1
|
Luo H, Wang X, You C, Wu X, Pan D, Lv Z, Li T, Zhang D, Shen Z, Zhang X, Liu G, He K, Ye Q, Jia Y, Zhao Q, Deng X, Cao X, Song X, Huang G. Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance. SCIENCE CHINA. LIFE SCIENCES 2024; 67:149-160. [PMID: 37897613 DOI: 10.1007/s11427-023-2463-y] [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: 07/20/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023]
Abstract
Alkaline soils pose an increasing problem for agriculture worldwide, but using stress-tolerant plants as green manure can improve marginal land. Here, we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and, when used as a green manure, substantially improves alkaline soil. To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume, we generated the first telomere-to-telomere genome assembly of S. cannabina spanning ∼2,087 Mb. The assembly included all centromeric regions, which contain centromeric satellite repeats, and complete chromosome ends with telomeric characteristics. Further genome analysis distinguished A and B subgenomes, which diverged approximately 7.9 million years ago. Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events (>10 Mb) and a significant, transposon-driven size expansion of the chromosome 5A homoeolog. We further identified four specific alkali-induced phosphate transporter genes in S. cannabina; these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil. Our work highlights the significance of S. cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.
Collapse
Affiliation(s)
- Haofei Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofei Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Changqing You
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuedan Wu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Duofeng Pan
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Zhiyao Lv
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Tong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongmei Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Zhongbao Shen
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xiaodong Zhang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257345, China
- Shandong Green Manure Ecological Technology Co., Ltd, Dongying, 257345, China
| | - Guodao Liu
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Kaixuan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Qingtong Ye
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yajun Jia
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Qinghua Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Gai Huang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
2
|
Wang Y, Yang Y, Zhao D, Li Z, Sui X, Zhang H, Liu J, Li Y, Zhang CS, Zheng Y. Ensifer sp. GMS14 enhances soybean salt tolerance for potential application in saline soil reclamation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 349:119488. [PMID: 37939476 DOI: 10.1016/j.jenvman.2023.119488] [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: 08/01/2023] [Revised: 10/10/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
Rhizosphere microbiomes play an important role in enhancing plant salt tolerance and are also commonly employed as bio-inoculants in soil remediation processes. Cultivated soybean (Glycine max) is one of the major oilseed crops with moderate salt tolerance. However, the response of rhizosphere microbes me to salt stress in soybean, as well as their potential application in saline soil reclamation, has been rarely reported. In this study, we first investigated the microbial communities of salt-treated and non-salt-treated soybean by 16S rRNA gene amplicon sequencing. Then, the potential mechanism of rhizosphere microbes in enhancing the salt tolerance of soybean was explored based on physiological analyses and transcriptomic sequencing. Our results suggested that Ensifer and Novosphingobium were biomarkers in salt-stressed soybean. One corresponding strain, Ensifer sp. GMS14, showed remarkable growth promoting characteristics. Pot experiments showed that GMS14 significantly improved the growth performance of soybean in saline soils. Strain GMS14 alleviated sodium ions (Na+) toxicity by maintaining low a Na+/K+ ratio and promoted nitrogen (N) and phosphorus (P) uptake by soybean in nutrient-deficient saline soils. Transcriptome analyses indicated that GMS14 improved plant salt tolerance mainly by ameliorating salt stress-mediated oxidative stress. Interestingly, GMS14 was evidenced to specifically suppress hydrogen peroxide (H2O2) production to maintain reactive oxygen species (ROS) homeostasis in plants under salt stress. Field experiments with GMS14 applications showed its great potential in saline soil reclamation, as evidenced by the increased biomass and nodulation capacity of GMS14-inoculated soybean. Overall, our findings provided valuable insights into the mechanisms underlying plant-microbes interactions, and highlighted the importance of microorganisms recruited by salt-stressed plant in the saline soil reclamation.
Collapse
Affiliation(s)
- Youqiang Wang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China
| | - Yanzhe Yang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Donglin Zhao
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China
| | - Zhe Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xiaona Sui
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Han Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Jin Liu
- Shandong Baiwo Bio-technology Co., Ltd., Linyi, 273423, China
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China.
| | - Yanfen Zheng
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China.
| |
Collapse
|
3
|
Msaddak A, Quiñones MA, Mars M, Pueyo JJ. The Beneficial Effects of Inoculation with Selected Nodule-Associated PGPR on White Lupin Are Comparable to Those of Inoculation with Symbiotic Rhizobia. PLANTS (BASEL, SWITZERLAND) 2023; 12:4109. [PMID: 38140436 PMCID: PMC10747367 DOI: 10.3390/plants12244109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Nodule endophytes and associated bacteria are non-symbiotic bacteria that colonize legume nodules. They accompany nodulating rhizobia and can form beneficial associations, as some of them are plant growth-promoting rhizobacteria (PGPR) that are able to promote germination and plant growth and increase tolerance to biotic and abiotic stress. White lupin (Lupinus albus) is a legume crop that is gaining relevance as a suitable alternative to soybean as a plant protein source. Eleven nodule-associated bacteria were isolated from white lupin nodules grown in a Tunisian soil. They belonged to the genera Rhizobium, Ensifer, Pseudomonas and Bacillus. Their plant growth-promoting (PGP) and enzymatic activities were tested in vitro. Strains Pseudomonas sp., L1 and L12, displayed most PGP activities tested, and were selected for in planta assays. Inoculation with strains L1 or L12 increased seed germination and had the same positive effects on all plant growth parameters as did inoculation with symbiotic Bradyrhizobium canariense, with no significant differences among treatments. Inoculation with efficient nitrogen-fixing rhizobia must compete with rhizobia present in the soil that sometimes nodulate efficiently but fix nitrogen poorly, leading to a low response to inoculation. In such cases, inoculation with highly effective PGPR might represent a feasible alternative to boost crop productivity.
Collapse
Affiliation(s)
- Abdelhakim Msaddak
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia;
| | - Miguel A. Quiñones
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
| | - Mohamed Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia;
| | - José J. Pueyo
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
| |
Collapse
|
4
|
Duo L, Yang Y, Gao Y, Zhao S. Graphene oxide affects the symbiosis of legume-rhizobium and associated rhizosphere rhizobial communities. CHEMOSPHERE 2023; 342:140166. [PMID: 37714489 DOI: 10.1016/j.chemosphere.2023.140166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
The large-scale production and utilization of graphene oxide (GO) have raised concerns regarding its environmental exposure and potential risks. However, existing research on GO toxicity has primarily focused on individual organisms. Little attention has been given to the interaction between GO and the nitrogen-fixing symbiosis of legume-rhizobium. In this study, we focused on alfalfa (Medicago sativa L.), a typical leguminous nitrogen-fixing plant, to investigate the effects of GO on various aspects of this symbiotic relationship, including root nodulation, rhizobial viability, nodule nitrogen fixation, DNA damage, and the composition of the rhizobial community in the rhizosphere. As the dosage of GO increased, a significant inhibition in nodulation development was observed. Exposure to GO resulted in decreased growth and viability of rhizobia, as well as induced DNA damage in nodule cells. Furthermore, with increasing GO dosage, there were significant reductions in nitrogenase activity, leghemoglobin level, and cytoplasmic ammonia content within the root nodules. Additionally, the presence of GO led to notable changes in the rhizobial community in the rhizosphere. Our findings support the existence of the damage promoted by GO in the symbiosis of nitrogen fixing rhizobia with legumes. This underscores the importance of careful soil GO management.
