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Hale B, Watts C, Conatser M, Brown E, Wijeratne AJ. Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing. ENVIRONMENTAL MICROBIOME 2024; 19:46. [PMID: 38997772 PMCID: PMC11241880 DOI: 10.1186/s40793-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions. RESULTS Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi - a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties. CONCLUSIONS This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.
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Affiliation(s)
- Brett Hale
- AgriGro Incorporated, Doniphan, MO, USA
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA
- College of Science and Mathematics, Arkansas State University, State University, AR, USA
| | - Caitlin Watts
- College of Agriculture, Arkansas State University, State University, AR, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew Conatser
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Edward Brown
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Asela J Wijeratne
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA.
- College of Science and Mathematics, Arkansas State University, State University, AR, USA.
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Bünger W, Sarkar A, Grönemeyer JL, Zielinski J, Revermann R, Hurek T, Reinhold-Hurek B. Root Nodule Rhizobia From Undomesticated Shrubs of the Dry Woodlands of Southern Africa Can Nodulate Angolan Teak Pterocarpus angolensis, an Important Source of Timber. Front Microbiol 2021; 12:611704. [PMID: 33584615 PMCID: PMC7876412 DOI: 10.3389/fmicb.2021.611704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/06/2021] [Indexed: 11/17/2022] Open
Abstract
Pterocarpus angolensis, a leguminous tree native to the dry woodlands of Southern Africa, provides valuable timber, but is threatened by land conversion and overharvesting while showing limited natural regeneration. Nitrogen-fixing root nodule symbionts that could improve establishment of young seedlings have not yet been described. Therefore, we investigated the ability of P. angolensis to form nodules with a diverse range of rhizobia. In drought-prone areas under climate change with higher temperatures, inoculants that are heat-tolerant and adapted to these conditions are likely to be of advantage. Sources of bacterial isolates were roots of P. angolensis from nurseries in the Kavango region, other shrubs from this area growing near Pterocarpus such as Indigofera rautanenii, Desmodium barbatum, Chamaecrista sp., or shrubs from drought-prone areas in Namaqualand (Wiborgia monoptera, Leobordea digitata) or Kalahari (Indigofera alternans). Only slight protrusions were observed on P. angolensis roots, from which a non-nodulating Microbacterium sp. was isolated. Rhizobia that were isolated from nodules of other shrubs were affiliated to Bradyrhizobium ripae WR4T, Bradyrhizobium spp. (WR23/WR74/WR93/WR96), or Ensifer/Mesorhizobium (WR41/WR52). As many plant growth-promoting rhizobacteria (PGPR), nodule isolates produced siderophores and solubilized phosphate. Among them, only the Bradyrhizobium strains nodulated P. angolensis under controlled conditions in the laboratory. Isolates were further characterized by multilocus sequence analysis and were found to be distant from known Bradyrhizobium species. Among additional reference species tested for nodulation on P. angolensis, Bradyrhizobium vignae 7-2T and Bradyrhizobium namibiense 5-10T from the Kavango region of Namibia as well as Bradyrhizobium elkanii LMG6234T and Bradyrhizobium yuanmingense LMG21728T induced nitrogen-fixing nodules, while Bradyrhizobium diazoefficiens USDA110T and Bradyrhizobium tropiciagri SEMIA6148T did not. This suggests a broad microsymbiont range from Bradyrhizobium japonicum and B. elkanii lineages. Phylogenetic analysis of nodC genes indicated that nodulating bradyrhizobia did not belong to a specific symbiovar. Also, for I. rautanenii and Wiborgia, nodule isolates B. ripae WR4T or Mesorhizobium sp. WR52, respectively, were authenticated. Characterization of symbionts inducing effective root nodules in P. angolensis and other shrubs from Subsahara Africa (SSA) give insights in their symbiotic partners for the first time and might help in future to develop bioinoculants for young seedlings in nurseries, and for reforestation efforts in Southern Africa.
