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Ahmad F, Yang GY, Liang SY, Zhou QH, Gaal HA, Mo JC. Multipartite symbioses in fungus-growing termites (Blattodea: Termitidae, Macrotermitinae) for the degradation of lignocellulose. INSECT SCIENCE 2021; 28:1512-1529. [PMID: 33236502 DOI: 10.1111/1744-7917.12890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/06/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Fungus-growing termites are among the most successful herbivorous animals and improve crop productivity and soil fertility. A range of symbiotic organisms can be found inside their nests. However, interactions of termites with these symbionts are poorly understood. This review provides detailed information on the role of multipartite symbioses (between termitophiles, termites, fungi, and bacteria) in fungus-growing termites for lignocellulose degradation. The specific functions of each component in the symbiotic system are also discussed. Based on previous studies, we argue that the enzymatic contribution from the host, fungus, and bacteria greatly facilitates the decomposition of complex polysaccharide plant materials. The host-termitophile interaction protects the termite nest from natural enemies and maintains the stability of the microenvironment inside the colony.
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Affiliation(s)
- Farhan Ahmad
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
- Entomology Section, Central Cotton Research Institute, Sakrand, Shaheed Benazirabad, Sindh, Pakistan
| | - Gui-Ying Yang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shi-You Liang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qi-Huan Zhou
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hassan Ahmed Gaal
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
- Department of Entomology, Faculty of Veterinary and Animal Husbandry, Somali National University, Mogadishu, Somalia
| | - Jian-Chu Mo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
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Baleeiro FCF, Ardila MS, Kleinsteuber S, Sträuber H. Effect of Oxygen Contamination on Propionate and Caproate Formation in Anaerobic Fermentation. Front Bioeng Biotechnol 2021; 9:725443. [PMID: 34568301 PMCID: PMC8460912 DOI: 10.3389/fbioe.2021.725443] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/19/2021] [Indexed: 01/19/2023] Open
Abstract
Mixed microbial cultures have become a preferred choice of biocatalyst for chain elongation systems due to their ability to convert complex substrates into medium-chain carboxylates. However, the complexity of the effects of process parameters on the microbial metabolic networks is a drawback that makes the task of optimizing product selectivity challenging. Here, we studied the effects of small air contaminations on the microbial community dynamics and the product formation in anaerobic bioreactors fed with lactate, acetate and H2/CO2. Two stirred tank reactors and two bubble column reactors were operated with H2/CO2 gas recirculation for 139 and 116 days, respectively, at pH 6.0 and 32°C with a hydraulic retention time of 14 days. One reactor of each type had periods with air contamination (between 97 ± 28 and 474 ± 33 mL O2 L−1 d−1, lasting from 4 to 32 days), while the control reactors were kept anoxic. During air contamination, production of n-caproate and CH4 was strongly inhibited, whereas no clear effect on n-butyrate production was observed. In a period with detectable O2 concentrations that went up to 18%, facultative anaerobes of the genus Rummeliibacillus became predominant and only n-butyrate was produced. However, at low air contamination rates and with O2 below the detection level, Coriobacteriia and Actinobacteria gained a competitive advantage over Clostridia and Methanobacteria, and propionate production rates increased to 0.8–1.8 mmol L−1 d−1 depending on the reactor (control reactors 0.1–0.8 mmol L−1 d−1). Moreover, i-butyrate production was observed, but only when Methanobacteria abundances were low and, consequently, H2 availability was high. After air contamination stopped completely, production of n-caproate and CH4 recovered, with n-caproate production rates of 1.4–1.8 mmol L−1 d−1 (control 0.7–2.1 mmol L−1 d−1). The results underline the importance of keeping strictly anaerobic conditions in fermenters when consistent n-caproate production is the goal. Beyond that, micro-aeration should be further tested as a controllable process parameter to shape the reactor microbiome. When odd-chain carboxylates are desired, further studies can develop strategies for their targeted production by applying micro-aerobic conditions.
