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Zhang Y, Chen Y, Penttinen P, Wang X, Quan Y, Wen L, Yang M, Zhang X, Chen Q, Zhang L, Zhang J, Zhang X, Xu K. Ciceribacter sichuanensis sp. nov., a plant growth promoting rhizobacterium isolated from root nodules of soybean in Sichuan, China. Antonie Van Leeuwenhoek 2024; 117:46. [PMID: 38427093 DOI: 10.1007/s10482-024-01941-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
The fast-growing rhizobia-like strains S101T and S153, isolated from root nodules of soybean (Glycine max) in Sichuan, People's Republic of China, underwent characterization using a polyphasic taxonomy approach. The strains exhibited growth at 20-40 °C (optimum, 28 °C), pH 4.0-10.0 (optimum, pH 7.0) and up to 2.0% (w/v) NaCl (optimum, 0.01%) on Yeast Mannitol Agar plates. The 16S rRNA gene of strain S101T showed 98.4% sequence similarity to the closest type strain, Ciceribacter daejeonense L61T. Major cellular fatty acids in strain S101T included summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. The predominant quinone was ubiquinone-10. The polar lipids of strain S101T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethyl ethanolamine, phosphatidyl ethanolamine, amino phospholipid, unidentified phosphoglycolipid and unidentified amino-containing lipids. The DNA G + C contents of S101T and S153 were 61.1 and 61.3 mol%, respectively. Digital DNA-DNA hybridization relatedness and average nucleotide identity values between S101T and C. daejeonense L61T were 46.2% and 91.4-92.2%, respectively. In addition, strain S101T promoted the growth of soybean and carried nitrogen fixation genes in its genome, hinting at potential applications in sustainable agriculture. We propose that strains S101T and S153 represent a novel species, named Ciceribacter sichuanensis sp. nov., with strain S101T as the type strain (= CGMCC 1.61309 T = JCM 35649 T).
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Affiliation(s)
- Yanqin Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Yuanxue Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Xing Wang
- 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, People's Republic of China
| | - Ying Quan
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Licheng Wen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Miao Yang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Lingzi Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450000, People's Republic of 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, People's Republic of China.
| | - Kaiwei Xu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
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Ma T, Xue H, Piao C, Jiang N, Li Y. Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov. Front Microbiol 2023; 14:1207256. [PMID: 37601364 PMCID: PMC10434624 DOI: 10.3389/fmicb.2023.1207256] [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: 04/17/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T).
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Affiliation(s)
| | | | | | | | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
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3
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Yang E, Liu J, Chen D, Wang S, Xu L, Ma K, Zhan X, Sun L, Wang W. Rhizobium cremeum sp. nov., isolated from sewage and capable of acquisition of heavy metal and aromatic compounds resistance genes. Syst Appl Microbiol 2022; 45:126322. [DOI: 10.1016/j.syapm.2022.126322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 10/18/2022]
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Rahi P, Khairnar M, Hagir A, Narayan A, Jain KR, Madamwar D, Pansare A, Shouche Y. Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae. Arch Microbiol 2021; 203:3591-3604. [PMID: 33966089 DOI: 10.1007/s00203-021-02349-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 11/27/2022]
Abstract
A novel bacterial strain designated as ADMK78T was isolated from the saline desert soil. The cells were rod-shaped, Gram-stain-negative, and non-motile. The strain ADMK78T grows best at 28 °C. Phylogeny of 16S rRNA gene placed the strain ADMK78T with the members of genera Ciceribacter and Rhizobium, while the highest sequence similarity was with Rhizobium wuzhouense W44T (98.7%) and Rhizobium ipomoeae shin9-1 T (97.9%). Phylogenetic analysis based on 92 core-genes extracted from the genome sequences and average amino acid identity (AAI) revealed that the strain ADMK78T forms a distinct cluster including five species of Rhizobium, which is separate from the cluster of the genera Rhizobium and Ciceribacter. We propose re-classification of Rhizobium ipomoeae, R. wuzhouense, R. rosettiformans and R. rhizophilum into the novel genus Peteryoungia. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of ADMK78T were less than 82 and 81%, respectively, among all type strains included in the genus Peteryoungia. The strain ADMK78T showed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78T represents a novel species, Peteryoungia desertarenae sp. nov. The type strain is ADMK78T (= MCC 3400T; KACC 21383T; JCM 33657T). We also proposed the reclassification of Rhizobium daejeonense, R. naphthalenivorans and R. selenitireducens, into the genus Ciceribacter, based on core gene phylogeny and AAI values.