Collapse
Affiliation(s)
- Lian Duo
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Yaqian Yang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Yingyue Gao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Shulan Zhao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China.
| |
Collapse
|
5
|
Zheng Y, Cao X, Zhou Y, Li Z, Yang Y, Zhao D, Li Y, Xu Z, Zhang CS. Effect of planting salt-tolerant legumes on coastal saline soil nutrient availability and microbial communities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118574. [PMID: 37423189 DOI: 10.1016/j.jenvman.2023.118574] [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: 04/07/2023] [Revised: 06/28/2023] [Accepted: 07/02/2023] [Indexed: 07/11/2023]
Abstract
Soil salinization is a serious global environmental problem affecting sustainable development of agriculture. Legumes are excellent candidates for the phytoremediation of saline soils; however, how soil microbes mediate the amelioration of coastal saline ecosystems is unknown. In this study, two salt-tolerant legumes, Glycine soja and Sesbania cannabina were planted in coastal saline soil for three years. Soil nutrient availability and microbiota structure (including bacteria, fungi, and diazotrophs) were compared between the phytoremediated soils and control soil (barren land). Planting legumes reduced soil salinity, and increased total carbon, total nitrogen, and NO3--N contents. Among the soil microbiota, some nitrogen-fixing bacteria (e.g., Azotobacter) were enriched in legumes, which were probably responsible for soil nitrogen accumulation. The complexity of the bacterial, fungal, and diazotrophic networks increased significantly from the control to the phytoremediated soils, suggesting that the soil microbial community formed closer ecological interactions during remediation. Furthermore, the dominant microbial functions were chemoheterotrophy (24.75%) and aerobic chemoheterotrophy (21.97%) involved in the carbon cycle, followed by nitrification (13.68%) and aerobic ammonia oxidation (13.34%) involved in the nitrogen cycle. Overall, our findings suggested that G. soja and S. cannabina legumes were suitable for ameliorating saline soils as they decreased soil salinity and increased soil nutrient content, with microorganisms especially nitrogen-fixing bacteria, playing an important role in this remediation process.
Collapse
Affiliation(s)
- Yanfen Zheng
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China
| | - Xuwen Cao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266200, China
| | - Yanan Zhou
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Zhe Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Yanzhe Yang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Donglin Zhao
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China
| | - Zongchang Xu
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China.
| | - Cheng-Sheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257300, China.
| |
Collapse
|
6
|
Ye X, Meng J, Ma R, Wu M. Effects of Clipping an Invasive Plant Species on the Growth of Planted Plants of Two Co-Occurring Species in a Greenhouse Study. BIOLOGY 2023; 12:1282. [PMID: 37886992 PMCID: PMC10604010 DOI: 10.3390/biology12101282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
The restoration of native plants in invaded habitats is constrained with the presence of highly competitive exotic species. Aboveground removal, such as clipping or mowing, of invasive plants is required for successful restoration. The effects of clipping an invasive plant species, Solidago canadensis, grown at five densities (1-5 plants per pot), and planting two co-occurring and competitive species, Sesbania cannabina and Imperata cylindrica, on the growth of both the invasive species and the co-occurring species were investigated in a greenhouse experiment. The established S. canadensis suppressed the growth of planted seedlings with 47.8-94.4% reduction in biomass, with stronger effects at higher densities; clipping significantly reduced 97.5-97.4% of biomass of S. canadensis and ameliorated the suppression effects (with only 8.7-52.7% reduction in biomass of the co-occurring plants), irrespective of density. Both the aboveground and belowground part of S. canadensis contributed to its suppression effects on planted co-occurring species. Seed sowing of co-occurring species reduced the belowground growth, but not the underground growth of S. canadensis. S. cannabina appeared to be more effective at reducing the growth of S. canadensis than I. cylindrica. Therefore, clipping together with planting competitive species that can overcome the belowground priority effects of S. canadensis could be a promising strategy for controlling S. canadensis invasion and restoring native plant communities.
Collapse
Affiliation(s)
| | | | | | - Ming Wu
- Research Station of Hangzhou Bay Wetland Ecosystems, Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; (X.Y.); (J.M.); (R.M.)
| |
Collapse
|
7
|
Wang W, Yang X, Mo Q, Li Y, Meng D, Li H. Intercropping efficiency of Pteris vittata with two legume plants: Impacts of soil arsenic concentrations. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 259:115004. [PMID: 37196521 DOI: 10.1016/j.ecoenv.2023.115004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Intercropping of hyperaccumulators with crops has emerged as a promising method for remediating arsenic (As)-contaminated soil in agroecosystems. However, the response of intercropping hyperaccumulators with different types of legume plants to diverse gradients of As-contaminated soil remains poorly understood. In this study, we assessed the response of plant growth and accumulation of an As hyperaccumulator (Pteris vittata L.) intercropped with two legume plants to three gradients of As-contaminated soil. Results indicated that soil As concentration had a substantial effect on the As uptake by plants. P. vittata growing in slightly As-contaminated soil (80 mg kg-1) exhibited higher As accumulation (1.52-5.49 folds) than those in higher As-contaminated soil (117 and 148 mg kg-1), owing to the lower soil pH in high As-contaminated soil. Intercropping with Sesbania cannabina L. increased As accumulation in P. vittata by 19.3%- 53.9% but decreased in intercropping with Cassia tora L. This finding was attributed to S. cannabina providing more NO3--N to P. vittata to support its growth, and higher resistance to As. The decreased rhizosphere pH in the intercropping treatment also resulted in the increased As accumulation in P. vittata. Meanwhile, the As concentrations in the seeds of the two legume plants met the national food standards(<0.5 mg kg-1). Therefore, the intercropping P. vittata with S. cannabina is a highly effective intercropping system in slightly As-contaminated soil and provides a potent method for As phytoremediation.
Collapse
Affiliation(s)
- Wenjuan Wang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture of China, Guangzhou 510642, China
| | - Xu Yang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Qifeng Mo
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Yinshi Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture of China, Guangzhou 510642, China
| | - Dele Meng
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture of China, Guangzhou 510642, China
| | - Huashou Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture of China, Guangzhou 510642, China.
| |
Collapse
|
8
|
Han K, Li Y, Zhang Z, Sun L, Wang ET, Li Y. Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids. Microb Genom 2023; 9. [PMID: 37133904 DOI: 10.1099/mgen.0.001004] [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: 05/04/2023] Open
Abstract
Symbiotic nitrogen fixation between legumes and rhizobia makes a great contribution to the terrestrial ecosystem. The successful symbiosis between the partners mainly depends on the nod and nif genes in rhizobia, while the specific symbiosis is mainly determined by the structure of Nod factors and the corresponding secretion systems (type III secretion system; T3SS), etc. These symbiosis genes are usually located on symbiotic plasmids or a chromosomal symbiotic island, both could be transferred interspecies. In our previous studies, Sesbania cannabina-nodulating rhizobia across the world were classified into 16 species of four genera and all the strains, especially those of Rhizobium spp., harboured extraordinarily highly conserved symbiosis genes, suggesting that horizontal transfer of symbiosis genes might have happened among them. In order to learn the genomic basis of diversification of rhizobia under the selection of host specificity, we performed this study to compare the complete genome sequences of four Rhizobium strains associated with S. cannabina, YTUBH007, YTUZZ027, YTUHZ044 and YTUHZ045. Their complete genomes were sequenced and assembled at the replicon level. Each strain represents a different species according to the average nucleotide identity (ANI) values calculated using the whole-genome sequences; furthermore, except for YTUBH007, which was classified as Rhizobium binae, the remaining three strains were identified as new candidate species. A single symbiotic plasmid sized 345-402 kb containing complete nod, nif, fix, T3SS and conjugal transfer genes was detected in each strain. The high ANI and amino acid identity (AAI) values, as well as the close phylogenetic relationships among the entire symbiotic plasmid sequences, indicate that they have the same origin and the entire plasmid has been transferred among different Rhizobium species. These results indicate that S. cannabina stringently selects a certain symbiosis gene background of the rhizobia for nodulation, which might have forced the symbiosis genes to transfer from some introduced rhizobia to the related native or local-condition-adapted bacteria. The existence of almost complete conjugal transfer related elements, but not the gene virD, indicated that the self-transfer of the symbiotic plasmid in these rhizobial strains may be realized via a virD-independent pathway or through another unidentified gene. This study provides insight for the better understanding of high-frequency symbiotic plasmid transfer, host-specific nodulation and the host shift for rhizobia.