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Affiliation(s)
- Wiebke Bünger
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Abhijit Sarkar
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Jann Lasse Grönemeyer
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Janina Zielinski
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Rasmus Revermann
- Department of Biodiversity, Ecology and Evolution of Plants, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
- Faculty of Natural Resources and Spatial Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
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Sugiyama A. The soybean rhizosphere: Metabolites, microbes, and beyond-A review. J Adv Res 2019; 19:67-73. [PMID: 31341671 PMCID: PMC6630087 DOI: 10.1016/j.jare.2019.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 11/17/2022] Open
Abstract
Rhizosphere microbial communities are important for plant health. Specialized metabolites in the rhizosphere influence the microbial communities. Isoflavones and saponins are major specialized metabolites secreted by soybean. Secretion is regulated developmentally and nutritionally. Possible links between specialized metabolites and microbial communities are highlighted.
The rhizosphere is the region close to a plant’s roots, where various interactions occur. Recent evidence indicates that plants influence rhizosphere microbial communities by secreting various metabolites and, in turn, the microbes influence the growth and health of the plants. Despite the importance of plant-derived metabolites in the rhizosphere, relatively little is known about their spatiotemporal distribution and dynamics. In addition to being an important crop, soybean (Glycine max) is a good model plant with which to study these rhizosphere interactions, because soybean plants have symbiotic relationships with rhizobia and arbuscular mycorrhizal fungi and secrete various specialized metabolites, such as isoflavones and saponins, into the soil. This review summarizes the characteristics of the soybean rhizosphere from the viewpoint of specialized metabolites and microbes and discusses future research perspectives. In sum, secretion of these metabolites is developmentally and nutritionally regulated and potentially alters the rhizosphere microbial communities.
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Affiliation(s)
- Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
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Sugiyama A, Ueda Y, Takase H, Yazaki K. Do soybeans select specific species of Bradyrhizobium during growth? Commun Integr Biol 2015; 8:e992734. [PMID: 26841977 PMCID: PMC4594333 DOI: 10.4161/19420889.2014.992734] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 09/19/2014] [Indexed: 11/19/2022] Open
Abstract
Soybean is an important crop, with processed soybeans being the second largest source of vegetable oil and the largest source of animal protein feed in the world. Nodules on soybean roots are responsible for symbiotic nitrogen fixation, enabling soybean plants to obtain sufficient nitrogen for growth and seed production. Because nitrogen is an essential, but often limiting, nutrient for plant growth, improvements in nitrogen fixation are highly required in agriculture. We recently reported a comprehensive analysis of rhizosphere bacterial communities during soybean growth in a field in Kyoto prefecture, Japan. The bacterial communities of the rhizosphere changed significantly during growth, with potential plant growth-promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, increasing in a stage-specific manner. In this addendum, we focus on changes in Bradyrhizobium during soybean growth, suggesting that soybean plants select for symbiotic partners.
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Affiliation(s)
- Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere; Kyoto University ; Kyoto, Japan
| | - Yoshikatsu Ueda
- Research Institute for Sustainable Humanosphere; Kyoto University ; Kyoto, Japan
| | - Hisabumi Takase
- Faculty of Bioenvironmental Science; Kyoto Gakuen University ; Kyoto, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere; Kyoto University ; Kyoto, Japan
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Shiro S, Matsuura S, Saiki R, Sigua GC, Yamamoto A, Umehara Y, Hayashi M, Saeki Y. Genetic diversity and geographical distribution of indigenous soybean-nodulating bradyrhizobia in the United States. Appl Environ Microbiol 2013; 79:3610-8. [PMID: 23563944 PMCID: PMC3675916 DOI: 10.1128/aem.00236-13] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/26/2013] [Indexed: 11/20/2022] Open
Abstract
We investigated the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia and their geographical distribution in the United States using nine soil isolates from eight states. The bradyrhizobia were inoculated on three soybean Rj genotypes (non-Rj, Rj(2)Rj(3), and Rj(4)). We analyzed their genetic diversity and community structure by means of restriction fragment length polymorphisms of PCR amplicons to target the 16S-23S rRNA gene internal transcribed spacer region, using 11 USDA Bradyrhizobium strains as reference strains. We also performed diversity analysis, multidimensional scaling analysis based on the Bray-Curtis index, and polar ordination analysis to describe the structure and geographical distribution of the soybean-nodulating bradyrhizobial community. The major clusters were Bradyrhizobium japonicum Bj123, in the northern United States, and Bradyrhizobium elkanii, in the middle to southern regions. Dominance of bradyrhizobia in a community was generally larger for the cluster belonging to B. elkanii than for the cluster belonging to B. japonicum. The indigenous American soybean-nodulating bradyrhizobial community structure was strongly correlated with latitude. Our results suggest that this community varies geographically.