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Affiliation(s)
- Flávio C F Baleeiro
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Process Engineering in Life Science 2, Technical Biology, Karlsruhe Institute of Technology - KIT, Karlsruhe, Germany
| | - Magda S Ardila
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Process Engineering in Life Science 2, Technical Biology, Karlsruhe Institute of Technology - KIT, Karlsruhe, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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Cheng M, Sun Y, Wang L, Tan L, Jin H, Yan S, Li S, Xiao X. Integrative analysis of microbiome and metabolome in rats with Gest-Aid Plus Oral Liquid supplementation reveals mechanism of its healthcare function. FOOD QUALITY AND SAFETY 2021. [DOI: 10.1093/fqsafe/fyab010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Abstract
Objective
This study aimed to elucidate the possible mechanism of Gest-Aid Plus Oral Liquid (GAP) on healthcare function.
Method
Ultrahigh-performance liquid chromatography–quadrupole time-of-flight mass spectrometry-based metabolomics and 16S rDNA sequencing of gut microbiota were performed on serum and fecal samples of GAP and control rats. Additionally, short-chain fatty acids (SCFAs) and inflammatory cytokines in fecal samples were determined through gas chromatography–mass spectrometry and enzyme-linked immunosorbent assay kits.
Result
Metabolomics discovered 41 metabolites, which mainly involved amino acid metabolism, lipid metabolism, coenzyme factors, and vitamin metabolism. Administration of GAP increased abundance of Prevotella_9, Alloprevotella, Blautia, Phascolarctobacterium, Parabacteroides, and Fusicatenibacter, and six SCFAs were increased in the GAP group. Measurement of inflammatory cytokines showed that GAP had an anti-inflammatory effect in rats.
Conclusion
Administration of GAP greatly affects the aspartate metabolism and microecology of rats, enhances intestinal motility and gut barrier integrity and anti-inflammation. These findings not only have possible implications for further application of GAP, but also provide a link between the gut microbiome, SCFAs, inflammation and serum metabolites in rats.
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He C, Zhang B, Yan W, Ding D, Guo J. Enhanced Microbial Chromate Reduction Using Hydrogen and Methane as Joint Electron Donors. JOURNAL OF HAZARDOUS MATERIALS 2020; 395:122684. [PMID: 32330782 DOI: 10.1016/j.jhazmat.2020.122684] [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: 01/12/2020] [Revised: 03/19/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Hydrogen and methane commonly co-exist in aquifer. Either hydrogen or methane has been individually utilized as electron donor for bio-reducing chromate. However, little is known whether microbial chromate reduction would be suppressed or promoted when both hydrogen and methane are simultaneously supplied as joint electron donors. This study for the first time demonstrated microbial chromate reduction rate could be accelerated by both hydrogen and methane donating electrons. The maximum chromate reduction rate (4.70 ± 0.03 mg/L·d) with a volume ratio of hydrogen to methane at 1:1 was significantly higher than that with pure hydrogen (2.53 ± 0.02 mg/L·d) or pure methane (2.01 ± 0.02 mg/L·d) as the sole electron donor (p < 0.01). High-throughput 16S rRNA gene amplicon sequencing detected potential chromate reducers (e.g., Spirochaetaceae, Delftia and Azonexus) and hydrogenotrophic bacteria (e.g., Acetoanaerobium) and methane-metabolizing microorganisms (e.g., Methanobacterium), indicating that these microorganisms might play important roles on microbial chromate reduction using both hydrogen and methane as electron donors. Abundant hupL and mcrA genes responsible for hydrogen oxidation and methane conversion were harbored, together with chrA gene for chromate reduction. More abundant extracellular cytochrome c and intracellular NADH were detected with joint electron donors, suggesting more active electron transfers.
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Affiliation(s)
- Chao He
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Baogang Zhang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, China.