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Affiliation(s)
- Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India.
| | - Mitesh Khairnar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Ashwini Hagir
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Avinash Narayan
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India
| | - Kunal R Jain
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India
| | - Datta Madamwar
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India
| | - Aabeejjeet Pansare
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra, 411007, India
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Ramoneda J, Roux JJL, Frossard E, Frey B, Gamper HA. Geographical patterns of root nodule bacterial diversity in cultivated and wild populations of a woody legume crop. FEMS Microbiol Ecol 2021; 96:5874250. [PMID: 32691840 DOI: 10.1093/femsec/fiaa145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
There is interest in understanding how cultivation, plant genotype, climate and soil conditions influence the biogeography of root nodule bacterial communities of legumes. For crops from regions with relict wild populations, this is of even greater interest because the effects of cultivation on symbiont communities can be revealed, which is of particular interest for bacteria such as rhizobia. Here, we determined the structure of root nodule bacterial communities of rooibos (Aspalathus linearis), a leguminous shrub endemic to South Africa. We related the community dissimilarities of the root nodule bacteria of 18 paired cultivated and wild rooibos populations to pairwise geographical distances, plant ecophysiological characteristics and soil physicochemical parameters. Using next-generation sequencing data, we identified region-, cultivation- and farm-specific operational taxonomic units for four distinct classes of root nodule bacterial communities, dominated by members of the genus Mesorhizobium. We found that while bacterial richness was locally increased by organic cultivation, strong biogeographical differentiation in the bacterial communities of wild rooibos disappeared with cultivation of one single cultivar across its entire cultivation range. This implies that expanding rooibos farming has the potential to endanger wild rooibos populations through the homogenisation of root nodule bacterial diversity.
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Affiliation(s)
- Josep Ramoneda
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland
| | - Johannes J Le Roux
- Department of Biological Sciences, Macquarie University, Balaclava Rd, Macquarie Park NSW 2109, Sydney, Australia
| | - Emmanuel Frossard
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Hannes Andres Gamper
- Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315 Lindau, Zurich, Switzerland.,Faculty of Science and Technology, Free University of Bolzen-Bolzano, Piazza Università, 1, 39100 Bolzano BZ, Italy
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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Meglouli H, Fontaine J, Verdin A, Magnin-Robert M, Tisserant B, Hijri M, Sahraoui ALH. Aided Phytoremediation to Clean Up Dioxins/Furans-Aged Contaminated Soil: correlation between microbial communities and pollutant dissipation. Microorganisms 2019; 7:E523. [PMID: 31684182 PMCID: PMC6920798 DOI: 10.3390/microorganisms7110523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/24/2019] [Accepted: 10/31/2019] [Indexed: 11/16/2022] Open
Abstract
To restore and clean up polluted soils, aided phytoremediation was found to be an effective, eco-friendly, and feasible approach in the case of many organic pollutants. However, little is known about its potential efficiency regarding polychlorinated dibenzo-p-dioxins and furans-contaminated soils. Thus, phytoremediation of aged dioxins/furans-contaminated soil was carried out through microcosm experiments vegetated with alfalfa combined with different amendments: an arbuscular mycorrhizal fungal inoculum (Funneliformis mosseae), a biosurfactant (rhamnolipids), a dioxins/furans degrading-bacterium (Sphingomonas wittichii RW1), and native microbiota. The total dioxins/furans dissipation was estimated to 23%, which corresponds to 48 ng.kg-1 of soil, after six months of culture in the vegetated soil combined with the four amendments compared to the non-vegetated soil. Our findings showed that the dioxins/furans dissipation resulted from the stimulation of soil microbial enzyme activities (fluorescein diacetate hydrolase and dehydrogenase) and the increase of bacterial abundance, richness, and diversity, as well as fungal diversity. Amplicon sequencing using Illumina MiSeq analysis led to identification of several bacterial (Bacillaceae, Sphingomonadaceae) and fungal (Chaetomium) groups known to be involved in dioxins/furans degradation. Furthermore, concomitant cytotoxicity and dioxins/furans concentration decreases were pointed out in the phytoremediated soil. The current study demonstrated the usefulness of combining different types of amendments to improve phytoremediation efficacy of aged dioxins/furans-contaminated soils.
