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Alon M, Waitz Y, Finkel OM, Sheffer E. The native distribution of a common legume shrub is limited by the range of its nitrogen-fixing mutualist. THE NEW PHYTOLOGIST 2024; 242:77-92. [PMID: 38339826 DOI: 10.1111/nph.19577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 01/20/2024] [Indexed: 02/12/2024]
Abstract
Plant-microbe mutualisms, such as the legume-rhizobium symbiosis, are influenced by the geographical distributions of both partners. However, limitations on the native range of legumes, resulting from the absence of a compatible mutualist, have rarely been explored. We used a combination of a large-scale field survey and controlled experiments to determine the realized niche of Calicotome villosa, an abundant and widespread legume shrub. Soil type was a major factor affecting the distribution and abundance of C. villosa. In addition, we found a large region within its range in which neither C. villosa nor Bradyrhizobium, the bacterial genus that associates with it, were present. Seedlings grown in soil from this region failed to nodulate and were deficient in nitrogen. Inoculation of this soil with Bradyrhizobium isolated from root nodules of C. villosa resulted in the formation of nodules and higher growth rate, leaf N and shoot biomass compared with un-inoculated plants. We present evidence for the exclusion of a legume from parts of its native range by the absence of a compatible mutualist. This result highlights the importance of the co-distribution of both the host plant and its mutualist when attempting to understand present and future geographical distributions of legumes.
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Affiliation(s)
- Moshe Alon
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Yoni Waitz
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Omri M Finkel
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Efrat Sheffer
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
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2
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Mousavi SA, Ramula S. The invasive legume Lupinus polyphyllus has minor site-specific impacts on the composition of soil bacterial communities. Ecol Evol 2024; 14:e11030. [PMID: 38357596 PMCID: PMC10864723 DOI: 10.1002/ece3.11030] [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: 03/01/2023] [Revised: 01/26/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Plant invasions can have major impacts on ecosystems, both above- and belowground. In particular, invasions by legumes, which often host nitrogen-fixing symbionts (rhizobia), are known to modify soil bacterial communities. Here, we examined the effect of the invasive herbaceous legume Lupinus polyphyllus on the alpha diversity and community composition of soil bacteria. We also explored the relationships between these bacterial communities and vegetation cover, the cover of other (non-invasive) legumes, or the number of vascular plants present. For this, we sampled rhizosphere soil and surveyed vegetation from ten paired sites (uninvaded versus invaded more than 10 years ago) in southwestern Finland, and identified bacterial DNA using 16S rRNA gene amplicon sequencing. The presence of the plant invader and the three vegetation variables considered had no effect on the alpha diversity of soil bacteria in terms of bacterial richness or Shannon and Inverse Simpson diversity indices. However, the composition of soil bacterial communities differed between invaded and uninvaded soils at four out of the ten sites. Interestingly, the relative abundances of the top bacterial families in invaded and uninvaded soils were inconsistent across sites, including for legume-associated rhizobia in the family Bradyrhizobiaceae. Other factors-such as vegetation cover, legume cover (excluding L. polyphyllus), number of plant species-also explained a small proportion of the variation in bacterial community composition. Our findings indicate that L. polyphyllus has the potential to modify the composition of local soil bacterial community, at least in sites where it has been present for more than a decade.
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Affiliation(s)
| | - Satu Ramula
- Department of BiologyUniversity of TurkuTurkuFinland
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3
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Mpongwana S, Manyevere A, Mupangwa J, Mpendulo CT, Mashamaite CV. Improving soil fertility through dual inoculation with arbuscular mycorrhizal fungi and Rhizobium on a eutric cambisol cultivated with forage legumes in a semi-arid region. Heliyon 2024; 10:e24817. [PMID: 38312554 PMCID: PMC10834816 DOI: 10.1016/j.heliyon.2024.e24817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 02/06/2024] Open
Abstract
The Sub-Saharan region of southern Africa is characterized by high temperatures, low rainfall, and poor land-use management practices such as continuous cropping without replenishment of soil nutrients. The combination of these factors has resulted in nutrient depletion and land degradation. The current study aimed at investigating the effect of arbuscular mycorrhizal fungi (AMF) and Rhizobium bacteria inoculation on soil chemical properties in field-grown forage legumes, namely, Mucuna pruriens (mucuna), Lablab purpureus (lablab) and Vigna unguiculata (cowpea), in the semi-arid region of the Eastern Cape Province (South Africa). Forage legumes were inoculated with the AMF species Paraglomus occulum and the Rhizobia bacteria species Bradyrhizobium strain and grown for 120 days. Soil samples were collected in the following sequence: prior to planting, before flowering and after harvesting the forage legumes in each of the two seasons (2017/2018 and 2018/2019) and soil chemical properties were determined using standard procedures. The results showed that the addition of dual inoculation over time greatly improved soil chemical properties when compared to the control treatment. This was advocated by the significant (P ≤ 0.05) increase in soil pH, soil organic carbon, soil organic matter, total nitrogen, phosphorus, calcium, potassium, magnesium, sodium, sulfur and iron in soils. The concentration of cation exchange capacity was significantly (P ≤ 0.05) higher in cowpea treated with Rhizobium as compared to other treatment combinations. The control treatment of mucuna forage greatly improved the concentrations of manganese, boron, copper, molybdenum, and zinc over other treatment combinations only before the flowering stage. However, the concentrations of micronutrients were significantly higher on the treatment combination of lablab and single inoculation of AMF after harvesting. Generally, dual inoculation with AMF and Rhizobia enhanced soil properties when compared to a single inoculation or untreated control.