| | - Wenyue Yan
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Dahu Ding
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland, 4072, Australia
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5
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Zeng W, Liu B, Zhong J, Li Q, Li Z. A Natural High-Sugar Diet Has Different Effects on the Prokaryotic Community Structures of Lower and Higher Termites (Blattaria). ENVIRONMENTAL ENTOMOLOGY 2020; 49:21-32. [PMID: 31782953 DOI: 10.1093/ee/nvz130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 06/10/2023]
Abstract
The lignocellulosic digestive symbiosis in termites is a dynamic survival adaptation system. While the contribution of hereditary and habitat factors to the development of the symbiotic bacterial community of termites had been confirmed, the manner in which these factors affect functional synergism among different bacterial lineages has still not been fully elucidated. Therefore, the 16S rRNA gene libraries of Odontotermes formosanus Shiraki (Blattodea: Termitidae) and Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) sampled from sugarcane fields (high sugar) or pine tree forests (no free sugar) were sequenced. The results verify that the prokaryotic community structures of termites could be significantly reshaped by native dietary isolation within a species. Although the most dominant phyla are convergent in all samples, their relative abundances in these two termite species exhibited a reverse variation pattern when the termite hosts were fed on the high-sugar diet. Furthermore, we showed that the taxonomic composition of the dominant phyla at the family or genus level differentiate depending on the diet and the host phylogeny. We hypothesize that the flexible bacterial assemblages at low taxonomic level might exert variable functional collaboration to accommodate to high-sugar diet. In addition, the functional predictions of Tax4Fun suggest a stable metabolic functional structure of the microbial communities of the termites in both different diet habitats and taxonomy. We propose that the symbiotic bacterial community in different host termites developed a different functional synergistic pattern, which may be essential to maintain the stability of the overall metabolic function for the survival of termites.
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Affiliation(s)
- Wenhui Zeng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Bingrong Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Junhong Zhong
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Qiujian Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Zhiqiang Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
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6
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Yang Z, Zhang Y, Lv Y, Yan W, Xiao X, Sun B, Ma H. H 2 Metabolism revealed by metagenomic analysis of subglacial sediment from East Antarctica. J Microbiol 2019; 57:1095-1104. [PMID: 31758395 DOI: 10.1007/s12275-019-9366-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/14/2019] [Accepted: 11/06/2019] [Indexed: 01/17/2023]
Abstract
Subglacial ecosystems harbor diverse chemoautotrophic microbial communities in areas with limited organic carbon, and lithological H2 produced during glacial erosion has been considered an important energy source in these ecosystems. To verify the H2-utilizing potential there and to identify the related energy-converting metabolic mechanisms of these communities, we performed metagenomic analysis on subglacial sediment samples from East Antarctica with and without H2 supplementation. Genes coding for several [NiFe]-hydrogenases were identified in raw sediment and were enriched after H2 incubation. All genes in the dissimilatory nitrate reduction and denitrification pathways were detected in the subglacial community, and the genes coding for these pathways became enriched after H2 was supplied. Similarly, genes transcribing key enzymes in the Calvin cycle were detected in raw sediment and were also enriched. Moreover, key genes involved in H2 oxidization, nitrate reduction, oxidative phosphorylation, and the Calvin cycle were identified within one metagenome-assembled genome belonging to a Polaromonas sp. As suggested by our results, the microbial community in the subglacial environment we investigated consisted of chemoautotrophic populations supported by H2 oxidation. These results further confirm the importance of H2 in the cryosphere.
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Affiliation(s)
- Zhifeng Yang
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, P. R. China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Yu Zhang
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Yongxin Lv
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Wenkai Yan
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xiang Xiao
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Bo Sun
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, P. R. China
| | - Hongmei Ma
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, P. R. China.
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7
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Chen F, Jin W, Gao H, Guo Z, Lin H, Li J, Hu K, Guan X, Kalia VC, Lee JK, Zhang L, Li Y. Cloning, Expression and Characterization of Two Beta Carbonic Anhydrases from a Newly Isolated CO 2 Fixer, Serratia marcescens Wy064. Indian J Microbiol 2019; 59:64-72. [PMID: 30728632 DOI: 10.1007/s12088-018-0773-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/06/2018] [Indexed: 12/20/2022] Open
Abstract
Bacterial strains from karst landform soil were enriched via chemostat culture in the presence of sodium bicarbonate. Two chemolithotrophic strains were isolated and identified as Serratia marcescens Wy064 and Bacillus sp. Wy065. Both strains could grow using sodium bicarbonate as the sole carbon source. Furthermore, the supplement of the medium with three electron donors (Na2S, NaNO2, and Na2S2O3) improved the growth of both strains. The activities of carbonic anhydrase (CA) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) could be detected in the crude enzyme of strain Wy064, implying that the strain Wy064 might employ Calvin cycle to fix CO2. S. marcescens genome mining revealed four potential CA genes designated CA1-CA4. The proteins encoded by genes CA1-3 were cloned and expressed in Escherichia coli. The purified recombinant enzymes of CA1 and CA3 exhibited CO2 hydration activities, whereas enzyme CA2 was expressed in inclusion bodies. A CO2 hydration assay demonstrated that the specific activity of CA3 was significantly higher than that of CA1. The maximum CO2 hydration activities for CA1 and CA3 were observed at pH 7.5 and 40 °C. The activities of CA1 and CA3 were significantly enhanced by several metal ions, especially Zn2+, which resulted in 21.1-fold and 26.1-fold increases of CO2 hydration activities, respectively. The apparent K m and V max for CO2 as substrate were 27 mM and 179 WAU/mg for CA1, and 14 mM and 247 WAU/mg for CA3, respectively. Structure modeling combined with sequence analysis indicated that CA1 and CA3 should belong to the Type II β-CA.