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Affiliation(s)
- Sokichi Shiro
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Japan
| | - Syota Matsuura
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Rina Saiki
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Gilbert C. Sigua
- USDA Agricultural Research Service, Coastal Plains Soil Water & Plant Research Center, Florence, South Carolina, USA
| | - Akihiro Yamamoto
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Yosuke Umehara
- National Institute of Agrobiological Sciences, Ibaraki, Japan
| | - Masaki Hayashi
- National Institute of Agrobiological Sciences, Ibaraki, Japan
| | - Yuichi Saeki
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
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Biochemical and molecular characterization of a rhizobitoxine-producing Bradyrhizobium from pigeon pea plants. Folia Microbiol (Praha) 2010; 55:233-8. [DOI: 10.1007/s12223-010-0034-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 11/19/2009] [Indexed: 10/19/2022]
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Abstract
Legume nodules, specialized structures for nitrogen fixation, are probably the result of coevolution of plants and ancestral rhizobia. Among the evolutionary processes leading to legume radiation and divergence, coevolution with rhizobia might have occurred. Alternatively, bacteria could have been constantly selected by plants, with bacteria slightly influencing plant evolution (required to fulfill the criteria for a coevolutionary hypothesis). Evidence of bacterial effects on plant evolution is scarce but being searched for. Bacterial genetic plasticity may be indicative of the large capacity of Rhizobium to adapt to legumes. Events such as symbiotic replacement, easy recruitment of symbiotic bacteria by legume plants, and lateral transfer of symbiotic genes seem to erase the coevolutionary or selected relationships in rhizobial-legume symbiosis. In particular, the hypotheses proposed are (1) Rhizobium replaced Bradyrhizobium in a few hosts of the Phaseoleae tribe, Phaseolus vulgaris and P. coccineus; (2) Rhizobium etli as a species did not coevolve with bean; and (3) beta-Proteobacteria replaced alpha-Proteobacteria in South American mimosas. Novel results on symbiosis suggest a more complex evolutionary process for nodulation that may include multiple organisms, such as mycorrhiza, nematodes, and other bacteria in addition to rhizobia.
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Yasuta T, Okazaki S, Mitsui H, Yuhashi K, Ezura H, Minamisawa K. DNA sequence and mutational analysis of rhizobitoxine biosynthesis genes in Bradyrhizobium elkanii. Appl Environ Microbiol 2001; 67:4999-5009. [PMID: 11679318 PMCID: PMC93263 DOI: 10.1128/aem.67.11.4999-5009.2001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We cloned and sequenced a cluster of genes involved in the biosynthesis of rhizobitoxine, a nodulation enhancer produced by Bradyrhizobium elkanii. The nucleotide sequence of the cloned 28.4-kb DNA region encompassing rtxA showed that several open reading frames (ORFs) were located downstream of rtxA. A large-deletion mutant of B. elkanii, USDA94 Delta rtx::Omega 1, which lacks rtxA, ORF1 (rtxC), ORF2, and ORF3, did not produce rhizobitoxine, dihydrorhizobitoxine, or serinol. The broad-host-range cosmid pLAFR1, which contains rtxA and these ORFs, complemented rhizobitoxine production in USDA94 Delta rtx::Omega 1. Further complementation experiments involving cosmid derivatives obtained by random mutagenesis with a kanamycin cassette revealed that at least rtxA and rtxC are necessary for rhizobitoxine production. Insertional mutagenesis of the N-terminal and C-terminal regions of rtxA indicated that rtxA is responsible for two crucial steps, serinol formation and dihydrorhizobitoxine biosynthesis. An insertional mutant of rtxC produced serinol and dihydrorhizobitoxine but no rhizobitoxine. Moreover, the rtxC product was highly homologous to the fatty acid desaturase of Pseudomonas syringae and included the copper-binding signature and eight histidine residues conserved in membrane-bound desaturase. This result suggested that rtxC encodes dihydrorhizobitoxine desaturase for the final step of rhizobitoxine production. In light of results from DNA sequence comparison, gene disruption experiments, and dihydrorhizobitoxine production from various substrates, we discuss the biosynthetic pathway of rhizobitoxine and its evolutionary significance in bradyrhizobia.