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Affiliation(s)
- Sanele Mpongwana
- Department of Livestock and Pasture Science, University of Fort Hare, Private Bag X 1314, Alice 5700, South Africa
| | - Alen Manyevere
- Department of Agronomy, University of Fort Hare, Private Bag X 1314, Alice 5700, South Africa
| | - Johnfisher Mupangwa
- Department of Livestock and Pasture Science, University of Fort Hare, Private Bag X 1314, Alice 5700, South Africa
- Department of Animal Production, Agribusiness & Economics, University of Namibia, Neudamm Campus, Private Bag 13188, Windhoek, Namibia
| | - Conference Thando Mpendulo
- Department of Livestock and Pasture Science, University of Fort Hare, Private Bag X 1314, Alice 5700, South Africa
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NIANG D, GUEDDOU A, NIANG N, NZEPANG D, SAMBOU A, DIOUF A, ZAIYA AZ, CISSOKO M, GULLY D, NGUEPJOP JR, SVISTOONOFF S, FONCEKA D, HOCHER V, DIOUF D, FALL S, TISA LS. Permanent draft genome sequence of Bradyrhizobium vignae, strain ISRA 400, an elite nitrogen-fixing bacterium, isolated from the groundnut growing area in Senegal. J Genomics 2023; 11:52-57. [PMID: 37915957 PMCID: PMC10615618 DOI: 10.7150/jgen.88302] [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: 07/21/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
A new Bradyrhizobium vignae strain called ISRA400 was isolated from groundnut (Arachis hypogaea L.) root nodules obtained by trapping the bacteria from soil samples collected in the Senegalese groundnut basin. In this study, we present the draft genome sequence of this strain ISRA400, which spans approximatively 7.9 Mbp and exhibits a G+C content of 63.4%. The genome analysis revealed the presence of 48 tRNA genes and one rRNA operon (16S, 23S, and 5S). The nodulation test revealed that this strain ISRA400 significantly improves the nodulation parameters and chlorophyll content of the Arachis hypogaea variety Fleur11. These findings suggest the potential of Bradyrhizobium vignae strain ISRA400 as an effective symbiotic partner for improving the growth and productivity of groundnut crop.