Collapse
Affiliation(s)
- Kunming Han
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Zhenpeng Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, PR China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| |
Collapse
|
9
|
An X, Sun M, Ren K, Xu M, Wang Z, Li Y, Liu H, Lian B. Effect and mechanism of the improvement of coastal silt soil by application of organic fertilizer and gravel combined with Sesbania cannabina cultivation. FRONTIERS IN PLANT SCIENCE 2022; 13:1092089. [PMID: 36618651 PMCID: PMC9815860 DOI: 10.3389/fpls.2022.1092089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Jiangsu Province of China has a large area of coastal silt soil (CSS) with poor permeability, high salinity, and poor nutrients, which brings great difficulties to the development and utilization of coastal zones, so that needs to be improved as a matter of urgency. In this study, river-sand, serpentine, and organic fertilizer were used as additives in CSS, and Sesbania cannabina, a salt-tolerant cash crop, was planted in these differently treated soils. Through high-throughput sequencing, analysis of soil physico-chemical properties, and detection of plant growth status, the rhizosphere bacterial diversity of S. cannabina growing in CSS under different treatments and their environmental impact factors were studied, while exploring the effect and mechanism of organic fertilizer combined with gravel as a CSS modifier. The results implied that single application of organic fertilizer could significantly increase the fertility levels of total nitrogen (TN), total organic carbon (TOC) and Avail. P in CSS; then, the application of organic fertilizer with river-sand significantly reduced salt content and alkalinity of soil; meanwhile, in the treatment of single application of organic fertilizer and application of organic fertilizer combined with river-sand, the rhizosphere of S. cannabina enriched the bacterial communities of organic matter degradation and utilization to varying degrees. The soil moisture content and indicators related to saline-alkali soil (including total salt, electrical conductivity (EC), exchangeable sodium percentage (ESP), Avail. Na and Avail. K, etc.) were further reduced significantly by the application of organic fertilizer combined with river-sand and serpentine. The method has greatly improved the growth conditions of S. cannabina and promoted the positive development of its rhizosphere bacterial community. Among them, in the treatment of organic fertilizer combined with river-sand and serpentine, a variety of plant growth-promoting rhizobacteria (PGPR, such as Sphingomonas, Ensifer, and Rhodobacter) and nitrogen-cycle-related bacteria (such as nitrate-reduction-related bacteria, nitrogen-fixing bacteria like Ensifer, and purple non-sulfur photosynthetic bacteria like Rhodobacter) were enriched in the rhizosphere of S. cannabina; moreover, the mutual association and robustness of bacterial co-occurrence networks have been significantly enhanced. The results provide a theoretical basis and reference model for the improvement of coastal saline-alkali silt soil.
Collapse
|
10
|
Dynamic Changes in Fermentation Quality and Structure and Function of the Microbiome during Mixed Silage of Sesbania cannabina and Sweet Sorghum Grown on Saline-Alkaline Land. Microbiol Spectr 2022; 10:e0248322. [PMID: 36190422 PMCID: PMC9604195 DOI: 10.1128/spectrum.02483-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Protein-rich Sesbania cannabina and sugar-rich sweet sorghum [Sorghum dochna (Forssk.) Snowden] are characterized by their higher tolerance to saline-alkaline stresses and simultaneous harvests. They could be utilized for coensiling because of their nutritional advantages, which are crucial to compensate protein-rich forage in saline-alkaline regions. The current study investigated the fermentation quality, microbial community succession, and predicted microbial functions of Sesbania cannabina and sweet sorghum in mixed silage during the fermentation process. Before ensiling, the mixtures were treated with compound lactic acid bacteria (LAB) inoculants followed by 3, 7, 14, 30, and 60 days of fermentation. The results revealed that the inoculated homofermentative species Lactobacillus plantarum and Lactobacillus farciminis dominated the early phase of fermentation, and these shifted to the heterofermentative species Lactobacillus buchneri and Lactobacillus hilgardii in the later phase of fermentation. As a result, the pH of the mixed silages decreased significantly, accompanied by the growth of acid-producing microorganisms, especially L. buchneri and L. hilgardii, which actively influenced the bacterial community structure and metabolic pathways. Moreover, the contents of lactic acid, acetic acid, 1,2-propanediol, and water-soluble carbohydrates increased, while the contents of ammonia-N and fiber were decreased, with increasing ratios of sweet sorghum in the mixed silage. Overall, coensiling Sesbania cannabina with >30% sweet sorghum is feasible to attain high-quality silage, and the relay action between homofermentative and heterofermentative LAB species could enhance fermentation quality and conserve the nutrients of the mixed silage. IMPORTANCE The coensiling of Sesbania cannabina and sweet sorghum is of great practical importance in order to alleviate the protein-rich forage deficiency in saline-alkaline regions. Furthermore, understanding the microbial community's dynamic changes, interactions, and metabolic pathways during ensiling will provide the theoretical basis to effectively regulate silage fermentation. Here, we established that coensiling Sesbania cannabina with >30% sweet sorghum was effective at ensuring better fermentation quality and preservation of nutrients. Moreover, the different fermentation types of LAB strains played a relay role during the fermentation process. The homofermentative species L. plantarum and L. farciminis dominated in the early phase of fermentation, while the heterofermentative species L. buchneri and L. hilgardii dominated in the later phase of fermentation. Their relay action in Sesbania cannabina-sweet sorghum mixed silage may help to improve fermentation quality and nutrient preservation.
Collapse
|
11
|
Liu Y, Liu X, Dong X, Yan J, Xie Z, Luo Y. The effect of Azorhizobium caulinodans ORS571 and γ-aminobutyric acid on salt tolerance of Sesbania rostrata. FRONTIERS IN PLANT SCIENCE 2022; 13:926850. [PMID: 36046585 PMCID: PMC9423025 DOI: 10.3389/fpls.2022.926850] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/18/2022] [Indexed: 05/27/2023]
Abstract
Salt stress seriously affects plant growth and crop yield, and has become an important factor that threatens the soil quality worldwide. In recent years, the cultivation of salt-tolerant plants such as Sesbania rostrata has a positive effect on improving coastal saline-alkali land. Microbial inoculation and GABA addition have been shown to enhance the plant tolerance in response to the abiotic stresses, but studies in green manure crops and the revelation of related mechanisms are not clear. In this study, the effects of inoculation with Azorhizobium caulinodans ORS571 and exogenous addition of γ-Aminobutyric Acid (GABA; 200 mg·L-1) on the growth and development of S. rostrata under salt stress were investigated using potting experiments of vermiculite. The results showed that inoculation with ORS571 significantly increased the plant height, biomass, chlorophyll content, proline content (PRO), catalase (CAT) activity, and superoxide dismutase (SOD) activity of S. rostrata and reduced the malondialdehyde (MDA) level of leaves. The exogenous addition of GABA also increased the height, biomass, and CAT activity and reduced the MDA and PRO level of leaves. In addition, exogenous addition of GABA still had a certain improvement on the CAT activity and chlorophyll content of the ORS571-S. rostrata symbiotic system. In conclusion, ORS571 inoculation and GABA application have a positive effect on improving the salt stress tolerance in S. rostrata, which are closely associated with increasing chlorophyll synthesis and antioxidant enzyme activity and changing the amino acid content. Therefore, it can be used as a potential biological measure to improve the saline-alkali land.
Collapse
Affiliation(s)
- Yanan Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xiaoyan Dong
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Jiaming Yan
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Yongming Luo
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| |
Collapse
|
12
|
Sun L, Zhang Z, Dong X, Tang Z, Ju B, Du Z, Wang E, Xie Z. Bradyrhizobium aeschynomenes sp. nov., a root and stem nodule microsymbiont of Aeschynomene indica. Syst Appl Microbiol 2022; 45:126337. [DOI: 10.1016/j.syapm.2022.126337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/15/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022]
|
13
|
The Genome of Bacillus velezensis SC60 Provides Evidence for Its Plant Probiotic Effects. Microorganisms 2022; 10:microorganisms10040767. [PMID: 35456817 PMCID: PMC9025316 DOI: 10.3390/microorganisms10040767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 12/10/2022] Open
Abstract
Root colonization and plant probiotic function are important traits of plant growth-promoting rhizobacteria (PGPR). Bacillus velezensis SC60, a plant endophytic strain screened from Sesbania cannabina, has a strong colonization ability on various plant roots, which indicates that SC60 has a preferable adaptability to plants. However, the probiotic function of the strain SC60 is not well-understood. Promoting plant growth and suppressing soil-borne pathogens are key to the plant probiotic functions. In this study, the genetic mechanism of plant growth-promoting and antibacterial activity of the strain SC60 was analyzed by biological and bioinformatics methods. The complete genome size of strain SC60 was 3,962,671 bp, with 4079 predicted genes and an average GC content of 46.46%. SC60 was designated as Bacillus velezensis according to the comparative analysis, including average nucleotide polymorphism (ANI), digital DNA–DNA hybridization (dDDH), and phylogenetic analysis. Genomic secondary metabolite analyses indicated two clusters encoding potential new antimicrobials. The antagonism experiments revealed that strain SC60 had the ability to inhibit the growth of a variety of plant pathogens and its closely related strains of Bacillus spp., which was crucial to the rhizospheric competitiveness and growth-promoting effect of the strain. The present results further suggest that B. velezensis SC60 could be used as a PGPR strain to develop new biocontrol agents or microbial fertilizers.
