 18.5-19.2%, and 59.0-62.3%, respectively. The complete circular genome of strain GM2-3-6-6T was 4,365,762 bp in length with a DNA G + C content of 35.0%. The respiratory quinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, two unidentified phospholipids, one unidentified aminoglycolipid, one unidentified aminolipid and four other unidentified lipids. The major fatty acids were iso-C15:0, iso-C15:1 G, summed feature 3 (C16:1ω7c and/or C16:1ω6c), and iso-C17:0 3-OH. Based on genomic, phenotypic, and chemotaxonomic characterizations, strain GM2-3-6-6T represents a novel species of a novel genus, for which the name Paracrocinitomix mangrovi gen. nov., sp. nov. is proposed. The type strain is GM2-3-6-6T (= MCCC 1K04831T = KCTC 82931T). Additionally, phylogenomic analysis of the type strains of the family Schleiferiaceae and family Cryomorphaceae related members including uncultivated bacteria, was performed using the Genome Taxonomic Database toolkit (GTDB-Tk). Based on 16S rRNA gene phylogeny and genomic features, two novel families, Phaeocystidibacteraceae fam. nov. and Owenweeksiaceae fam. nov. are proposed. An emended description of the family Schleiferiaceae is also proposed.
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Affiliation(s)
- Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, People's Republic of China. .,Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, Quanzhou, China.
| | - Yuanyuan Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, People's Republic of China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Aharon Oren
- The Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
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Kim H, Park YH, Yang JE, Kim HS, Kim SC, Oh EJ, Moon J, Cho W, Shin W, Yu C. Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health. TOXICS 2022; 10:toxics10030117. [PMID: 35324742 PMCID: PMC8953465 DOI: 10.3390/toxics10030117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 12/10/2022]
Abstract
The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-generation sequencing (NGS)-based molecular-biological methods have revealed information on soil biodiversity; however, whether this biodiversity is related to soil health remains unclear. In this study, we performed NGS on grassland surface soil to compare the prokaryotic and eukaryotic genetic diversity to determine the chemical soil quality and examined markers associated with soil health. Microorganisms associated with the nitrogen cycle, bioremediation, plant pathogenicity, antibiotic production, and material degradation showed potential for use as markers. To propose a framework for soil health assessment, we not only used traditional indicators, such as chemical and physical measures, but also assessed metagenomics data of soil by land use to identify the major factors influencing the microbial structure in soil. Moreover, major keystone species were identified. Furthermore, the microbial genetic diversity of generally healthy surface soil, such as forests, farmland, and parks, was determined. These findings provide basic data for exploring soil health-related biomarkers.
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Affiliation(s)
- Heejung Kim
- Department of Geology, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Korea; (H.K.); (J.M.); (W.C.); (W.S.); (C.Y.)
| | - Yong-Ha Park
- Korea Environment Institute, Sejong 30147, Korea;
- Correspondence: (Y.-H.P.); (J.E.Y.); Tel.: +82-44-425-7631 (Y.-H.P.)
| | - Jae E. Yang
- Department of Biological Environment, Kangwon National University, Chuncheon 24341, Korea;
- Correspondence: (Y.-H.P.); (J.E.Y.); Tel.: +82-44-425-7631 (Y.-H.P.)
| | - Hyuck-Soo Kim
- Department of Biological Environment, Kangwon National University, Chuncheon 24341, Korea;
| | - Sung-Chul Kim
- Department of Bio-Environmental Chemistry, Chungnam National University, Deajeon 34134, Korea;
| | - Eun-Ji Oh
- Korea Environment Institute, Sejong 30147, Korea;
| | - Jinah Moon
- Department of Geology, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Korea; (H.K.); (J.M.); (W.C.); (W.S.); (C.Y.)
| | - Wonsil Cho
- Department of Geology, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Korea; (H.K.); (J.M.); (W.C.); (W.S.); (C.Y.)
| | - Wonsik Shin
- Department of Geology, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Korea; (H.K.); (J.M.); (W.C.); (W.S.); (C.Y.)
| | - Chaerim Yu
- Department of Geology, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Korea; (H.K.); (J.M.); (W.C.); (W.S.); (C.Y.)
