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Wu Q, Wang F, Chen Y, Zou W, Zhu Z. Diazotrophic community in the sediments of Poyang Lake in response to water level fluctuations. Front Microbiol 2024; 15:1324313. [PMID: 38371932 PMCID: PMC10869460 DOI: 10.3389/fmicb.2024.1324313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 02/20/2024] Open
Abstract
Water level fluctuations (WLFs) are typical characteristic of floodplain lakes and dominant forces regulating the structure and function of lacustrine ecosystems. The sediment diazotrophs play important roles in contributing bioavailable nitrogen to the aquatic environment. However, the relationship between the diazotrophic community and WLFs in floodplain lakes is unknown. In this paper, we carried out a comprehensive investigation on the alpha diversity, abundance, composition and co-occurrence network of the sediment diazotrophs during different water level phases in Poyang Lake. There were no regular variation patterns in the alpha diversity and abundance of the sediment diazotrophs with the water level phase transitions. The relative abundance of some diazotrophic phyla (including Alphaproteobacteria, Deltaproteobacteri, Euryarchaeota, and Firmicutes) and genera (including Geobacter, Deferrisoma, Desulfuromonas, Rivicola, Paraburkholderia, Methylophilus, Methanothrix, Methanobacterium, and Clostridium) was found to change with the water level phase transitions. The results of ANOSIM, PerMANOVA, and DCA at the OTU level showed that the diazotrophic community structure in the low water level phase was significantly different from that in the two high water level phases, while there was no significant difference between the two high water level phases. These results indicated that the diazotrophic community was affected by the declining water level in terms of the composition, while the rising water level contributed to the recoveries of the diazotrophic community. The diazotrophs co-occurrence network was disrupted by the declining water level, but it was strengthened by the rising water level. Moreover, redundancy analysis showed that the variation of the diazotrophic community composition was mostly related to sediment total nitrogen (TN) and total phosphorous (TP). Interestingly, the levels of sediment TN and TP were also found to vary with the water level phase transitions. Therefore, it might be speculated that the WLFs may influence the sediment TN and TP, and in turn influence the diazotrophic community composition. These data can contribute to broadening our understanding of the ecological impacts of WLFs and the nitrogen fixation process in floodplain lakes.
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Affiliation(s)
- Qiang Wu
- School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
- Jiangxi Key Laboratory of Poyang Lake Water Resources and Environment, Jiangxi Academy of Water Science and Engineering, Nanchang, China
- Jiangxi Provincial Technology Innovation Center for Ecological Water Engineering in Poyang Lake Basin, Nanchang, China
| | - Fei Wang
- School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
- Jiangxi Provincial Technology Innovation Center for Ecological Water Engineering in Poyang Lake Basin, Nanchang, China
| | - Yuwei Chen
- School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
- Jiangxi Provincial Technology Innovation Center for Ecological Water Engineering in Poyang Lake Basin, Nanchang, China
| | - Wenxiang Zou
- School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
- Jiangxi Provincial Technology Innovation Center for Ecological Water Engineering in Poyang Lake Basin, Nanchang, China
| | - Zhigang Zhu
- School of Hydraulic and Ecological Engineering, Nanchang Institute of Technology, Nanchang, China
- Jiangxi Provincial Technology Innovation Center for Ecological Water Engineering in Poyang Lake Basin, Nanchang, China
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2
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Bromfield ESP, Cloutier S, Wasai-Hara S, Minamisawa K. Strains of Bradyrhizobium barranii sp. nov. associated with legumes native to Canada are symbionts of soybeans and belong to different subspecies (subsp. barranii subsp. nov. and subsp. apii subsp. nov.) and symbiovars (sv. glycinearum and sv. septentrionale). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soils of legumes native to Canada were previously identified as a novel
Bradyrhizobium
lineage consisting of symbiovars (sv.) glycinearum and septentrionale. Our purpose was to verify the taxonomic status of these strains using phylogenetic, genomic and phenotypic analyses. Multiple phylogenetic analyses including analysis of 51 full-length ribosome protein subunit (rps) gene sequences confirmed placement of the novel strains in a highly supported lineage distinct from named