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Affiliation(s)
- Fanbing Chen
- 1College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
| | - Wensong Jin
- 1College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
| | - Huifang Gao
- 1College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
| | - Zewang Guo
- 1College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
| | - Hui Lin
- 1College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
| | - Jiahuan Li
- 1College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
| | - Kaihui Hu
- 1College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
| | - Xiong Guan
- 1College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
| | - Vipin C Kalia
- 2Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- 2Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Liaoyuan Zhang
- 1College of Life Sciences, Gutian Edible Fungi Research Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
- 2Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Yongyu Li
- 3College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
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8
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Herrero J, Puigserver D, Nijenhuis I, Kuntze K, Carmona JM. Combined use of ISCR and biostimulation techniques in incomplete processes of reductive dehalogenation of chlorinated solvents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:819-829. [PMID: 30138882 DOI: 10.1016/j.scitotenv.2018.08.184] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/16/2018] [Accepted: 08/16/2018] [Indexed: 05/20/2023]
Affiliation(s)
- Jofre Herrero
- Department of Minerology, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona, Carrer Martí Franquès SN, Barcelona, Spain..
| | - Diana Puigserver
- Department of Minerology, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona, Carrer Martí Franquès SN, Barcelona, Spain
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry (ISOBIO), UFZ Centre for Environmental Research Leipzig-Halle, Permoserstr. 15, 04318 Leipzig, Germany
| | - Kevin Kuntze
- Department of Isotope Biogeochemistry (ISOBIO), UFZ Centre for Environmental Research Leipzig-Halle, Permoserstr. 15, 04318 Leipzig, Germany
| | - José M Carmona
- Department of Minerology, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona, Carrer Martí Franquès SN, Barcelona, Spain
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Ray AE, Connon SA, Neal AL, Fujita Y, Cummings DE, Ingram JC, Magnuson TS. Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment. Front Microbiol 2018; 9:1689. [PMID: 30174652 PMCID: PMC6107796 DOI: 10.3389/fmicb.2018.01689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/06/2018] [Indexed: 01/11/2023] Open
Abstract
The capability of microorganisms to alter metal speciation offers potential for the development of new strategies for immobilization of toxic metals in the environment. A metal-reducing microbe, "Pelosinus lilae" strain UFO1, was isolated under strictly anaerobic conditions from an Fe(III)-reducing enrichment established with uncontaminated soil from the Department of Energy Oak Ridge Field Research Center, Tennessee. "P. lilae" UFO1 is a rod-shaped, spore-forming, and Gram-variable anaerobe with a fermentative metabolism. It is capable of reducing the humic acid analog anthraquinone-2,6-disulfonate (AQDS) using a variety of fermentable substrates and H2. Reduction of Fe(III)-nitrilotriacetic acid occurred in the presence of lactate as carbon and electron donor. Ferrihydrite was not reduced in the absence of AQDS. Nearly complete reduction of 1, 3, and 5 ppm Cr(VI) occurred within 24 h in suspensions containing 108 cells mL-1 when provided with 10 mM lactate; when 1 mM AQDS was added, 3 and 5 ppm Cr(VI) were reduced to 0.1 ppm within 2 h. Strain UFO1 is a novel species within the bacterial genus Pelosinus, having 98.16% 16S rRNA gene sequence similarity with the most closely related described species, Pelosinus fermentans R7T. The G+C content of the genomic DNA was 38 mol%, and DNA-DNA hybridization of "P. lilae" UFO1 against P. fermentans R7T indicated an average 16.8% DNA-DNA similarity. The unique phylogenetic, physiologic, and metal-transforming characteristics of "P. lilae" UFO1 reveal it is a novel isolate of the described genus Pelosinus.
