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Dom SP, Ikenaga M, Lau SYL, Radu S, Midot F, Yap ML, Chin MY, Lo ML, Jee MS, Maie N, Melling L. Linking prokaryotic community composition to carbon biogeochemical cycling across a tropical peat dome in Sarawak, Malaysia. Sci Rep 2021; 11:6416. [PMID: 33742002 PMCID: PMC7979770 DOI: 10.1038/s41598-021-81865-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Tropical peat swamp forest is a global store of carbon in a water-saturated, anoxic and acidic environment. This ecosystem holds diverse prokaryotic communities that play a major role in nutrient cycling. A study was conducted in which a total of 24 peat soil samples were collected in three forest types in a tropical peat dome in Sarawak, Malaysia namely, Mixed Peat Swamp (MPS), Alan Batu (ABt), and Alan Bunga (ABg) forests to profile the soil prokaryotic communities through meta 16S amplicon analysis using Illumina Miseq. Results showed these ecosystems were dominated by anaerobes and fermenters such as Acidobacteria, Proteobacteria, Actinobacteria and Firmicutes that cover 80-90% of the total prokaryotic abundance. Overall, the microbial community composition was different amongst forest types and depths. Additionally, this study highlighted the prokaryotic communities' composition in MPS was driven by higher humification level and lower pH whereas in ABt and ABg, the less acidic condition and higher organic matter content were the main factors. It was also observed that prokaryotic diversity and abundance were higher in the more oligotrophic ABt and ABg forest despite the constantly waterlogged condition. In MPS, the methanotroph Methylovirgula ligni was found to be the major species in this forest type that utilize methane (CH4), which could potentially be the contributing factor to the low CH4 gas emissions. Aquitalea magnusonii and Paraburkholderia oxyphila, which can degrade aromatic compounds, were the major species in ABt and ABg forests respectively. This information can be advantageous for future study in understanding the underlying mechanisms of environmental-driven alterations in soil microbial communities and its potential implications on biogeochemical processes in relation to peatland management.
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Affiliation(s)
- Simon Peter Dom
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Sharon Yu Ling Lau
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Son Radu
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Frazer Midot
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Lan Yap
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei-Yee Chin
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei Lieng Lo
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Sie Jee
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Nagamitsu Maie
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Lulie Melling
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
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Chen Y, Huang Z, Li J, Su G, Feng B. Complete Genome Sequence of Kosakonia radicincitans GXGL-4A, a Nitrogen-Fixing Bacterium with Capability to Degrade TEX. Curr Microbiol 2020; 77:1848-1857. [PMID: 32170407 DOI: 10.1007/s00284-020-01942-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/03/2020] [Indexed: 11/26/2022]
Abstract
Kosakonia radicincitans GXGL-4A, a free-living nitrogen-fixing (NF) bacterial strain isolated from maize (Zea mays L.) roots was found to have ability to degrade aromatic hydrocarbons. In this study, we describe the main morphological characteristics of bacterium, aromatic hydrocarbon-degrading capability, and the complete genome of K. radicincitans GXGL-4A. The genome is consisted of only one 5,687,681 bp linear chromosome with a G + C content of 53.96%. The strain has two genetically distinct nitrogenase systems, one based on molybdenum (Mo) similar to nitrogenase isolated from a wide range of nitrogen-fixing organisms, and the other contains iron (Fe). The differences in transcriptional level of several important nitrogen fixation (nif) genes between LB (nitrogen-rich, NR) and A15 nitrogen-free (nitrogen-limited, NL) culture conditions were detected using Real-time Quantitative Reverse Transcription PCR (qRT-PCR). The bacterial cells of GXGL-4A can grow well in LB liquid medium containing 1% toluene, ethylbenzene or xylene, suggesting a good resistance to the tested aromatic hydrocarbons. The results of GC-MS analysis showed that K. radicincitans GXGL-4A has a good capability to degrade toluene, ethylbenzene, and xylene (TEX). Completion of the genome sequencing will no doubt contribute to the deep exploration and comprehensive utilization of this NF bacterium in sustainable agriculture and bioremediation of aromatic pollutants.
