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Li Y, Wang T, Jing H, Xiao Y. Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep-sea biosphere. Mol Ecol 2024; 33:e17372. [PMID: 38709214 DOI: 10.1111/mec.17372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/02/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
The NC10 phylum links anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophic pathway. Although numerous amplicon-based studies revealed the distribution of this phylum, comprehensive genomic insights and niche characterization in deep-sea environments were still largely unknown. In this study, we extensively surveyed the NC10 bacteria across diverse deep-sea environments, including waters, sediments, cold seeps, biofilms, rocky substrates, and subseafloor aquifers. We then reconstructed and analysed 38 metagenome-assembled genomes (MAGs), and revealed the extensive distribution of NC10 bacteria and their intense selective pressure in these harsh environments. Isotopic analyses combined with gene expression profiling confirmed that active nitrite-dependent anaerobic methane oxidation (n-DAMO) occurs within deep-sea sediments. In addition, the identification of the Wood-Ljungdahl (WL) and 3-hydroxypropionate/4-hydroxybutyrat (3HB/4HP) pathways in these MAGs suggests their capability for carbon fixation as chemoautotrophs in these deep-sea environments. Indeed, we found that for their survival in the oligotrophic deep-sea biosphere, NC10 bacteria encode two branches of the WL pathway, utilizing acetyl-CoA from the carbonyl branch for citric acid cycle-based energy production and methane from the methyl branch for n-DAMO. The observed low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS) in n-DAMO-related genes across these habitats suggest a pronounced purifying selection that is critical for the survival of NC10 bacteria in oligotrophic deep-sea environments. These findings not only advance our understanding of the evolutionary adaptations of NC10 bacteria but also underscore the intricate coupling between the carbon and nitrogen cycles within deep-sea ecosystems, driven by this bacterial phylum.
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Affiliation(s)
- Yingdong Li
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Ting Wang
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Yao Xiao
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
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Chen LB, OuYang YT, Liu L, Jin PJ, Huang RR, Pan WY, Wang Y, Xing JY, She TT, Jiao JY, Wang S, Li WJ. Methylobacterium nigriterrae sp. nov., isolated from black soil. Antonie Van Leeuwenhoek 2024; 117:83. [PMID: 38806744 DOI: 10.1007/s10482-024-01981-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/18/2024] [Indexed: 05/30/2024]
Abstract
An aerobic, Gram-stain-negative, motile rod bacterium, designated as SYSU BS000021T, was isolated from a black soil sample in Harbin, Heilongjiang province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Methylobacterium, and showed the highest sequence similarity to Methylobacterium segetis KCTC 62267 T (98.51%) and Methylobacterium oxalidis DSM 24028 T (97.79%). Growth occurred at 20-37℃ (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0% (w/v) NaCl. Polar lipids comprised of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified polar lipid. The major cellular fatty acids (> 5%) were C18:0 and C18:1 ω7c and/or C18:1 ω6c. The predominant respiratory quinone was Q-10. The genomic G + C content was 68.36% based on the whole genome analysis. The average nucleotide identity (≤ 83.5%) and digital DNA-DNA hybridization (≤ 27.3%) values between strain SYSU BS000021T and other members of the genus Methylobacterium were all lower than the threshold values recommended for distinguishing novel prokaryotic species. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain SYSU BS000021T represents a novel species of the genus Methylobacterium, for which the name Methylobacterium nigriterrae sp. nov. is proposed. The type strain of the proposed novel species is SYSU BS000021T (= GDMCC 1.3814 T = KCTC 8051 T).
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Affiliation(s)
- Le-Bin Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu-Ting OuYang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Pin-Jiao Jin
- Heilongjiang Academy of Black Soil Conservation & Utilization/Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin, 150086, People's Republic of China
| | - Rong-Rong Huang
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Wen-Yi Pan
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Ying Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Ying Xing
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ting-Ting She
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation & Utilization/Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin, 150086, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Chen Y, Lv AP, Li MM, OuYang YT, Lian ZH, Chen LB, Liu ZT, Liu L, Jiao JY, Li WJ. Ferviditalea candida gen. nov., sp. nov., a novel member of the family Paenibacillaceae isolated from a geothermal area. Anaerobe 2024:102866. [PMID: 38797261 DOI: 10.1016/j.anaerobe.2024.102866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
OBJECTIVE The family Paenibacillaceae is linked to the order Caryophanales. Paenibacillaceae members residing in compost or soil play crucial roles in nutrient recycling and breaking down complex organic materials. However, our understanding of Paenibacillaceae remains limited. METHODS Strain SYSU GA230002T was conclusively identified using a polyphasic taxonomic approach frequently utilized in bacterial systematics. Standard microbiological techniques were employed to characterize the morphology and biochemistry of strain SYSU GA230002T. RESULTS An anaerobic and Gram-stain-negative bacterium, designated SYSU GA230002T, was isolated from geothermally heated soil of Tengchong, Yunnan Province, south-west China. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain SYSU GA230002T belongs to the family Paenibacillaceae. 16S rRNA gene sequence similarity (<94.0%), ANI (<71.95%) and AAI values (<58.67%) between strain SYSU GA230002T with other members of the family were lower than the threshold values recommended for distinguishing novel species. Growth was observed at 30-45ºC (optimum, 37ºC), pH 7.0-8.0 (optimum, pH 7.5) and in 0-3.0% (w/v) NaCl concentrations (optimum, 0%). The major fatty acids detected were anteiso-C15:0, iso-C16:0 and iso-C17:0. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid, one unidentified aminolipid and two unidentified glycolipids. The respiratory quinone was MK-7. The DNA G+C content of strain SYSU GA230002T was 49.87%. CONCLUSION Based on the results of morphological, physiological properties, and chemotaxonomic characteristics, this strain is proposed to represent a new species of a new genus Ferviditalea candida gen. nov., sp. nov. The type strain of the type species is SYSU GA230002T (=KCTC 25726T=GDMCC 1.4160T).
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Yu-Ting OuYang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Le-Bin Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, PR China.
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Qi YL, Chen YT, Xie YG, Li YX, Rao YZ, Li MM, Xie QJ, Cao XR, Chen L, Qu YN, Yuan ZX, Xiao ZC, Lu L, Jiao JY, Shu WS, Li WJ, Hedlund BP, Hua ZS. Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes. Nat Commun 2024; 15:4066. [PMID: 38744885 PMCID: PMC11094006 DOI: 10.1038/s41467-024-48498-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.
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Affiliation(s)
- Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Ya-Ting Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang-Zhi Rao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Jun Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Xing-Ru Cao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lei Chen
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhen-Xuan Yuan
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhi-Chao Xiao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.
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Yang ZW, Liu WL, Zhang P, Guo DY, Wang HC, Li JL, Wang PD, Dong GX, Nie GX, Li WJ. Stomatohabitans albus gen. nov., sp. nov., an oral living facultative anaerobic actinobacteria isolated form Steller sea lion, and proposal of Stomatohabitantaceae fam. nov. and Stomatohabitantales ord. nov. Syst Appl Microbiol 2024; 47:126501. [PMID: 38460344 DOI: 10.1016/j.syapm.2024.126501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Two novel actinobacteria, designated as SYSU M7M538T and SYSU M7M531, were isolated from oral of Eumetopias jubatus in Zhuhai Chimelong Ocean Kingdom, China. The cells of these microorganisms stained Gram-positive and were rod shaped. These strains were facultative anaerobic, and catalase-positive. Optimal growth occurred at 37 °C and pH 7.0 over 7 days of cultivation. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol and phosphocholine as the major polar lipids. The main menaquinone was MK-9(H4). The major fatty acids were C16:0, C17:1w8c, C17:0, C18:1w9c and C18:0. Analyses of genome sequences revealed that the genome size of SYSU M7M538T was 2.1 Mbp with G + C content of 52.5 %, while the genome size of SYSU M7M531 was 2.3 Mbp with G + C content of 52.7 %. The ANI and 16S rRNA gene analysis results showed that the pairwise similarities between the two strains and other recognized Nitriliruptoria species were less than 64.9 % and 89.0 %, respectively. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strains SYSU M7M538T and SYSU M7M531 formed a well-separated phylogenetic branch distinct from other orders of Nitriliruptoria. Based on the data presented here, these two strains are considered to represent a novel species of a novel genus, for which the name Stomatohabitans albus gen. nov., sp. nov., with the type strain SYSU M7M538T (=KCTC 59113T = GDMCC 1.4286T), are proposed. We also propose that these organisms represent a novel family named Stomatohabitantaceae fam. nov. of a novel order Stomatohabitantales ord. nov.
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Affiliation(s)
- Zi-Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Li Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China
| | - Peng Zhang
- Guangdong Chimelong Group Co., Ltd., Guangzhou, 510275, PR China
| | - Dan-Yuan Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Hong-Chuan Wang
- Jiangsu Province Engineering Research Center for Marine Bio‑resources Sustainable Utilization and College of Oceanography, Hohai University, Nanjing 210098, PR China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Gui-Xin Dong
- Guangdong Chimelong Group Co., Ltd., Guangzhou, 510275, PR China.
| | - Guo-Xing Nie
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
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Wu W, Li Z, Liu G, Zhou L, Wang W. Regulation on C2-C8 carboxylic acid biosynthesis from anaerobic CO 2 fermentation. Eng Life Sci 2024; 24:2200069. [PMID: 38708418 PMCID: PMC11065331 DOI: 10.1002/elsc.202200069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Bioconversion of CO2 into liquid fuels or chemicals, preferred medium chain carboxylic acids (caproic and caprylic acid), is an attractive CO2 utilization technology. The present study aims to investigate the effects of different ratios of H2/CO2 on regulating the distribution of C2-C8 carboxylic acid products, while the headspace pressure of 1.5 bar was set to amplify the effect of different ratios. The H2/CO2 ratio of 4:1 was more suitable for preparing acetic acid, where the highest acetic acid yield was 17.5 g/L. And the H2/CO2 ratio of 2:1 showed excellent chain elongation ability with the highest n-caprylic yield of 2.4 g/L. Additionally, the actual H2/CO2 ratios of 4:1 reactors were higher than that in 2:1 may be course chain elongation often accompanied by H2 production. The 16S rRNA genes analysis shows that the genus Terrisporobacter and Coriobacteriales may be related to acetic acid production enriched in H2/CO2 ratio 4:1 reactors, and the genus Clostridium and Paenibacillaceae may associate with the chain elongation pathway were enriched in H2/CO2 ratio 2:1 reactors.