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Affiliation(s)
- Allison E. Ray
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- Idaho National Laboratory, Idaho Falls, ID, United States
| | - Stephanie A. Connon
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- California Institute of Technology, Pasadena, CA, United States
| | - Andrew L. Neal
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Yoshiko Fujita
- Idaho National Laboratory, Idaho Falls, ID, United States
| | - David E. Cummings
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Jani C. Ingram
- Idaho National Laboratory, Idaho Falls, ID, United States
| | - Timothy S. Magnuson
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
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10
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Tegtmeier D, Belitz A, Radek R, Heimerl T, Brune A. Ereboglobus luteus gen. nov. sp. nov. from cockroach guts, and new insights into the oxygen relationship of the genera Opitutus and Didymococcus ( Verrucomicrobia : Opitutaceae ). Syst Appl Microbiol 2018; 41:101-112. [DOI: 10.1016/j.syapm.2017.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/19/2017] [Accepted: 10/28/2017] [Indexed: 11/25/2022]
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11
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Mikkelson KM, Homme CL, Li D, Sharp JO. Propane biostimulation in biologically activated carbon (BAC) selects for bacterial clades adept at degrading persistent water pollutants. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2015; 17:1405-1414. [PMID: 26154499 DOI: 10.1039/c5em00212e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biologically activated carbon (BAC) can be used in both municipal water and hazardous waste remediation applications to enhance contaminant attenuation in water; however, questions remain about how selective pressures can be applied to increase the capabilities of microbial communities to attenuate recalcitrant contaminants. Here we utilized flow-through laboratory columns seeded with municipally derived BAC and exposed to water from a local drinking water facility to query how propane biostimulation impacts resident microorganisms. Ecological analyses using high throughput phylogenetic sequencing revealed that while propane did not increase the total number of microbiological species, it did select for bacterial communities that were distinct from those without propane. Temporal extractions demonstrated that microbial succession was rapid and established in approximately 2 months. A higher density of propane monooxygenase genes and bacterial clades including the Pelosinus and Dechloromonas genera suggest an enhanced potential for the degradation of persistent water pollutants in propane-stimulated systems. However, the ecological selective pressure was exhausted in less than 15 cm of transit in this flow-through scenario (25 hour retention) indicating a pronounced zonation that could limit the size of a biostimulated zone and require physical mixing, hydraulic manipulation, or other strategies to increase the spatial impact of biostimulation in flow-through scenarios.
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Affiliation(s)
- Kristin M Mikkelson
- ReNUWit Engineering Research Center, Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA.
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12
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Tetrachloromethane-Degrading Bacterial Enrichment Cultures and Isolates from a Contaminated Aquifer. Microorganisms 2015; 3:327-43. [PMID: 27682092 PMCID: PMC5023247 DOI: 10.3390/microorganisms3030327] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/09/2015] [Accepted: 06/18/2015] [Indexed: 01/05/2023] Open
Abstract
Abstract: The prokaryotic community of a groundwater aquifer exposed to high concentrations of tetrachloromethane (CCl4) for more than three decades was followed by terminal restriction fragment length polymorphism (T-RFLP) during pump-and-treat remediation at the contamination source. Bacterial enrichments and isolates were obtained under selective anoxic conditions, and degraded 10 mg·L−1 CCl4, with less than 10% transient formation of chloroform. Dichloromethane and chloromethane were not detected. Several tetrachloromethane-degrading strains were isolated from these enrichments, including bacteria from the Klebsiella and Clostridium genera closely related to previously described CCl4 degrading bacteria, and strain TM1, assigned to the genus Pelosinus, for which this property was not yet described. Pelosinus sp. TM1, an oxygen-tolerant, Gram-positive bacterium with strictly anaerobic metabolism, excreted a thermostable metabolite into the culture medium that allowed extracellular CCl4 transformation. As estimated by T-RFLP, phylotypes of CCl4-degrading enrichment cultures represented less than 7%, and archaeal and Pelosinus strains less than 0.5% of the total prokaryotic groundwater community.