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Toshchakov SV, Izotova AO, Vinogradova EN, Kachmazov GS, Tuaeva AY, Abaev VT, Evteeva MA, Gunitseva NM, Korzhenkov AA, Elcheninov AG, Patrushev MV, Kublanov IV. Culture-Independent Survey of Thermophilic Microbial Communities of the North Caucasus. BIOLOGY 2021; 10:biology10121352. [PMID: 34943267 PMCID: PMC8698779 DOI: 10.3390/biology10121352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 01/04/2023]
Abstract
Simple Summary The Republic of North Ossetia-Alania, located in the southern part of the North Caucasus, possess a number of hydrothermal habitats, including both subterranean thermal reservoirs and terrestrial hot springs. At the same time, reports on microbiology of numerous geothermal sites are rather scarce for the whole North Caucasus region. In this paper, we report on the first culture-independent metabarcoding study of thermal habitats in the North Caucasus, coupled with a chemical analysis of the elemental composition of water. The results of this work include the conclusions regarding key metabolic characteristics of these habitats as well as detection of few but abundant deep lineages of uncultivated microorganisms which could be regarded as endemic. This study may represent a first step in closing the knowledge gap in extremophilic microbial communities of the North Caucasus. Abstract The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot springs. However, there are only a limited number of scientific works reporting on the microbial communities of these habitats. Moreover, all these reports concern only studies of specific microbial taxa, carried out using classical cultivation approaches. In this work, we present first culture-independent study of hydrotherms in the Republic of North Ossetia-Alania, located in the southern part of the North Caucasus. Using 16S metabarcoding, we analyzed the composition of the microbial communities of two subterranean thermal aquifers and terrestrial hot springs of the Karmadon valley. Analysis of correlations between the chemical composition of water and the representation of key taxa allowed us to identify the key factors determining the formation of microbial communities. In addition, we were able to identify a significant number of highly abundant deep phylogenetic lineages. Our study represents a first glance on the thermophilic microbial communities of the North Caucasus and may serve as a basis for further microbiological studies of the extreme habitats of this region.
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Affiliation(s)
- Stepan V. Toshchakov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Correspondence: ; Tel.: +7-911-481-1809
| | - Anna O. Izotova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Elizaveta N. Vinogradova
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Gennady S. Kachmazov
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Albina Y. Tuaeva
- National Research Center Kurchatov Institute-GOSNIIGENETIKA, 1st Dorozhny Pr., 1, Moscow 117545, Russia;
| | - Vladimir T. Abaev
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named after K.L. Khetagurov, Vatutina str., 44-46, Vladikavkaz 362025, Russia; (G.S.K.); (V.T.A.)
| | - Martha A. Evteeva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Natalia M. Gunitseva
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Aleksei A. Korzhenkov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
| | - Maxim V. Patrushev
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Ac. Kurchatov Square, 1, Moscow 123098, Russia; (A.O.I.); (E.N.V.); (M.A.E.); (N.M.G.); (A.A.K.); (M.V.P.)
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 60-let Oktyzbrya Av., 7/2, Moscow 119071, Russia; (A.G.E.); (I.V.K.)
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Liu R, Lai Q, Gu L, Yan P, Shao Z. Croceimicrobium hydrocarbonivorans gen. nov., sp. nov., a novel marine bacterium isolated from a bacterial consortium that degrades polyethylene terephthalate. Int J Syst Evol Microbiol 2021; 71. [PMID: 33847553 DOI: 10.1099/ijsem.0.004770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1-8 %, at pH 6.5-8 and at temperatures of 10-40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae, and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA-DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).
