1
|
Atsbeha G, Kebede M, Samuel B, Baraki H, Tadesse H, Sbhatu DB. Analysis of promoter region and regulatory elements of Rhizobium giardinii DNA-binding response regulator A3AY_RS01 genes. J Genet Eng Biotechnol 2024; 22:100397. [PMID: 39179324 PMCID: PMC11231716 DOI: 10.1016/j.jgeb.2024.100397] [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: 12/23/2023] [Revised: 05/08/2024] [Accepted: 06/12/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUND Rhizobium giardinii has been demonstrated to colonize the roots of a variety of legume species, including common beans, and to increase nitrogen fixation. This suggests that Rhizobium giardinii might be a beneficial tool for sustainable agriculture by lowering dependency on synthetic nitrogen fertilizers and enhancing soil fertility. Understanding the regulatory components in the R. giardinii A3AY_RS01 genes might also lead to the creation of innovative ways for increasing the effectiveness of nitrogen fixation in other agriculturally important bacteria. Therefore, this study was aimed to predict regulatory element of R. giardinii DNA-binding response regulator A3AY_RS01 genes. RESULTS The locations for 19 % of the Transcriptional start site (TSSs) were within -300 bp relative to the start codon and ten candidate motifs were identified that are shared by at least 50 % of the R. giardinii A3AY_RS01 promoter input sequences from both strands. Motif 1 was revealed as the common promoter motif for all of R. giardinii A3AY_RS01 genes that serves as binding sites for TFs involved in the expression regulation of these genes. Hence, it was revealed that Motif 1 may serve as the binding site chiefly for Ferric uptake regulator (Fur) transcription factor family to regulate expression of A3AY_RS01 genes. High CpG density in the promoter than body regions were observed for most of the genes except for A3AY_RS0102950, A3AY_RS0120195 and A3AY_RS0131150 genes. Nonetheless, promoter areas were richer than body regions in both techniques. CONCLUSIONS MV1 motif can serve as a binding site for the Fur transcription factor gene family in R. giardinii to regulate the expression of R. giardinii A3AY_RS01 genes. R. giardinii A3AY_RS01 genes are rich in CpG Islands, and play an important role in the regulation of the gene expression of nitrogen fixing in this bacterium.
Collapse
Affiliation(s)
- Genet Atsbeha
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia.
| | - Mulugeta Kebede
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Behailu Samuel
- Department of Animal Science, College of Agriculture and Natural Resource, Salale University, Fitche, Ethiopia.
| | - Haftom Baraki
- Department of Biological and Chemical Engineering, Mekelle Institute of Technology, Mekelle University, Mekelle, Ethiopia.
| | - Hailekiros Tadesse
- Department of Biological and Chemical Engineering, Mekelle Institute of Technology, Mekelle University, Mekelle, Ethiopia.
| | - Desta Berhe Sbhatu
- Department of Biological and Chemical Engineering, Mekelle Institute of Technology, Mekelle University, Mekelle, Ethiopia.
| |
Collapse
|
2
|
Zhang YF, Dai YN, Pu JF, Yang XF, Liu HH, Pan H, Tian Y. Pararhizobium qamdonense sp. nov., Isolated from an Alpine Soil in Tibet and the Reclassification of Rhizobium gei Shi et al. 2016 as Pararhizobium gei comb. nov. Curr Microbiol 2023; 81:44. [PMID: 38117411 DOI: 10.1007/s00284-023-03567-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
A novel Gram-stain-negative, aerobic, rod-shaped bacterium named T808T was isolated from an alpine soil in Qamdo, Tibet, PR China. Strain T808T grew at 5-30℃, pH 5.0-9.0 (optimum, 25℃ and pH 7.0-8.0) with 0-2% (w/v) NaCl (optimum, 0%). The 16S rRNA gene sequences of strain T808T showed the highest similarity with Pararhizobium herbae CCBAU83011T (98.8%), followed by Pararhizobium polonicum F5.1T (98.7%), Pararhizobium giardinii H152T (98.5%), Rhizobium gei ZFJT-2 T (98.4%), and Pararhizobium antarcticum NAQVI59T (97.5%). The highest digital DNA-DNA hybridization (dDDH), core-proteome average amino acid identity (cpAAI) and average nucleotide identity (ANI) values between strain T808T and related strains were estimated as 28.0%, 92.1% and 84.4%, respectively. Phylogenetic analysis based on 16S rRNA, core-proteome and whole-genome indicated that strain T808T belonged to the genus Pararhizobium. The genome size was 6.24 Mbp with genomic DNA G + C content of 60.1%. The major cellular fatty acids were Summed feature 8 (C18:1 ω7c or C18:1 ω6c), C16:0 and C19:0 cyclo ω8c. The polar lipids were diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl choline and unidentified aminophospholipid. The isoprenoid quinone were ubiquinone-10 and ubiquinone-9. Based on phenotypic, phylogenetic, and genotypic data, strain T808T is considered to represent a novel species of the genus Pararhizobium, for which the name Pararhizobium qamdonense sp. nov. is proposed. The type strain is T808T (= JCM 36247 T = CICC 25216 T). According to phylogenetic coherence based on 16S rRNA, core-proteome and whole-genome, it is also proposed that the type strain Rhizobium gei Shi et al. 2016 should be reclassified as Pararhizobium gei comb. nov., the type strain is ZFJT-2 T (= CCTCC AB 2013015 T = KCTC 32301 T = LMG 27603 T).