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Affiliation(s)
- Yunpeng Chen
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhibo Huang
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiaoyong Li
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoxun Su
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Baoyun Feng
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Methylotrophic methanogens everywhere - physiology and ecology of novel players in global methane cycling. Biochem Soc Trans 2020; 47:1895-1907. [PMID: 31819955 DOI: 10.1042/bst20180565] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 01/14/2023]
Abstract
Research on methanogenic Archaea has experienced a revival, with many novel lineages of methanogens recently being found through cultivation and suggested via metagenomics approaches, respectively. Most of these lineages comprise Archaea (potentially) capable of methanogenesis from methylated compounds, a pathway that had previously received comparably little attention. In this review, we provide an overview of these new lineages with a focus on the Methanomassiliicoccales. These lack the Wood-Ljungdahl pathway and employ a hydrogen-dependent methylotrophic methanogenesis pathway fundamentally different from traditional methylotrophic methanogens. Several archaeal candidate lineages identified through metagenomics, such as the Ca. Verstraetearchaeota and Ca. Methanofastidiosa, encode genes for a methylotrophic methanogenesis pathway similar to the Methanomassiliicoccales. Thus, the latter are emerging as a model system for physiological, biochemical and ecological studies of hydrogen-dependent methylotrophic methanogens. Methanomassiliicoccales occur in a large variety of anoxic habitats including wetlands and animal intestinal tracts, i.e. in the major natural and anthropogenic sources of methane emissions, respectively. Especially in ruminant animals, they likely are among the major methane producers. Taken together, (hydrogen-dependent) methylotrophic methanogens are much more diverse and widespread than previously thought. Considering the role of methane as potent greenhouse gas, resolving the methanogenic nature of a broad range of putative novel methylotrophic methanogens and assessing their role in methane emitting environments are pressing issues for future research on methanogens.
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Munson E, Carroll KC. What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015. J Clin Microbiol 2017; 55:24-42. [PMID: 27795334 PMCID: PMC5228236 DOI: 10.1128/jcm.01379-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Azizi A, Kim W, Lee JH. Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions. World J Microbiol Biotechnol 2016; 32:158. [PMID: 27562592 DOI: 10.1007/s11274-016-2112-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/20/2016] [Indexed: 11/25/2022]
Abstract
Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH4/g volatile solids (VS) and 246.1 ± 11 mL CH4/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities.
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Affiliation(s)
- Aqil Azizi
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, PO Box 29, Ansan, 15627, Republic of Korea.,Korea University of Science and Technology, 217 Gajunro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Wonduck Kim
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, PO Box 29, Ansan, 15627, Republic of Korea.,Korea University of Science and Technology, 217 Gajunro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Jung Hyun Lee
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, PO Box 29, Ansan, 15627, Republic of Korea. .,Korea University of Science and Technology, 217 Gajunro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
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6
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Kwak Y, Park GS, Shin JH. High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium. Stand Genomic Sci 2016; 11:51. [PMID: 27555890 PMCID: PMC4994261 DOI: 10.1186/s40793-016-0173-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas lutea OK2(T) (=LMG 21974(T), CECT 5822(T)) is the type strain of the species and was isolated from the rhizosphere of grass growing in Spain in 2003 based on its phosphate-solubilizing capacity. In order to identify the functional significance of phosphate solubilization in Pseudomonas Plant growth promoting rhizobacteria, we describe here the phenotypic characteristics of strain OK2(T) along with its high-quality draft genome sequence, its annotation, and analysis. The genome is comprised of 5,647,497 bp with 60.15 % G + C content. The sequence includes 4,846 protein-coding genes and 95 RNA genes.
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Affiliation(s)
- Yunyoung Kwak
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 702-701 Republic of Korea
| | - Gun-Seok Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 702-701 Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 702-701 Republic of Korea
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Shukla S, Lee G, Song X, Park S, Kim M. Immunoliposome-based immunomagnetic concentration and separation assay for rapid detection of Cronobacter sakazakii. Biosens Bioelectron 2016; 77:986-94. [DOI: 10.1016/j.bios.2015.10.077] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 09/24/2015] [Accepted: 10/26/2015] [Indexed: 11/25/2022]
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Dione N, Sankar S, Lagier JC, Khelaifia S, Michele C, Armstrong N, Richez M, Abrahão J, Raoult D, Fournier PE. Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 2016; 10:66-76. [PMID: 26937282 PMCID: PMC4753391 DOI: 10.1016/j.nmni.2016.01.002] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/30/2015] [Accepted: 01/04/2016] [Indexed: 01/09/2023] Open
Abstract
Anaerosalibacter massiliensis sp. nov. strain ND1(T) (= CSUR P762 = DSM 27308) is the type strain of A. massiliensis sp. nov., a new species within the genus Anaerosalibacter. This strain, the genome of which is described here, was isolated from the faecal flora of a 49-year-old healthy Brazilian man. Anaerosalibacter massiliensis is a Gram-positive, obligate anaerobic rod and member of the family Clostridiaceae. With the complete genome sequence and annotation, we describe here the features of this organism. The 3 197 911 bp long genome (one chromosome but no plasmid) contains 3271 protein-coding and 62 RNA genes, including six rRNA genes.