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Wang YN, Wang L, Shan YN, Hu J, Tsang Y, Hu Y, Fu X, Le Y. Optimization of inorganic carbon sources to improve the carbon fixation efficiency of the non-photosynthetic microbial community with different electron donors. ENVIRONMENTAL TECHNOLOGY 2015; 36:1246-1255. [PMID: 25367398 DOI: 10.1080/09593330.2014.983991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
As the non-photosynthetic microbial community (NPMC) isolated from seawaters utilized inorganic carbon sources for carbon fixation, the concentrations and ratios of Na2CO3, NaHCO3, and CO2 were optimized by response surface methodology design. With H2 as the electron donor, the optimal carbon sources were 270 mg/L Na2CO3, 580 mg/L NaHCO3, and 120 mg/L CO2. The carbon fixation efficiency in response to total organic carbon (TOC) was up to 30.59 mg/L with optimal carbon sources, which was about 50% higher than that obtained with CO2 as the sole carbon source. The mixture of inorganic carbon sources developed a buffer system to prevent acidification or alkalization of the medium caused by CO2 or Na2CO3, respectively. Furthermore, CO2 and HCO3(-), the starting points of carbon fixation in the pathways of Calvin-Benson-Bassham and 3-hydroxypropionate cycles, were provided by the carbon source structure to facilitate carbon fixation by NPMC. However, in the presence of mixed electron donors composed of 1.25% Na2S, 0.50% Na2S2O3, and 0.457% NaNO2, the carbon source structure did not exhibit significant improvement in the carbon fixation efficiency, when compared with that achieved with CO2 as the sole carbon source. The positive effect of mixed electron donors on inorganic carbon fixation was much higher than that of the carbon source structure. Nevertheless, the carbon source structure could be used as an alternative to CO2 when using NPMC to fix carbon in industrial processes.
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Affiliation(s)
- Ya-nan Wang
- a State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering , Tongji University , Shanghai 200092 , People's Republic of China
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15
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Rosendale DI, Blatchford PA, Sims IM, Parkar SG, Carnachan SM, Hedderley D, Ansell J. Characterizing kiwifruit carbohydrate utilization in vitro and its consequences for human faecal microbiota. J Proteome Res 2012; 11:5863-75. [PMID: 23072625 DOI: 10.1021/pr300646m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
It is well accepted that our gut bacteria have coevolved with us in relation to our genetics, diet and lifestyle and are integrated metabolically with us to affect our gut health adversely or beneficially. "Who is there" may vary quite widely between individuals, as might "how they do it", but "what they make" may be less variable. Many different individual species of bacteria can perform the same saccharolytic functions and so the availability of substrate (host or diet-derived) along with the degradative enzymes they possess may be key drivers of gut ecology. In this case study, we discuss detailed microbial ecology and metabolism analysis for three individuals following 48 h of in vitro faecal fermentation, using green kiwifruit as the substrate. In parallel, we have analyzed the chemical changes to the kiwifruit carbohydrates present in the fermenta to close the circle on substrate usage/degradative enzymes possessed/microbes present/microbial byproducts produced. In the absence of host carbohydrate, we see that kiwifruit carbohydrates were differentially utilized to drive microbial diversity, yet resulted in similar byproduct production. The starting ecology of each individual influenced the quantitative and qualitative microbial changes; but not necessarily the metabolic byproduct production. Thus, we propose that it is the consistent functional changes that are relevant for assessment of gut health benefits of any food. We recommend that in this era of large scale genotype/-omics studies that hypothesis-driven, bottom-up research is best placed to interpret metagenomic data in parallel with functional, phenotypic data.