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Affiliation(s)
- Hacène Meglouli
- Université du Littoral Côte d'Opale, UCEIV-EA 4492, SFR Condorcet FR CNRS 3417, CS 80699, F-62228 Calais cedex, France.
| | - Joël Fontaine
- Université du Littoral Côte d'Opale, UCEIV-EA 4492, SFR Condorcet FR CNRS 3417, CS 80699, F-62228 Calais cedex, France.
| | - Anthony Verdin
- Université du Littoral Côte d'Opale, UCEIV-EA 4492, SFR Condorcet FR CNRS 3417, CS 80699, F-62228 Calais cedex, France.
| | - Maryline Magnin-Robert
- Université du Littoral Côte d'Opale, UCEIV-EA 4492, SFR Condorcet FR CNRS 3417, CS 80699, F-62228 Calais cedex, France.
| | - Benoit Tisserant
- Université du Littoral Côte d'Opale, UCEIV-EA 4492, SFR Condorcet FR CNRS 3417, CS 80699, F-62228 Calais cedex, France.
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada.
- AgroBioSciences, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir, 43150 Morocco.
| | - Anissa Lounès-Hadj Sahraoui
- Université du Littoral Côte d'Opale, UCEIV-EA 4492, SFR Condorcet FR CNRS 3417, CS 80699, F-62228 Calais cedex, France.
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Wang M, Chen S, Han Y, Chen L, Wang D. Responses of soil aggregates and bacterial communities to soil-Pb immobilization induced by biofertilizer. CHEMOSPHERE 2019; 220:828-836. [PMID: 30612052 DOI: 10.1016/j.chemosphere.2018.12.214] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 12/28/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
The objective of this study was to investigate how soil aggregates and bacterial communities responded to soil-lead (Pb) immobilization induced by biofertilizer. Wheat (Triticum spp.) was planted in Pb-polluted soil. The re-distribution of Pb in soil aggregates and change of soil microbial communities due to biofertilizers were believed to be responsible for immobilizing soil Pb and alleviating its phytotoxicity. Adding biofertilizer promoted the formation of large aggregates (0.20-2.0 mm) with more mass loading of Pb, and increased soil bacterial diversity and the abundance of beneficial taxa such as those from the phyla Bacteroidetes, Actinobacteria, and Proteobacteria. In addition, there was significant alleviation of Pb availability as indicated by decreases in the values of bioconcentration factors (BCF) (up to 35.7% and 42.3% for roots and shoots, respectively) of wheat and DTPA-extractable Pb in soil (up to 34.4%) receiving fertilizer treatments compared with the CK (no treatment). Similar bacterial community structures and alpha diversities for the biofertilizer treatments and their autoclaved controls were observed, suggesting that physicochemical properties drove the structure of the soil bacterial community. This study introduced a new idea for development of effective strategies to control or reduce soil Pb risks.