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Affiliation(s)
- Wanling Wu
- College of Chemical EngineeringBeijing University of Chemical TechnologyBeijingChina
- Biomass Energy and Environmental Engineering Research CenterBeijing University of Chemical TechnologyBeijingChina
| | - Zhiqi Li
- College of Chemical EngineeringBeijing University of Chemical TechnologyBeijingChina
| | - Guangqing Liu
- Biomass Energy and Environmental Engineering Research CenterBeijing University of Chemical TechnologyBeijingChina
| | - Ling Zhou
- Modern Agricultural Engineering Key Laboratory at Universities of Education Department of Xinjiang Uygur Autonomous RegionTarim UniversityAlarXinjiangChina
| | - Wen Wang
- College of Chemical EngineeringBeijing University of Chemical TechnologyBeijingChina
- Biomass Energy and Environmental Engineering Research CenterBeijing University of Chemical TechnologyBeijingChina
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Aguilar C, Alwali A, Mair M, Rodriguez-Orduña L, Contreras-Peruyero H, Modi R, Roberts C, Sélem-Mojica N, Licona-Cassani C, Parkinson EI. Actinomycetota bioprospecting from ore-forming environments. Microb Genom 2024; 10. [PMID: 38743050 DOI: 10.1099/mgen.0.001253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.
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Affiliation(s)
- César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Amir Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Madeline Mair
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Carson Roberts
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Elizabeth Ivy Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
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8
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Lv YQ, Hu CJ, Xian WD, Li MM, Liu L, Liu ZT, Tan S, Liu WQ, Jiao JY, Li WJ. Chelatococcus albus sp. nov., a bacterium isolated from hot spring microbial mat. Int J Syst Evol Microbiol 2024; 74. [PMID: 38530347 DOI: 10.1099/ijsem.0.006307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
A Gram-stain-negative, non-endospore-forming, motile, short rod-shaped strain, designated SYSU G07232T, was isolated from a hot spring microbial mat, sampled from Rehai National Park, Tengchong, Yunnan Province, south-western China. Strain SYSU G07232T grew at 25-50 °C (optimum, 37 °C), at pH 5.5-9.0 (optimum, pH 6.0) and tolerated NaCl concentrations up to 1.0 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SYSU G07232T showed closest genetic affinity with Chelatococcus daeguensis K106T. The genomic features and taxonomic status of this strain were determined through whole-genome sequencing and a polyphasic approach. The predominant quinone of this strain was Q-10. Major cellular fatty acids comprised C19 : 0 cyclo ω8c and summed feature 8. The whole-genome length of strain SYSU G07232T was 4.02 Mbp, and the DNA G+C content was 69.26 mol%. The average nucleotide identity (ANIm ≤84.85 % and ANIb ≤76.08 %) and digital DNA-DNA hybridization (≤ 21.9 %) values between strain SYSU G07232T and the reference species were lower than the threshold values recommended for distinguishing novel prokaryotic species. Thus, based on the provided phenotypic, phylogenetic, and genetic data, it is proposed that strain SYSU G07232T (=KCTC 8141T=GDMCC 1.4178T) be designated as representing a novel species within the genus Chelatococcus, named Chelatococcus albus sp. nov.
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Affiliation(s)
- Yi-Qing Lv
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- School of Ecology, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Chao-Jian Hu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- School of Ecology, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Dong Xian
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, PR China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wei-Qiu Liu
- School of Ecology, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
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9
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Li Y, Su W, Wang X, Lu J, Zhang W, Wei S. In situ topotactic formation of an inorganic intergrowth bulk NiS/FeS@MgFe-LDH heterojunction to simulate CODH for the photocatalytic reduction of CO 2. NANOSCALE 2024. [PMID: 38415719 DOI: 10.1039/d3nr06581b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Enzyme-mimetic photocatalysis has been attracting much attention in bionic research, in which carbon monoxide dehydrogenase (CODH) is a suitable prototype for simulation to meet environmental and energy needs. In this study, we utilized the structural memory effect of layered double hydroxides (LDHs) to build inorganic intergrowth bulk heterojunctions (IIBHs) NiS/FeS@MgFe-LDHs via a pyrolytic topological vulcanization (PTV) method that imitated active C-clusters [Ni-4Fe-4S] in CODH. Enzyme mimicry was evaluated in terms of the microstructure and catalytic reaction site. The similarity between the microstructure of NiS/FeS@MgFe-LDHs and the CODH active group was demonstrated through XRD, XAFS and other characterisations. Subsequently, the obtained in situ irradiated X-ray photoelectron spectra and transient absorption spectra indicated the photogenerated electron transfer of the IIBH, wherein electrons finally accumulated in the conduction band of the NiS domain for the photocatalytic CO2 reduction reaction, which was similar to that of C-clusters [Ni-4Fe-4S] in which the Ni2+ ion was the reactive site. As a result, NiS/FeS@MgFe-LDHs achieved a high yield of CO at a rate of 2151.974 μmol g-1 h-1, which was 39.8 and 9.7 times more than that of NiMgFe-LDHs and NiMgFe-MMO, respectively. The study offers an innovative design route for developing IIBHs, providing novel opportunities for enzyme-mimetic photocatalysis.
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Affiliation(s)
- Yuexian Li
- State Key Laboratory of Chemical Resource Engineering and College of Chemistry, Beijing University of Chemical Technology, P. Box 98, Beisanhuan East Road 15, Beijing 100029, P. R. China.
| | - Wenli Su
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Xinjiekou Outside Street 19, Beijing 100875, China.
| | - Xiaoyan Wang
- State Key Laboratory of Chemical Resource Engineering and College of Chemistry, Beijing University of Chemical Technology, P. Box 98, Beisanhuan East Road 15, Beijing 100029, P. R. China.
| | - Jun Lu
- State Key Laboratory of Chemical Resource Engineering and College of Chemistry, Beijing University of Chemical Technology, P. Box 98, Beisanhuan East Road 15, Beijing 100029, P. R. China.
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, P. Box 98, Beisanhuan East Road 15, Beijing 100029, P. R. China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Xinjiekou Outside Street 19, Beijing 100875, China.
| | - Shuo Wei
- College of Chemistry, Beijing Normal University, Xinjiekou Outside Street 19, Beijing 100875, P. R. China.
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10
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Zhang RY, Wang YR, Liu RL, Rhee SK, Zhao GP, Quan ZX. Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment. MICROBIOME 2024; 12:7. [PMID: 38191433 PMCID: PMC10773090 DOI: 10.1186/s40168-023-01728-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking. RESULTS In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways. CONCLUSIONS One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.
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Affiliation(s)
- Ru-Yi Zhang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan-Ren Wang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Ru-Long Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Guo-Ping Zhao
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhe-Xue Quan
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
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11
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Wu E, Wang K, Liu Z, Wang J, Yan H, Zhu X, Zhu X, Chen B. Metabolic and Microbial Profiling of Soil Microbial Community under Per- and Polyfluoroalkyl Substance (PFAS) Stress. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21855-21865. [PMID: 38086098 DOI: 10.1021/acs.est.3c07020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) represent significant stress to organisms and are known to disrupt microbial community structure and function. Nevertheless, a detailed knowledge of the soil microbial community responding to PFAS stress at the metabolism level is required. Here we integrated UPLC-HRMS-based metabolomics data with 16S rRNA and ITS amplicon data across soil samples collected adjacent to a fluoropolymer production facility to directly identify the biochemical intermediates in microbial metabolic pathways and the interactions with microbial community structure under PFAS stress. A strong correlation between metabolite and microbial diversity was observed, which demonstrated significant variations in soil metabolite profiles and microbial community structures along with the sampling locations relative to the facility. Certain key metabolites were identified in the metabolite-PFAS co-occurrence network, functioning on microbial metabolisms including lipid metabolism, amino acid metabolism, and secondary metabolite biosynthesis. These results provide novel insights into the impacts of PFAS contamination on soil metabolomes and microbiomes. We suggest that soil metabolomics is an informative and useful tool that could be applied to reinforce the chemical evidence on the disruption of microbial ecological traits.
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Affiliation(s)
- Enhui Wu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Kun Wang
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Zhengzheng Liu
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, People's Republic of China
| | - Jing Wang
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, People's Republic of China
| | - Huicong Yan
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Xiangyu Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Xiaomin Zhu
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Innovation Center of Yangtze River Delta, Zhejiang University, Haining, Zhejiang 311400, People's Republic of China
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12
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Cheng Y, Zhu W, Han S, Yang J, Wu G, Zhao G, He X. Roseomonas populi sp. nov., an acetate-degrading bacteria isolated from the stem of Populus tomentosa. Antonie Van Leeuwenhoek 2023; 117:2. [PMID: 38147266 DOI: 10.1007/s10482-023-01911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 12/27/2023]
Abstract
Strain CN29T, isolated from the stem of 5- to 6-year-old Populus tomentosa in Shandong, China, was characterized using a polyphasic taxonomic approach. Cells of CN29T were Gram-stain negative, aerobic, nonspore-forming, and nonmotile coccoid. Growth occurred at 20-37 °C, pH 4.0-9.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CN29T was closely related to members of the genus Roseomonas and closest to Roseomonas pecuniae N75T (96.6%). This classification was further supported by phylogenetic analysis using additional core genes. The average nucleotide identity and digital DNA‒DNA hybridization values between strain CN29T and Roseomonas populi CN29T were 82.7% and 27.8%, respectively. The genome size of strain CN29T was 5.87 Mb, with a G + C content of 70.9%. The major cellular fatty acids included summed feature 8 (C18:1 ω7c/C18:1 ω6c), C19:0 cyclo ω8c and C16:0. The major respiratory quinone was Q-10. The polar lipids were phosphatidylcholine, aminolipid, phosphatidylglycerol, and diphosphatidylglycerol. Strain CN29T can utilize acetate as a carbon source for growth and metabolism. Additionally, it contains acid phosphatase (2-naphthyl phosphate), which catalyzes the hydrolysis of phosphoric monoesters. The CN29T strain contains several genes, including maeB, gdhB, and cysJ, involved in carbon, nitrogen, and sulfur cycling. These findings suggest that the strain may actively participate in ecosystem cycling, leading to soil improvement and promoting the growth of poplar trees. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain CN29T is concluded to represent a novel species of the genus Roseomonas, for which the name Roseomonas populi sp. nov. is proposed. The type strain is CN29T (= JCM 35579T = GDMCC 1.3267T).
