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van Lill M, Venter SN, Muema EK, Palmer M, Chan WY, Beukes CW, Steenkamp ET. SeqCode facilitates naming of South African rhizobia left in limbo. Syst Appl Microbiol 2024; 47:126504. [PMID: 38593622 DOI: 10.1016/j.syapm.2024.126504] [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: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.
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Affiliation(s)
- Melandré van Lill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Esther K Muema
- Department of Soil Science, Faculty of AgriSciences, Stellenbosch University, South Africa
| | - Marike Palmer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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Li Y, Guo T, Sun L, Wang ET, Young JPW, Tian CF. Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species. BMC Genomics 2024; 25:419. [PMID: 38684951 PMCID: PMC11057113 DOI: 10.1186/s12864-024-10333-y] [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: 01/31/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUD The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. RESULTS The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. CONCLUSION The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.
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Affiliation(s)
- Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China.
| | - Tingyan Guo
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovation Utilization, Jiaodong Microbial Resource Center of Yantai University, College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, 11340, México
| | - J Peter W Young
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Chang-Fu Tian
- State Key Laboratory of Plant Environmental Resilience, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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Luo Q, Wang H, Lu X, Wang C, Chen R, Cheng J, He T, Fu T. Potential of combined reactor and static composting applications for the removal of heavy metals and antibiotic resistance genes from chicken manure. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120592. [PMID: 38508009 DOI: 10.1016/j.jenvman.2024.120592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Chicken manure (CM) can pose a serious threat to environmental and human health, and need to be managed properly. The compost can effectively treat CM. However, there is limited research on the heavy metals and antibiotic resistance genes (ARGs) during compost CM. In this study, the combined application of reactor and static composting (RSC) was used to produce organic fertilizer of CM (OCM), and heavy metals, ARGs and bacterial community structure was investigated. The results show that RSC could be used to produce OCM, and OCM meet the National organic fertilizer standard (NY/T525-2021). Compared to the initial CM, DTPA-Cu, DTPA-Zn, DTPA-Pb, DTPA-Cr, DTPA-Ni and DTPA-As in OCM decreased by 40.83%, 23.73%, 34.27%, 38.62%, 16.26%, and 43.35%, respectively. RSC decreased the relative abundance of ARGs in CM by 84.06%, while the relative abundance of sul1 and ermC increased. In addition, the relative abundance and diversity of ARGs were mainly influenced by the bacterial community, with Actinobacteria, Firmicutes, and Proteobacteria becoming the dominant phyla during composting, and probably being the main carriers and dispersers of most of the ARGs. Network analyses confirmed that Gracilibacillus, Lactobacillus, Nocardiopsis, Mesorhizobium and Salinicoccus were the main potential hosts of ARGs, with the main potential hosts of sul1 and ermC being Mesorhizobium and Salinicoccus. The passivation and physicochemical properties of heavy metals contribute to the removal of ARGs, with sul1 and ermC being affected by the toal heavy metals. Application of RSC allows CM to produce mature, safe organic fertilizer after 32 d and reduces the risk of rebound from ARGs, but the issues of sul1 and ermC gene removal cannot be ignored.
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Affiliation(s)
- Qu Luo
- College of Resource and Environmental Engineering, Guizhou University, Guiyang, 550025, Guizhou, China; Guizhou Engineering Laboratory of Mountain Livestock and Poultry Farming Pollution Control and Resource Technology, Institute of New Rural Development, Guizhou University, Guiyang, 550025, China
| | - Hu Wang
- Guizhou Chuyang Ecological Environmental Protection Technology Co., Ltd., Guizhou, 550003, China
| | - Xiaoqing Lu
- College of Resource and Environmental Engineering, Guizhou University, Guiyang, 550025, Guizhou, China; Guizhou Engineering Laboratory of Mountain Livestock and Poultry Farming Pollution Control and Resource Technology, Institute of New Rural Development, Guizhou University, Guiyang, 550025, China
| | - Can Wang
- Lijiang Agricultural Environmental Protection Monitoring Station, Lijiang, Yunnan, 674100, China
| | - Ruiying Chen
- College of Resource and Environmental Engineering, Guizhou University, Guiyang, 550025, Guizhou, China; Guizhou Engineering Laboratory of Mountain Livestock and Poultry Farming Pollution Control and Resource Technology, Institute of New Rural Development, Guizhou University, Guiyang, 550025, China
| | - Jianbo Cheng
- Guizhou Engineering Laboratory of Mountain Livestock and Poultry Farming Pollution Control and Resource Technology, Institute of New Rural Development, Guizhou University, Guiyang, 550025, China
| | - Tengbing He
- College of Resource and Environmental Engineering, Guizhou University, Guiyang, 550025, Guizhou, China; Guizhou Engineering Laboratory of Mountain Livestock and Poultry Farming Pollution Control and Resource Technology, Institute of New Rural Development, Guizhou University, Guiyang, 550025, China
| | - Tianling Fu
- College of Resource and Environmental Engineering, Guizhou University, Guiyang, 550025, Guizhou, China; Guizhou Engineering Laboratory of Mountain Livestock and Poultry Farming Pollution Control and Resource Technology, Institute of New Rural Development, Guizhou University, Guiyang, 550025, China.