Collapse
|
14
|
Egamberdieva D, Alimov J, Shurigin V, Alaylar B, Wirth S, Bellingrath-Kimura SD. Diversity and Plant Growth-Promoting Ability of Endophytic, Halotolerant Bacteria Associated with Tetragonia tetragonioides (Pall.) Kuntze. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010049. [PMID: 35009054 PMCID: PMC8747539 DOI: 10.3390/plants11010049] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/14/2021] [Accepted: 12/22/2021] [Indexed: 05/24/2023]
Abstract
The diversity of salt-tolerant cultivable endophytic bacteria associated with the halophyte New Zealand spinach (Tetragonia tetragonioides (Pall.) Kuntze) was studied, and their plant beneficial properties were evaluated. The bacteria isolated from leaves and roots belonged to Agrobacterium, Stenotrophomonas, Bacillus, Brevibacterium, Pseudomonas, Streptomyces, Pseudarthrobacter, Raoultella, Curtobacterium, and Pantoea. Isolates exhibited plant growth-promoting traits, including the production of a phytohormone (indole 3-acetic-acid), cell wall degrading enzymes, and hydrogen cyanide production. Furthermore, antifungal activity against the plant pathogenic fungi Fusarium solani, F. oxysporum, and Verticillium dahliae was detected. Ten out of twenty bacterial isolates were able to synthesize ACC deaminase, which plays a vital role in decreasing ethylene levels in plants. Regardless of the origin of isolated bacteria, root or leaf tissue, they stimulated plant root and shoot growth under 200 mM NaCl conditions. Our study suggests that halophytes such as New Zealand spinach are a promising source for isolating halotolerant plant-beneficial bacteria, which can be considered as potentially efficient biofertilizers in the bioremediation of salt-affected soils.
Collapse
Affiliation(s)
- Dilfuza Egamberdieva
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Muncheberg, Germany; (S.W.); (S.D.B.-K.)
- Faculty of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan; (J.A.); (V.S.)
| | - Jakhongir Alimov
- Faculty of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan; (J.A.); (V.S.)
| | - Vyacheslav Shurigin
- Faculty of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan; (J.A.); (V.S.)
| | - Burak Alaylar
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Agri Ibrahim Cecen University, Agri 04100, Turkey;
| | - Stephan Wirth
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Muncheberg, Germany; (S.W.); (S.D.B.-K.)
| | - Sonoko Dorothea Bellingrath-Kimura
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Muncheberg, Germany; (S.W.); (S.D.B.-K.)
- Faculty of Life Science, Humboldt University of Berlin, 10115 Berlin, Germany
| |
Collapse
|
15
|
Patterns in the Microbial Community of Salt-Tolerant Plants and the Functional Genes Associated with Salt Stress Alleviation. Microbiol Spectr 2021; 9:e0076721. [PMID: 34704793 PMCID: PMC8549722 DOI: 10.1128/spectrum.00767-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salinity is an important abiotic stress affecting plant growth. We have known that plants can recruit beneficial microbes from the surrounding soil. However, the ecological functions of the core microbiome in salt-tolerant plants, together with their driving factors, remain largely unexplored. Here, we employed both amplicon and shotgun metagenomic sequencing to investigate the microbiome and function signatures of bulk soil and rhizocompartment samples from three salt-tolerant plants (legumes Glycine soja and Sesbania cannabina and nonlegume Sorghum bicolor). Strong filtration effects for microbes and functional genes were found in the rhizocompartments following a spatial gradient. The dominant bacteria belonged to Ensifer for legumes and Bacillus for S. bicolor. Although different salt-tolerant plants harbored distinct bacterial communities, they all enriched genes involved in cell motility, Na+ transport, and plant growth-promoting function (e.g., nitrogen fixation and phosphate solubilization) in rhizoplane soils, implying that the microbiome assembly of salt-tolerant plants might depend on the ecological functions of microbes rather than microbial taxa. Moreover, three metagenome-assembled genomes affiliated to Ensifer were obtained, and their genetic basis for salt stress alleviation were predicted. Soil pH, electrical conductivity, and total nitrogen were the most important driving factors for explaining the above microbial and functional gene selection. Correspondingly, the growth of an endophyte, Ensifer meliloti CL09, was enhanced by providing root exudates, suggesting that root exudates might be one of factors in the selection of rhizosphere and endosphere microbiota. Overall, this study reveals the ecological functions of the populations inhabiting the root of salt-tolerant plants. IMPORTANCE Salinity is an important but little-studied abiotic stressor affecting plant growth. Although several previous reports have examined salt-tolerant plant microbial communities, we still lack a comprehensive understanding about the functional characteristics and genomic information of this population. The results of this study revealed the root-enriched and -depleted bacterial groups, and found three salt-tolerant plants harbored different bacterial populations. The prediction of three metagenome-assembled genomes confirmed the critical role of root dominant species in helping plants tolerate salt stress. Further analysis indicated that plants enriched microbiome from soil according to their ecological functions but not microbial taxa. This highlights the importance of microbial function in enhancing plant adaptability to saline soil and implies that we should pay more attention to microbial function and not only to taxonomic information. Ultimately, these results provide insight for future agriculture using the various functions of microorganisms on the saline soil.
Collapse
|
16
|
Liu G, Liu X, Liu W, Gao K, Chen X, Wang ET, Zhao Z, Du W, Li Y. Biodiversity and Geographic Distribution of Rhizobia Nodulating With Vigna minima. Front Microbiol 2021; 12:665839. [PMID: 34017318 PMCID: PMC8129581 DOI: 10.3389/fmicb.2021.665839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Vigna minima is a climbing annual plant widely distributed in barren wilderness, grass land, and shrub bush of China and other countries such as Japan. However, the rhizobia nodulating with this plant has never been systematically studied. In order to reveal the biodiversity of nodulating rhizobia symbiosis with V. minima, a total of 874 rhizobium isolates were obtained from root nodules of the plant spread in 11 sampling sites of Shandong Peninsula, China, and they were designated as 41 haplotypes in the genus Bradyrhizobium based upon recA sequence analyses. By multilocus sequence analysis (MLSA) of five housekeeping genes (dnaK, glnII, gyrB, recA, and rpoB), the 41 strains representing different recA haplotypes were classified into nine defined species and nine novel genospecies. Bradyrhizobium elkanii, Bradyrhizobium ferriligni, and Bradyrhizobium pachyrhizi were the predominant and universally distributed groups. The phylogeny of symbiotic genes of nodC and nifH showed similar topology and phylogenetic relationships, in which all the representative strains were classified into two clades grouped with strains nodulating with Vigna spp., demonstrating that Vigna spp. shared common nodulating groups in the natural environment. All the representative strains formed nodules with V. minima in a nodulation test performed in green house conditions. The correlation between V. minima nodulating rhizobia and soil characteristics analyzed by CANOCO indicates that available nitrogen, total nitrogen, and organic carbon in the soil samples were the main factors affecting the distribution of rhizobia isolated in this study. This study systematically uncovered the biodiversity and distribution characteristics of V. minima nodulating rhizobia for the first time, which provided novel information for the formation of the corresponding rhizobium community.