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Affiliation(s)
- Diariatou NIANG
- Université Cheikh Anta Diop (UCAD/FST), Département de Biologie Végétale, École doctorale Sciences de la Vie, de la Santé et de l'Environnement (EDSEV), B.P.: 5005 Dakar-Fann, Senegal
- Institut Sénégalais de Recherche Agricole (ISRA), Laboratoire National de Recherches sur la Productions Végétales (LNRPV), Campus ISRA-IRD de Bel air, Dakar
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
| | - Abdellatif GUEDDOU
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Nogaye NIANG
- Université Cheikh Anta Diop (UCAD/FST), Département de Biologie Végétale, École doctorale Sciences de la Vie, de la Santé et de l'Environnement (EDSEV), B.P.: 5005 Dakar-Fann, Senegal
- Institut Sénégalais de Recherche Agricole (ISRA), Laboratoire National de Recherches sur la Productions Végétales (LNRPV), Campus ISRA-IRD de Bel air, Dakar
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
| | - Darius NZEPANG
- Université Cheikh Anta Diop (UCAD/FST), Département de Biologie Végétale, École doctorale Sciences de la Vie, de la Santé et de l'Environnement (EDSEV), B.P.: 5005 Dakar-Fann, Senegal
- Institut Sénégalais de Recherche Agricole (ISRA), Laboratoire National de Recherches sur la Productions Végétales (LNRPV), Campus ISRA-IRD de Bel air, Dakar
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Aissatou SAMBOU
- Institut Sénégalais de Recherche Agricole (ISRA), Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse, CERAAS - Route de Khombole, BP3320 Thiès, Senegal
| | - Adama DIOUF
- Université Cheikh Anta Diop (UCAD/FST), Département de Biologie Végétale, École doctorale Sciences de la Vie, de la Santé et de l'Environnement (EDSEV), B.P.: 5005 Dakar-Fann, Senegal
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
| | - Arlette Z ZAIYA
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
- Institut Sénégalais de Recherche Agricole (ISRA), Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse, CERAAS - Route de Khombole, BP3320 Thiès, Senegal
- Present address: Institute of Agricultural Research for Development (IRAD), Yaounde, Cameroon
| | - Maimouna CISSOKO
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
| | - Djamel GULLY
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
| | - Joel-Romaric NGUEPJOP
- Institut Sénégalais de Recherche Agricole (ISRA), Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse, CERAAS - Route de Khombole, BP3320 Thiès, Senegal
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
- CIRAD, UMRAGAP, CIRAD/Univ Montpellier/ INRAE, Institut Agro, F-34398 Montpellier, France
| | - Sergio SVISTOONOFF
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
| | - Daniel FONCEKA
- Institut Sénégalais de Recherche Agricole (ISRA), Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse, CERAAS - Route de Khombole, BP3320 Thiès, Senegal
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
- CIRAD, UMRAGAP, CIRAD/Univ Montpellier/ INRAE, Institut Agro, F-34398 Montpellier, France
| | - Valérie HOCHER
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
- Institut de Recherche pour le Développement (IRD), UMR PHIM IRD/INRAE/CIRAD/U.Montpellier/Institut Agro , Montpellier, France
| | - Diégane DIOUF
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
- Université du Sine Saloum El Hadj Ibrahima Niass (USSEIN), UFR Sciences sociales et environnementales, Centre d'Excellence Africain "Agriculture pour la Sécurité Alimentaire et Nutritionnelle" (CEA-AGRISAN), Kaolack
| | - Saliou FALL
- Institut Sénégalais de Recherche Agricole (ISRA), Laboratoire National de Recherches sur la Productions Végétales (LNRPV), Campus ISRA-IRD de Bel air, Dakar
- Laboratoire Commun de Microbiologie (LCM: IRD - ISRA - UCAD), B. P. 3120, Campus ISRA-IRD de Bel air, Dakar
| | - Louis S. TISA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Claassens R, Venter SN, Beukes CW, Stępkowski T, Chan WY, Steenkamp ET. Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa. Syst Appl Microbiol 2023; 46:126452. [PMID: 37634485 DOI: 10.1016/j.syapm.2023.126452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023]
Abstract
A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1T, B. betae PL7HG1T, B. ganzhouense CCBAU 51670 T, B. cytisi CTAW11T and B. rifense CTAW71T) resulted in values well below 95-96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14ABT (=LMG 31415 T = SARCC-753 T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.
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Affiliation(s)
- Ricu Claassens
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa
| | | | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Poland
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa; Right to Care, Centurion, Gauteng, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa.