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Affiliation(s)
- Yao Cheng
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wen Zhu
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuo Han
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jingjing Yang
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Guanqi Wu
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Guozhu Zhao
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiangwei He
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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13
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Zhu S, Sun X, Li Y, Feng X, Gao B. The common origin and degenerative evolution of flagella in Actinobacteria. mBio 2023; 14:e0252623. [PMID: 38019005 PMCID: PMC10746217 DOI: 10.1128/mbio.02526-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/19/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Flagellar motility plays an important role in the environmental adaptation of bacteria and is found in more than 50% of known bacterial species. However, this important characteristic is sparsely distributed within members of the phylum Actinobacteria, which constitutes one of the largest bacterial groups. It is unclear why this important fitness organelle is absent in most actinobacterial species and the origin of flagellar genes in other species. Here, we present detailed analyses of the evolution of flagellar genes in Actinobacteria, in conjunction with the ecological distribution and cell biological features of major actinobacterial lineages, and the co-evolution of signal transduction systems. The results presented in addition to clarifying the puzzle of sporadic distribution of flagellar motility in Actinobacteria, also provide important insights into the evolution of major lineages within this phylum.
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Affiliation(s)
- Siqi Zhu
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian Sun
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Yuqian Li
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Xueyin Feng
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
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14
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Zhang L, Dong T, Yang J, Hao S, Sun Z, Peng Y. Anammox Coupled with Photocatalyst for Enhanced Nitrogen Removal and the Activated Aerobic Respiration of Anammox Bacteria Based on cbb3-Type Cytochrome c Oxidase. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17910-17919. [PMID: 37463493 DOI: 10.1021/acs.est.3c02435] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
This study introduced photogenerated electrons into the anammox system by coupling them to a g-C3N4 nanoparticle photocatalyst. A high nitrogen removal efficiency (94.25%) was achieved, exceeding the biochemical limit of 89% imposed by anammox stoichiometry. Photogenerated electrons boosted anammox metabolic activity by empowering key enzymes (NIR, HZS, and WLP-related proteins) and triggered rapid algal enrichment by enhancing the algal Calvin cycle, thus developing multiple anammox-algae synergistic nitrogen removal processes. Remarkably, the homologous expression of cbb3-type cytochrome c oxidase (CcO) in anammox bacteria was discovered and reported in this study for the first time. This conferred aerobic respiration capability to anammox bacteria and rendered them the principal oxygen consumer under 7.9-19.8 mg/L dissolved oxygen, originating from algal photosynthesis. Additionally, photogenerated electrons selectively targeted the cb1 complex and cbb3-type CcO as activation sites while mobilizing the RegA/B regulatory system to activate the expression of cbb3-type CcO. Furthermore, cbb3-type CcO blocked oxidative stress in anammox by depleting intracellular oxygen, a substrate for reactive oxygen species synthesis. This optimized the environmental sensitivity of anammox bacteria and maintained their high metabolic activity. This study expands our understanding of the physiological aptitudes of anammox bacteria and provides valuable insights into applying solar energy for enhanced wastewater treatment.
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Affiliation(s)
- Li Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing 100124, China
| | - Tingjun Dong
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing 100124, China
| | - Jiachun Yang
- Shuifa Shandong Water Development Group Co. Ltd., Shandong 274200, China
- Shandong Jianzhu University, Shandong 250101, China
| | - Shiwei Hao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing 100124, China
| | - Zaicheng Sun
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Beijing 100124, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing 100124, China
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15
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Ma B, Lu C, Wang Y, Yu J, Zhao K, Xue R, Ren H, Lv X, Pan R, Zhang J, Zhu Y, Xu J. A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources. Nat Commun 2023; 14:7318. [PMID: 37951952 PMCID: PMC10640626 DOI: 10.1038/s41467-023-43000-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023] Open
Abstract
Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservo)ir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.
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Affiliation(s)
- Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Caiyu Lu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Jingwen Yu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Ran Xue
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Hao Ren
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, 310018, China
| | - Ronghui Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yongguan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
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16
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Deng QQ, Luo XQ, Li SH, Li JL, Wang PD, Yuan Y, Yang ZW, Li WJ. Alsobacter ponti sp. nov., a novel denitrification and sulfate reduction bacterium isolated from Pearl River sediment. Antonie Van Leeuwenhoek 2023; 116:987-994. [PMID: 37568066 DOI: 10.1007/s10482-023-01861-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
A Gram-staining negative, aerobic, motile, and short rods strain, designated SYSU M60028T, was isolated from a Pearl River sediment sample in Guangzhou, Guangdong, China. The isolate could be able to grow at pH 6.0-8.0 (optimum, pH 7.0), 25-37 °C (optimum, 28 °C) and in the presence of 0-2% (w/v) NaCl (optimum, 0% NaCl). The cellular polar lipids of this strain were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and three unidentified lipids. The respiratory quinone of SYSU M60028T was found to be Q-10. The major fatty acids (> 5% of total) were summed feature 8, C16:0, and C18:1 ω7c 11-methy1. The genomic DNA G + C content was 69.9%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M60028T belonged to the genus Alsobacter and had the highest sequences similarities to Alsobacter metallidurans SK200a-9T (96.87%) and Alsobacter soli SH9T (96.87%). Based on the phenotypic, genotypic, and phylogenetic data, strain SYSU M0028T should be considered to represent a novel species of the genus Alsobacter, for which the name Alsobacter ponti sp. nov. is proposed. The type strain is SYSU M60028T (= CGMCC 1.19341T = KCTC 92046T).
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Affiliation(s)
- Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shan-Hui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yang Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zi-Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Diao M, Dyksma S, Koeksoy E, Ngugi DK, Anantharaman K, Loy A, Pester M. Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. FEMS Microbiol Rev 2023; 47:fuad058. [PMID: 37796897 PMCID: PMC10591310 DOI: 10.1093/femsre/fuad058] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023] Open
Abstract
Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.
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Affiliation(s)
- Muhe Diao
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Stefan Dyksma
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Elif Koeksoy
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - David Kamanda Ngugi
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna A-1030, Austria
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig D-38124, Germany
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig D-38106, Germany
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Liu WL, Yang ZW, Guo DY, Deng QQ, Li JL, Wang PD, Chen SH, Liu L, Nie GX, Li WJ. Cereibacter flavus sp. nov., a novel member of the family Rhodobacteraceae isolated from seawater of the South China Sea and reclassification of Rhodobacter alkalitolerans as Cereibacter alkalitolerans comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37773605 DOI: 10.1099/ijsem.0.006051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023] Open
Abstract
A Gram-stain-negative, aerobic, motile, ovoid-shaped and yellow-coloured strain, designated SYSU M79828T, was isolated from seawater collected from the South China Sea. Growth of this strain was observed at 4-37 °C (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-6% NaCl (optimum, 3.0 %, w/v). The respiratory quinone was found to be Q-10. Major fatty acid constituents were C18 : 1 ω7c/C18 : 1 ω6c, C18 : 1 ω7c11-methyl and C18 : 0 (>5 % of total). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphoglycolipid, two unidentified phospholipid, one unidentified lipid and an unidentified glycolipid. The genomic DNA G+C content was 64.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M79828T belonged to the genus Cereibacter and had the highest sequences similarity to 'Rhodobacter xinxiangensis' TJ48T (98.41 %). Based on 16S rRNA gene phylogeny, physiological and chemotaxonomic characterizations, we consider that strain SYSU M79828T represents a novel species of the genus Cereibacter, for which the name Cereibacter flavus sp. nov. is proposed. The type strain is SYSU M79828T (=GDMCC 1.3803T=KCTC 92893T). In addition, according to the results of phylogenetic analysis and similar taxonomic characteristics, we propose that Rhodobacter alkalitolerans should be reclassified as Cereibacter alkalitolerans comb. nov.
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Affiliation(s)
- Wen-Li Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China
| | - Zi-Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Dan-Yuan Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Sen-Hua Chen
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519000, PR China
| | - Lan Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519000, PR China
| | - Guo-Xing Nie
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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19
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OuYang YT, Lv AP, Liu L, Li TT, Zhou Y, She TT, Cao LX, Jiao JY, Wang S, Li WJ. Isoptericola croceus sp. nov., a novel actinobacterium isolated from saline-alkali soil. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01849-6. [PMID: 37247101 DOI: 10.1007/s10482-023-01849-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/18/2023] [Indexed: 05/30/2023]
Abstract
A novel actinomycete, designated strain q2T, was isolated from the saline-alkaline soil, collected from Daqing, Heilongjiang province, China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain q2T belongs to the genus Isoptericola, and showed the highest sequence similarity to Isoptericola halotolerans KCTC 19046T (98.48%) and Isoptericola chiayiensis KCTC 19740T (98.13%), respectively. The average nucleotide identity values between strain q2T and other members of the genus Isoptericola were lower than 95% recommended for distinguishing novel prokaryotic species. Cells of strain q2T were Gram-staining-positive, aerobic, non-motile, rod-shaped and non-spore-forming. Colonies of strain q2T were golden-yellow pigmented, tidy edged and smooth surfaced. Growth occurred at 15-37 °C (optimum, 29 °C), pH 7.0-10.0 (optimum, pH 8.0). The predominant respiratory quinones were MK-9(H4) and MK-9(H2). The main detected polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannoside. The peptidoglycan compositions were L-alanine, D-aspartic, L-glutamic acid and L-lysine (type A4α). The major cellular fatty acids (> 10%) were anteiso-C15:0, iso-C15:0, and anteiso-C17:0. The G+C content of the genomic DNA was determined to be 69.7%. Based on the phenotypic, physiological, genotypic, and phylogenetic data, strain q2T represents a novel species of the genus Isoptericola, for which the name Isoptericola croceus sp. nov. is proposed. The type strain is q2T (= GDMCC 1.2923T = KCTC 49759T).