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Affiliation(s)
- Meng Wang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture / Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Shibao Chen
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture / Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
| | - Yun Han
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture / Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Li Chen
- Institute of Plant Protection and Environmental Protection, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, PR China
| | - Duo Wang
- College of Energy, Xiamen University, Xiamen, Fujian, 361102, PR China
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Wang M, Li S, Chen S, Meng N, Li X, Zheng H, Zhao C, Wang D. Manipulation of the rhizosphere bacterial community by biofertilizers is associated with mitigation of cadmium phytotoxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:413-421. [PMID: 30176454 DOI: 10.1016/j.scitotenv.2018.08.174] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 05/13/2023]
Abstract
The objective of this study was to understand the effect of biofertilizers on cadmium (Cd)-induced phytotoxicity and the rhizosphere bacterial community. The crop specie rice (Oryza sativa L.) was planted in Cd-contaminated soils, and Illumina high-throughput sequencing was performed to investigate how the composition of the rhizosphere bacterial community responded to the addition of biofertilizers. Biofertilizers were effective in alleviating Cd phytotoxicity as indicated by the significant increase in plant biomass (up to 85.2% and 48.4% for roots and shoots, respectively) and decrease in tissue Cd concentration (up to 72.2% in roots) of rice receiving fertilizer treatments compared with the CK (no treatment). These positive effects were likely due to the increase in soil pH, which can be attributed primarily to Cd immobilization, and the promotion of beneficial taxa such as Proteobacteria, Bacteroidetes, Gemmatimonadetes, and Firmicutes. In addition, autoclaved biofertilizers tended to have similar beneficial effects and similar bacterial community alpha diversities as the original biofertilizer treatments. This suggests that the change in soil physicochemical properties by biofertilizer addition might drive the structure of rhizosphere bacterial community, and not the biofertilizer microbes themselves. In both the original and sterilized biofertilizer treatments, the effectiveness in mitigating of Cd phytotoxicity was found to be dependent on the type of biofertilizer applied. Comparatively, the biofertilizer denoted as DY was more effective in mitigating Cd phytotoxicity than others. These results demonstrate that biofertilizer addition could be a promising approach to immobilize soil Cd by manipulating the rhizosphere bacterial community, thus to facilitate plant growth.
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Affiliation(s)
- Meng Wang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shanshan Li
- School of Land Science and Technology, China University of Geosciences, Beijing 100083, PR China
| | - Shibao Chen
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
| | - Nan Meng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoyue Li
- School of Land Science and Technology, China University of Geosciences, Beijing 100083, PR China
| | - Han Zheng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Chunmei Zhao
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Duo Wang
- College of Energy, Xiamen University, Xiamen, Fujian 361102, PR China
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de Lajudie PM, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of rhizobia and agrobacteria Minutes of the closed meeting, Granada, 4 September 2017. Int J Syst Evol Microbiol 2018; 68:3363-3368. [DOI: 10.1099/ijsem.0.002974] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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11
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2018; 68:693-694. [PMID: 29493486 DOI: 10.1099/ijsem.0.002570] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Wang Y, Yu Z, Li Y, Wang G, Liu J, Liu J, Liu X, Jin J. Microbial association with the dynamics of particulate organic carbon in response to the amendment of elevated CO 2-derived wheat residue into a Mollisol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:972-981. [PMID: 28724229 DOI: 10.1016/j.scitotenv.2017.07.087] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