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Pulido-Suárez L, Notario Del Pino J, Díaz-Peña FJ, Perdomo-González A, González-Rodríguez ÁM, León-Barrios M. High Diversity of Bradyrhizobial Species Fix Nitrogen with Woody Legume Spartocytisus supranubius in a High Mountain Ecosystem. Microorganisms 2023; 11:1244. [PMID: 37317218 DOI: 10.3390/microorganisms11051244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
The symbiosis between rhizobia and legumes is of pivotal importance in nitrogen-poor ecosystems. Furthermore, as it is a specific process (most legumes only establish a symbiosis with certain rhizobia), it is of great interest to know which rhizobia are able to nodulate key legumes in a specific habitat. This study describes the diversity of the rhizobia that are able to nodulate the shrub legume Spartocytisus supranubius in the harsh environmental conditions of the high mountain ecosystem of Teide National Park (Tenerife). The diversity of microsymbionts nodulating S. supranubius was estimated from a phylogenetic analysis of root nodule bacteria isolated from soils at three selected locations in the park. The results showed that a high diversity of species of Bradyrhizobium and two symbiovars can nodulate this legume. Phylogenies of ribosomal and housekeeping genes showed these strains distributed into three main clusters and a few isolates on separate branches. These clusters consist of strains representing three new phylogenetic lineages of the genus Bradyrhizobium. Two of these lineages belong to the B. japonicum superclade, which we refer to as B. canariense-like and B. hipponense-like, as the type strains of these species are the closest species to our isolates. The third main group was clustered within the B. elkanii superclade and is referred to as B. algeriense-like as B. algeriense is its closest species. This is the first time that bradyrhizobia of the B. elkanii superclade have been reported for the canarian genista. Furthermore, our results suggest that these three main groups might belong to potential new species of the genus Bradyrhizobium. Analysis of the soil physicochemical properties of the three study sites showed some significant differences in several parameters, which, however, did not have a major influence on the distribution of bradyrhizobial genotypes at the different locations. The B. algeriense-like group had a more restrictive distribution pattern, while the other two lineages were detected in all of the soils. This suggests that the microsymbionts are well adapted to the harsh environmental conditions of Teide National Park.
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Affiliation(s)
- Laura Pulido-Suárez
- Department of Biochemistry, Microbiology, Genetics and Cellular Biology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Jesús Notario Del Pino
- Department of Animal Biology, Soil Science and Geology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Francisco J Díaz-Peña
- Department of Animal Biology, Soil Science and Geology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Adolfo Perdomo-González
- Department of Animal Biology, Soil Science and Geology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Águeda M González-Rodríguez
- Department of Botany, Ecology and Plant Physiology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Milagros León-Barrios
- Department of Biochemistry, Microbiology, Genetics and Cellular Biology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
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Msaddak A, Mars M, Quiñones MA, Lucas MM, Pueyo JJ. Lupin, a Unique Legume That Is Nodulated by Multiple Microsymbionts: The Role of Horizontal Gene Transfer. Int J Mol Sci 2023; 24:ijms24076496. [PMID: 37047476 PMCID: PMC10094711 DOI: 10.3390/ijms24076496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Lupin is a high-protein legume crop that grows in a wide range of edaphoclimatic conditions where other crops are not viable. Its unique seed nutrient profile can promote health benefits, and it has been proposed as a phytoremediation plant. Most rhizobia nodulating Lupinus species belong to the genus Bradyrhizobium, comprising strains that are phylogenetically related to B. cytisi, B. hipponenese, B. rifense, B. iriomotense/B. stylosanthis, B. diazoefficiens, B. japonicum, B. canariense/B. lupini, and B. retamae/B. valentinum. Lupins are also nodulated by fast-growing bacteria within the genera Microvirga, Ochrobactrum, Devosia, Phyllobacterium, Agrobacterium, Rhizobium, and Neorhizobium. Phylogenetic analyses of the nod and nif genes, involved in microbial colonization and symbiotic nitrogen fixation, respectively, suggest that fast-growing lupin-nodulating bacteria have acquired their symbiotic genes from rhizobial genera other than Bradyrhizobium. Horizontal transfer represents a key mechanism allowing lupin to form symbioses with bacteria that were previously considered as non-symbiotic or unable to nodulate lupin, which might favor lupin’s adaptation to specific habitats. The characterization of yet-unstudied Lupinus species, including microsymbiont whole genome analyses, will most likely expand and modify the current lupin microsymbiont taxonomy, and provide additional knowledge that might help to further increase lupin’s adaptability to marginal soils and climates.