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Volpiano CG, Sant'Anna FH, Ambrosini A, de São José JFB, Beneduzi A, Whitman WB, de Souza EM, Lisboa BB, Vargas LK, Passaglia LMP. Genomic Metrics Applied to Rhizobiales ( Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains. Front Microbiol 2021; 12:614957. [PMID: 33841347 PMCID: PMC8026895 DOI: 10.3389/fmicb.2021.614957] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) “Bartonella vinsonii” subsp. arupensis and “B. vinsonii” subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 (“Mesorhizobium loti LMG 6125T”), GCF_003024595.1 (“Mesorhizobium plurifarium LMG 11892T”), GCF_003096615.1 (“Methylobacterium organophilum DSM 760T”), and GCF_000373025.1 (“R. gallicum R-602 spT”) are not from the genuine type strains used for the respective species descriptions; and v) “Xanthobacter autotrophicus” Py2 and “Aminobacter aminovorans” KCTC 2477T represent cases of misuse of the term “type strain”. Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.
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Affiliation(s)
- Camila Gazolla Volpiano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernando Hayashi Sant'Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriana Ambrosini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Anelise Beneduzi
- Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Centro Politécnico, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Bruno Brito Lisboa
- Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | - Luciano Kayser Vargas
- Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
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Oren A, Garrity GM. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication. Int J Syst Evol Microbiol 2020; 70:5596-5600. [DOI: 10.1099/ijsem.0.004484] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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de Lajudie P, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019. Int J Syst Evol Microbiol 2020; 70:3563-3571. [DOI: 10.1099/ijsem.0.004157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Minutes of the closed meeting of the ICSP Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference on 17 July 2019, and list of recent species.
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Yang X, Jiang Z, Zhang J, Zhou X, Zhang X, Wang L, Yu T, Wang Z, Bei J, Dong B, Dai Z, Yang Q, Chen Z. Mesorhizobium alexandrii sp. nov., isolated from phycosphere microbiota of PSTs-producing marine dinoflagellate Alexandrium minutum amtk4. Antonie Van Leeuwenhoek 2020; 113:907-917. [PMID: 32193664 DOI: 10.1007/s10482-020-01400-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/04/2020] [Indexed: 11/26/2022]
Abstract
An aerobic, Gram-stain-negative, motile and rod-shaped bacterial strain, designated as Z1-4T, was isolated from the phycosphere microbiota of marine dinoflagellate Alexandrium minutum that produces paralytic shellfish poisoning toxins. Phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate belongs to the genus Mesorhizobium, and it was closely related to Mesorhizobium waimense LMG 28228T and Mesorhizobium amorphae LMG 18977T with both 16S rRNA gene sequence similarities of 97.3%. The values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness between strain Z1-4T and its relatives are both well below the thresholds used for the delineation of a new species. A genome-based phylogenetic tree constructed by up-to-date bacterial core gene set (UBCG) indicates that strain Z1-4T forms an independent branch within the genus Mesorhizobium. The respiratory quinone of strain Z1-4T was Q-10. The major fatty acids were similar to other members of the genus Mesorhizobium containing the summed feature 8, C16:0, C19:0cycloω8c, C17:0 and summed feature 3. The polar lipids are phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, five glycolipids and seven unknown polar lipids. The DNA G + C content was determined to be 62.1 mol % based on its genomic sequence. Combined evidences based on the genotypic, chemotaxonomic and phenotypic characteristics clearly indicates that strain Z1-4T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium alexandrii sp. nov. is proposed. The type strain is Z1-4T (= KCTC 72512T = CCTCC AB 2019101T).
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Affiliation(s)
- Xi Yang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Zhiwei Jiang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Jing Zhang
- Comprehensive Technology Service Center of Zhoushan Customs, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Xin Zhou
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Xiaoling Zhang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Lei Wang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Ting Yu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Zhilin Wang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Jinlong Bei
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Bo Dong
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Zhangyan Dai
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Qiao Yang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China.
| | - Zhuang Chen
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China.
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