As the chemical quality of crop residue is likely to be affected by elevated CO2 (eCO2), residue amendments may influence soil organic carbon (SOC) sequestration. However, in Mollisols, the dynamics of the SOC fractions in response to amendment with wheat residue produced under eCO2 and the corresponding microbial community composition remain unknown. Such investigation is essential to residue management, which affects the soil quality and productivity of future farming systems. To narrow this knowledge gap, 13C-labeled shoot and root residue derived from ambient CO2 (aCO2) or eCO2 were amended into Mollisols and incubated for 200days. The soil was sampled during the incubation period to determine the residue-C retained in the three SOC fractions, i.e., coarse intra-aggregate particulate organic C (coarse iPOC), fine iPOC and mineral-associated organic C (MOC). The soil bacterial community was assessed using a MiSeq sequencing instrument. The results showed that the increase in SOC concentrations attributable to the application of the wheat residue primarily occurred in the coarse iPOC fraction. Compared with the aCO2-derived shoot residue, the amendment of eCO2-derived shoot residue resulted in greater SOC concentrations, whereas no significant differences (P>0.05) were observed between the aCO2- and eCO2-derived roots. Principal coordinates analysis (PCoA) showed that the residue amendment significantly (P≤0.05) altered the bacterial community composition compared with the non-residue amendment. Additionally, the bacterial community in the aCO2-derived shoot treatment differed from those in the other residue treatments until day 200 of the incubation period. The eCO2-derived shoot treatment significantly increased (P≤0.05) the relative abundances of the genera Acidobacteriaceae_(Subgroup_1)_uncultured, Bryobacter, Candidatus_Solibacter, Gemmatimonas and Nitrosomonadaceae_uncultured, whereas the opposite trend was observed in Nonomuraea, Actinomadura, Streptomyces and Arthrobacter (P≤0.05). These results imply that the response of the microbial community to the eCO2-derived shoot treatment is associated with its contribution to the POC fractions.
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Affiliation(s)
- Yanhong Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Yansheng Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Judong Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; Centre for AgriBioscience, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia.
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13
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Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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An arsenate-reducing and alkane-metabolizing novel bacterium, Rhizobium arsenicireducens sp. nov., isolated from arsenic-rich groundwater. Arch Microbiol 2016; 199:191-201. [PMID: 27663709 DOI: 10.1007/s00203-016-1286-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 01/09/2023]
Abstract
A novel arsenic (As)-resistant, arsenate-respiring, alkane-metabolizing bacterium KAs 5-22T, isolated from As-rich groundwater of West Bengal was characterized by physiological and genomic properties. Cells of strain KAs 5-22T were Gram-stain-negative, rod-shaped, motile, and facultative anaerobic. Growth occurred at optimum of pH 6.0-7.0, temperature 30 °C. 16S rRNA gene affiliated the strain KAs 5-22T to the genus Rhizobium showing maximum similarity (98.4 %) with the type strain of Rhizobium naphthalenivorans TSY03bT followed by (98.0 % similarity) Rhizobium selenitireducens B1T. The genomic G + C content was 59.4 mol%, and DNA-DNA relatedness with its closest phylogenetic neighbors was 50.2 %. Chemotaxonomy indicated UQ-10 as the major quinone; phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; C16:0, C17:0, 2-OH C10:0, 3-OH C16:0, and unresolved C18:1 ɷ7C/ɷ9C as predominant fatty acids. The cells were found to reduce O2, As5+, NO3-, SO42- and Fe3+ as alternate electron acceptors. The strain's ability to metabolize dodecane or other alkanes as sole carbon source using As5+ as terminal electron acceptor was supported by the presence of genes encoding benzyl succinate synthase (bssA like) and molybdopterin-binding site (mopB) of As5+ respiratory reductase (arrA). Differential phenotypic, chemotaxonomic, genotypic as well as physiological properties revealed that the strain KAs 5-22T is separated from its nearest recognized Rhizobium species. On the basis of the data presented, strain KAs 5-22T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium arsenicireducens sp. nov. is proposed as type strain (=LMG 28795T=MTCC 12115T).