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Affiliation(s)
- Abdelhakim Msaddak
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia
| | - Mohamed Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia
| | - Miguel A. Quiñones
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
| | - M. Mercedes Lucas
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
| | - José J. Pueyo
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
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8
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Liebrenz K, Gómez C, Brambilla S, Frare R, Stritzler M, Maguire V, Ruiz O, Soldini D, Pascuan C, Soto G, Ayub N. Whole-Genome Resequencing of Spontaneous Oxidative Stress-Resistant Mutants Reveals an Antioxidant System of Bradyrhizobium japonicum Involved in Soybean Colonization. MICROBIAL ECOLOGY 2022; 84:1133-1140. [PMID: 34782938 DOI: 10.1007/s00248-021-01925-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Soybean is the most inoculant-consuming crop in the world, carrying strains belonging to the extremely related species Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens. Currently, it is well known that B. japonicum has higher efficiency of soybean colonization than B. diazoefficiens, but the molecular mechanism underlying this differential symbiotic performance remains unclear. In the present study, genome resequencing of four spontaneous oxidative stress-resistant mutants derived from the commercial strain B. japonicum E109 combined with molecular and physiological studies allowed identifying an antioxidant cluster (BjAC) containing a transcriptional regulator (glxA) that controls the expression of a catalase (catA) and a phosphohydrolase (yfbR) related to the hydrolysis of hydrogen peroxide and oxidized nucleotides, respectively. Integrated synteny and phylogenetic analyses supported the fact that BjAC emergence in the B. japonicum lineage occurred after its divergence from the B. diazoefficiens lineage. The transformation of the model bacterium B. diazoefficiens USDA110 with BjAC from E109 significantly increased its ability to colonize soybean roots, experimentally recapitulating the beneficial effects of the occurrence of BjAC in B. japonicum. In addition, the glxA mutation significantly increased the nodulation competitiveness and plant growth-promoting efficiency of E109. Finally, the potential applications of these types of non-genetically modified mutant microbes in soybean production worldwide are discussed.
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Affiliation(s)
- Karen Liebrenz
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Cristina Gómez
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Silvina Brambilla
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Romina Frare
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Margarita Stritzler
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Vanina Maguire
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Oscar Ruiz
- Instituto Tecnológico Chascomús (INTECH-CONICET), Buenos Aires, Argentina
| | - Diego Soldini
- Estación Experimental Agropecuaria Marcos Juárez, INTA, Córdoba, Argentina
| | - Cecilia Pascuan
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Nicolás Ayub
- Instituto de Agrobiotecnología Y Biología Molecular (INTA-CONICET), Buenos Aires, Argentina.
- Instituto de Genética (IGEAF), INTA, De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina.
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9
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Tighilt L, Boulila F, De Sousa BFS, Giraud E, Ruiz-Argüeso T, Palacios JM, Imperial J, Rey L. The Bradyrhizobium Sp. LmicA16 Type VI Secretion System Is Required for Efficient Nodulation of Lupinus Spp. MICROBIAL ECOLOGY 2022; 84:844-855. [PMID: 34697646 DOI: 10.1007/s00248-021-01892-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/30/2021] [Indexed: 05/06/2023]
Abstract
Many bacteria of the genus Bradyrhizobium are capable of inducing nodules in legumes. In this work, the importance of a type VI secretion system (T6SS) in a symbiotic strain of the genus Bradyrhizobium is described. T6SS of Bradyrhizobium sp. LmicA16 (A16) is necessary for efficient nodulation with Lupinus micranthus and Lupinus angustifolius. A mutant in the gene vgrG, coding for a component of the T6SS nanostructure, induced less nodules and smaller plants than the wild-type (wt) strain and was less competitive when co-inoculated with the wt strain. A16 T6SS genes are organized in a 26-kb DNA region in two divergent gene clusters of nine genes each. One of these genes codes for a protein (Tsb1) of unknown function but containing a methyltransferase domain. A tsb1 mutant showed an intermediate symbiotic phenotype regarding vgrG mutant and higher mucoidity than the wt strain in free-living conditions. T6SS promoter fusions to the lacZ reporter indicate expression in nodules but not in free-living cells grown in different media and conditions. The analysis of nodule structure revealed that the level of nodule colonization was significantly reduced in the mutants with respect to the wt strain.
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Affiliation(s)
- L Tighilt
- Laboratoire d'Ecologie Microbienne, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, 06000, Bejaia, Algeria
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
| | - F Boulila
- Laboratoire d'Ecologie Microbienne, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, 06000, Bejaia, Algeria
| | - B F S De Sousa
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - E Giraud
- IRD, Laboratoire Des Symbioses Tropicales Et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J-Campus International de Baillarguet, 34398Cedex 5, Montpellier, France
| | - T Ruiz-Argüeso
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - J M Palacios
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - J Imperial
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Instituto de Ciencias Agrarias, CSIC, 28006, Madrid, Spain
| | - L Rey
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain.
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain.