Collapse
Affiliation(s)
- Guohua Liu
- College of Life Science, Yantai University, Yantai, China
| | - Xiaoling Liu
- College of Life Science, Yantai University, Yantai, China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Kangning Gao
- College of Resources and Environment, Shijiazhuang University, Shijiazhuang, China
| | - Xiaoli Chen
- The Fruit Trees Work Station of Penglai, Yantai, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Zhenjun Zhao
- College of Life Science, Yantai University, Yantai, China
| | - Wenxiao Du
- College of Life Science, Yantai University, Yantai, China
| | - Yan Li
- College of Life Science, Yantai University, Yantai, China.,Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| |
Collapse
|
17
|
Hailu Gunnabo A, Geurts R, Wolde-meskel E, Degefu T, E. Giller K, van Heerwaarden J. Phylogeographic distribution of rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia. FEMS Microbiol Ecol 2021; 97:fiab046. [PMID: 33724341 PMCID: PMC8016211 DOI: 10.1093/femsec/fiab046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/13/2021] [Indexed: 11/19/2022] Open
Abstract
Rhizobia are soilborne bacteria that form symbiotic relations with legumes and fix atmospheric nitrogen. The nitrogen fixation potential depends on several factors such as the type of host and symbionts and on environmental factors that affect the distribution of rhizobia. We isolated bacteria nodulating common bean in Southern Ethiopia to evaluate their genetic diversity and phylogeography at nucleotide, locus (gene/haplotype) and species levels of genetic hierarchy. Phylogenetically, eight rhizobial genospecies (including previous collections) were determined that had less genetic diversity than found among reference strains. The limited genetic diversity of the Ethiopian collections was due to absence of many of the Rhizobium lineages known to nodulate beans. Rhizobium etli and Rhizobiumphaseoli were predominant strains of bean-nodulating rhizobia in Ethiopia. We found no evidence for a phylogeographic pattern in strain distribution. However, joint analysis of the current and previous collections revealed differences between the two collections at nucleotide level of genetic hierarchy. The differences were due to genospecies Rhizobium aethiopicum that was only isolated in the earlier collection.
Collapse
Affiliation(s)
- Ashenafi Hailu Gunnabo
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Endalkachew Wolde-meskel
- World Agroforestry Centre (ICRAF), c/o ILRI Campus, Gurd Shola PO Box 5689, Addis Ababa, 4 Ethiopia
| | - Tulu Degefu
- International Crops Research Institute for the Semi-Arid Tropics, c/o ILRI Campus, Gurd Shola PO Box 5689, Addis Ababa, Ethiopia
| | - Ken E. Giller
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| | - Joost van Heerwaarden
- Plant Production Systems Group, Wageningen University & Research, Wageningen, Gelderland, The Netherlands, Postal code: 6708 PB
| |
Collapse
|
18
|
The leguminous trees Vachellia seyal (Del.) and Prosopis juliflora (Swartz) DC and their association with rhizobial strains from the root-influence zone of the grass Sporobolus robustus Kunth. Symbiosis 2021. [DOI: 10.1007/s13199-021-00763-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
19
|
Cui Q, Xia J, Yang H, Liu J, Shao P. Biochar and effective microorganisms promote Sesbania cannabina growth and soil quality in the coastal saline-alkali soil of the Yellow River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:143801. [PMID: 33307496 DOI: 10.1016/j.scitotenv.2020.143801] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 05/24/2023]
Abstract
Soil salinization and nutrient deficiency have emerged as the major factors negatively impacting soil quality and primary productivity in the coastal saline-alkali soil of the Yellow River Delta. Biochar has been proposed as an efficient strategy for promoting plant growth and restoring degraded saline-alkali soil. However, knowledge is inadequate regarding the effects of adding Spartina alterniflora-derived biochar alone or in combination with effective microorganisms (EM) on the growth of Sesbania cannabina and soil quality in saline-alkali soil. To enhance this knowledge, a pot experiment with different EM treatments (without EM addition, EM-; with EM addition, EM+) and a gradient of biochar treatments (0%, B0; 0.5%, B1; 1.5%, B2; and 3%, B3; biochar weight/soil weight) was conducted. Our results showed that biochar addition alone and in combination with EM significantly increased seed germination, plant height, stem diameter, total biomass and plant nutrient uptake of S. cannabina. Biochar addition, EM addition and their interaction significantly decreased soil salt content efficiently and increased soil total carbon (TC), total nitrogen (TN), available phosphorus (AP) and available potassium (AK) but had little effect on soil pH. Biochar addition increased soil organic carbon, soil NH4+ and NO3-, microbial biomass carbon, and soil enzyme activities and these effects increased in strength when biochar and EM were present simultaneously. Of the treatments, the EM + B3 treatment had the largest effects in terms of inhibiting salinization, increasing soil fertility, elevating soil nutrients and enzyme activities, and improving plant growth. Moreover, the application of biochar and EM promoted the growth of S. cannabina by enhancing plant nutrient uptake, improving soil fertility (e.g., TN, AP, AK, NH4+ and NO3-), and elevating soil enzyme activities (urease and alkaline phosphatase activity). Overall, the integrated use of an appropriate biochar rate (3%) and EM for coastal saline-alkali soil could be an effective strategy to ameliorate soil salinity, improve soil quality and promote plant productivity.
Collapse
Affiliation(s)
- Qian Cui
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou 256603, PR China
| | - Jiangbao Xia
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou 256603, PR China.
| | - Hongjun Yang
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou 256603, PR China
| | - Jingtao Liu
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou 256603, PR China
| | - Pengshuai Shao
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou 256603, PR China
| |
Collapse
|
20
|
Yang Y, Liu L, Singh RP, Meng C, Ma S, Jing C, Li Y, Zhang C. Nodule and Root Zone Microbiota of Salt-Tolerant Wild Soybean in Coastal Sand and Saline-Alkali Soil. Front Microbiol 2020; 11:2178. [PMID: 33071999 PMCID: PMC7536311 DOI: 10.3389/fmicb.2020.523142] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Soil salinization limits crop growth and yield in agro-ecosystems worldwide by reducing soil health and altering the structure of microbial communities. Salt-tolerant plant growth-promoting rhizobacteria (PGPR) alleviate plant salinity stress. Wild soybean (Glycine soja Sieb. and Zucc.) is unique in agricultural ecosystems owing to its ability to grow in saline-alkali soils and fix atmospheric nitrogen via symbiotic interactions with diverse soil microbes. However, this rhizosphere microbiome and the nodule endosymbionts have not been investigated to identify PGPR. In this study, we investigated the structural and functional rhizosphere microbial communities in saline-alkali soil from the Yellow River Delta and coastal soil in China, as well as wild soybean root nodule endosymbionts. To reveal the composition of the microbial ecosystem, we performed 16S rRNA and nifH gene amplicon sequencing on root nodules and root zones under different environmental conditions. In addition, we used culture-independent methods to examine the root bacterial microbiome of wild soybean. For functional characterization of individual members of the microbiome and their impact on plant growth, we inoculated isolates from the root microbiome with wild soybean and observed nodulation. Sinorhizobium/Ensifer accounted for 97% of the root nodule microbiome, with other enriched members belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes; the genera Sphingomonas, Microbacterium, Arthrobacter, Nocardioides, Streptomyces, Flavobacterium, Flavisolibacter, and Pseudomonas; and the family Enterobacteriaceae. Compared to saline-alkali soil from the Yellow River Delta, coastal soil was highly enriched for soybean nodules and displayed significant differences in the abundance and diversity of β-proteobacteria, δ-proteobacteria, Actinobacteria, and Bacteroidetes. Overall, the wild soybean root nodule microbiome was dominated by nutrient-providing Sinorhizobium/Ensifer and was enriched for bacterial genera that may provide salt resistance. Thus, this reductionist experimental approach provides an avenue for future systematic and functional studies of the plant root microbiome.
Collapse
Affiliation(s)
- Yingjie Yang
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lei Liu
- Bureau of Agriculture and Rural Affairs of Laoshan District, Qingdao, China
| | - Raghvendra Pratap Singh
- Department of Research and Development, Biotechnology, Uttaranchal University, Dehradun, India
| | - Chen Meng
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Siqi Ma
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Changliang Jing
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Chengsheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| |
Collapse
|
21
|
Zhang Z, Liu W, Shao S, Wang ET, Li Y. Diverse Genomic Backgrounds Vs. Highly Conserved Symbiotic Genes in Sesbania-Nodulating Bacteria: Shaping of the Rhizobial Community by Host and Soil Properties. MICROBIAL ECOLOGY 2020; 80:158-168. [PMID: 31996939 DOI: 10.1007/s00248-020-01489-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/19/2020] [Indexed: 06/10/2023]
Abstract
Aiming at investigating the overall diversity, biogeography, and symbiosis gene evolutionary history of the Sesbania cannabina-nodulating rhizobia in China, a total of 874 rhizobial isolates originating from the root nodules of this plant grown at different sites were characterized and compared with those of some reference strains. All of the S. cannabina-nodulating rhizobia were classified into 16 (geno) species, including seven novel genospecies in the genera Ensifer, Rhizobium, Neorhizobium, and Agrobacterium, with Ensifer sesbaniae and Neorhizobium huautlense as the dominant and universal species. Ten of these species were found to nodulate other leguminous hosts or to lack nodulating abilities and were defined as symbiovar sesbania. Biogeographic patterns were observed, for which pH, TN, AK, and AP were the main determinants. The effects of pH were opposite to those of TN and AK, while AP presented effects independently of TN, AK, and pH. Symbiotic genes of these rhizobia showed a common origin, but nodA evolved faster than nifH. Point mutation is the main driving force in the evolution of both nodA and nifH, and lateral transfer of symbiotic genes might play an important role in the formation of diverse S. cannabina-nodulating rhizobial species. S. cannabina only nodulates with Sesbania rhizobia, demonstrating its severe selection on rhizobial symbiosis genes. Soil pH and physiochemical characteristics could affect rhizobial survival and competitive nodulation. This study provides insight into the community shifts and evolution of rhizobia in relation to their host and soil environments.