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Affiliation(s)
- N. Dione
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - S.A. Sankar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - S. Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - C. Michele
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - N. Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - M. Richez
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - J. Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
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Söllinger A, Schwab C, Weinmaier T, Loy A, Tveit AT, Schleper C, Urich T. Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences. FEMS Microbiol Ecol 2016; 92:fiv149. [PMID: 26613748 DOI: 10.1093/femsec/fiv149] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2015] [Indexed: 01/30/2023] Open
Abstract
Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems.
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Affiliation(s)
- Andrea Söllinger
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Clarissa Schwab
- Institute of Food, Nutrition and Health, ETH Zürich, 8092 Zurich, Switzerland
| | - Thomas Weinmaier
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Christa Schleper
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald, 17489 Greifswald, Germany
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Lin CY, Zhang XY, Liu A, Liu C, Song XY, Su HN, Qin QL, Xie BB, Zhang YZ, Chen XL. Haliea atlantica sp. nov., isolated from seawater, transfer of Haliea mediterranea to Parahaliea gen. nov. as Parahaliea mediterranea comb. nov. and emended description of the genus Haliea. Int J Syst Evol Microbiol 2015; 65:3413-3418. [DOI: 10.1099/ijsem.0.000431] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chao-Yi Lin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Ang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan 250100, PR China
| | - Xiu-Lan Chen
- Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan 250100, PR China
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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11
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Kämpfer P, McInroy JA, Glaeser SP. Enterobacter muelleri sp. nov., isolated from the rhizosphere of Zea mays. Int J Syst Evol Microbiol 2015; 65:4093-4099. [PMID: 26294947 DOI: 10.1099/ijsem.0.000547] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A beige-pigmented, oxidase-negative bacterial strain (JM-458T), isolated from a rhizosphere sample, was studied using a polyphasic taxonomic approach. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain JM-458T with sequences of the type strains of closely related species of the genus Enterobacter showed that it shared highest sequence similarity with Enterobacter mori (98.7 %), Enterobacter hormaechei (98.3 %), Enterobacter cloacae subsp. dissolvens, Enterobacter ludwigii and Enterobacter asburiae (all 98.2 %). 16S rRNA gene sequence similarities to all other Enterobacter species were below 98 %. Multilocus sequence analysis based on concatenated partial rpoB, gyrB, infB and atpD gene sequences showed a clear distinction of strain JM-458T from its closest related type strains. The fatty acid profile of the strain consisted of C16 : 0, C17 : 0 cyclo, iso-C15 : 0 2-OH/C16 : 1ω7c and C18 : 1ω7c as major components. DNA-DNA hybridizations between strain JM-458T and the type strains of E. mori, E. hormaechei and E. ludwigii resulted in relatedness values of 29 % (reciprocal 25 %), 24 % (reciprocal 43 %) and 16 % (reciprocal 17 %), respectively. DNA-DNA hybridization results together with multilocus sequence analysis results and differential biochemical and chemotaxonomic properties showed that strain JM-458T represents a novel species of the genus Enterobacter, for which the name Enterobacter muelleri sp. nov. is proposed. The type strain is JM-458T ( = DSM 29346T = CIP 110826T = LMG 28480T = CCM 8546T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
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12
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Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions. Appl Microbiol Biotechnol 2015; 99:5801-15. [DOI: 10.1007/s00253-015-6739-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/23/2015] [Accepted: 05/29/2015] [Indexed: 12/11/2022]
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13
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Singh N, Goel G, Raghav M. Insights into virulence factors determining the pathogenicity of Cronobacter sakazakii. Virulence 2015; 6:433-40. [PMID: 25950947 PMCID: PMC4601314 DOI: 10.1080/21505594.2015.1036217] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 02/07/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen associated with outbreaks of life-threatening necrotizing enterocolitis, meningitis and sepsis in neonates and infants. The pathogen possesses an array of virulence factors which aid in tissue adhesion, invasion and host cell injury. Although the identification and validation of C. sakazakii virulence factors has been hindered by availability of suitable neonatal animal model, various studies has reported outer membrane protein A (ompA) as a potential virulence marker. Various other plasmid associated genes such as filamentous hemagglutinin (fhaBC), Cronobacter plasminogen activator (cpa) and genes responsible for iron acquisition (eitCBAD and iucABD/iutA) have been reported in different strains of C. sakazakii. Besides these proposed virulence factors, several biophysical growth factors such as formation of biofilms and resistance to various environmental stresses also contributes to the pathogenic potential of this pathogen. This review provides an update on virulence determinants associated with the pathogenesis of C. sakazakii. The potential reservoirs of the pathogen, mode of transmission and epidemiology are also discussed.