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Affiliation(s)
- Renju Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,School of Environmental Science, Harbin Institute of Technology, Harbin, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Li Gu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Peisheng Yan
- School of Environmental Science, Harbin Institute of Technology, Harbin, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.,School of Environmental Science, Harbin Institute of Technology, Harbin, PR China
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Han X, Qu Y, Wu J, Li D, Ren N, Feng Y. Nitric oxide reduction by microbial fuel cell with carbon based gas diffusion cathode for power generation and gas purification. JOURNAL OF HAZARDOUS MATERIALS 2020; 399:122878. [PMID: 32937696 DOI: 10.1016/j.jhazmat.2020.122878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Nitric oxide (NO) from anthropogenic emission is one of the main air contaminants and induces many environmental problems. Microbial fuel cells (MFCs) with gas diffusion cathode provide an alternative technology for NO reduction. In this work, pure NO as the sole electron acceptor of MFCs with gas diffusion cathode (NO-MFCs) was verified. The NO-MFCs obtained a maximum power density of 489 ± 50 mW/m2. Compared with MFCs using O2 in air as electron acceptor (Air-MFCs), the columbic efficiency increased from 23.2% ± 4.3% (Air-MFCs) to 55.7% ± 4.6% (NO-MFCs). The NO removal rate was 12.33 ± 0.14 mg/L/h and N2 was the main reduction product. Cathode reduction was the dominant pathway of NO conversion in NO-MFCs, including abiotic electrochemical reduction and microbial denitrification process. The predominant genera in anodic microbial community changed from exoelectrogenic bacteria in Air-MFCs to denitrifying bacteria in NO-MFCs and effected the power generation.
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Affiliation(s)
- Xiaoyu Han
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No 73 Huanghe Road, Nangang District, Harbin 150090, China
| | - Youpeng Qu
- School of Life Science and Technology, Harbin Institute of Technology, No. 2 Yikuang Street, Nangang District, Harbin 150080, China.
| | - Jing Wu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No 73 Huanghe Road, Nangang District, Harbin 150090, China
| | - Da Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No 73 Huanghe Road, Nangang District, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No 73 Huanghe Road, Nangang District, Harbin 150090, China
| | - Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No 73 Huanghe Road, Nangang District, Harbin 150090, China.
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Microbiota of the Therapeutic Euganean Thermal Muds with a Focus on the Main Cyanobacteria Species. Microorganisms 2020; 8:microorganisms8101590. [PMID: 33076380 PMCID: PMC7650686 DOI: 10.3390/microorganisms8101590] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/17/2022] Open
Abstract
The Euganean Thermal District has been known since Roman times for the therapeutic properties of peloids, obtained from natural clays that have undergone a traditional maturation process. This leads to the growth of a green microbial biofilm with Cyanobacteria and the target species Phormidium sp. ETS-05 as fundamental components for their ability to synthetize anti-inflammatory molecules. Currently, in-depth studies on the microbiota colonizing Euganean peloids, as in general on peloids utilized worldwide, are missing. This is the first characterization of the microbial community of Euganean thermal muds, also investigating the effects of environmental factors on its composition. We analysed 53 muds from 29 sites (Spas) using a polyphasic approach, finding a stable microbiota peculiar to the area. Differences among mud samples mainly depended on two parameters: water temperature and shading of mud maturation plants. In the range 37-47 °C and in the case of irradiance attenuation due to the presence of protective roofs, a statistically significant higher mud Chl a content was detected. Moreover, in these conditions, a characteristic microbial and Cyanobacteria population composition dominated by Phormidium sp. ETS-05 was observed. We also obtained the complete genome sequence of this target species using a mixed sequencing approach based on Illumina and Nanopore sequencing.
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Quigley CTC, Capistrant-Fossa KA, Morrison HG, Johnson LE, Morozov A, Hertzberg VS, Brawley SH. Bacterial Communities Show Algal Host ( Fucus spp.)/Zone Differentiation Across the Stress Gradient of the Intertidal Zone. Front Microbiol 2020; 11:563118. [PMID: 33072025 PMCID: PMC7541829 DOI: 10.3389/fmicb.2020.563118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
The intertidal zone often has varying levels of environmental stresses (desiccation, temperature, light) that result in highly stress-tolerant macrobiota occupying the upper zone while less tolerant species occupy the lower zone, but little comparative information is available for intertidal bacteria. Here we describe natural (unmanipulated) bacterial communities of three Fucus congeners (F. spiralis, high zone; F. vesiculosus, mid zone; F. distichus, low zone) as well as those of F. vesiculosus transplanted to the high zone (Dry and Watered treatments) and to the mid zone (Procedural Control) during summer in Maine (United States). We predicted that bacterial communities would be different among the differently zoned natural congeners, and that higher levels of desiccation stress in the high zone would cause bacterial communities of Dry transplants to become similar to F. spiralis, whereas relieving desiccation stress on Watered transplants would maintain the mid-zone F. vesiculosus bacterial community. Bacteria were identified as amplicon sequence variants (ASVs) after sequencing the V4 hypervariable region of the 16S rRNA gene. Microbiome composition and structure were significantly different between the differently zoned congeners at each tissue type (holdfasts, receptacles, vegetative tips). ASVs significantly associated with the mid-zone congener were frequently also present on the high-zone or low-zone congener, whereas overlap in ASVs between the high-zone and low-zone congeners was rare. Only 7 of 6,320 total ASVs were shared among tissues over all congeners and transplant treatments. Holdfast bacterial community composition of Dry transplants was not significantly different from that of F. spiralis, but Watered holdfast communities were significantly different from those of F. spiralis and not significantly different from those of procedural controls. Additional stressor(s) appeared important, because bacterial communities of Dry and Watered transplants were only marginally different from each other (p = 0.059). The relative abundance of Rhodobacteraceae associated with holdfasts generally correlated with environmental stress with highest abundance associated with F. spiralis and the two high-zone transplant treatments. These findings suggest that the abiotic stressors that shape distributional patterns of host species also affect their bacterial communities.