Collapse
Affiliation(s)
- Zhenpeng Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Shuai Shao
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Life Science College, Yantai University, Yantai, 264005, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C. D. Mexico, 11340, Mexico City, Mexico
| | - Yan Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| |
Collapse
|
22
|
Shao S, Chen M, Liu W, Hu X, Wang ET, Yu S, Li Y. Long-term monoculture reduces the symbiotic rhizobial biodiversity of peanut. Syst Appl Microbiol 2020; 43:126101. [PMID: 32847777 DOI: 10.1016/j.syapm.2020.126101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 11/17/2022]
Abstract
Long-term monoculture (LTM) decreases the yield and quality of peanut, even resulting in changes in the microbial community. However, the effect of LTM on peanut rhizobial communities has still not been elucidated. In this study, we isolated and characterized peanut rhizobia from 6 sampling plots with different monoculture cropping durations. The community structure and diversity index for each sampling site were analyzed, and the correlations between a peanut rhizobium and soil characteristics were evaluated to clarify the effects on peanut rhizobial communities. The competitive abilities among representative strains were also analyzed. A total of 283 isolates were obtained from 6 sampling plots. Nineteen recA haplotypes were defined and were grouped into 8 genospecies of Bradyrhizobium, with B. liaoningense and B. ottawaense as the dominant groups in each sample. The diversity indexes of the rhizobial community decreased, and the dominant groups of B. liaoningense and B. ottawaense were enriched significantly with extended culture duration. Available potassium (AK), available phosphorus (AP), available nitrogen (AN), total nitrogen (TN) and organic carbon (OC) gradually increased with increasing monoculture duration. OC, TN, AP and AK were the main soil characteristics affecting the distribution of rhizobial genospecies in the samples. A competitive nodulation test indicated that B. liaoningense presented an excellent competitive ability, which was congruent with its high isolation frequency. This study revealed that soil characteristics and the competitive ability of rhizobia shape the symbiotic rhizobial community and provides information on community formation and the biogeographic properties of rhizobia.
Collapse
Affiliation(s)
- Shuai Shao
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Life Science College, Yantai University, Yantai, 264005, China
| | - Mingna Chen
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City D.F, 11340, Mexico
| | - Shanlin Yu
- Shandong Peanut Research Institute, Qingdao, 266100, China.
| | - Yan Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| |
Collapse
|
23
|
The Root Nodule Microbiome of Cultivated and Wild Halophytic Legumes Showed Similar Diversity but Distinct Community Structure in Yellow River Delta Saline Soils. Microorganisms 2020; 8:microorganisms8020207. [PMID: 32028717 PMCID: PMC7074777 DOI: 10.3390/microorganisms8020207] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/01/2020] [Accepted: 02/01/2020] [Indexed: 12/31/2022] Open
Abstract
Symbiotic associations between leguminous plants and their nodule microbiome play a key role in sustainable agriculture by facilitating the fixation of atmospheric nitrogen and enhancing plant stress resistance. This study aimed to decipher the root nodule microbiome of two halophytic legumes, Sesbania cannabina and Glycine soja, which grow in saline soils of the Yellow River Delta, China, using PacBio’s circular consensus sequencing for full-length bacterial 16S rRNA gene to obtain finer taxonomic information. The cultivated legume Glycine max was used for comparison. We identified 18 bacterial genera and 55 species in nodule samples, which mainly classified to Proteobacteria, and rhizobial genus Ensifer was the predominant group. The three legumes showed similarity in operational taxonomic unit (OTU) diversity but distinction in OTU richness, indicating that they harbor similar bacterial species with different relative contents. The results of principal coordinates analysis and ANOSIM tests indicated that G. soja and G. max have similar nodule bacterial communities, and these communities differ from that of S. cannabina. Wild legumes S. cannabina and G. soja both harbored a higher number of rhizobia, while G. max possessed more non-rhizobial bacteria. These differences could be associated with their adaptability to saline–alkali stress and revealed clues on the nodule endophytes with relative importance of culturable rhizobial symbionts.
Collapse
|
24
|
Aeschynomene indica-Nodulating Rhizobia Lacking Nod Factor Synthesis Genes: Diversity and Evolution in Shandong Peninsula, China. Appl Environ Microbiol 2019; 85:AEM.00782-19. [PMID: 31562167 DOI: 10.1128/aem.00782-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/04/2019] [Indexed: 02/02/2023] Open
Abstract
Aeschynomene indica is a semiaquatic legume that forms both stem and root nodules with rhizobia. Some A. indica rhizobia (AIRs) have been reported to nodulate the host using a Nod factor-independent pathway and possess photosynthetic abilities. To investigate the diversity and community structure of AIRs in China, a total of 300 rhizobial isolates were acquired from the root and stem nodules of A. indica grown at 4 sites in Shandong Peninsula, China. Nineteen representative strains were selected according to their recA phylogeny. With further classification in comparison with reference strains, 10 Bradyrhizobium genospecies were defined based on the 16S rRNA gene phylogeny and multilocus sequence analysis (MLSA) of housekeeping genes (HKGs) recA, atpD, glnII, dnaK, gyrB, and rpoB In addition, 6 genospecies were found only in China. No nodulation gene (nodA, nodB, nodC, or nodZ) was detected in the AIRs isolates by PCR amplification and Southern blotting. Phylogenetic analysis of nifH and the photosynthesis-related gene pufLM revealed their common origins. All representative strains formed root nodules, but only 9 representative strains for 4 genospecies formed stem nodules on A. indica, indicating that the stem nodulation process of A. indica is limited to some strains. The nucleotide diversity and recombination events of the HKGs, as well as nifH and pufLM genes, showed that mutation contributes more than recombination in evolution. The distribution of dominant AIR genospecies was mainly affected by available nitrogen, organic carbon, total nitrogen, and pH. Our study helps to characterize the diversity and evolution of AIRs.IMPORTANCE Aeschynomene indica rhizobia (AIRs) can form both root and stem nodules via Nod factor-independent processes, which distinguishes them from other rhizobia. This study systematically uncovered the diversity and community composition of A. indica rhizobia distributed in eastern China. Our results reclassified all the A. indica rhizobia across the world and represent a useful contribution to evaluating the diversity and distribution of the symbiont. The presence of novel genospecies specifically distributed in China enriched the A. indica rhizobia resources and provided insight into the geographic distribution of rhizobia. The phylogenetic relationship between nifH and pufLM of A. indica rhizobia across the world provides insight into the evolution of their nitrogen fixation and photosynthetic abilities.