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Affiliation(s)
- Niharika Singh
- Department of Biotechnology and Bioinformatics; Jaypee University of Information Technology; Waknaghat, Solan, India
| | - Gunjan Goel
- Department of Biotechnology and Bioinformatics; Jaypee University of Information Technology; Waknaghat, Solan, India
| | - Mamta Raghav
- Department of Biotechnology and Bioinformatics; Jaypee University of Information Technology; Waknaghat, Solan, India
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Singh N, Goel G, Raghav M. Prevalence and Characterization of Cronobacter spp. from Various Foods, Medicinal Plants, and Environmental Samples. Curr Microbiol 2015; 71:31-8. [PMID: 25855303 DOI: 10.1007/s00284-015-0816-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 02/26/2015] [Indexed: 11/26/2022]
Abstract
Dairy or non-dairy based products were explored to determine the prevalence, molecular characterization, and antibiotic susceptibility of Cronobacter spp. The isolation was done as per ISO 22964:2006 on chromogenic media followed by further confirmation by biochemical- and 16S rRNA-based identification. From 219 samples, the chromogenic agar assay and biochemical tests yielded presumptive 45 isolates. Among them, only 36 isolates showed 282 bp band amplified from ITS-G gene confirming as Cronobacter sakazakii. The Cronobacter spp. prevalence was highest in herbs and spices (34 %) while environmental samples had contamination rates of 23 % indicating plants as a possible reservoir of this pathogen. All the isolates were resistant to β-lactam derivatives (68 %), macrolides (88.6 %), and aminoglycosides (79.9 %) but susceptible to phenicoles (31.6 %) and tetracyclines (15 %) derivatives. The results emphasize the screening of plant materials before their incorporation in food matrices.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacterial Typing Techniques
- Cluster Analysis
- Cronobacter/classification
- Cronobacter/drug effects
- Cronobacter/genetics
- Cronobacter/isolation & purification
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Environmental Microbiology
- Food Microbiology
- Microbial Sensitivity Tests
- Phylogeny
- Plants, Medicinal/microbiology
- Prevalence
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Niharika Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
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15
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Lang K, Schuldes J, Klingl A, Poehlein A, Daniel R, Brune A. New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. Appl Environ Microbiol 2015; 81:1338-52. [PMID: 25501486 PMCID: PMC4309702 DOI: 10.1128/aem.03389-14] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/08/2014] [Indexed: 11/20/2022] Open
Abstract
The recently discovered seventh order of methanogens, the Methanomassiliicoccales (previously referred to as “Methanoplasmatales”), so far consists exclusively of obligately hydrogen-dependent methylotrophs. We sequenced the complete genome of “Candidatus Methanoplasma termitum” from a highly enriched culture obtained from the intestinal tract of termites and compared it with the previously published genomes of three other strains from the human gut, including the first isolate of the order. Like all other strains, “Ca. Methanoplasma termitum” lacks the entire pathway for CO2 reduction to methyl coenzyme Mand produces methane by hydrogen-dependent reduction of methanol or methylamines, which is consistent with additional physiological data. However, the shared absence of cytochromes and an energy-converting hydrogenase for the reoxidation of the ferredoxin produced by the soluble heterodisulfide reductase indicates that Methanomassiliicoccales employ a new mode of energy metabolism, which differs from that proposed for the obligately methylotrophic Methanosphaera stadtmanae. Instead, all strains possess a novel complex that is related to the F420:methanophenazine oxidoreductase (Fpo) of Methanosarcinales butlacks an F420-oxidizing module, resembling the apparently ferredoxin-dependent Fpo-like homolog in Methanosaeta thermophila. Since all Methanomassiliicoccales also lack the subunit E of the membrane-bound heterodisulfide reductase (HdrDE), wepropose that the Fpo-like complex interacts directly with subunit D, forming an energy-converting ferredoxin: heterodisulfideoxidoreductase. The dual function of heterodisulfide in Methanomassiliicoccales, which serves both in electron bifurcation and as terminal acceptor in a membrane-associated redox process, may be a unique characteristic of the novel order.