Collapse
Affiliation(s)
- Yi-Fan Zhang
- Institute of Agricultural Quality Standard and Testing, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850032, China
- Agricultural and Livestock Products Engineering Technology Research Center of Tibet Autonomous Region, Lhasa, 850032, China
| | - Yan-Na Dai
- Institute of Agricultural Quality Standard and Testing, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850032, China
- Agricultural and Livestock Products Engineering Technology Research Center of Tibet Autonomous Region, Lhasa, 850032, China
| | - Ji-Feng Pu
- Institute of Agricultural Quality Standard and Testing, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850032, China
- Agricultural and Livestock Products Engineering Technology Research Center of Tibet Autonomous Region, Lhasa, 850032, China
| | - Xiao-Feng Yang
- Institute of Agricultural Quality Standard and Testing Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Hu-Hu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Hu Pan
- Institute of Agricultural Quality Standard and Testing, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850032, China.
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Agricultural and Livestock Products Engineering Technology Research Center of Tibet Autonomous Region, Lhasa, 850032, China.
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
| |
Collapse
|
3
|
Wang M, Eyre AW, Thon MR, Oh Y, Dean RA. Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds. Front Microbiol 2020; 11:559728. [PMID: 33013792 PMCID: PMC7506108 DOI: 10.3389/fmicb.2020.559728] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/17/2020] [Indexed: 12/26/2022] Open
Abstract
Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents.
Collapse
Affiliation(s)
- Mengying Wang
- Fungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
| | - Alexander W Eyre
- Fungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
| | - Michael R Thon
- Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Villamayor, Spain
| | - Yeonyee Oh
- Fungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
| | - Ralph A Dean
- Fungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
4
|
Naqvi SUEK, Qin Y, Tahir A, Stougaard P. Pararhizobium antarcticum sp. nov., isolated from Antarctic water samples. Int J Syst Evol Microbiol 2017; 67:1650-1655. [PMID: 28141485 DOI: 10.1099/ijsem.0.001828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains were isolated from sediments and microbial mats of Kingfisher Pond, Antarctica and characterized in a taxonomic study using a polyphasic approach. Cells were strictly aerobic, Gram-stain-negative, rod-shaped, motile (+50 flagellum-specific genes present in the genome sequence; motility observed under microscope) and formed creamy white, half-transparent colonies. Growth occurred at 4 to 28 °C with an optimum at 20 °C, with 0-5.0 % (w/v) NaCl (optimum at 0-1.0 %) and at pH 4.0-11.0 (optimum pH 7.0-9.0). The major fatty acid was C18 : 1ω7c. The respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C content was 60.7 mol %. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmethanolamine in addition to three unidentified lipids, one unknown glycolipid and five unidentified phospholipids. Comparative analysis of 16S rRNA gene sequences showed highest sequence similarity (98.1 %) to Pararhizobium giardinii H152T, Pararhizobium herbae CCBAU 83011T, and 'Pararhizobium polonicum' F5.1. In silico average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC) showed 81.1 % identity (ANI) and 22.6 % identity (GGDC) to the closest relative, 'P. polonicum' F5.1. On the basis of phenotypic, phylogenetic, genomic and chemotaxonomic data, the two strains represent a novel species of the genus Pararhizobium, for which the name Pararhizobium antarcticum sp. nov. is proposed. The type strain is NAQVI 59T(=DSM 103442T=LMG 29675T).