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Affiliation(s)
| | | | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Ladd E Johnson
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Aleksey Morozov
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Vicki S Hertzberg
- Center for Data Science, Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States
| | - Susan H Brawley
- School of Marine Sciences, University of Maine, Orono, ME, United States
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Bowman JP. Out From the Shadows - Resolution of the Taxonomy of the Family Cryomorphaceae. Front Microbiol 2020; 11:795. [PMID: 32431677 PMCID: PMC7214798 DOI: 10.3389/fmicb.2020.00795] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
The family Cryomorphaceae for many years has been a poorly defined taxonomic group within the order Flavobacteriales, phylum Bacteroidetes. Members of the Cryomorphaceae, apparently consisting of multiple-family level clades, have been mostly but not exclusively detected in saline ecosystems. The problems with the taxonomy of this group have stemmed from inadequate resolution of taxonomic groups using 16S rRNA gene sequences, sparse numbers of cultivated taxa, and limited phenotypic distinctiveness. The Genome Tiaxonomc Database (GTDB), which is based on normalized taxonomic ranks includes Cryomorphaceae as containing the genera Owenweeksia and Schleiferia. This is at odds with the official taxonomy that places these genera in the family Schleiferiaceae. The other Cryomorphaceae affiliated species have even more uncertain taxonomic positions including Cryomorpha ignava. To clarify the taxonomy of Cryomorphaceae, genomes were generated for all type strains of the family Cryomorphaceae lacking such data. The GTDB-toolkit (GTDB-tk) was used to place taxa in the GTDB, which revealed novelty at the family level for some of these type strains. 16S rRNA gene sequences and concatenated protein sequences were used to further evaluate the taxonomy of the order Flavobacteriales. From the data, the GTDB enabled successful clarification of the taxonomy of the family Cryomorphaceae. A number of placeholder families were given Latinized names. It is proposed that the family Cryomorphaceae is emended to include only the species Cryomorpha ignava. The family Schleiferiaceae is emended to account for the expansion of its membership. Luteibaculum oceani represents a new family designated Luteibaculaceae fam. nov. Vicingus serpentipes is the representative of Vicingaceae fam. nov. while Salibacter halophilus represents Salibacteraceae fam. nov.