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Affiliation(s)
- Kristina Lang
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörg Schuldes
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Andreas Klingl
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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16
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Persicke M, Albersmeier A, Bednarz H, Niehaus K, Kalinowski J, Rückert C. Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T). Stand Genomic Sci 2015; 10:5. [PMID: 26203323 PMCID: PMC4510995 DOI: 10.1186/1944-3277-10-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/21/2014] [Indexed: 11/23/2022] Open
Abstract
Corynebacterium callunae DSM 20147(T) is a member of the genus Corynebacterium which contains Gram-positive and non-spore forming bacteria with a high G + C content. C. callunae was isolated during a screening for l-glutamic acid producing bacteria and belongs to the aerobic and non-haemolytic corynebacteria. As this is a type strain in a subgroup of industrial relevant bacteria for many of which there are also complete genome sequence available, knowledge of the complete genome sequence might enable genome comparisons to identify production relevant genetic loci. This project, describing the 2.84 Mbp long chromosome and the two plasmids, pCC1 (4.11 kbp) and pCC2 (85.02 kbp), with their 2,647 protein-coding and 82 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Marcus Persicke
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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Gaci N, Borrel G, Tottey W, O’Toole PW, Brugère JF. Archaea and the human gut: New beginning of an old story. World J Gastroenterol 2014; 20:16062-16078. [PMID: 25473158 PMCID: PMC4239492 DOI: 10.3748/wjg.v20.i43.16062] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/14/2014] [Accepted: 07/22/2014] [Indexed: 02/06/2023] Open
Abstract
Methanogenic archaea are known as human gut inhabitants since more than 30 years ago through the detection of methane in the breath and isolation of two methanogenic species belonging to the order Methanobacteriales, Methanobrevibacter smithii and Methanosphaera stadtmanae. During the last decade, diversity of archaea encountered in the human gastrointestinal tract (GIT) has been extended by sequence identification and culturing of new strains. Here we provide an updated census of the archaeal diversity associated with the human GIT and their possible role in the gut physiology and health. We particularly focus on the still poorly characterized 7th order of methanogens, the Methanomassiliicoccales, associated to aged population. While also largely distributed in non-GIT environments, our actual knowledge on this novel order of methanogens has been mainly revealed through GIT inhabitants. They enlarge the number of final electron acceptors of the gut metabolites to mono- di- and trimethylamine. Trimethylamine is exclusively a microbiota-derived product of nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, from which seems originate two diseases, trimethylaminuria (or Fish-Odor Syndrome) and cardiovascular disease through the proatherogenic property of its oxidized liver-derived form. This therefore supports interest on these methanogenic species and its use as archaebiotics, a term coined from the notion of archaea-derived probiotics.
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Zimmermann J, Schmidt H, Loessner MJ, Weiss A. Development of a rapid detection system for opportunistic pathogenic Cronobacter spp. in powdered milk products. Food Microbiol 2014; 42:19-25. [DOI: 10.1016/j.fm.2014.02.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/13/2014] [Accepted: 02/15/2014] [Indexed: 11/29/2022]
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Borrel G, Parisot N, Harris HMB, Peyretaillade E, Gaci N, Tottey W, Bardot O, Raymann K, Gribaldo S, Peyret P, O’Toole PW, Brugère JF. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 2014; 15:679. [PMID: 25124552 PMCID: PMC4153887 DOI: 10.1186/1471-2164-15-679] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 07/18/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of methanogens and belong to a large evolutionary branch composed by lineages of non-methanogenic archaea such as Thermoplasmatales, the Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2, Aciduliprofundum boonei) and the Marine Group-II (MG-II). To better understand this new order and its relationship to other archaea, we manually curated and extensively compared the genome sequences of three Methanomassiliicoccales representatives derived from human GIT microbiota, "Candidatus Methanomethylophilus alvus", "Candidatus Methanomassiliicoccus intestinalis" and Methanomassiliicoccus luminyensis. RESULTS Comparative analyses revealed atypical features, such as the scattering of the ribosomal RNA genes in the genome and the absence of eukaryotic-like histone gene otherwise present in most of Euryarchaeota genomes. Previously identified in Thermoplasmatales genomes, these features are presently extended to several completely sequenced genomes of this large evolutionary branch, including MG-II and DHVE2. The three Methanomassiliicoccales genomes share a unique composition of genes involved in energy conservation suggesting an original combination of two main energy conservation processes previously described in other methanogens. They also display substantial differences with each other, such as their codon usage, the nature and origin of their CRISPRs systems and the genes possibly involved in particular environmental adaptations. The genome of M. luminyensis encodes several features to thrive in soil and sediment conditions suggesting its larger environmental distribution than GIT. Conversely, "Ca. M. alvus" and "Ca. M. intestinalis" do not present these features and could be more restricted and specialized on GIT. Prediction of the amber codon usage, either as a termination signal of translation or coding for pyrrolysine revealed contrasted patterns among the three genomes and suggests a different handling of the Pyl-encoding capacity. CONCLUSIONS This study represents the first insights into the genomic organization and metabolic traits of the seventh order of methanogens. It suggests contrasted evolutionary history among the three analyzed Methanomassiliicoccales representatives and provides information on conserved characteristics among the overall methanogens and among Thermoplasmata.