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Affiliation(s)
- Yu-Ting OuYang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ting-Ting Li
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Yi Zhou
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Ting-Ting She
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Li-Xiang Cao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization/Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin, 150086, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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20
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Singavarapu B, Du J, Beugnon R, Cesarz S, Eisenhauer N, Xue K, Wang Y, Bruelheide H, Wubet T. Functional Potential of Soil Microbial Communities and Their Subcommunities Varies with Tree Mycorrhizal Type and Tree Diversity. Microbiol Spectr 2023; 11:e0457822. [PMID: 36951585 PMCID: PMC10111882 DOI: 10.1128/spectrum.04578-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/11/2023] [Indexed: 03/24/2023] Open
Abstract
Soil microbial communities play crucial roles in the earth's biogeochemical cycles. Yet, their genomic potential for nutrient cycling in association with tree mycorrhizal type and tree-tree interactions remained unclear, especially in diverse tree communities. Here, we studied the genomic potential of soil fungi and bacteria with arbuscular (AM) and ectomycorrhizal (EcM) conspecific tree species pairs (TSPs) at three tree diversity levels in a subtropical tree diversity experiment (BEF-China). The soil fungi and bacteria of the TSPs' interaction zone were characterized by amplicon sequencing, and their subcommunities were determined using a microbial interkingdom co-occurrence network approach. Their potential genomic functions were predicted with regard to the three major nutrients carbon (C), nitrogen (N), and phosphorus (P) and their combinations. We found the microbial subcommunities that were significantly responding to different soil characteristics. The tree mycorrhizal type significantly influenced the functional composition of these co-occurring subcommunities in monospecific stands and two-tree-species mixtures but not in mixtures with more than three tree species (here multi-tree-species mixtures). Differentiation of subcommunities was driven by differentially abundant taxa producing different sets of nutrient cycling enzymes across the tree diversity levels, predominantly enzymes of the P (n = 11 and 16) cycles, followed by the N (n = 9) and C (n = 9) cycles, in monospecific stands and two-tree-species mixtures, respectively. Fungi of the Agaricomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes and bacteria of the Verrucomicrobia, Acidobacteria, Alphaproteobacteria, and Actinobacteria were the major differential contributors (48% to 62%) to the nutrient cycling functional abundances of soil microbial communities across tree diversity levels. Our study demonstrated the versatility and significance of microbial subcommunities in different soil nutrient cycling processes of forest ecosystems. IMPORTANCE Loss of multifunctional microbial communities can negatively affect ecosystem services, especially forest soil nutrient cycling. Therefore, exploration of the genomic potential of soil microbial communities, particularly their constituting subcommunities and taxa for nutrient cycling, is vital to get an in-depth mechanistic understanding for better management of forest soil ecosystems. This study revealed soil microbes with rich nutrient cycling potential, organized in subcommunities that are functionally resilient and abundant. Such microbial communities mainly found in multi-tree-species mixtures associated with different mycorrhizal partners can foster soil microbiome stability. A stable and functionally rich soil microbiome is involved in the cycling of nutrients, such as carbon, nitrogen, and phosphorus, and their combinations could have positive effects on ecosystem functioning, including increased forest productivity. The new findings could be highly relevant for afforestation and reforestation regimes, notably in the face of growing deforestation and global warming scenarios.
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Affiliation(s)
- Bala Singavarapu
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Jianqing Du
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Rémy Beugnon
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Leipzig Institute for Meteorology, Universität Leipzig, Leipzig, Germany
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources, Chinese Academy of Sciences, Beijing, China
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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21
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Yi Y, Dolfing J, Jin G, Fang X, Han W, Liu L, Tang Y, Cheng L. Thermodynamic restrictions determine ammonia tolerance of methanogenic pathways in Methanosarcina barkeri. WATER RESEARCH 2023; 232:119664. [PMID: 36775717 DOI: 10.1016/j.watres.2023.119664] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Ammonia is a ubiquitous potential inhibitor of anaerobic digestion processes, mainly exhibiting inhibition towards methanogenic activity. However, knowledge as to how ammonia affects the methanogens is still limited. In this study, we cultured a multitrophic methanogen, Methanosarcina barkeri DSM 800, with acetate, H2/CO2, and methanol to evaluate the influence of ammonia on different methanogenic pathways. Aceticlastic methanogenesis was more sensitive to increased ammonia concentrations than hydrogenotrophic and methylotrophic methanogenesis. Theoretical maximum NH3 tolerances of M. barkeri fed with acetate, H2/CO2, and methanol were calculated to be 39.1 ± 9.0, 104.3 ± 7.4, and 85.7 ± 1.0 mg/L, respectively. The order of the ΔG range of M. barkeri under three methanogenic pathways reflected the order of ammonia tolerance of M. barkeri. Our results provide insights into the role of the thermodynamic potential of methanogenesis on the tolerance of ammonia stress; and shed light on the mechanism of ammonia inhibition on anaerobic digestion.
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Affiliation(s)
- Yue Yi
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China; College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Wynne Jones 2.11, Ellison Place, Newcastle-upon-Tyne NE1 8QH, UK
| | - Ge Jin
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - XiaoYu Fang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - WenHao Han
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - LaiYan Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - YueQin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China.
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China.
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Deng QQ, Li SH, Luo XQ, Yang ZW, She TT, Li JL, Wang PD, Wang Y, Jiang H, Li WJ. Ectobacillus ponti sp. nov., a novel bacterium isolated from Pearl River Estuary. Int J Syst Evol Microbiol 2023; 73. [PMID: 37067995 DOI: 10.1099/ijsem.0.005836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
A Gram-staining-positive, aerobic, motile, and rod-shaped strain, designated SYSU M60031T, was isolated from a Pearl River Estuary sediment sample, Guangzhou, Guangdong, China. The isolate could grow at pH 5.0-8.0 (optimum, pH 7.0), 25-37 °C (optimum, 28 °C) and in the presence of 0-1 % (w/v) NaCl (optimum, 0 %). The predominant respiratory menaquinone of SYSU M60031T was MK-7. The cellular polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, and one unidentified aminolipid. The major fatty acids (>10 % of total) were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and C16 : 0. The genomic DNA G+C content was 51.2 %. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M60031T belonged to the genus Ectobacillus and showed the highest sequence similarity to Ectobacillus funiculus NAF001T (96.16%), followed by Ectobacillus antri SYSU K30001T (95.08 %). Based on the phenotypic, genotypic, and phylogenetic data, strain SYSU M60031T should be considered to represent a novel species of the genus Ectobacillus, for which the name Ectobacillus ponti sp. nov. is proposed. The type strain of the proposed novel isolate is SYSU M60031T (=CGMCC 1.19243T =NBRC 115614T).
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Affiliation(s)
- Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Shan-Hui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zi-Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ting-Ting She
- Biology and Food Engineering Institute, Guangdong University of Education, Guangzhou, 510303, PR China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Yu Wang
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Hongchen Jiang
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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23
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Wang W, Cheng X, Song Y, Wang H, Wu M, Ma L, Lu X, Liu X, Tuovinen OH. Elevated antimony concentration stimulates rare taxa of potential autotrophic bacteria in the Xikuangshan groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161105. [PMID: 36566853 DOI: 10.1016/j.scitotenv.2022.161105] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/29/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Microbial communities composed of few abundant and many rare species are widely involved in the biogeochemical cycles of elements. Yet little is known about the ecological roles of rare taxa in antimony (Sb) contaminated groundwater. Groundwater samples were collected along an Sb concentration gradient in the Xikuangshan antimony mine area and subjected to high through-put sequencing of 16S rRNA genes to investigate the bacterial communities. Results suggested that both abundant and rare sub-communities were dominated by Betaproteobacteria, Gammaproteobacteria, and Alphaproteobacteria, whereas rare sub-communities showed higher alpha-diversities. Multivariate analysis showed that both the abundant and rare taxa were under the stress of Sb, but the impact on rare taxa was greater. Nitrate explained a large part for the variation of the abundant sub-communities, indicating the critical role of nitrate for their activities under anoxic conditions. In contrast, bicarbonate significantly impacted rare sub-communities, suggesting their potential autotrophic characteristics. To further explore the role of rare taxa in the communities and the mechanism of affecting the community composition, a network was constructed to display the co-occurrence pattern of bacterial communities. The rare taxa contributed most of the network nodes and served as keystone species to maintain the stability of community. Abiotic factors (mainly Sb and pH) and bacterial interspecific interactions (interactions between keystone species and other bacterial groups) jointly affect the community dynamics. Functional prediction was performed to further reveal the ecological function of rare taxa in the Sb-disturbed groundwater environment. The results indicated that the rare taxa harbored much more diverse functions than their abundant counterparts. Notably, elevated Sb concentration promoted some potential autotrophic functions in rare taxa such as the oxidation of S-, N-, and Fe(II)-compounds. These results offer new insights into the roles of rare species in elemental cycles in the Sb-impacted groundwater.