Bradyrhizobium
species with
B. japonicum
USDA 6T as the closest relative. The results of genomic and phylogenomic analyses based on digital DNA–DNA hybridization and genome blast distance phylogeny showed that novel strains in comparisons with type strains of closest relatives were below the established threshold (70 %) for species delineation. Moreover, the novel strains were divided into two subspecies clusters based on the established threshold of 79 %. The genomes of strains 144S4T, 323S2, 1S5 and 38S5T have sizes of 11 399 526, 11 474 152, 10580853 and 10 530 141 bp with DNA G+C contents of 63.1, 63.0, 63.4 and 63.3 mol%, respectively. These strains possess symbiosis islands harbouring key nodulation, nitrogen-fixation and type III secretion system genes as well as abundant insertion sequences and between two and four putative plasmids. Strains 144S4T and 323S2 (sv. glycinearum) are effective with regard to nitrogen fixation in symbiotic association with soybeans whereas strains 1S5 and 38S5T (sv. septentrionale) are ineffective. Data for morphological, physiological and symbiotic characteristics complement the sequence-based results. The data presented here support the description of a new species and two new subspecies for which the names Bradyrhizobium barranii sp. nov. subsp. barranii subsp. nov. (sv. glycinearum) and Bradyrhizobium barranii sp. nov. subsp. apii subsp. nov. (sv. septentrionale) are proposed with strain 144S4T (=LMG 31552T=HAMBI 3722T) as the species type strain and type strain of subsp. barranii subsp. nov., and strain 38S5T (=LMG 31556T=HAMBI 3721T) as the type strain of subsp. apii subsp. nov.
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Affiliation(s)
- Eden S. P. Bromfield
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Sawa Wasai-Hara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8604, Japan
- Graduate School of Life Sciences, Tohoku University,, Katahira, Aoba-ku, Sendai 980–8577, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University,, Katahira, Aoba-ku, Sendai 980–8577, Japan
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Mburu SW, Koskey G, Njeru EM, Ombori O, Maingi J, Kimiti JM. Genetic and phenotypic diversity of microsymbionts nodulating promiscuous soybeans from different agro-climatic conditions. J Genet Eng Biotechnol 2022; 20:109. [PMID: 35849206 PMCID: PMC9294079 DOI: 10.1186/s43141-022-00386-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/20/2022] [Indexed: 11/10/2022]
Abstract
Background Global food supply is highly dependent on field crop production that is currently severely threatened by changing climate, poor soil quality, abiotic, and biotic stresses. For instance, one of the major challenges to sustainable crop production in most developing countries is limited nitrogen in the soil. Symbiotic nitrogen fixation of legumes such as soybean (Glycine max (L.) Merril) with rhizobia plays a crucial role in supplying nitrogen sufficient to maintain good crop productivity. Characterization of indigenous bradyrhizobia is a prerequisite in the selection and development of effective bioinoculants. In view of this, bradyrhizobia were isolated from soybean nodules in four agro-climatic zones of eastern Kenya (Embu Upper Midland Zone, Embu Lower Midland Zone, Tharaka Upper Midland Zone, and Tharaka Lower Midland Zone) using two soybean varieties (SB8 and SB126). The isolates were characterized using biochemical, morphological, and genotypic approaches. DNA fingerprinting was carried out using 16S rRNA gene and restricted by enzymes HaeIII, Msp1, and EcoRI. Results Thirty-eight (38) bradyrhizobia isolates obtained from the trapping experiments were placed into nine groups based on their morphological and biochemical characteristics. Most (77%) of the isolates had characteristics of fast-grower bradyrhizobia while 23% were slow-growers. Restriction digest revealed significant (p < 0.015) variation within populations and not among the agro-climatic zones based on analysis of molecular variance. Principal coordinate analysis demonstrated sympatric speciation of indigenous bradyrhizobia isolates. Embu Upper Midland Zone bradyrhizobia isolates had the highest polymorphic loci (80%) and highest genetic diversity estimates (H’ = 0.419) compared to other agro-climatic zones. Conclusion The high diversity of bradyrhizobia isolates depicts a valuable genetic resource for selecting more effective and competitive strains to improve promiscuous soybean production at a low cost through biological nitrogen fixation.