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Affiliation(s)
- Guillaume Borrel
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
- />School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Nicolas Parisot
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
- />CNRS, UMR 6023, Université Blaise Pascal, 63000 Clermont-Ferrand, France
| | - Hugh MB Harris
- />School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Eric Peyretaillade
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Nadia Gaci
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - William Tottey
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Olivier Bardot
- />GReD, CNRS, UMR 6293, Inserm, UMR 1103, Clermont Université, Université d’Auvergne 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Kasie Raymann
- />Département de Microbiologie, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Paris Cedex 15, 75724 France
- />Cellule Pasteur UPMC, Université Pierre et Marie Curie, Paris Cedex 15, 75724 France
| | - Simonetta Gribaldo
- />Département de Microbiologie, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Paris Cedex 15, 75724 France
- />Cellule Pasteur UPMC, Université Pierre et Marie Curie, Paris Cedex 15, 75724 France
| | - Pierre Peyret
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Paul W O’Toole
- />School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Jean-François Brugère
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
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Montero-Calasanz MDC, Hofner B, Göker M, Rohde M, Spröer C, Hezbri K, Gtari M, Schumann P, Klenk HP. Geodermatophilus poikilotrophi sp. nov.: a multitolerant actinomycete isolated from dolomitic marble. BIOMED RESEARCH INTERNATIONAL 2014; 2014:914767. [PMID: 25114928 PMCID: PMC4119925 DOI: 10.1155/2014/914767] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/03/2014] [Accepted: 06/09/2014] [Indexed: 12/02/2022]
Abstract
A novel Gram-reaction-positive, aerobic actinobacterium, tolerant to mitomycin C, heavy metals, metalloids, hydrogen peroxide, desiccation, and ionizing- and UV-radiation, designated G18T, was isolated from dolomitic marble collected from outcrops in Samara (Namibia). The growth range was 15-35°C, at pH 5.5-9.5 and in presence of 1% NaCl, forming greenish-black coloured colonies on GYM Streptomyces agar. Chemotaxonomic and molecular characteristics of the isolate matched those described for other representatives of the genus Geodermatophilus. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diaminoacid. The main phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, and small amount of diphosphatidylglycerol. MK-9(H4) was the dominant menaquinone and galactose was detected as diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids iso-C16:0 and iso-C15:0 and the unsaturated C17:1 ω8c and C16:1 ω7c. The 16S rRNA gene showed 97.4-99.1% sequence identity with the other representatives of genus Geodermatophilus. Based on phenotypic results and 16S rRNA gene sequence analysis, strain G18T is proposed to represent a novel species, Geodermatophilus poikilotrophi. Type strain is G18T (=DSM 44209T=CCUG 63018T). The INSDC accession number is HF970583. The novel R software package lethal was used to compute the lethal doses with confidence intervals resulting from tolerance experiments.
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Affiliation(s)
- Maria del Carmen Montero-Calasanz
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Instituto de Investigacióon y Formacióon Agraria y Pesquera (IFAPA), Centro Las Torres-Tomejil, Carretera Sevilla-Cazalla de la Sierra, Km 12.2, 41200 Alcalá del Río, Sevilla, Spain
| | - Benjamin Hofner
- Institut für Medizininformatik, Biometrie und Epidemiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Waldstraße 6, 91054 Erlangen, Germany
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Manfred Rohde
- Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Karima Hezbri
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis Elmanar (FST) et Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis Elmanar (FST) et Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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