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Affiliation(s)
- Weiqi Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Yuyang Song
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.
| | - Mengxiaojun Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Liyuan Ma
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaolu Lu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaoyan Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus 43210, USA
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Wang P, Li X, Li Y, Su Y, Wu D, Xie B. Enhanced anaerobic digestion performance of food waste by zero-valent iron and iron oxides nanoparticles: Comparative analyses of microbial community and metabolism. BIORESOURCE TECHNOLOGY 2023; 371:128633. [PMID: 36657585 DOI: 10.1016/j.biortech.2023.128633] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
The effects of zero-valent iron (ZVI) and iron oxides nanoparticles on anaerobic digestion (AD) performance of food waste (FW) were comparably clarified in this study. Results indicated that the nanoparticles supplement effectively enhanced the methane yields. As observed, these nanoparticles accelerated organics transformation and alleviated acidification process. Also, the enriched total methanogens and functional bacteria (e.g., Proteiniphilum) were consistent with the promotion of oxidative phosphorylation, citrate cycle, coenzymes biosynthesis and the metabolisms of amino acid, carbohydrate, methane. Additionally, these nanoparticles stimulated electron transfer potential via enriching syntrophic genera (e.g., Geobacter, Syntrophomonas), primary acetate-dependent methanogens (Methanosaeta, Methanosarcina) and related functions (pilus assembly protein, ferredoxins). By comparison, ZVI nanoparticle presented the excellent performance on methanogenesis. This study provides comprehensive understanding of the methanogenesis facilitated by ZVI and iron oxides nanoparticles through the enhancement of key microbes and microbial metabolisms, while ZVI is an excellent option for promoting the methane production.
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Affiliation(s)
- Panliang Wang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Xunan Li
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Ye Li
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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Baleeiro FCF, Varchmin L, Kleinsteuber S, Sträuber H, Neumann A. Formate-induced CO tolerance and methanogenesis inhibition in fermentation of syngas and plant biomass for carboxylate production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:26. [PMID: 36805806 PMCID: PMC9936662 DOI: 10.1186/s13068-023-02271-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/29/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Production of monocarboxylates using microbial communities is highly dependent on local and degradable biomass feedstocks. Syngas or different mixtures of H2, CO, and CO2 can be sourced from biomass gasification, excess renewable electricity, industrial off-gases, and carbon capture plants and co-fed to a fermenter to alleviate dependence on local biomass. To understand the effects of adding these gases during anaerobic fermentation of plant biomass, a series of batch experiments was carried out with different syngas compositions and corn silage (pH 6.0, 32 °C). RESULTS Co-fermentation of syngas with corn silage increased the overall carboxylate yield per gram of volatile solids (VS) by up to 29% (0.47 ± 0.07 g gVS-1; in comparison to 0.37 ± 0.02 g gVS-1 with a N2/CO2 headspace), despite slowing down biomass degradation. Ethylene and CO exerted a synergistic effect in preventing methanogenesis, leading to net carbon fixation. Less than 12% of the electrons were misrouted to CH4 when either 15 kPa CO or 5 kPa CO + 1.5 kPa ethylene was used. CO increased the selectivity to acetate and propionate, which accounted for 85% (electron equivalents) of all products at 49 kPa CO, by favoring lactic acid bacteria and actinobacteria over n-butyrate and n-caproate producers. Inhibition of n-butyrate and n-caproate production by CO happened even when an inoculum preacclimatized to syngas and lactate was used. Intriguingly, the effect of CO on n-butyrate and n-caproate production was reversed when formate was present in the broth. CONCLUSIONS The concept of co-fermenting syngas and plant biomass shows promise in three aspects: by making anaerobic fermentation a carbon-fixing process, by increasing the yields of short-chain carboxylates (propionate and acetate), and by minimizing electron losses to CH4. Moreover, a model was proposed for how formate can alleviate CO inhibition in certain acidogenic bacteria. Testing the fermentation of syngas and plant biomass in a continuous process could potentially improve selectivity to n-butyrate and n-caproate by enriching chain-elongating bacteria adapted to CO and complex biomass.
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Affiliation(s)
- Flávio C. F. Baleeiro
- grid.7492.80000 0004 0492 3830Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany ,grid.7892.40000 0001 0075 5874Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology – KIT, Karlsruhe, Germany
| | - Lukas Varchmin
- grid.7892.40000 0001 0075 5874Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology – KIT, Karlsruhe, Germany
| | - Sabine Kleinsteuber
- grid.7492.80000 0004 0492 3830Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Heike Sträuber
- grid.7492.80000 0004 0492 3830Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Anke Neumann
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology - KIT, Karlsruhe, Germany.
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26
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Lv AP, Ming YZ, Liu ZT, Ouyang YT, Li MM, Lian ZH, Jiao JY, She TT, Liu L, Li WJ. Clostridium caldaquaticum sp. nov., a thermophilic bacterium isolated from a hot spring sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748593 DOI: 10.1099/ijsem.0.005684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A novel anaerobic bacterium, designated SYSU GA19001T, was isolated from a hot spring sediment sample. Phylogenetic analysis indicated that the isolate belongs to the genus Clostridium, and showed the highest sequence similarity to Clostridium swellfunianum CICC 10730T (96.63 %) and Clostridium prolinivorans PYR-10T (96.11 %). Cells of strain SYSU GA19001T were Gram-stain-positive, spore-forming, rod-shaped (0.6-0.8×2.6-4.0 µm) and motile. Growth was observed at pH 5.0-9.0 (optimum, pH 7.0), 37-55 °C (optimum, 45 °C) and in NaCl concentrations of 0-2.0 % (optimum, 0 %). The genomic DNA G+C content was 31.62 %. The major cellular fatty acids of strain SYSU GA19001T were C14 : 0, iso-C15 : 0, C16 : 0 and summed feature 8. The prominent polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol. Meso-diaminopimelic acid was the diamino acid in peptidoglycan. Based on the results of phylogenetic, chemotaxonomic and phenotypic analyses, strain SYSU GA19001T represents a novel species of the genus Clostridium, for which the name Clostridium caldaquaticum sp. nov. is proposed. The type strain of the proposed novel species is SYSU GA19001T (=NBRC 115040T= CGMCC 1.17864T).
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Affiliation(s)
- Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Yu-Zhen Ming
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Yu-Ting Ouyang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ting-Ting She
- Biology and Food Engineering Institute, Guangdong University of Education, Guangzhou, 510303, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
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27
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Xu Z, Wu X, Zhang J, Cheng P, Xu Z, Sun W, Zhong Y, Wang Y, Yu G, Liu H. Microplastics existence intensified bloom of antibiotic resistance in livestock feces transformed by black soldier fly. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120845. [PMID: 36496063 DOI: 10.1016/j.envpol.2022.120845] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/27/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Efficient degradation of residual antibiotics in livestock and poultry feces by black soldier flies (BSFs) has been widely reported. Nevertheless, the effects of widely detected microplastics in feces on the dynamic reduction of antibiotics and the transfer of gut bacterial resistome remain unclear. In this study, red fluorescence-labeled microplastics are observed to be abundantly distributed in BSFs gut, which caused epithelial cell damage along with gut peristalsis and friction, thereby releasing reactive oxygen species and activating the antioxidant enzyme system. In addition, they result in not only in inflammatory cytokine release to induce gut inflammation, but fecal hardening because of mucus released from the BSFs, thereby hindering organic mineralization and antibiotic degradation. Besides, the gut pathogenic bacteria easily obtain growth energy and crowded out ecological niches by reducing nitrate produced by inflammatory host cells to nitrite with nitrate reductase. Consequently, linear discriminant analysis effect size and detrended correspondence analysis found that microplastic intake significantly reshape the microbial community structure and cause the significant reduction of several important organic-decomposing bacteria and probiotics (e.g., Pseudomonadales, Coriobacteriales, Lachnospirales, and Ruminococcaceae). In addition, a large number of pathogenic bacteria (e.g., Enterococcaceae, Hungateiclostridiaceae, and Clostridia) are enriched in feces and BSFs gut. Weighted correlation network analysis and bubble diagram analysis indicate that microplastic intake intensified gut colonization of pathogenic bacteria carrying antibiotic-resistant genes/mobile genetic elements, driving the bloom of antibiotic resistance in transformed fecal piles. Therefore, microplastics in feces should be isolated as much as possible before insect transformation.
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Affiliation(s)
- Zhimin Xu
- College of Resources and Environment, Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xinyue Wu
- College of Resources and Environment, Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jiexiang Zhang
- Guangzhou Radio & TV Measurement & Testing Co., Ltd., Guangzhou, 510656, China
| | - Ping Cheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Zhihao Xu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinggangshan University, Jian, 343009, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management Institute of Environmental and Soil Sciences, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Yuming Zhong
- College of Resources and Environment, Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Yifan Wang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Hui Liu
- College of Resources and Environment, Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
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Lian WH, Mohamad OAA, Dong L, Zhang LY, Wang D, Liu L, Han MX, Li S, Wang S, Antunes A, Fang BZ, Jiao JY, Li WJ. Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems. ENVIRONMENTAL MICROBIOME 2023; 18:4. [PMID: 36639807 PMCID: PMC9840269 DOI: 10.1186/s40793-023-00463-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/08/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants. RESULTS The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different. CONCLUSION Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.
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Affiliation(s)
- Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Osama Abdalla Abdelshafy Mohamad
- Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Arish, 45511, Egypt
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ling-Yu Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dong Wang
- College of Life Science and Technology, Honghe University, Mengzi, 661199, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ming-Xian Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, People's Republic of China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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29
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Liu X, Luo H, Yu D, Tan J, Yuan J, Li H. Synthetic biology promotes the capture of CO2 to produce fatty acid derivatives in microbial cell factories. BIORESOUR BIOPROCESS 2022; 9:124. [PMID: 38647643 PMCID: PMC10992411 DOI: 10.1186/s40643-022-00615-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/27/2022] [Indexed: 12/07/2022] Open
Abstract
Environmental problems such as greenhouse effect, the consumption of fossil energy, and the increase of human demand for energy are becoming more and more serious, which force researcher to turn their attention to the reduction of CO2 and the development of renewable energy. Unsafety, easy to lead to secondary environmental pollution, cost inefficiency, and other problems limit the development of conventional CO2 capture technology. In recent years, many microorganisms have attracted much attention to capture CO2 and synthesize valuable products directly. Fatty acid derivatives (e.g., fatty acid esters, fatty alcohols, and aliphatic hydrocarbons), which can be used as a kind of environmentally friendly and renewable biofuels, are sustainable substitutes for fossil energy. In this review, conventional CO2 capture techniques pathways, microbial CO2 concentration mechanisms and fixation pathways were introduced. Then, the metabolic pathway and progress of direct production of fatty acid derivatives from CO2 in microbial cell factories were discussed. The synthetic biology means used to design engineering microorganisms and optimize their metabolic pathways were depicted, with final discussion on the potential of optoelectronic-microbial integrated capture and production systems.