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Affiliation(s)
- Simon W Mburu
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P.O. Box 43844 (00100), Nairobi, Kenya. .,Department of Biological Sciences, Chuka University, P.O Box 109, Chuka, -60400, Kenya.
| | - Gilbert Koskey
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri Della Libertà, 33, 56127, Pisa, Italy
| | - Ezekiel M Njeru
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P.O. Box 43844 (00100), Nairobi, Kenya
| | - Omwoyo Ombori
- Department of Plant Sciences, Kenyatta University, P.O. Box 43844 (00100), Nairobi, Kenya
| | - John Maingi
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P.O. Box 43844 (00100), Nairobi, Kenya
| | - Jacinta M Kimiti
- Department of Forestry and Land Resources Management, South Eastern Kenya University, P.O. Box 170, Kitui, -90200, Kenya
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4
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Bromfield ESP, Cloutier S. Bradyrhizobium septentrionale sp. nov. (sv. septentrionale) and Bradyrhizobium quebecense sp. nov. (sv. septentrionale) associated with legumes native to Canada possess rearranged symbiosis genes and numerous insertion sequences. Int J Syst Evol Microbiol 2021; 71. [PMID: 34106824 PMCID: PMC8374602 DOI: 10.1099/ijsem.0.004831] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soil of legumes native to Canada were previously characterized and 1) placed in two novel lineages within the genus Bradyrhizobium and 2) assigned to symbiovar septentrionale. Here we verified the taxonomic status of these strains using genomic and phenotypic analyses. Phylogenetic analyses of five protein encoding partial gene sequences as well as 52 full length ribosome protein subunit gene sequences confirmed placement of the novel strains in two highly supported lineages distinct from named Bradyrhizobium species. The highest average nucleotide identity values of strains representing these two lineages relative to type strains of closest relatives were 90.7 and 92.3% which is well below the threshold value for bacterial species circumscription. The genomes of representative strains 1S1T, 162S2 and 66S1MBT have sizes of 10598256, 10733150 and 9032145 bp with DNA G+C contents of 63.5, 63.4 and 63.8 mol%, respectively. These strains possess between one and three plasmids based on copy number of plasmid replication and segregation (repABC) genes. Novel strains also possess numerous insertion sequences, and, relative to reference strain Bradyrhizobium diazoefficiens USDA110T, exhibit inversion and fragmentation of nodulation (nod) and nitrogen-fixation (nif) gene clusters. Phylogenetic analyses of nodC and nifH gene sequences confirmed placement of novel strains in a distinct lineage corresponding to symbiovar septentrionale. Data for morphological, physiological and symbiotic characteristics complement the sequence-based results. The data presented here support the description of two new species for which the names Bradyrhizobium septentrionale sp. nov. (sv. septentrionale) and Bradyrhizobium quebecense sp. nov. (sv. septentrionale) are proposed, with 1S1T (=LMG 29930T=HAMBI 3676T) and 66S1MBT (=LMG 31547T=HAMBI 3720T) as type strains, respectively.
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Affiliation(s)
- Eden S P Bromfield
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
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5
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Mayhood P, Mirza BS. Soybean Root Nodule and Rhizosphere Microbiome: Distribution of Rhizobial and Nonrhizobial Endophytes. Appl Environ Microbiol 2021; 87:e02884-20. [PMID: 33674438 PMCID: PMC8117765 DOI: 10.1128/aem.02884-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/02/2021] [Indexed: 11/20/2022] Open
Abstract
Soybean root nodules are known to contain a high diversity of both rhizobial endophytes and nonrhizobial endophytes (NREs). Nevertheless, the variation of these bacteria among different root nodules within single plants has not been reported. So far, it is unclear whether the selection of NREs among different root nodules within single plants is a random process or is strictly controlled by the host plant to favor a few specific NREs based on their beneficial influence on plant growth. As well, it is also unknown if the relative frequency of NREs within different root nodules is consistent or if it varies based on the location or size of a root nodule. We assessed the microbiomes of 193 individual soybean root nodules from nine plants using high-throughput DNA sequencing. Bradyrhizobium japonicum strains occurred in high abundance in all root nodules despite the presence of other soybean-compatible rhizobia, such as Ensifer, Mesorhizobium, and other species of Bradyrhizobium in soil. Nitrobacter and Tardiphaga were the two nonrhizobial genera that were uniformly detected within almost all root nodules, though they were in low abundance. DNA sequences related to other NREs that have frequently been reported, such as Bacillus, Pseudomonas, Flavobacterium, and Variovorax species, were detected in a few nodules. Unlike for Bradyrhizobium, the low abundance and inconsistent occurrence of previously reported NREs among different root nodules within single plants suggest that these microbes are not preferentially selected as endophytes by host plants and most likely play a limited part in plant growth as endophytes.IMPORTANCE Soybean (Glycine max L.) is a valuable food crop that also contributes significantly to soil nitrogen by developing a symbiotic association with nitrogen-fixing rhizobia. Bacterial endophytes (both rhizobial and nonrhizobial) are considered critical for the growth and resilience of the legume host. In the past, several studies have suggested that the selection of bacterial endophytes within root nodules can be influenced by factors such as soil pH, nutrient availability, host plant genotype, and bacterial diversity in soil. However, the influence of size or location of root nodules on the selection of bacterial endophytes within soybean roots is unknown. It is also unclear whether the selection of nonrhizobial endophytes within different root nodules of a single plant is a random process or is strictly regulated by the host. This information can be useful in identifying potential bacterial species for developing bioinoculants that can enhance plant growth and soil nitrogen.