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Affiliation(s)
- Douglas I Rosendale
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
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16
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Genomic and physiological characterization of the chromate-reducing, aquifer-derived Firmicute Pelosinus sp. strain HCF1. Appl Environ Microbiol 2012; 79:63-73. [PMID: 23064329 DOI: 10.1128/aem.02496-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pelosinus spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with aquifer sediment. Strain HCF1 ferments lactate to propionate and acetate (the methylmalonyl-coenzyme A [CoA] pathway was identified in the genome), and its genome encodes two [NiFe]- and four [FeFe]-hydrogenases for H(2) cycling. The reduction of Cr(VI) and Fe(III) may be catalyzed by a flavoprotein with 42 to 51% sequence identity to both ChrR and FerB. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides, including dissimilatory reduction of nitrate to ammonium (two copies of NrfH and NrfA were identified along with NarGHI) and a nitric oxide reductase (NorCB). In this strain, either H(2) or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of hydrogenases and nitrate and nitrite reductases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.
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17
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Moe WM, Stebbing RE, Rao JU, Bowman KS, Nobre MF, da Costa MS, Rainey FA. Pelosinus
defluvii sp. nov., isolated from chlorinated solvent-contaminated groundwater, emended description of the genus
Pelosinus
and transfer of
Sporotalea propionica
to Pelosinus
propionicus comb. nov. Int J Syst Evol Microbiol 2012; 62:1369-1376. [DOI: 10.1099/ijs.0.033753-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two anaerobic bacterial strains, designated SHI-1T and SHI-2, were isolated from chlorinated solvent-contaminated groundwater. They were found to be identical in phenotypic properties and shared high (98.5–99.8 %) pairwise 16S rRNA gene sequence similarity. Multiple 16S rRNA genes were found to be present in the isolates as well as
Pelosinus fermentans
DSM 17108T and
Sporotalea propionica
DSM 13327T. Strains SHI-1T and SHI-2 could be differentiated from their closest phylogenetic relatives,
P. fermentans
DSM 17108T and
S. propionica
DSM 13327T, on the basis of their phenotypic and phylogenetic properties. The isolates were Gram-negative, spore-forming, motile rods with peritrichous flagella. Growth occurred at 10–42 °C and pH 5.5–8.5. Fermentative growth was observed on Casamino acids, fructose, fumarate, glucose, glycerol, pyruvate and yeast extract. The major organic acids produced from glucose and glycerol fermentation were propionate and acetate. The major organic acids produced from fermentation of fumarate were propionate, acetate and succinate. The major cellular fatty acids were summed feature 4 (consisting of C15 : 1ω8c and/or C15 : 2), summed feature 8 (consisting of C17 : 1ω8c and/or C17 : 2) and C14 : 0 dimethyl aldehyde. The polar lipids comprised aminophospholipids, including phosphatidylethanolamine and phosphatidylserine, and an unknown phospholipid. The genomic DNA G+C content was 39.2 mol%. We propose that strains SHI-1T and SHI-2 are assigned to a novel species of the genus
Pelosinus
, with the name Pelosinus
defluvii sp. nov. (type strain SHI-1T = NRRL Y-59407T = LMG 25549T). The description of the genus
Pelosinus
is emended. We also propose the transfer of
S. propionica
to the genus
Pelosinus
as Pelosinus
propionicus comb. nov. (type strain TmPN3T = DSM 13327T = ATCC BAA-626T), on the basis of phylogenetic, chemotaxonomic and phenotypic properties.
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Affiliation(s)
- William M. Moe
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Rachael E. Stebbing
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jyoti U. Rao
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kimberly S. Bowman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Civil and Environmental Engineering, 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
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal
| | - Fred A. Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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Hu JJ, Wang L, Zhang SP, Fu XH, Le YQ, Li HR. Enhanced CO2 fixation by a non-photosynthetic microbial community under anaerobic conditions: optimization of electron donors. BIORESOURCE TECHNOLOGY 2011; 102:3220-3226. [PMID: 21115242 DOI: 10.1016/j.biortech.2010.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Revised: 11/01/2010] [Accepted: 11/03/2010] [Indexed: 05/30/2023]
Abstract
To enhance the CO(2) fixation efficiency of the non-photosynthetic microbial community (NPMC) isolated from sea water under anaerobic conditions without hydrogen, the concentration of inorganic compounds as electron donors and their ratios were optimized by response surface methodology design (RSMD). The results indicated that the CO(2) fixation efficiency of NPMC using NaNO(2), Na(2)S(2)O(3) and Na(2)S as the electron donors was increased about 90%, 75% and 207%, respectively. Additionally, there were interactions between two electron donors and three electron donors. Central composite RSMD experimentation predicted that the optimal concentration and ratios of these inorganic compounds was 1.04% NaNO(2), 1.07% Na(2)S(2)O(3) and 0.98% Na(2)S. Under these conditions, the fixed CO(2) was 139.89 mg/L, which obviously exceeded the amount prior to optimization, as well as when H(2) was used as an electron donor. The established electron donor system can effectively enhance the CO(2) fixation efficiency of NPMC without hydrogen under anaerobic conditions.