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Affiliation(s)
- Xiaofang Liu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insects of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, Guizhou, China.
| | - Hangyu Luo
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insects of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, Guizhou, China
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Dayong Yu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insects of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, Guizhou, China
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Jinyu Tan
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Junfa Yuan
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China
| | - Hu Li
- State Key Laboratory Breeding Base of Green Pesticide & Agricultural Bioengineering, Key Laboratory of Green Pesticide & Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for Research & Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou, China.
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30
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Yin X, Gong W, Zhan Z, Wei W, Li M, Jiao J, Chen B, Liu L, Li W, Gao Z. Mining and engineering of valine dehydrogenases from a hot spring sediment metagenome for the synthesis of chiral non-natural L-amino acids. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Li BB, Zhang XJ, Wu D, Zhang DD, Fang BZ, Liu HC, Zhou YG, Cai M, Li WJ, Nie GX. Devosia ureilytica sp. nov., isolated from Kuche River in China. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748494 DOI: 10.1099/ijsem.0.005663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Two novel strains, designated XJ19-45T and XJ19-1, were isolated from water of Kuche River in Xinjiang Uygur Autonomous Region, China. Their cells were Gram-stain-negative, aerobic and motile rods. The phylogenetic analyses based on 16S rRNA genes and genomes showed that the two isolates belonged to the genus Devosia and the closest relative was Devosia subaequoris HST3-14T. The 16S rRNA genes sequences pairwise similarities, average nucleotide identities, digital DNA-DNA hybridizations and average amino acid identities between type strain XJ19-45T and other relatives were all less than 98.3, 80.3, 23.6 and 85.7 %, respectively, all below the species delineation thresholds. Pan-genomic analysis indicated that the novel isolate XJ19-45T shared 1594 core gene clusters with the 11 closely related type strains in Devosia, and the number of strain-specific clusters was 390. The major cellular fatty acids (>10 %) of the two isolates were summed feature 8, C18 : 1 ω7c 11-methyl and C16 : 0. Diphosphatidylglycerol, phosphatidylglycerol and glycolipids were the major polar lipids, and Q10 was the detected respiratory quinone. Based on the results of phenotypic, physiological, chemotaxonomic and genotypic characterizations, we propose that the isolates represent a novel species, for which the name Devosia ureilytica sp. nov. is proposed. The type strain is XJ19-45T (=CGMCC 1.19388T=KCTC 92263T).
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Affiliation(s)
- Bin-Bin Li
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China.,China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiao-Juan Zhang
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Danni Wu
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Dan-Dan Zhang
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Man Cai
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen-Jun Li
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
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32
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Khomyakova MA, Zavarzina DG, Merkel AY, Klyukina AA, Pikhtereva VA, Gavrilov SN, Slobodkin AI. The first cultivated representatives of the actinobacterial lineage OPB41 isolated from subsurface environments constitute a novel order Anaerosomatales. Front Microbiol 2022; 13:1047580. [PMID: 36439822 PMCID: PMC9686372 DOI: 10.3389/fmicb.2022.1047580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/24/2022] [Indexed: 08/01/2023] Open
Abstract
The continental subsurface harbors microbial populations highly enriched in uncultured taxa. OPB41 is an uncultured order-level phylogenetic lineage within the actinobacterial class Coriobacteriia. OPB41 bacteria have a wide geographical distribution, but the physiology and metabolic traits of this cosmopolitan group remain elusive. From two contrasting subsurface environments, a terrestrial mud volcano and a deep subsurface aquifer, located in the central part of Eurasia, within the Caucasus petroleum region, we have isolated two pure cultures of anaerobic actinobacteria belonging to OPB41. The cells of both strains are small non-motile rods forming numerous pili-like appendages. Strain M08DHBT is mesophilic, while strain Es71-Z0120T is a true thermophile having a broad temperature range for growth (25-77°C). Strain M08DHBT anaerobically reduces sulfur compounds and utilizes an aromatic compound 3,4-dihydroxybenzoic acid. Strain Es71-Z0120T is an obligate dissimilatory Fe(III) reducer that is unable to utilize aromatic compounds. Both isolates grow lithotrophically and consume molecular hydrogen or formate using either thiosulfate, elemental sulfur, or Fe(III) as an electron acceptor. Genomes of the strains encode the putative reductive glycine pathway for autotrophic CO2 fixation, Ni-Fe hydrogenases, putative thiosulfate/polysulfide reductases, and multiheme c-type cytochromes presumably involved in dissimilatory Fe(III) reduction. We propose to assign the isolated strains to the novel taxa of the species-order levels and describe strain M08DHBT as Anaerosoma tenue gen. nov., sp. nov., and strain Es71-Z0120T as Parvivirga hydrogeniphila gen. nov., sp. nov., being members of Anaerosomatales ord. nov. This work expands the knowledge of the diversity, metabolic functions, and ecological role of the phylum Actinomycetota.
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Affiliation(s)
- Maria A. Khomyakova
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daria G. Zavarzina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Valeria A. Pikhtereva
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander I. Slobodkin
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
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33
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Yue W, Han F. Effects of monoglucoside and diglucoside anthocyanins from Yan 73 (Vitis Vinifera L.) and spine grape (Vitis davidii Foex) skin on intestinal microbiota in vitro. Food Chem X 2022; 16:100501. [DOI: 10.1016/j.fochx.2022.100501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/13/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
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34
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Xie YG, Luo ZH, Fang BZ, Jiao JY, Xie QJ, Cao XR, Qu YN, Qi YL, Rao YZ, Li YX, Liu YH, Li A, Seymour C, Palmer M, Hedlund BP, Li WJ, Hua ZS. Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota. MICROBIOME 2022; 10:172. [PMID: 36242054 PMCID: PMC9563170 DOI: 10.1186/s40168-022-01376-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/22/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria. Aside from hypersaline environments, Ca. Nanohaloarchaeota can also have been discovered from deep-subsurface marine sediments. RESULTS Three metagenome-assembled genomes (MAGs) representing a new order within the Ca. Nanohaloarchaeota were reconstructed from a stratified salt crust and proposed to represent a novel order, Nucleotidisoterales. Genomic features reveal them to be anaerobes capable of catabolizing nucleotides by coupling nucleotide salvage pathways with lower glycolysis to yield free energy. Comparative genomics demonstrated that these and other Ca. Nanohaloarchaeota inhabiting saline habitats use a "salt-in" strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. In contrast, previously described Ca. Nanohaloarchaeota MAGs from geothermal environments were enriched with basic amino acids to counter heat stress. Evolutionary history reconstruction revealed that functional differentiation of energy conservation strategies drove diversification within Ca. Nanohaloarchaeota, further leading to shifts in the catabolic strategy from nucleotide degradation within deeper lineages to polysaccharide degradation within shallow lineages. CONCLUSIONS This study provides deeper insight into the ecological functions and evolution of the expanded phylum Ca. Nanohaloarchaeota and further advances our understanding on the functional and genetic associations between potential symbionts and hosts. Video Abstract.
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Affiliation(s)
- Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Qi-Jun Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Xing-Ru Cao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yan-Lin Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Andrew Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Cale Seymour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, People's Republic of China.
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35
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Song ZQ, Wang L, Liang F, Zhou Q, Pei D, Jiang H, Li WJ. nifH gene expression and diversity in geothermal springs of Tengchong, China. Front Microbiol 2022; 13:980924. [PMID: 36160261 PMCID: PMC9493357 DOI: 10.3389/fmicb.2022.980924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/08/2022] [Indexed: 11/20/2022] Open
Abstract
Terrestrial hot springs have been suggested to harbor diverse diazotrophic lineages by using DNA-based nifH gene phylogenetic analysis. However, only a small amount of diazotrophs were ever confirmed to perform nitrogen fixation. In order to explore the compositions of active diazotrophic populations in hot springs, the in situ expression and diversity of nifH and 16S rRNA genes were investigated in the sediments of hot springs (pH 4.3-9.1; temperature 34-84°C) in Tengchong, China, by using high-throughput sequencing. The results showed that active diazotrophs were diverse in the studied Tengchong hot springs. The main active diazotrophs in high-temperature hot springs were affiliated with Aquificae, while those in low-temperature hot springs belonged to Cyanobacteria and Nitrospirae. Such dominance of Aquificae and Nitrospirae of diazotrophs has not been reported in other ecosystems. This suggests that hot springs may harbor unique active diazotrophs in comparison with other type of ecosystems. Furthermore, there were significant differences in the phylogenetic lineages of diazotrophs between hot springs of Tengchong and other regions, indicating that diazotrophs have geographical distribution patterns. Statistical analysis suggests that the expression and distribution of nifH gene were influenced by temperature and concentrations of ammonia and sulfur seem in Tengchong hot springs. These findings avail us to understand element cycling mediated by diazotrophs in hot spring ecosystems.