Collapse
|
25
|
Dang X, Xie Z, Liu W, Sun Y, Liu X, Zhu Y, Staehelin C. The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations. BMC Genomics 2019; 20:643. [PMID: 31405380 PMCID: PMC6689892 DOI: 10.1186/s12864-019-6004-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022] Open
Abstract
Background Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green manure and for soil remediation. E. alkalisoli YIC4027 can grow in saline-alkaline soils and is a narrow-host-range strain that establishes a symbiotic relationship with S. cannabina. The complete genome of this strain was sequenced to better understand the genetic basis of host specificity and adaptation to saline-alkaline soils. Results E. alkalisoli YIC4027 was found to possess a 6.1-Mb genome consisting of three circular replicons: one chromosome (3.7 Mb), a chromid (1.9 Mb) and a plasmid (0.46 Mb). Genome comparisons showed that strain YIC4027 is phylogenetically related to broad-host-range Ensifer fredii strains. Synteny analysis revealed a strong collinearity between chromosomes of E. alkalisoli YIC4027 and those of the E. fredii NGR234 (3.9 Mb), HH103 (4.3 Mb) and USDA257 (6.48 Mb) strains. Notable differences were found for genes required for biosynthesis of nodulation factors and protein secretion systems, suggesting a role of these genes in host-specific nodulation. In addition, the genome analysis led to the identification of YIC4027 genes that are presumably related to adaptation to saline-alkaline soils, rhizosphere colonization and nodulation competitiveness. Analysis of chemotaxis cluster genes and nodulation tests with constructed che gene mutants indicated a role of chemotaxis and flagella-mediated motility in the symbiotic association between YIC4027 and S. cannabina. Conclusions This study provides a basis for a better understanding of host specific nodulation and of adaptation to a saline-alkaline rhizosphere. This information offers the perspective to prepare optimal E. alkalisoli inocula for agriculture use and soil remediation. Electronic supplementary material The online version of this article (10.1186/s12864-019-6004-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiaoxiao Dang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China. .,Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, People's Republic of China.
| | - Wei Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Yu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Xiaolin Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Yongqiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Christian Staehelin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| |
Collapse
|
26
|
Genetic diversity of rhizobia associated with root nodules of white lupin (Lupinus albus L.) in Tunisian calcareous soils. Syst Appl Microbiol 2019; 42:448-456. [DOI: 10.1016/j.syapm.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 11/30/2022]
|
27
|
Liu Z, Chen W, Jiao S, Wang X, Fan M, Wang E, Wei G. New Insight into the Evolution of Symbiotic Genes in Black Locust-Associated Rhizobia. Genome Biol Evol 2019; 11:1736-1750. [PMID: 31192354 PMCID: PMC6698633 DOI: 10.1093/gbe/evz116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2019] [Indexed: 11/29/2022] Open
Abstract
Nitrogen fixation in legumes occurs via symbiosis with rhizobia. This process involves packages of symbiotic genes on mobile genetic elements that are readily transferred within or between rhizobial species, furnishing the recipient with the ability to interact with plant hosts. However, it remains elusive whether plant host migration has played a role in shaping the current distribution of genetic variation in symbiotic genes. Herein, we examined the genetic structure and phylogeographic pattern of symbiotic genes in 286 symbiotic strains of Mesorhizobium nodulating black locust (Robinia pseudoacacia), a cross-continental invasive legume species that is native to North America. We conducted detailed phylogeographic analysis and approximate Bayesian computation to unravel the complex demographic history of five key symbiotic genes. The sequencing results indicate an origin of symbiotic genes in Germany rather than North America. Our findings provide strong evidence of prehistoric lineage splitting and spatial expansion events resulting in multiple radiations of descendent clones from founding sequence types worldwide. Estimates of the timescale of divergence in North American and Chinese subclades suggest that black locust-specific symbiotic genes have been present in these continent many thousands of years before recent migration of plant host. Although numerous crop plants, including legumes, have found their centers of origin as centers of evolution and diversity, the number of legume-specific symbiotic genes with a known geographic origin is limited. This work sheds light on the coevolution of legumes and rhizobia.
Collapse
Affiliation(s)
- Zhenshan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinye Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Miaochun Fan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México, D.F., Mexico
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
28
|
Fall F, Le Roux C, Bâ AM, Fall D, Bakhoum N, Faye MN, Kane A, Ndoye I, Diouf D. The rhizosphere of the halophytic grass Sporobolus robustus Kunth hosts rhizobium genospecies that are efficient on Prosopis juliflora (Sw.) DC and Vachellia seyal (Del.) P.J.H. Hurter seedlings. Syst Appl Microbiol 2018; 42:232-239. [PMID: 30384991 DOI: 10.1016/j.syapm.2018.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 01/01/2023]
Abstract
The aim of this study was to survey the abundance and genetic diversity of legume-nodulating rhizobia (LNR) in the rhizosphere of a salt-tolerant grass, Sporobolus robustus Kunth, in the dry and rainy seasons along a salinity gradient, and to test their effectiveness on Prosopis juliflora (SW.) DC and Vachellia seyal (Del.) P.J.H. Hurter seedlings. The results showed a significant decrease in LNR population density and diversity in response to salinity, particularly during the dry season. A phylogenetic analysis of the 16S-23S rRNA ITS region clustered the 232 rhizobium isolates into three genera and 12 distinct representative genotypes: Mesorhizobium (8 genotypes), Ensifer (2 genotypes) and Rhizobium (2 genotypes). Of these genotypes, 2 were only found in the dry season, 4 exclusively in the rainy season and 6 were found in both seasons. Isolates of the Mesorhizobium and Ensifer genera were more abundant than those of Rhizobium, with 55%, 44% and 1% of the total strains, respectively. The abundance of the Mesorhizobium isolates appeared to increase in the dry season, suggesting that they were more adapted to environmental aridity than Ensifer genospecies. Conversely, Ensifer genospecies were more tolerant of high salinity levels than the other genospecies. However, Ensifer genospeciesproved to be the most efficient strains on P. juliflora and V. seyal seedlings. We concluded that S. robustus hosts efficient rhizobium strains in its rhizosphere, suggesting its ability to act as a nurse plant to facilitate seedling recruitment of P. juliflora and V. seyal in saline soils.
Collapse
Affiliation(s)
- Fatoumata Fall
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Senegal.
| | | | - Amadou Mustapha Bâ
- CIRAD, UMR LSTM, F-34398 Montpellier, France; Laboratoire de Biologie et Physiologie Végétales, Université des Antilles, Guadeloupe, France
| | - Dioumacor Fall
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Centre National de Recherches Agronomiques (CNRA), Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
| | - Niokhor Bakhoum
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Mathieu Ndigue Faye
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
| | - Aboubacry Kane
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Senegal
| | - Ibrahima Ndoye
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Senegal
| | - Diegane Diouf
- Laboratoire Commun de Microbiologie (LCM) IRD/ISRA/UCAD, Centre de Recherche de Bel-Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; Département de Biologie Végétale, Université Cheikh Anta Diop de Dakar, Senegal
| |
Collapse
|
29
|
Isolation, characterization and in vitro anticancer activity of an aqueous galactomannan from the seed of Sesbania cannabina. Int J Biol Macromol 2018; 113:1241-1247. [DOI: 10.1016/j.ijbiomac.2018.03.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/05/2018] [Accepted: 03/13/2018] [Indexed: 11/15/2022]
|
30
|
Andrews M, De Meyer S, James EK, Stępkowski T, Hodge S, Simon MF, Young JPW. Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance. Genes (Basel) 2018; 9:E321. [PMID: 29954096 PMCID: PMC6071183 DOI: 10.3390/genes9070321] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/17/2023] Open
Abstract
Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume⁻rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.
Collapse
Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch 6150, Australia.
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium.
| | - Euan K James
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland.
| | - Simon Hodge
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Marcelo F Simon
- Embrapa Genetic Resources and Biotechnology, Brasilia DF 70770-917, Brazil.
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK.
| |
Collapse
|
31
|
Guo Y, Matsuoka Y, Nishizawa T, Ohta H, Narisawa K. Effects of Rhizobium Species Living with the Dark Septate Endophytic Fungus Veronaeopsis simplex on Organic Substrate Utilization by the Host. Microbes Environ 2018; 33:102-106. [PMID: 29459501 PMCID: PMC5877336 DOI: 10.1264/jsme2.me17144] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 09/13/2017] [Indexed: 01/04/2023] Open
Abstract
Bacteria harbored in/on the hyphae of the dark septate endophyte, Veronaeopsis simplex Y34, were identified as a single Rhizobium species by molecular analyses of bacterial 16S rRNA genes, and were successfully isolated from the endophyte. The Rhizobium-cured fungus was prepared thoroughly by an antibiotic treatment, thereby allowing an examination of their effects on organic substrate utilization. Assays with Biolog® FF microplates revealed that the respiration potential for 52.6% of the tested compounds were significantly different between Rhizobium-harboring and -cured fungal hosts, indicating that organic substrate utilization by V. simplex Y34 was significantly influenced by the presence of the associated Rhizobium sp. VsBac-Y9.