Collapse
Affiliation(s)
- Syeda Um-E-Kalsoom Naqvi
- Department of Environmental Science, Lahore College for Women University, Lahore, Pakistan.,Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Yanan Qin
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Arifa Tahir
- Department of Environmental Science, Lahore College for Women University, Lahore, Pakistan
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| |
Collapse
|
5
|
de Lajudie P, Martinez-Romero E. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Agrobacterium and Rhizobium Minutes of the meeting, 7 September 2014, Tenerife, Spain. Int J Syst Evol Microbiol 2017; 67:516-520. [DOI: 10.1099/ijsem.0.001597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Philippe de Lajudie
- IRD, LSTM, Campus International de Baillarguet TA A-82/J, 34398 Montpellier Cédex 5, France
| | | |
Collapse
|
6
|
Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
7
|
Shi X, Li C, Zhao L, Si M, Zhu L, Xin K, Chen C, Wang Y, Shen X, Zhang L. Rhizobium gei sp. nov., a bacterial endophyte of Geum aleppicum. Int J Syst Evol Microbiol 2016; 66:4282-4288. [PMID: 27474082 DOI: 10.1099/ijsem.0.001348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated as ZFJT-2T, was isolated from the stem of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain ZFJT-2T were Gram-stain-negative, strictly aerobic, rod-shaped and motile by means of a single polar flagellum. The major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, 11-methyl C18 : 1ω7c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), and the DNA G+C content was 58.3 mol% (HPLC). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFJT-2T was a member of the genus Rhizobium and was most closely related to Rhizobium giardinii KACC 10720T (98.6 % similarity) and Rhizobium herbae CCBAU 83011T (98.5 %). The low levels of sequence similarity found between the atpD, recA and glnII gene sequences of strain ZFJT-2T and those of recognized species of the genus Rhizobium (no more than 94.4, 87.2 and 89.5 %, respectively) indicated that it may represent a separate species of the genus Rhizobium. The DNA-DNA relatedness values for strain ZFJT-2T with respect to R. giardinii KACC 10720T and R. herbae CCBAU 83011T were 17.6 and 41.9 %, respectively. On the basis of phenotypic, phylogenetic and genotypic data, strain ZFJT-2T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium gei sp. nov. is proposed. The type strain is ZFJT-2T (=CCTCC AB 2013015T=KCTC 32301T=LMG 27603T).
Collapse
Affiliation(s)
- Xu Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Changfu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Liang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Meiru Si
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lingfang Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Kaiyun Xin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Chaoqiong Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| |
Collapse
|
8
|
Pararhizobium polonicum sp. nov. isolated from tumors on stone fruit rootstocks. Syst Appl Microbiol 2016; 39:164-169. [PMID: 27026286 DOI: 10.1016/j.syapm.2016.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 02/29/2016] [Accepted: 03/04/2016] [Indexed: 11/20/2022]
Abstract
Five Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from galls on different stone fruit rootstocks in Poland: strains F5.1(T) and F5.3 from Prunus avium F12/1, strains CP3.5 and CP17.2.1 from Prunus avium and strain AL5.1.8 from Prunus cerasifera. On the basis of 16S rDNA phylogeny, the strains cluster together and belong to the genus Pararhizobium with type strain of Pararhizobium herbae (99.6-99.8%) as their closest relative. Phylogenetic analysis of the novel strains using housekeeping genes atpD, recA and rpoB revealed their distinct position separate from other known Rhizobium species and confirmed their relation to P. herbae. DNA-DNA hybridization of strains F5.1(T), with the type strain of P. herbae LMG 25718(T) and Pararhizobium giardinii R-4385(T) revealed 28.3% and 27.9% of DNA-DNA relatedness, respectively. Phenotypic and physiological properties differentiate the novel isolates from other closely related species. On the basis of the results obtained, the five isolates are considered to represent a novel species of the genus Pararhizobium, for which the name Pararhizobium polonicum sp. nov. (type strain F5.1(T)=LMG 28610(T)=CFBP 8359(T)) is proposed.
Collapse
|
9
|
Rhizobium puerariae sp. nov., an endophytic bacterium from the root nodules of the medicinal plant Pueraria candollei var. candollei. Int J Syst Evol Microbiol 2016; 66:1236-1241. [DOI: 10.1099/ijsem.0.000863] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
10
|
Naamala J, Jaiswal SK, Dakora FD. Antibiotics Resistance in Rhizobium: Type, Process, Mechanism and Benefit for Agriculture. Curr Microbiol 2016; 72:804-16. [DOI: 10.1007/s00284-016-1005-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/07/2016] [Indexed: 11/29/2022]
|
11
|
Yan H, Ji ZJ, Jiao YS, Wang ET, Chen WF, Guo BL, Chen WX. Genetic diversity and distribution of rhizobia associated with the medicinal legumes Astragalus spp. and Hedysarum polybotrys in agricultural soils. Syst Appl Microbiol 2016; 39:141-9. [PMID: 26915496 DOI: 10.1016/j.syapm.2016.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 01/28/2016] [Accepted: 01/29/2016] [Indexed: 10/22/2022]
Abstract
With the increasing cultivation of medicinal legumes in agricultural fields, the rhizobia associated with these plants are facing new stresses, mainly from fertilization and irrigation. In this study, investigations on the nodulation of three cultivated medicinal legumes, Astragalus mongholicus, Astragalus membranaceus and Hedysarum polybotrys were performed. Bacterial isolates from root nodules of these legumes were subjected to genetic diversity and multilocus sequence analyses. In addition, the distribution of nodule bacteria related to soil factors and host plants was studied. A total 367 bacterial isolates were obtained and 13 genospecies were identified. The predominant microsymbionts were identified as Mesorhizobium septentrionale, Mesorhizobium temperatum, Mesorhizobium tianshanense, Mesorhizobium ciceri and Mesorhizobium muleiense. M. septentrionale was found in most root nodules especially from legumes grown in the barren soils (with low available nitrogen and low organic carbon contents), while M. temperatum was predominant in nodules where the plants were grown in the nitrogen-rich fields. A. mongholicus tended to be associated with M. septentrionale, M. temperatum and M. ciceri in different soils, while A. membranaceus and H. polybotrys tended to be associated with M. tianshanense and M. septentrionale, respectively. This study showed that soil fertility may be the main determinant for the distribution of rhizobia associated with these cultured legume plants.