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Affiliation(s)
- Zhao-Qi Song
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Li Wang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Feng Liang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Qingfeng Zhou
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Dongli Pei
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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36
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Description of five novel thermophilic species of the genus Thermus: Thermus hydrothermalis sp. nov., Thermus neutrinimicus sp. nov., Thermus thalpophilus sp. nov., Thermus albus sp. nov., and Thermus altitudinis sp. nov., isolated from hot spring sediments. Syst Appl Microbiol 2022; 45:126361. [DOI: 10.1016/j.syapm.2022.126361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/27/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022]
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37
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Oceanobacillus saliphilus sp. nov., Isolated from Saline-Alkali Soil in Heilongjiang Province, China. Curr Microbiol 2022; 79:301. [PMID: 36002665 DOI: 10.1007/s00284-022-02997-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/08/2022] [Indexed: 11/03/2022]
Abstract
A novel bacterium, designated strain APA_H-1(4)T, was isolated from the saline-alkaline soil, Zhaodong, Heilongjiang Province, China. Phenotypic and chemotaxonomic analyses, and whole-genome sequencing were used to determine the taxonomic position of the strain. Phylogenetic analysis indicated that the isolate belongs to the genus Oceanobacillus, and showed the highest sequence similarity to O. damuensis KCTC 33146T (98.35%, similarity) and 'O. massiliensis' DSM 24644 (98.32%). The average nucleotide identity values between strain APA_H-1(4)T and other members of the genus Oceanobacillus were lower than 82% recommended for distinguishing novel prokaryotic species. The digital DNA-DNA hybridization values of strain APA_H-1(4)T with O. damuensis KCTC 33146T and 'O. massiliensis' DSM 24644 were 13.60 and 17.60%, respectively. Cells of strain APA_H-1(4)T were Gram-staining positive, motile, aerobic, spore-forming rods (0.5-0.7 × 1.8-2.6 μm) with flagella. The growth was found to occur optimally at 37 °C. The whole-cell hydrolysate contained meso-diaminopimelic acid as the diagnostic cell wall diamino acid. The main detected polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified polar lipid. The predominant respiratory quinone was identified as menaquinone-7 (MK-7). The major cellular fatty acid (>10%) was anteiso-C15:0. The G + C content of the genomic DNA was determined to be 38.4% based on the draft genome sequence. Based on the comparative analysis of polyphasic taxonomic data, strain APA_H-1(4)T represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus saliphilus sp. nov. is proposed. The type strain is APA_H-1(4)T (=GDMCC 1.2239T = KCTC 43254T).
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38
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Pi HW, Lin JJ, Chen CA, Wang PH, Chiang YR, Huang CC, Young CC, Li WH. Origin and evolution of nitrogen fixation in prokaryotes. Mol Biol Evol 2022; 39:6673025. [PMID: 35993177 PMCID: PMC9447857 DOI: 10.1093/molbev/msac181] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.
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Affiliation(s)
- Hong Wei Pi
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Jinn Jy Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chi An Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Po Hsiang Wang
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, Taiwan 32001.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan 145-0061
| | - Yin Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chieh Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan 402
| | - Chiu Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan 402
| | - Wen Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Department of Ecology and Evolution, University of Chicago, Chicago 60637, USA
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39
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Jin PJ, Sun L, Rao MPN, Jiao JY, Sun XJ, Li WJ, Wang S. Oceanobacillus alkalisoli sp. nov., an alkaliphilic bacterium isolated from saline-alkaline soil. Int J Syst Evol Microbiol 2022; 72. [PMID: 36018779 DOI: 10.1099/ijsem.0.005518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023] Open
Abstract
Two alkaliphilic strains, designated APA_J-2 (6-2)T and APA_J-5 (13-2), were isolated from saline-alkali soil sampled in Jilin Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains APA_J-2 (6-2)T and APA_J-5(13–2) were closely related to members of the genus
Oceanobacillus
, and had the highest sequence similarity to
Oceanobacillus indicireducens
JCM 17251T (96.8 and 96.9 %, respectively). The 16S rRNA gene sequence similarity between the two novel isolates was 99.6 %, indicating that they were similar species. Cells were Gram-stain-positive, aerobic, motile and rod-shaped. The strains grew at 15–45 °C (optimum, 37 °C), pH 8.0–11.0. (optimum, pH 9) and with 0–10 % (w/v) NaCl (optimum, 5 %). The strains contained menaquinone-7 as the respiratory quinone and anteiso-C15 : 0 as the predominant cellular fatty acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The genomic DNA G+C content was 40.0 mol%. The average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values of strain APA_J-2 (6-2)T with
O. indicireducens
JCM 17251T were 85.5, 87.9 and 30.7 %, respectively. The ANI, AAI and dDDH values of strain APA_J-5 (13-2) with
O. indicireducens
JCM 17251T were 85.7, 87.7 and 30.8 %, respectively. Based on the phylogenetic, phenotypic, biochemical, chemotaxonomic and genome data, strains APA_J-2 (6-2)T and APA_J-5 (13-2) represent a novel species of the genus
Oceanobacillus
, for which the name Oceanobacillus alkalisoli sp. nov. is proposed. The type strain is APA_J-2 (6-2)T (=KCTC 43253T=GDMCC 1.2242T).
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Affiliation(s)
- Pin-Jiao Jin
- Heilongjiang Academy of Black Soil Conservation & Utilization, Postdoctoral Station of Heilongjiang Academy of Agricultural Sciences/ Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin 150086, PR China
| | - Lei Sun
- Heilongjiang Academy of Black Soil Conservation & Utilization, Postdoctoral Station of Heilongjiang Academy of Agricultural Sciences/ Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin 150086, PR China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xiu-Jun Sun
- Heilongjiang Academy of Black Soil Conservation & Utilization, Postdoctoral Station of Heilongjiang Academy of Agricultural Sciences/ Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin 150086, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation & Utilization, Postdoctoral Station of Heilongjiang Academy of Agricultural Sciences/ Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin 150086, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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40
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Wang S, Wang J, Liu Z, Zhang B. Unraveling diverse survival strategies of microorganisms to vanadium stress in aquatic environments. WATER RESEARCH 2022; 221:118813. [PMID: 35810633 DOI: 10.1016/j.watres.2022.118813] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/25/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Worldwide vanadium contamination is posing serious risks to ecosystems. Although abilities of microbial communities to cope with vanadium stress using specific survival strategies have been reported, little is known regarding their relative importance and the underlying detoxification/tolerance mechanisms. Herein, we investigated the potential survival strategies of microbial communities and associated pathways in aquatic environments based on geochemistry and molecular biology. High vanadium content was observed for both water (12.6 ± 1.15 mg/L) and sediment (1.18 × 103 ± 10.4 mg/kg) in the investigated polluted stream. Co-occurrence network investigation implied that microbial communities showed cooperative interactions to adapt to the vanadium-polluted condition. Vanadium was also characterized as one of the vital factors shaping the community structure via redundancy analysis and structural equation models. Based on the metagenomic technology, three survival strategies including denitrification pathway, electron transfer, and metal resistance in innate microbes under the vanadium stress were revealed, with comprehensively summarized vanadium detoxification/tolerance genes. Remarkable role of electron transfer genes and the prevalent existence of resistance genes during detoxifying vanadium were highlighted. Overall, these findings provide novel insights into survival strategies under the vanadium contamination in aquatic environments, which can be of great significance for the identification, isolation, and application of vanadium reducing bacteria in vanadium bioremediation.
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Affiliation(s)
- Song Wang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences Beijing, Beijing 100083, China
| | - Jiawen Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Ziqi Liu
- 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.
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41
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Liu ZT, Dai JY, Lian ZH, Liu L, Xian WD, Li MM, Fang BZ, Jiao JY, Li WJ. Thermomonas flagellata sp. nov. and Thermomonas alba sp. nov., two novel members of the phylum Pseudomonadota isolated from hot spring sediments. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005444] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel species, designated strains SYSU G04041T and SYSU G04536T, were isolated from hot spring sediments collected in Yunnan, PR China. Phenotypic and chemotaxonomic analyses, and whole-genome sequencing were used to determine the taxonomic positions of the candidate strains. Phylogenetic analysis using 16S rRNA gene sequence indicated that strain SYSU G04041T showed the highest sequence similarity to
Thermomonas haemolytica
A50-7-3T (97.5 %), and SYSU G04536T showed the highest sequence similarity to
Thermomonas hydrothermalis
SGM-6T (98.2 %). The strains could be differentiated from other species of the genus
Thermomonas
by their distinct phenotypic and genotypic characteristics. Cells of strains SYSU G04041T and SYSU G04536T were aerobic, motile and Gram-stain-negative. Growth both occurred optimally at 45 °C and pH 7.0 for SYSU G04041T and SYSU G04536T. In addition, the predominant respiratory quinone in both isolates was ubiquinone Q-8. The major fatty acids (>10 %) of strain SYSU G04041T were C16 : 0, iso-C15 : 0 and iso-C16 : 0, while the major fatty acids (>10 %) of strain SYSU G04536T were iso-C15 : 0 and iso-C16 : 0. The main detected polar lipids in strains SYSU G04041T and SYSU G04536T included phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The G+C contents of the genomic DNA of strains SYSU G04041T and SYSU G04536T based on draft genomic sequences were 72.5 and 68.3 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU G04041T and SYSU G04536T represent two novel species of the genus
Thermomonas
, for which the names Thermomonas flagellata sp. nov. and Thermomonas alba sp. nov. are proposed, with the type strains SYSU G04041T (=CGMCC 1.19366T=KCTC 92228T) and SYSU G04536T (=CGMCC 1.19367T=KCTC 82839T), respectively.
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Affiliation(s)
- Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Jun-Yi Dai
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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Rhodoflexus caldus gen. nov., sp. nov., a new member of the phylum Bacteroidota isolated from a hot spring sediment. Antonie van Leeuwenhoek 2022; 115:889-898. [PMID: 35562517 DOI: 10.1007/s10482-022-01742-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/15/2022] [Indexed: 10/18/2022]
Abstract
A thermophilic bacterium, designated strain SYSU G04325T, was isolated from a hot spring sediment in Yunnan, China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomic position of the strain. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SYSU G04325T shows high sequence similarity to Thermoflexibacter ruber NBRC 16677T (86.2%). The strain can be differentiated from other species of the family Thermoflexibacteraceae by its distinct phenotypic and genotypic characteristics. Cells of the strain SYSU G04325T were observed to be aerobic, Gram-stain negative and filamentous. Growth was found to occur optimally at 45 ºC and pH 7.0. In addition, the respiratory quinone was identified as menaquinone-7, while the major fatty acids (> 10%) were identified as iso-C15:0, iso-C17:0 and Summed Feature 9 (iso-C17:1ω9c). The polar lipids detected included phosphatidylethanolamine, three unidentified phospholipids, one unidentified glycolipid, five unidentified aminolipids and four unidentified polar lipids. The G + C content of the genomic DNA was determined to be 47.6% based on the draft genome sequence. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU G04325T is concluded to represent a novel species of a novel genus in the family Thermoflexibacteraceae, for which the name Rhodoflexus caldus gen. nov., sp. nov. is proposed. The type strain of Rhodoflexus caldus is SYSU G04325T (= MCCC 1K06127T = KCTC 82848T).