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Affiliation(s)
- Jia-Jun Hu
- School of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China
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A simple and rapid GC/MS method for the simultaneous determination of gaseous metabolites. J Microbiol Methods 2010; 84:46-51. [PMID: 20971136 DOI: 10.1016/j.mimet.2010.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/13/2010] [Accepted: 10/13/2010] [Indexed: 11/20/2022]
Abstract
We modified and tuned a commercial model of a gas chromatography/mass spectrometry (GC/MS) instrument to develop a simple and rapid method for the simultaneous quantification of a variety of gas species. Using the developed method with the newly modified instrument, gas species such as H(2), N(2), O(2), CO, NO, CH(4), CO(2), and N(2)O, which are common components of microbial metabolism, were accurately identified based on their retention times and/or mass-to-charge ratios (m/z) in less than 2.5 min. By examining the sensitivities and dynamic ranges for the detection of H(2), N(2), O(2), CH(4), CO(2), and N(2)O, it was demonstrated that the method developed in this study was sufficient for accurately monitoring the production and the consumption of these gaseous species during microbial metabolism. The utility of the new method was demonstrated by a denitrification study with Pseudomonas aureofaciens ATCC 13985(T). This method will be suitable for a variety of applications requiring the identification of gaseous metabolites in microorganisms, microbial communities, and natural ecosystems.
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Ray AE, Connon SA, Sheridan PP, Gilbreath J, Shields M, Newby DT, Fujita Y, Magnuson TS. Intragenomic heterogeneity of the 16S rRNA gene in strain UFO1 caused by a 100-bp insertion in helix 6. FEMS Microbiol Ecol 2010; 72:343-53. [PMID: 20557571 DOI: 10.1111/j.1574-6941.2010.00868.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Two different versions of the 16S rRNA gene, one of which contained an unusual 100-bp insertion in helix 6, were detected in isolate UFO1 acquired from the Oak Ridge Integrated Field-Research Challenge (ORIFRC) site in Tennessee. rRNA was extracted from UFO1 and analyzed by reverse transcriptase-quantitative PCR with insert- and non-insert-specific primers; only the noninsert 16S rRNA gene sequence was detected. Similarly, PCR-based screening of a cDNA library (190 clones) constructed from reverse-transcribed rRNA from UFO1 did not detect any clones containing the 100-bp insert. Examination of cDNA with primers specific to the insert-bearing 16S rRNA gene, but downstream of the insert, suggests that the insert was excised from rRNA. Inspection of other 16S rRNA genes in the GenBank database revealed that a homologous insert sequence, also found in helix 6, has been reported in other environmental clones, including those acquired from ORIFRC enrichments. These findings demonstrate the existence of widely divergent copies of the 16S rRNA gene within the same organism, which may confound 16S rRNA gene-based methods of estimating microbial diversity in environmental samples.
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Affiliation(s)
- Allison E Ray
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA.
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21
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Bifidobacteria in the digestive tract of bumblebees. Anaerobe 2010; 16:165-70. [DOI: 10.1016/j.anaerobe.2009.07.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 07/15/2009] [Accepted: 07/20/2009] [Indexed: 11/22/2022]
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Naphthalecin, a Novel Antibiotic Produced by the Anaerobic Bacterium, Sporotalea colonica sp. nov. J Antibiot (Tokyo) 2008; 61:207-12. [DOI: 10.1038/ja.2008.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Tholen A, Pester M, Brune A. Simultaneous methanogenesis and oxygen reduction by Methanobrevibacter cuticularis at low oxygen fluxes. FEMS Microbiol Ecol 2007; 62:303-12. [DOI: 10.1111/j.1574-6941.2007.00390.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2007; 57:893-897. [PMID: 17473228 DOI: 10.1099/ijs.0.65207-0] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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