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15
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Ren H, Su Y, Zhang J, Pan H, Chen B, Wang Y. Recombinant protein, AlnA, combined with transgenic alfalfa remediates polychlorinated biphenyl-contaminated soils: efficiency and rhizosphere microbial community response. Biotechnol Lett 2016; 38:1893-1901. [PMID: 27432168 DOI: 10.1007/s10529-016-2169-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 06/30/2016] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To investigate the remediation efficiency of polychlorinated biphenyl (PCB)-contaminated soils by the combination of a bioemulsifying protein, AlnA, and alfalfa expressing bphC. RESULT The combination of AlnA and transgenic alfalfa promoted PCB soil remediation through the pot experiments. The removal rates of tri-PCBs (PCB 16/PCB 32 and PCB 31/PCB 28) and tetra-PCB (PCB 49) in transgenic alfalfa/AlnA treatment were 3.6-, 1.1-, and 2-fold higher than in transgenic alfalfa treatment alone. Analysis of gene copy number revealed that the PCB-degrading gene, bphC, of Pseudomonas-like bacterial populations in transgenic alfalfa/AlnA treatment increased 1.5-fold compared with that of unplanted soils. Bacterial community Illumina sequencing showed Pseudomonas, Arthrobacter, and Sphingomonas positively correlated with the removal rates of PCBs. CONCLUSIONS PCB removal was unrelated to bacterial community diversity but positively correlated with their specific degraders and bphC gene expression.
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Affiliation(s)
- Hejun Ren
- Key Laboratory of Groud Water Resources and Environment of the Ministry of Education, College of Environment and Resources, Jilin University, 2519 Jiefang Road, Changchun, 130021, Jilin, People's Republic of China
| | - Yu Su
- Key Laboratory of Groud Water Resources and Environment of the Ministry of Education, College of Environment and Resources, Jilin University, 2519 Jiefang Road, Changchun, 130021, Jilin, People's Republic of China
| | - Junxing Zhang
- College of Plant Sciences, Jilin University, 5333, Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Hongyu Pan
- College of Plant Sciences, Jilin University, 5333, Xi'an Road, Changchun, 130062, Jilin, People's Republic of China
| | - Baoyu Chen
- College of Plant Sciences, Jilin University, 5333, Xi'an Road, Changchun, 130062, Jilin, People's Republic of China.,Research Institute of Agricultural Resources and Environment, Key Laboratory of Plant Nutrition and Agro-Environment in Northeast Region, Jilin Academy of Agricultural Sciences, MOA, Changchun, Jilin, People's Republic of China
| | - Yan Wang
- Key Laboratory of Groud Water Resources and Environment of the Ministry of Education, College of Environment and Resources, Jilin University, 2519 Jiefang Road, Changchun, 130021, Jilin, People's Republic of China. .,College of Plant Sciences, Jilin University, 5333, Xi'an Road, Changchun, 130062, Jilin, People's Republic of China.
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16
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Tang WJ, Zhang LS, Fang Y, Zhou Y, Ye BC. Biodegradation of phthalate esters by newly isolated Rhizobium
sp. LMB-1 and its biochemical pathway of di-n
-butyl phthalate. J Appl Microbiol 2016; 121:177-86. [DOI: 10.1111/jam.13123] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 02/23/2016] [Accepted: 03/04/2016] [Indexed: 11/29/2022]
Affiliation(s)
- W.-J. Tang
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
| | - L.-S. Zhang
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
| | - Y. Fang
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
| | - Y. Zhou
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
| | - B.-C. Ye
- Lab of Biosystems and Microanalysis; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai China
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17
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Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant. Int J Syst Evol Microbiol 2014; 64:3160-3167. [DOI: 10.1099/ijs.0.064154-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19T was distinct from other taxa within the class
Alphaproteobacteria
. Strain E19T showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera
Rhizobium
(≤93.5 %),
Labrenzia
(≤93.1 %),
Stappia
(≤93.1 %),
Aureimonas
(≤93.1 %) and
Mesorhizobium
(≤93.0 %) and was most closely related to
Rhizobium rhizoryzae
(93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19T was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19T ( = LMG 27460T = KACC 17263T).
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Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
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