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Zhao ZY, Xia TT, Jiao JY, Liu L, Su QY, Li MM, Lv AP, Ouyang YT, Li WJ, Ming H. Qipengyuania thermophila sp. nov., isolated from a Chinese hot spring. Arch Microbiol 2022; 204:305. [PMID: 35532844 DOI: 10.1007/s00203-022-02927-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/02/2022]
Abstract
A novel Gram-stain-negative, non-motile, short rod-shaped and aerobic bacterial strain, designated as CFH 74456 T, was isolated from sediment of a hot spring, Tengchong, Yunnan Province, south-western China. Growth occurred at 20-53 ºC (optimum 45 ºC), pH 7.0-9.0 (optimum pH 8.0) and up to 2.0% (w/v) NaCl (optimum 0-1.0%, w/v). The predominant respiratory quinone was ubiquinone 10 (Q-10). The major fatty acids (> 10%) were C17:1 ω6c (17.9%) and summed feature 8 (38.6%). The polar lipid profile of strain CFH 74456 T was identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, three unidentified glycolipids and three unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CFH 74456 T belongs to the genus Qipengyuania, and was most closely related to Qipengyuania sediminis CGMCC 1.12928 T (95.7%). The draft genome size of the isolate was 2.29 Mb with G + C content of 68.5%. The amino acid identity, average nucleotide identity and the digital DNA-DNA hybridization values between strain CFH 74456 T and the closest relatives ranged from 67.0 to 67.9%, 73.0 to 74.2% and 18.2-19.3%, respectively. On the basis of phenotypic, phylogenetic and genotypic analyses, it is concluded that strain CFH 74456 T represents a new species of the genus Qipengyuania, for which the name Qipengyuania thermophila sp. nov. is proposed. The type strain is CFH 74456 T (= KCTC 62921 T = CCTCC AB 2018237 T).
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Affiliation(s)
- Zi-Yu Zhao
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China
| | - Ting-Ting Xia
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Qing-Yang Su
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu-Ting Ouyang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Hong Ming
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China.
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Ornithinimicrobium sediminis sp. nov., a novel actinobacterium isolated from a saline lake sediment. Arch Microbiol 2022; 204:277. [PMID: 35460374 DOI: 10.1007/s00203-022-02898-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/13/2022] [Accepted: 04/05/2022] [Indexed: 11/02/2022]
Abstract
An actinobacterium, designated strain EGI L100131T, was isolated from saline lake sediment in Xinjiang Province, China. The taxonomic position of the isolate was determined using analysis based on the polyphasic taxonomy and phylogenomics. Phylogenetic analysis and 16S rRNA gene sequence similarities indicated that strain EGI L100131T formed a distinct clade with Ornithinimicrobium murale DSM 22056T and Ornithinimicrobium cavernae CFH 30183T, and shared sequence identities of 97.8% and 97.0%, respectively. The novel isolate could be distinguished from other species of the genus Ornithinimicrobium by its distinct phenotypic, physiological, and genotypic characteristics. Cells of strain EGI L100131T were aerobic, Gram-staining positive, and coccoid to rod-shaped. Optimal growing conditions of strain EGI L100131T occurred at pH 8.0 and 28 ºC. Ornithine was the diagnostic diamino acid in the cell-wall peptidoglycan. The respiratory quinone was MK-8 (H4), while the major fatty acids (> 10%) were C17:1 ω8c, C17:0, iso-C16:0, and iso-C15:0. The detected polar lipids included diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, and a glycophospholipid. The G + C content based on genomic DNA was 71.5%. According to the phenotypic, physiological, genotypic, and phylogenetic data, strain EGI L100131T represents a new species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium sediminis sp. nov. is proposed. The type strain is EGI L100131T (= KCTC 49716 T = CGMCC 1.19241T).
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Genome-based reclassification of the genus Meiothermus along with the proposal of a new genus Allomeiothermus gen. nov. Antonie van Leeuwenhoek 2022; 115:645-659. [PMID: 35348967 DOI: 10.1007/s10482-022-01723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/23/2022] [Indexed: 10/18/2022]
Abstract
Phylogenomic analyses were performed on the nine species of the genus Meiothermus and four species of the genus Calidithermus. Phylogenetic analysis, low values of genomic relatedness indices and functional diversity analysis indicated that Meiothermus silvanus should not be classified within the clades for Meiothermus and Calidithermus but instead be reclassified as a new genus, for which we propose the name Allomeiothermus gen. nov., with Allomeiothermus silvanus comb. nov. as type species. In addition, the species Meiothermus cateniformans Zhang et al. (Int J Syst Evol Microbial 60:840-844, 2010) should also be reclassified as a later heterotypic synonym of Meiothermus taiwanensis Chen et al. (Int J Syst Evol Microbiol 52:1647-1654, 2002) emend. Raposo et al. (2019). This reclassification is based on the high genomic relatedness indices (98.8% ANI; 90.2% dDDH; 99% AAI) that are above the threshold values necessary for defining a new species, as well as on the observation of overlapping functions on Principal Coordinate Analysis plot generated from Clusters of Orthologous Genes.
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Thermus brevis sp. nov., a moderately thermophilic bacterium isolated from a hot spring microbial mat. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005265] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three closely related, facultative anaerobic, Gram-stain-negative, twitching motile, short rod-shaped, non-endospore-forming, moderately thermophilic bacteria, designated strains SYSU G05001T, SYSU G05003 and SYSU G05004, were isolated from a hot spring microbial mat, collected from Rehai National Park, Tengchong, Yunnan Province, south-western China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that these three strains were closely related to
Thermus scotoductus
SE-1T (97.97, 98.18, 97.90 % sequence similarity). Whole genome sequencing and polyphasic taxonomic approach were used to determine the genomic profile and taxonomic status of the novel strain SYSU G05001T. Cell growth occurred at 37–80 °C (optimum, 55 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–3.0 % (w/v) NaCl (optimum, 1%). Thiosulfate enhanced cell growth. MK-8 was the predominant menaquinone. The major cellular fatty acids included iso-C15 : 0, iso-C17 : 0 and anteiso-C15 : 0. The major polar lipids were consisted of aminophospholipid, glycolipid and phospholipids. The whole genome of strain SYSU G05001T consisted of 2.55 Mbp and the DNA G+C content was 64.94 mol%. The average nucleotide identity (≤94.95 %) and digital DNA–DNA hybridization (≤62.3 %) values between strain SYSU G05001T and other members of the genus
Thermus
were all lower than the threshold values recommended for distinguishing novel prokaryotic species. On the basis of the presented polyphasic evidence and genotypic data, it is proposed that strain SYSU G05001T (=KCTC 82627T=MCCC 1K06118T) represents a novel species of the genus
Thermus
, for which the name Thermus brevis sp. nov. is proposed.
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Liu L, Lv AP, Narsing Rao MP, Ming YZ, Salam N, Li MM, Liu ZT, Zhang XT, Zhang JY, Xian WD, Jiao JY, Li WJ. Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China. Front Microbiol 2022; 12:739234. [PMID: 35145488 PMCID: PMC8822059 DOI: 10.3389/fmicb.2021.739234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 104 to 1.20 × 107 copies L–1. Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs.
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Affiliation(s)
- Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yu-Zhen Ming
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Tong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Jian-Yu Jiao,
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- *Correspondence: Wen-Jun Li,
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Wu D, Liu H, Zhou Y, Wu X, Nie Y, Cai M. Roseomonas oleicola sp. nov., isolated from an oil production mixture in Yumen Oilfield, and emended description of Roseomonas frigidaquae. Int J Syst Evol Microbiol 2021; 71. [PMID: 34710024 DOI: 10.1099/ijsem.0.005064] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pink, ovoid-shaped, Gram-stain-negative, strictly aerobic and motile bacterial strain, designated ROY-5-3T, was isolated from an oil production mixture from Yumen Oilfield in PR China. The strain grew at 4-42 °C (optimum, 30 °C), at pH 5-10 (optimum, 7) and with 0-5 % (w/v) NaCl (optimum, 0%). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that ROY-5-3T belongs to the genus Roseomonas and shared the highest pairwise similarities with Roseomonas frigidaquae CW67T (98.1%), Roseomonas selenitidurans BU-1T (97.8%), Roseomonas tokyonensis K-20T (97.7%) and Roseomonas stagni HS-69T (97.3%). The average nucleotide identity and digital DNA-DNA hybridization values between ROY-5-3T and other related type strains of Roseomonas species were less than 84.08 and 28.60 %, respectively, both below the species delineation threshold. Pan-genomic analysis showed that the novel isolate ROY-5-3T shared 3265 core gene families with the four closely related type strains in Roseomonas, and the number of strain-specific gene families was 513. The major fatty acids were identified as summed feature 8 (C18 : 1 ω6c/C18 : 1 ω7c), summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and C16 : 0. Strain ROY-5-3T contained Q-10 as the main ubiquinone and the genomic DNA G+C content was 69.8 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Based on the phylogenetic, morphological, physiological, chemotaxonomic and genome analyses, strain ROY-5-3T represents a novel species of the genus Roseomonas for which the name Roseomonas oleicola sp. nov. is proposed. The type strain is ROY-5-3T (=CGMCC 1.13459T =KCTC 82484T).
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Affiliation(s)
- Danni Wu
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hongcan Liu
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiaolei Wu
- College of Engineering, Peking University, Beijing 100871, PR China
| | - Yong Nie
- College of Engineering, Peking University, Beijing 100871, PR China
| | - Man Cai
- China General Microbiological Culture Collection Center, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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