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Affiliation(s)
- Parris Mayhood
- Department of Biology, Missouri State University, Springfield, Missouri, USA
| | - Babur S Mirza
- Department of Biology, Missouri State University, Springfield, Missouri, USA
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6
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Gohar D, Pent M, Põldmaa K, Bahram M. Bacterial community dynamics across developmental stages of fungal fruiting bodies. FEMS Microbiol Ecol 2021; 96:5894922. [PMID: 32816035 DOI: 10.1093/femsec/fiaa175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
Increasing evidence suggest that bacteria form diverse communities in various eukaryotic hosts, including fungi. However, little is known about their succession and the functional potential at different host development stages. Here we examined the effect of fruiting body parts and developmental stages on the structure and potential function of fungus-associated bacterial communities. Using high-throughput sequencing, we characterized bacterial communities and their associated potential functions in fruiting bodies from ten genera belonging to four major mushroom-forming orders and three different developmental stages of a model host species Cantharellus cibarius. Our results demonstrate that bacterial community structure differs between internal and external parts of the fruiting body but not between inner tissues. The structure of the bacterial communities showed significant variation across fruiting body developmental stages. We provide evidence that certain functional groups, such as those related to nitrogen fixation, persist in fruiting bodies during the maturation, but are replaced by putative parasites/pathogens afterwards. These data suggest that bacterial communities inhabiting fungal fruiting bodies may play important roles in their growth and development.
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Affiliation(s)
- Daniyal Gohar
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
| | - Mari Pent
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
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7
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Rejili M, Off K, Brachmann A, Marín M. Bradyrhizobium hipponense sp. nov., isolated from Lupinus angustifolius growing in the northern region of Tunisia. Int J Syst Evol Microbiol 2020; 70:5539-5550. [PMID: 32897848 DOI: 10.1099/ijsem.0.004445] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Strain aSej3T was isolated from a root nodule of a Lupinus angustifolius plant growing in Bizerte, Tunisia. 16S rRNA gene analysis placed this strain within the genus Bradyrhizobium. Multilocus sequence analysis (MLSA) including three housekeeping genes (glnII, gyrB and recA) grouped aSej3T together with Bradyrhizobium rifense CTAW71T, Bradyrhizobium cytisi CTAW11T, Bradyrhizobium ganzhouense RITF806T, Bradyrhizobium lupini USDA 3051T and Bradyrhizobium canariense BTA-1T. MLSA with five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed that this strain shares less than 93.5 % nucleotide identity with other type strains. Genome sequencing and inspection revealed a genome size of 8.83 Mbp with a G+C content of 62.8 mol%. Genome-wide average nucleotide identity and digital DNA-DNA hybridization values were below 87.5 and 36.2 %, respectively, when compared to described Bradyrhizobium species. Strain aSej3T nodulated L. angustifolius plants under axenic conditions and its nodC gene clustered within the genistearum symbiovar. Altogether, the phylogenetic data and the chemotaxonomic characteristics of this strain support that aSej3T represents a new species for which we propose the name Bradyrhizobium hipponense sp. nov. with the type strain aSej3T (=DSM 108913T=LMG 31020T).