Collapse
Affiliation(s)
- Hui Yan
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Zhao Jun Ji
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Yin Shan Jiao
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - En Tao Wang
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China; Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., Mexico
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China.
| | - Bao Lin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| |
Collapse
|
12
|
Xu KW, Zou L, Penttinen P, Zeng X, Liu M, Zhao K, Chen C, Chen YX, Zhang X. Diversity and phylogeny of rhizobia associated with Desmodium spp. in Panxi, Sichuan, China. Syst Appl Microbiol 2015; 39:33-40. [PMID: 26654528 DOI: 10.1016/j.syapm.2015.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 10/24/2015] [Accepted: 10/26/2015] [Indexed: 11/19/2022]
Abstract
Thirty-four rhizobial isolates were obtained from root nodules of four wild Desmodium species growing in Panxi, Sichuan, China. According to the combined ARDRA and IGS-RFLP (CACAI) cluster analysis, Rhizobium, Pararhizobium and Mesorhizobium isolates outnumbered Bradyrhizobium isolates. In general, the isolates representing the same species from the same site clustered together. Furthermore, the four Desmodium species were all nodulated by more than one rhizobial species. AFLP and phenotypic analyses showed that the 34 isolates represented at least 32 distinct strains. None of the strains were found from more than one site or host, indicating a high degree of rhizobial diversity in Panxi. In the multilocus sequence analysis, the isolates were assigned to Pararhizobium giardinii, Bradyrhizobium japonicum, Mesorhizobium septentrionale, and to undescribed species of the genera Rhizobium, Bradyrhizobium and Agrobacterium.
Collapse
Affiliation(s)
- Kai Wei Xu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 625014, China.
| | - Lan Zou
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 625014, China
| | - Petri Penttinen
- Department of Environmental Sciences, University of Helsinki, Helsinki Fin-00014, Finland
| | - Xiangzhong Zeng
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Ming Liu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 625014, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 625014, China
| | - Cuiping Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 625014, China
| | - Yuan Xue Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 625014, China.
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 625014, China.
| |
Collapse
|
13
|
Mousavi SA, Willems A, Nesme X, de Lajudie P, Lindström K. Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst Appl Microbiol 2015; 38:84-90. [DOI: 10.1016/j.syapm.2014.12.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/07/2014] [Accepted: 12/12/2014] [Indexed: 01/26/2023]
|
14
|
Fukano T, Gomi M, Osaki Y, Morikawa M. Isolation and characterization of an early colonizing Rhizobium sp. R8 from a household toilet bowl. Biosci Biotechnol Biochem 2015; 79:1207-15. [PMID: 25707633 DOI: 10.1080/09168451.2015.1012151] [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: 10/23/2022]
Abstract
The bacterial community structure was compared between the third days', one week', and three weeks' biofilm samples from the surface of a household toilet bowl. It was found that the PCR-DGGE band pattern of 16S rRNA gene was dramatically changed after the third day and was not further changed until three weeks. This result suggests that there are early and late colonizing bacterial groups. One of the early colonizers isolated from the third days' sample was Rhizobium sp. R8, a closest relative to Rhizobium giardinii, which exhibited the highest biofilm formation activity in an artificial urine condition. R8 produced extracellular polysaccharides containing galactose, glucose, and mannose at the molar ratio of 8:1:1, which were probably responsible for the biofilm formation. Its excelled biofilm formation and urease activities together with the lack of nodulation and nitrogen fixing genes in R8 suggest that this strain has been specifically adapted to urine condition in a toilet bowl.
Collapse
Affiliation(s)
- Toru Fukano
- a Graduate School of Environmental Science , Hokkaido University , Sapporo 060-0810 , Japan
| | | | | | | |
Collapse
|
15
|
Qin W, Deng ZS, Xu L, Wang NN, Wei GH. Rhizobium helanshanense sp. nov., a bacterium that nodulates Sphaerophysa salsula (Pall.) DC. in China. Arch Microbiol 2011; 194:371-8. [DOI: 10.1007/s00203-011-0766-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 11/29/2022]
|