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Affiliation(s)
- T Yasuta
- Institute of Genetic Ecology, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan
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Ezura H, Nukui N, Yuhashi K, Minamisawa K. In vitro plant regeneration in Macroptilium atropurpureum, a legume with a broad symbiont range for nodulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2000; 159:21-27. [PMID: 11011089 DOI: 10.1016/s0168-9452(00)00299-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Macroptilium atropurpureum is a model legume with a broad symbiont range for nodulation. We have achieved the first in vitro plant regeneration of this species using cv. Siratro. Hypocotyl explants excised from dark-grown seedlings generated slimy, friable calli after three weeks' culture on B5 medium containing 1-2 mg/l kinetin and 0.05 mg/l alpha-naphthaleneacetic acid. This was followed by the generation of green organogenic callus with shoot buds by subculturing the explants to hormone-free B5 medium 20 days after the start of culture. The green organogenic calli with shoot buds were maintained as organogenic callus by subculturing on the same medium, and shoots were elongated on hormone-free B5 medium. Elongated shoots were rooted on half-strength B5 medium. Most regenerated plants were morphologically normal, diploid and fertile, although tetraploid plants appeared at a low frequency (8%).
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Affiliation(s)
- H Ezura
- Plant Biotechnology Institute, Ibaraki Agricultural Center, Iwama, 319-0292, Nishi-ibaraki, Japan
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Nukui N, Ezura H, Yuhashi K, Yasuta T, Minamisawa K. Effects of ethylene precursor and inhibitors for ethylene biosynthesis and perception on nodulation in Lotus japonicus and Macroptilium atropurpureum. PLANT & CELL PHYSIOLOGY 2000; 41:893-7. [PMID: 10965947 DOI: 10.1093/pcp/pcd011] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Inhibitors of ethylene synthesis or its physiological function enhanced nodulation in Lotus japonicus and Macroptilium atropurpureum. In contrast, the application of 1-aminocyclopropane-1-carboxylic acid, a precursor of ethylene biosynthesis, reduced the nodule number in these legumes. These results suggest that an ethylene-mediated signaling pathway is involved in the nodulation process even in the determinate nodulators.
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Affiliation(s)
- N Nukui
- Institute of Genetic Ecology, Tohoku University Katahira, Sendai, Japan
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Yuhashi K, Ichikawa N, Ezura H, Akao S, Minakawa Y, Nukui N, Yasuta T, Minamisawa K. Rhizobitoxine production by Bradyrhizobium elkanii enhances nodulation and competitiveness on Macroptilium atropurpureum. Appl Environ Microbiol 2000; 66:2658-63. [PMID: 10831453 PMCID: PMC110596 DOI: 10.1128/aem.66.6.2658-2663.2000] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Application of 1-aminoocyclopropane-1-carboxylic acid, an ethylene precursor, decreased nodulation of Macroptilium atropurpureum by Bradyrhizobium elkanii. B. elkanii produces rhizobitoxine, an ethylene synthesis inhibitor. Elimination of rhizobitoxine production in B. elkanii increased ethylene evolution and decreased nodulation and competitiveness on M. atropurpureum. These results suggest that rhizobitoxine enhances nodulation and competitiveness of B. elkanii on M. atropurpureum.
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Affiliation(s)
- K Yuhashi
- Institute of Genetic Ecology, Tohoku University, Katahira, Aoba-ku, Sendai, 980-8577, Japan
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