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Affiliation(s)
- Mokhtar Rejili
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA), Faculty of Sciences, Gabes University, Tunisia
| | - Katja Off
- Chair of Genetics, Faculty of Biology, Ludwig Maximilians University Munich, Germany
| | - Andreas Brachmann
- Chair of Genetics, Faculty of Biology, Ludwig Maximilians University Munich, Germany
| | - Macarena Marín
- Chair of Genetics, Faculty of Biology, Ludwig Maximilians University Munich, Germany
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8
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Wasai-Hara S, Minamisawa K, Cloutier S, Bromfield ESP. Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands. Int J Syst Evol Microbiol 2020; 70:5063-5074. [PMID: 32804606 PMCID: PMC7656271 DOI: 10.1099/ijsem.0.004380] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
The taxonomic status of two previously characterized Bradyrhizobium strains (58S1T and S23321) isolated from contrasting habitats in Canada and Japan was verified by genomic and phenotypic analyses. Phylogenetic analyses of five and 27 concatenated protein-encoding core gene sequences placed both strains in a highly supported lineage distinct from named species in the genus Bradyrhizobium with Bradyrhizobium betae as the closest relative. Average nucleotide identity values of genome sequences between the test and reference strains were between 84.5 and 94.2 %, which is below the threshold value for bacterial species circumscription. The complete genomes of strains 58S1T and S23321 consist of single chromosomes of 7.30 and 7.23 Mbp, respectively, and do not have symbiosis islands. The genomes of both strains have a G+C content of 64.3 mol%. Present in the genome of these strains is a photosynthesis gene cluster (PGC) containing key photosynthesis genes. A tRNA gene and its partial tandem duplication were found at the boundaries of the PGC region in both strains, which is likely the hallmark of genomic island insertion. Key nitrogen-fixation genes were detected in the genomes of both strains, but nodulation and type III secretion system genes were not found. Sequence analysis of the nitrogen fixation gene, nifH, placed 58S1T and S23321 in a novel lineage distinct from described Bradyrhizobium species. Data for phenotypic tests, including growth characteristics and carbon source utilization, supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium cosmicum sp. nov. is proposed with 58S1T (=LMG 31545T=HAMBI 3725T) as the type strain.
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Affiliation(s)
- Sawa Wasai-Hara
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980–8577, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980–8577, Japan
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Eden S. P. Bromfield
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
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9
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Banerjee G, Basak S, Roy T, Chattopadhyay P. Intrinsic role of bacterial secretion systems in phylogenetic niche conservation of Bradyrhizobium spp. FEMS Microbiol Ecol 2020; 95:5586991. [PMID: 31609448 DOI: 10.1093/femsec/fiz165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/13/2019] [Indexed: 11/12/2022] Open
Abstract
Bradyrhizobium is a biologically important bacterial genus. Different Bradyrhizobium strains exhibit distinct niche selection like free living, root nodular and stem nodular. The present in-silico study was undertaken to identify the role of bacterial secretome in the phylogenetic niche conservation (PNC) of Bradyrhizobium sp. Analysis was carried out with the publicly available 19 complete genome assembly and annotation reports. A protocol was developed to screen the secretome related genes using three different database, viz. genome, proteome and gene ortholog. This resulted into 139 orthologs that include type secretion systems (T1SS-T6SS) along with flagella (Flg), type IV pili (T4P) and tight adherence (Tad) systems. Multivariate analysis using bacterial secretome was undertaken to find out the role of these secretion systems in PNC. In free living strains, T3SS, T4SS and T6SS were completely absent. Whereas, in the stem nodulating strains, T3SS and T6SS were absent, but T4SS was found to be present. On the other hand, the T3SS was found to be present only in the root-nodulating strains. The present investigation clearly demonstrated a pattern of PNC based on the distribution of secretion system components. To the best of our knowledge, this is the first report on PNC of Bradyrhizobium using the multivariate analysis of secretome.