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Affiliation(s)
- John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
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Iino T, Kawai S, Yuki M, Dekio I, Ohkuma M, Haruta S. Thermaurantimonas aggregans gen. nov., sp. nov., a moderately thermophilic heterotrophic aggregating bacterium isolated from microbial mats at a terrestrial hot spring. Int J Syst Evol Microbiol 2020; 70:1117-1121. [DOI: 10.1099/ijsem.0.003888] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Itaru Dekio
- Skin Microbe Laboratory, Mildix Skin Clinic, 3rd Floor, 3-98 Senju, Adachi-ku, Tokyo 120-0034, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes 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 proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium 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. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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11
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Sun L, Toyonaga M, Ohashi A, Tourlousse DM, Matsuura N, Meng XY, Tamaki H, Hanada S, Cruz R, Yamaguchi T, Sekiguchi Y. Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:2635-2642. [DOI: 10.1099/ijsem.0.001103] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Liwei Sun
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
- School of Energy & Environment, Southeast University, Nanjing, Jiangsu 210096, PR China
| | - Mayu Toyonaga
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Akiko Ohashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Dieter M. Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Norihisa Matsuura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Satoshi Hanada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Rodrigo Cruz
- EPAS International NV, Dok-Noord 4, Gent 9000, Belgium
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
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12
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Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016; 39:281-96. [PMID: 27287844 DOI: 10.1016/j.syapm.2016.04.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/01/2016] [Accepted: 04/05/2016] [Indexed: 11/21/2022]
Abstract
Members of the phylum Bacteroidetes, which was originally defined as a monophyletic branch encompassing the genera Cytophaga, Flavobacterium and Bacteroides (CFB), are widely studied due to their importance in environmental and gut microbiology. As a consequence, the number of species names with standing in nomenclature has doubled in the past five years. In this study, a revision of an earlier phylogeny of Bacteroidetes has been performed using the 16S rRNA gene as a backbone in combination with the 23S rRNA gene, as well as multilocus sequence analysis (MLSA) of 29 orthologous protein sequences, and indels in the sequences of the beta subunit of the F-type ATPase and the alanyl-tRNA synthetase. In addition, taxonomic data for Bacteroidetes has been updated by considering the orphan species list, signature nucleotides in the 16S rRNA sequence, the list of outlier species, and discrepancies with the current taxonomy at the genus rank level. As a result, seven new taxa are proposed within Bacteroidetes (Chitinophagia classis nov., Chitinophagales ord. nov., Crocinitomicaceae fam. nov., Odoribacteraceae fam. nov., Hymenobacteraceae fam. nov., Thermonemataceae fam. nov. and Persicobacteraceae fam. nov.), as well as one new phylum Rhodothermaeota phyl. nov. that contains two classes, two orders, four families and a new genus with two new combinations.
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13
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Baito K, Imai S, Matsushita M, Otani M, Sato Y, Kimura H. Biogas production using anaerobic groundwater containing a subterranean microbial community associated with the accretionary prism. Microb Biotechnol 2014; 8:837-45. [PMID: 25267392 PMCID: PMC4554471 DOI: 10.1111/1751-7915.12179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 08/12/2014] [Accepted: 08/24/2014] [Indexed: 11/05/2022] Open
Abstract
In a deep aquifer associated with an accretionary prism, significant methane (CH4) is produced by a subterranean microbial community. Here, we developed bioreactors for producing CH4 and hydrogen (H2) using anaerobic groundwater collected from the deep aquifer. To generate CH4, the anaerobic groundwater amended with organic substrates was incubated in the bioreactor. At first, H2 was detected and accumulated in the gas phase of the bioreactor. After the H2 decreased, rapid CH4 production was observed. Phylogenetic analysis targeting 16S rRNA genes revealed that the H2-producing fermentative bacterium and hydrogenotrophic methanogen were predominant in the reactor. The results suggested that syntrophic biodegradation of organic substrates by the H2-producing fermentative bacterium and the hydrogenotrophic methanogen contributed to the CH4 production. For H2 production, the anaerobic groundwater, amended with organic substrates and an inhibitor of methanogens (2-bromoethanesulfonate), was incubated in a bioreactor. After incubation for 24 h, H2 was detected from the gas phase of the bioreactor and accumulated. Bacterial 16S rRNA gene analysis suggested the dominance of the H2-producing fermentative bacterium in the reactor. Our study demonstrated a simple and rapid CH4 and H2 production utilizing anaerobic groundwater containing an active subterranean microbial community.
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Affiliation(s)
- Kyohei Baito
- Department of Geosciences, Graduate School of Science, Shizuoka University, Shizuoka, Japan
| | - Satomi Imai
- Department of Geosciences, Graduate School of Science, Shizuoka University, Shizuoka, Japan
| | - Makoto Matsushita
- Department of Geosciences, Graduate School of Science, Shizuoka University, Shizuoka, Japan
| | - Miku Otani
- Department of Geosciences, Graduate School of Science, Shizuoka University, Shizuoka, Japan
| | - Yu Sato
- Department of Geosciences, Graduate School of Science, Shizuoka University, Shizuoka, Japan
| | - Hiroyuki Kimura
- Department of Geosciences, Graduate School of Science, Shizuoka University, Shizuoka, Japan.,Center for Integrated Research and Education of Natural Hazards, Shizuoka University, Shizuoka, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
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14
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Draft Genome Sequence of the Moderately Thermophilic Bacterium Schleiferia thermophila Strain Yellowstone (Bacteroidetes). GENOME ANNOUNCEMENTS 2014; 2:2/4/e00860-14. [PMID: 25169864 PMCID: PMC4148732 DOI: 10.1128/genomea.00860-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes), isolated from Octopus Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 2,617,694 bp in 35 contigs. The draft genome is predicted to encode 2,457 protein coding genes and 37 tRNA encoding genes and two rRNA operons.