Collapse
Affiliation(s)
- Yong Guo
- Ibaraki University College of AgricultureIbaraki, Japan, 3–21–1 Chuou, Ami, Ibaraki 300–0393Japan
| | - Yuuto Matsuoka
- Graduate School of Agriculture, Ibaraki UniversityIbaraki, Japan, 3–21–1 Chuou, Ami, Ibaraki 300–0393Japan
| | - Tomoyasu Nishizawa
- Ibaraki University College of AgricultureIbaraki, Japan, 3–21–1 Chuou, Ami, Ibaraki 300–0393Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu-shi, Tokyo 183–8509Japan
| | - Hiroyuki Ohta
- Ibaraki University College of AgricultureIbaraki, Japan, 3–21–1 Chuou, Ami, Ibaraki 300–0393Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu-shi, Tokyo 183–8509Japan
| | - Kazuhiko Narisawa
- Ibaraki University College of AgricultureIbaraki, Japan, 3–21–1 Chuou, Ami, Ibaraki 300–0393Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu-shi, Tokyo 183–8509Japan
| |
Collapse
|
32
|
Yan J, Li Y, Yan H, Chen WF, Zhang X, Wang ET, Han XZ, Xie ZH. Agrobacterium salinitolerans sp. nov., a saline–alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina. Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001885] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, PR China
| | - Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| | - Hui Yan
- Rhizobium Research Center and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory for Agro-Biotechnology, Beijing 100193, PR China
| | - Wen Feng Chen
- Rhizobium Research Center and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory for Agro-Biotechnology, Beijing 100193, PR China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, México DF, México
| | - Xiao Zeng Han
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, PR China
| | - Zhi Hong Xie
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China
| |
Collapse
|
33
|
Yan J, Li Y, Han XZ, Chen WF, Zou WX, Xie Z, Li M. Agrobacterium deltaense sp. nov., an endophytic bacteria isolated from nodule of Sesbania cannabina. Arch Microbiol 2017; 199:1003-1009. [DOI: 10.1007/s00203-017-1367-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/05/2017] [Accepted: 03/15/2017] [Indexed: 10/19/2022]
|
34
|
Andrews M, Andrews ME. Specificity in Legume-Rhizobia Symbioses. Int J Mol Sci 2017; 18:E705. [PMID: 28346361 PMCID: PMC5412291 DOI: 10.3390/ijms18040705] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.
Collapse
Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| | - Morag E Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| |
Collapse
|
35
|
Yang CW, Lee CC, Ku H, Chang BV. Bacterial communities associated with anaerobic debromination of decabromodiphenyl ether from mangrove sediment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:5391-5403. [PMID: 28013469 DOI: 10.1007/s11356-016-8259-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/13/2016] [Indexed: 06/06/2023]
Abstract
This study evaluated decabromodiphenyl ether (BDE-209) anaerobic debromination and bacterial community changes in mangrove sediment. BDE-209 debromination rates were enhanced with zerovalent iron compared to without zerovalent iron in the sediment. BDE-209 debromination rates in microcosms constructed with sediments collected in autumn were higher than in microcosms constructed with sediments collected in spring and were higher at the Bali sampling site than the Guandu sampling site. The intermediate products resulting from the reductive debromination of BDE-209 in sediment were nona-BDE (BDE-206, BDE-207), octa-BDEs (BDE-196, BDE-197), hepta-BDEs (BDE-183, BDE-184, BDE-191), hexa-BDEs (BDE-137, BDE-138, BDE-154, BDE-157), penta-BDEs (BDE-85, BDE-99, BDE-100, BDE-126), tetra-BDEs (BDE-47, BDE-49, BDE-66, BDE-77), tri-BDEs (BDE-17, BDE-28), and di-BDEs (BDE-15). Fifty bacterial genera associated with BDE-209 debromination were identified. Overall, 12 of the 50 bacterial genera were reported to be involved in dehalogenation of aromatic compounds. These bacteria have high potential to be BDE-209 debromination bacteria. Different combinations of bacterial community composition exhibit different abilities for BDE-209 anaerobic debromination.
Collapse
Affiliation(s)
- Chu-Wen Yang
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Ching-Chang Lee
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - His Ku
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Bea-Ven Chang
- Department of Microbiology, Soochow University, Taipei, Taiwan.
| |
Collapse
|
36
|
Yan J, Chen W, Han X, Wang E, Zou W, Zhang Z. Genetic diversity of indigenous soybean-nodulating rhizobia in response to locally-based long term fertilization in a Mollisol of Northeast China. World J Microbiol Biotechnol 2017; 33:6. [PMID: 27848139 DOI: 10.1007/s11274-016-2170-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/03/2016] [Indexed: 01/03/2023]
Abstract
The influences of five different fertilizer treatments on diversity of rhizobia in soybean nodule were investigated in a long-term experiment with with four replicates: (1) control (without fertilization), (2) balanced NPK fertilizer (NPK), and (3-5) unbalanced chemical fertilizers without one of the major elements (NP, PK, and NK) in Mollisol in Northeast China. The highest soybean yield was observed in the NPK treatment. Total of 200 isolates were isolated and grouped into four Bradyrhizobium genospecies corresponding to B. japonicum, B. diazoefficiens, B. ottawaense and Bradyrhizobium sp. I, based upon the multilocus sequence analysis of 6 housekeeping genes. The Bradyrhizobium sp. I was extensively distributed throughout the study site and was recorded as the dominant soybean rhizobia (82.5-87.5%). Except the NK treatment, the other fertilizer treatments had no effect on rhizobial species composition. Compared with the CK treatment, all the fertilizer treatments decreased species richness, diversity and evenness. The soil organic carbon contents, available N content and pH were the key soil factors to rhizobial community structure. Results suggest that long-term fertilization can decrease rhizobial species diversity, while balanced fertilization with NPK is the most suitable fertilization regime if taking both soybean yields and rhizobial diversity into account.
Collapse
Affiliation(s)
- Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - WenFeng Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - XiaoZeng Han
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - EnTao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, México D.F., Mexico
| | - WenXiu Zou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - ZhiMing Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| |
Collapse
|
37
|
Multi locus sequence analysis and symbiotic characterization of novel Ensifer strains nodulating Tephrosia spp. in the Indian Thar Desert. Syst Appl Microbiol 2016; 39:534-545. [DOI: 10.1016/j.syapm.2016.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 11/23/2022]
|
38
|
Li Y, Yan J, Yu B, Wang ET, Li X, Yan H, Liu W, Xie Z. Ensifer alkalisoli sp. nov. isolated from root nodules of Sesbania cannabina grown in saline–alkaline soils. Int J Syst Evol Microbiol 2016; 66:5294-5300. [DOI: 10.1099/ijsem.0.001510] [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
Affiliation(s)
- Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, PR China
| | - Bing Yu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico City, D.F., México
| | - Xiangyue Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - Hui Yan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, PR China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| |
Collapse
|
39
|
Li Y, Wang ET, Liu Y, Li X, Yu B, Ren C, Liu W, Li Y, Xie Z. Rhizobium anhuiense as the predominant microsymbionts of Lathyrus maritimus along the Shandong Peninsula seashore line. Syst Appl Microbiol 2016; 39:384-90. [PMID: 27480059 DOI: 10.1016/j.syapm.2016.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 10/21/2022]
Abstract
Beach pea [Lathyrus maritimus Bigelow, or Lathyrus japonicus subsp. maritimus (L.) P.W. Ball] is a wild legume distributed on the seashore line, and the rhizobia nodulating with this plant have been reported only rarely. In order to reveal the diversity of beach pea rhizobia on the seashore line of Shandong Peninsula, China, a total of 124 bacterial strains were isolated from the root nodules of beach pea plants collected from five sites. All the isolates were divided into five recA types after screening by recA gene sequence analysis and they consisted of Rhizobium anhuiense covering 122 symbiotic isolates in three recA types, as well as two single isolates Rhizobium sp. and Rhizobium lusitanum representing distinct recA types. The recA genotype III of R. anhuiense (103 isolates) represented by strain YIC11270 was dominant at all five sampling sites. Identical symbiotic genes (nodC and nifH) were detected in the three recA genotypes of R. anhuiense isolates that were closely related to those of the pea and faba rhizobia. This study clarified that R. anhuiense was the main symbiont for beach pea rhizobia on the seashore line of Shandong Peninsula. The low level genetic diversity of beach pea rhizobia revealed by both MLSA and the symbiotic genes might be related to the strong selection pressure produced by the saline-alkaline environment and the host plants.
Collapse
Affiliation(s)
- Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C. P. 11340, Mexico City, Mexico
| | - Yajing Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Xiangyue Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Bing Yu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Chenggang Ren
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Yunzhao Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, China.
| |
Collapse
|