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Affiliation(s)
- Goutam Banerjee
- Department of Biochemistry, University of Calcutta, West Bengal 700019, India
| | - Swarnendu Basak
- Department of Medical Zoology, Kyung Hee University, School of Medicine, Seoul 02447, Republic of Korea
| | - Tathagato Roy
- Member of Jeevak Herb Welfare Society (registration number S/1L/78148 OF 2010-2011), Santiniketan, 731235, India.,Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, U.S
| | - Pritam Chattopadhyay
- Department of Biotechnology, Gauhati University, Guwahati, Assam 781014, India.,Department of Botany, M.U.C. Women's College, University of Bardhaman, Bardhaman, West Bengal 713104, India
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10
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Bromfield ESP, Cloutier S, Nguyen HDT. Description and complete genome sequences of Bradyrhizobium symbiodeficiens sp. nov., a non-symbiotic bacterium associated with legumes native to Canada. Int J Syst Evol Microbiol 2020; 70:442-449. [PMID: 31626586 PMCID: PMC7395627 DOI: 10.1099/ijsem.0.003772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/09/2019] [Accepted: 09/17/2019] [Indexed: 12/22/2022] Open
Abstract
Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soil of either Amphicarpaea bracteata (Hog Peanut) or Desmodium canadense (Showy Tick Trefoil) growing in Canada, were previously characterized and placed in a novel lineage within the genus Bradyrhizobium. The taxonomic status of the novel strains was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated housekeeping gene sequences (atp D, gln II, rec A, gyr B and rpo B) placed all novel strains in a highly supported lineage distinct from named Bradyrhizobium species. Data for sequence similarities of concatenated housekeeping genes of novel strains relative to type strains of named species were consistent with the phylogenetic data. Average nucleotide identity values of genome sequences (84.5-93.7 %) were below the threshold value of 95-96 % for bacterial species circumscription. Close relatives to the novel strains are Bradyrhizobium amphicarpaeae, Bradyrhizobium ottawaense and Bradyrhizobium shewense. The complete genomes of strains 85S1MBT and 65S1MB consist of single chromosomes of size 7.04 and 7.13 Mbp, respectively. The genomes of both strains have a G+C content of 64.3 mol%. These strains lack a symbiosis island as well as key nodulation, nitrogen-fixation and photosystem genes. Data from various phenotypic tests including growth characteristics and carbon source utilization supported the sequence-based analyses. Based on the data presented here, the four strains represent a novel species for which the name B radyrhizobium symbiodeficiens sp. nov., is proposed, with 85S1MBT (=LMG 29937T=HAMBI 3684T) as the type strain.
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Affiliation(s)
- Eden S. P. Bromfield
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Hai D. T. Nguyen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
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11
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Bromfield ESP, Cloutier S, Nguyen HDT. Description and complete genome sequence of Bradyrhizobium amphicarpaeae sp. nov., harbouring photosystem and nitrogen-fixation genes. Int J Syst Evol Microbiol 2019; 69:2841-2848. [PMID: 31251718 DOI: 10.1099/ijsem.0.003569] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated 39S1MBT, isolated from a root nodule of a soybean plant that had been inoculated with root-zone soil of Amphicarpaea bracteata (hog peanut) growing in Canada, was previously characterized and placed in a novel lineage within the genus Bradyrhizobium. The taxonomic status of strain 39S1MBT was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated protein-encoding gene sequences (atpD, glnII, recA, gyrB and rpoB) placed 39S1MBT in a lineage distinct from named species. Data for sequence similarities of concatenated genes relative to type strains of named species supported the phylogenetic data. Average nucleotide identity values of genome sequences (84.5-91.7 %) were well below the threshold value for bacterial species circumscription. Based on these data, Bradyrhizobium ottawaense OO99T and Bradyrhizobium shewense ERR11T are close relatives of 39S1MBT. The complete genome of 39S1MBT consists of a single 7.04 Mbp chromosome without a symbiosis island; G+C content is 64.7 mol%. Present in the genome are key photosystem and nitrogen-fixation genes, but not nodulation and type III secretion system genes. Sequence analysis of the nitrogen fixation gene, nifH, placed 39S1MBT in a novel lineage distinct from named Bradyrhizobium species. Data for phenotypic tests including growth characteristics and carbon source utilization supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium amphicarpaeae sp. nov. is proposed with 39S1MBT (=LMG 29934T=HAMBI 3680T) as the type strain.