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15
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Anders H, Dunfield PF, Lagutin K, Houghton KM, Power JF, MacKenzie AD, Vyssotski M, Ryan JLJ, Hanssen EG, Moreau JW, Stott MB. Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes. Int J Syst Evol Microbiol 2014; 64:1264-1270. [PMID: 24425740 DOI: 10.1099/ijs.0.057463-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, thermophilic, moderately acidophilic, non-spore-forming bacterium, strain P373(T), was isolated from geothermally heated soil at Waikite, New Zealand. Cells were filamentous rods, 0.2-0.4 µm in diameter and grew in chains up to 80 µm in length. On the basis of 16S rRNA gene sequence similarity, strain P373(T) was shown to belong to the family Chitinophagaceae (class Sphingobacteriia) of the phylum Bacteroidetes, with the most closely related cultivated strain, Chitinophaga pinensis UQM 2034(T), having 87.6 % sequence similarity. Cells stained Gram-negative, and were catalase- and oxidase-positive. The major fatty acids were i-15 : 0 (10.8 %), i-17 : 0 (24.5 %) and i-17 : 0 3-OH (35.2 %). Primary lipids were phosphatidylethanolamine, two unidentified aminolipids and three other unidentified polar lipids. The presence of sulfonolipids (N-acyl-capnines) was observed in the total lipid extract by mass spectrometry. The G+C content of the genomic DNA was 47.3 mol% and the primary respiratory quinone was MK-7. Strain P373(T) grew at 35-63 °C with an optimum temperature of 60 °C, and at pH 5.5-8.7 with an optimum growth pH of 7.3-7.4. NaCl tolerance was up to 5 % (w/v) with an optimum of 0.1-0.25 % (w/v). Cell colonies were non-translucent and pigmented vivid yellow-orange. Cells displayed an oxidative chemoheterotrophic metabolism. The distinct phylogenetic position and the phenotypic characteristics separate strain P373(T) from all other members of the phylum Bacteroidetes and indicate that it represents a novel species in a new genus, for which the name Thermoflavifilum aggregans gen. nov., sp. nov. is proposed. The type strain of the type species is P373(T) ( = ICMP 20041(T) = DSM 27268(T)).
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Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, Canada
| | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Karen M Houghton
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Jean F Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | | | | | - Jason L J Ryan
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Eric G Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
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16
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Leandro T, França L, Nobre MF, Rainey FA, da Costa MS. Heliimonas saccharivorans gen. nov., sp. nov., a member of the family
Chitinophagaceae
isolated from a mineral water aquifer, and emended description of
Filimonas lacunae. Int J Syst Evol Microbiol 2013; 63:3793-3799. [DOI: 10.1099/ijs.0.050021-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates, with optimum growth temperature and pH of about 30 °C and 6.0–7.0, were recovered from a borehole head of a mineral water aquifer in Portugal. The closest relatives based on 16S rRNA gene sequence analysis were species of genera of the family
Chitinophagaceae
. Strains L2-4T and L2-109 formed translucent colonies and non-motile pleomorphic cells. Strains were strictly aerobic, and oxidase- and catalase-positive. The major fatty acids of strains L2-4T and L2-109 were 17 : 0 iso 3-OH, 15 : 0 iso and 15 : 1 iso G. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid, four unidentified aminophospholipids, four unidentified aminolipids and three unidentified polar lipids. Menaquinone 7 was the only respiratory quinone. The G+C content of the DNA of strains L2-4T and L2-109 was 42.0 and 41.4 mol%, respectively. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, strains L2-4T ( = CECT 8122T = LMG 26919T) and L2-109 ( = CECT 8121 = LMG 26920) are considered to represent a novel species of a new genus, for which the name Heliimonas saccharivorans gen. nov., sp. nov. is proposed. The type strain of Heliimonas saccharivorans is L2-4T. Due to additional results obtained in this study an emended description of
Filimonas lacunae
is provided.