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Affiliation(s)
- Eden S P Bromfield
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Hai D T Nguyen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
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Avontuur JR, Palmer M, Beukes CW, Chan WY, Coetzee MPA, Blom J, Stępkowski T, Kyrpides NC, Woyke T, Shapiro N, Whitman WB, Venter SN, Steenkamp ET. Genome-informed Bradyrhizobium taxonomy: where to from here? Syst Appl Microbiol 2019; 42:427-439. [PMID: 31031014 DOI: 10.1016/j.syapm.2019.03.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 02/06/2023]
Abstract
Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in the number of described species. Although it was one of the first rhizobial genera recognised, its taxonomy remains complex. Various contemporary studies are showing that genome sequence information may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. In this study, we addressed two aims: first, we reviewed the availability and quality of available genomic resources for Bradyrhizobium. This was achieved by comparing genome sequences in terms of sequencing technologies used and estimated level of completeness for inclusion in genome-based phylogenetic analyses. Secondly, we utilized these genomes to investigate the taxonomic standing of Bradyrhizobium in light of its diverse lifestyles. Although genome sequences differed in terms of their quality and completeness, our data indicate that the use of these genome sequences is adequate for taxonomic purposes. By using these resources, we inferred a fully resolved, well-supported phylogeny. It separated Bradyrhizobium into seven lineages, three of which corresponded to the so-called supergroups known for the genus. Wide distribution of key lifestyle traits such as nodulation, nitrogen fixation and photosynthesis revealed that these traits have complicated evolutionary histories. We present the first robust Bradyrhizobium species phylogeny based on genome sequence information for investigating the evolution of this important assemblage of bacteria. Furthermore, this study provides the basis for using genome sequence information as a resource to make important taxonomic decisions, particularly at the species and genus levels.
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Affiliation(s)
- Juanita R Avontuur
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; Biotechnology Platform, Agricultural Research Council Onderstepoort Veterinary Institute (ARC-OVI), Onderstepoort 0110, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Poland
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa. http://emma.steenkamp.up.ac.za
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Tchagang CF, Xu R, Overy D, Blackwell B, Chabot D, Hubbard K, Doumbou CL, Bromfield ESP, Tambong JT. Diversity of bacteria associated with corn roots inoculated with Canadian woodland soils, and description of Pseudomonas aylmerense sp. nov. Heliyon 2018; 4:e00761. [PMID: 30186983 PMCID: PMC6120581 DOI: 10.1016/j.heliyon.2018.e00761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/24/2018] [Accepted: 08/24/2018] [Indexed: 11/15/2022] Open
Abstract
Bacteria associated with corn roots inoculated with soils collected from the Canadian woodlands were isolated and characterized. Genus-level identification based on 16S rRNA sequence analysis classified the 161 isolates in 19 genera. The majority (64%) of the isolates were affiliated with the genus Pseudomonas. Further analysis of the Pseudomonas isolates based on BLASTn and rpoD-rpoB-gyrB concatenated gene phylogeny revealed three unique clusters that could not be assigned to known species. This study reports the taxonomic description of one of the distinct lineages represented by two strains (S1E40T and S1E44) with P. lurida LMG 21995T, P. costantinii LMG 22119T, P. palleroniana LMG 23076T, P. simiae CCUG 50988T and P. extremorientalis LMG 19695T as the closest taxa. Both strains showed low ANIm (<90%) and genome-based DNA-DNA hybridization (<50%) values, which unequivocally delineated the new strains from the closest relatives. These findings were supported by multilocus sequence analysis (MLSA) and DNA fingerprinting. In addition, growth characteristics and biochemical tests revealed patterns that differed from the related species. Strains S1E40T and S1E44 are Gram-negative, aerobic, rod-shaped and motile by at least one flagellum; and grew optimally at 30 °C. The predominant polar lipid is phosphatidylethanolamine while the major respiratory quinone is ubiquinone-9. Based on phenotypic and genotypic data presented here, strains S1E40T and S1E44 represent a novel species for which the name Pseudomonas aylmerense sp. nov. is proposed. The type strain is S1E40T (= LMG 30784T = DOAB 703T = HAMI 3696T) with a G + C content of 61.6%.
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Affiliation(s)
- Caetanie F Tchagang
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada.,Institut des sciences de la santé et de la vie, Collège La Cité, 801 Aviation Parkway, Ottawa, Ontario, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - David Overy
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Barbara Blackwell
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Denise Chabot
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Cyr Lézin Doumbou
- Institut des sciences de la santé et de la vie, Collège La Cité, 801 Aviation Parkway, Ottawa, Ontario, Canada
| | - Eden S P Bromfield
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - James T Tambong
- Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
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