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Affiliation(s)
- Tânia Leandro
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Luís França
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - M. Fernanda Nobre
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Fred A. Rainey
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
| | - Milton S. da Costa
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
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17
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Coman C, Drugă B, Hegedus A, Sicora C, Dragoş N. Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania. Extremophiles 2013; 17:523-34. [DOI: 10.1007/s00792-013-0537-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/26/2013] [Indexed: 11/30/2022]
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18
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Albuquerque L, Tiago I, Nobre MF, Veríssimo A, da Costa MS. Cecembia calidifontis sp. nov., isolated from a hot spring runoff, and emended description of the genus Cecembia. Int J Syst Evol Microbiol 2012; 63:1431-1436. [PMID: 22843720 DOI: 10.1099/ijs.0.044537-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two red-pigmented isolates, designated RQ-33(T) and TU-13, were recovered from hot spring runoffs on the Island of São Miguel in the Azores, Portugal. These organisms have an optimum growth temperature of approximately 45 °C and an optimum pH for growth between 7.5 and 8.5. Based on 16S rRNA gene sequence analysis, the novel isolates were most closely related to the type strain of Cecembia lonarensis at 96.4 % pairwise similarity. Cells of the two isolates were non-motile, rod-shaped, Gram-stain-negative, strictly aerobic, and oxidase- and catalase-positive. The major fatty acids were iso-C15 : 0 and C15 : 0, phosphatidylethanolamine was the major polar lipid, and menaquinone 7 was the major respiratory quinone. Based on phylogenetic analyses, and physiological and biochemical characteristics, these isolates from the Azores represent a novel species of the genus Cecembia for which the name Cecembia calidifontis is proposed with strain RQ-33(T) ( = DSM 21411(T) = LMG 24596(T)) as the type strain. The description of the genus Cecembia is also emended.
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Affiliation(s)
- Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Igor Tiago
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - M Fernanda Nobre
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - António Veríssimo
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Milton S da Costa
- Microbiology Unit, BIOCANT Biotechnological Park, 3060-197 Cantanhede, Portugal.,Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
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19
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Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Hydrotalea sandarakina sp. nov., isolated from a hot spring runoff, and emended descriptions of the genus Hydrotalea and the species Hydrotalea flava. Int J Syst Evol Microbiol 2011; 62:1603-1608. [PMID: 21890728 DOI: 10.1099/ijs.0.034496-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial isolates, designated AF-51(T) and AF-50, with an optimum growth temperature of about 45 °C and an optimum pH for growth between 6.0 and 6.5, were recovered from a hot spring in the Furnas, Área da Fonte 1825, on the Island of São Miguel in the Azores. Based on 16S rRNA gene sequence analysis, these strains were related most closely to the type strain of Hydrotalea flava at a pairwise similarity of 95.7%. The two strains were orange-pigmented and formed non-motile, rod-shaped cells that stained Gram-negative and were aerobic and oxidase- and catalase-positive. The major fatty acids were iso-C(15:0), iso-C(17:0) 3-OH and iso-C(16:0). The major respiratory quinone was menaquinone 7. Based on phylogenetic, physiological and biochemical characteristics, these strains from the Azores are considered to represent a single novel species of the genus Hydrotalea, for which the name Hydrotalea sandarakina sp. nov. is proposed. The type strain is AF-51(T) (=DSM 23241(T)=LMG 25526(T)). We provide emended descriptions of the genus Hydrotalea and of H. flava to reflect new results obtained in this study.
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Affiliation(s)
- Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Fred A Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M Fernanda Nobre
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Milton S da Costa
- Microbiology Unit, BIOCANT Biotechnological Park, 3060-197 Cantanhede, Portugal.,Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
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20
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The Extraction and Identification of Respiratory Lipoquinones of Prokaryotes and Their Use in Taxonomy. J Microbiol Methods 2011. [DOI: 10.1016/b978-0-12-387730-7.00009-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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