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10
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Kawaka F. Characterization of symbiotic and nitrogen fixing bacteria. AMB Express 2022; 12:99. [PMID: 35907164 PMCID: PMC9339069 DOI: 10.1186/s13568-022-01441-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
Symbiotic nitrogen fixing bacteria comprise of diverse species associated with the root nodules of leguminous plants. Using an appropriate taxonomic method to confirm the identity of superior and elite strains to fix nitrogen in legume crops can improve sustainable global food and nutrition security. The current review describes taxonomic methods preferred and commonly used to characterize symbiotic bacteria in the rhizosphere. Peer reviewed, published and unpublished articles on techniques used for detection, classification and identification of symbiotic bacteria were evaluated by exploring their advantages and limitations. The findings showed that phenotypic and cultural techniques are still affordable and remain the primary basis of species classification despite their challenges. Development of new, robust and informative taxonomic techniques has really improved characterization and identification of symbiotic bacteria and discovery of novel and new species that are effective in biological nitrogen fixation (BNF) in diverse conditions and environments.
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Affiliation(s)
- Fanuel Kawaka
- Department of Biological Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210-40601, Bondo, Kenya.
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11
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Adjei JA, Aserse AA, Yli-Halla M, Ahiabor BDK, Abaidoo RC, Lindstrom K. Phylogenetically diverse Bradyrhizobium genospecies nodulate Bambara groundnut (Vigna subterranea L. Verdc) and soybean (Glycine max L. Merril) in the northern savanna zones of Ghana. FEMS Microbiol Ecol 2022; 98:fiac043. [PMID: 35404419 PMCID: PMC9329091 DOI: 10.1093/femsec/fiac043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
A total of 102 bacterial strains isolated from nodules of three Bambara groundnut and one soybean cultivars grown in nineteen soil samples collected from northern Ghana were characterized using multilocus gene sequence analysis. Based on a concatenated sequence analysis (glnII-rpoB-recA-gyrB-atpD-dnaK), 54 representative strains were distributed in 12 distinct lineages, many of which were placed mainly in the Bradyrhizobium japonicum and Bradyrhizobium elkanii supergroups. Twenty-four of the 54 representative strains belonged to seven putative novel species, while 30 were conspecific with four recognized Bradyrhizobium species. The nodA phylogeny placed all the representative strains in the cosmopolitan nodA clade III. The strains were further separated in seven nodA subclusters with reference strains mainly of African origin. The nifH phylogeny was somewhat congruent with the nodA phylogeny, but both symbiotic genes were mostly incongruent with the core housekeeping gene phylogeny indicating that the strains acquired their symbiotic genes horizontally from distantly related Bradyrhizobium species. Using redundancy analysis, the distribution of genospecies was found to be influenced by the edaphic factors of the respective sampling sites. In general, these results mainly underscore the high genetic diversity of Bambara groundnut-nodulating bradyrhizobia in Ghanaian soils and suggest a possible vast resource of adapted inoculant strains.
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Affiliation(s)
- Josephine A Adjei
- Department of Crop and Soil Sciences, Faculty of Agriculture, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana
- Faculty of Biological and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, PO Box 52, Tamale, Ghana
| | - Aregu A Aserse
- Faculty of Biological and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Markku Yli-Halla
- Department of Agricultural Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Benjamin D K Ahiabor
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, PO Box 52, Tamale, Ghana
| | - Robert C Abaidoo
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana
- International Institute of Tropical Agriculture, PMB 5320, Ibadan, Nigeria
| | - Kristina Lindstrom
- Faculty of Biological and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
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12
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Sun L, Zhang Z, Dong X, Tang Z, Ju B, Du Z, Wang E, Xie Z. Bradyrhizobium aeschynomenes sp. nov., a root and stem nodule microsymbiont of Aeschynomene indica. Syst Appl Microbiol 2022; 45:126337. [DOI: 10.1016/j.syapm.2022.126337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/15/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022]
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13
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Phylogenetic and symbiotic diversity of Lupinus albus and L. angustifolius microsymbionts in the maamora forest, morocco. Syst Appl Microbiol 2022; 45:126338. [DOI: 10.1016/j.syapm.2022.126338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/28/2022] [Accepted: 05/23/2022] [Indexed: 11/22/2022]
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14
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Dependence on Nitrogen Availability and Rhizobial Symbiosis of Different Accessions of Trifolium fragiferum, a Crop Wild Relative Legume Species, as Related to Physiological Traits. PLANTS 2022; 11:plants11091141. [PMID: 35567142 PMCID: PMC9099520 DOI: 10.3390/plants11091141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022]
Abstract
Biological nitrogen fixation by legume-rhizobacterial symbiosis in temperate grasslands is an important source of soil nitrogen. The aim of the present study was to characterize the dependence of different accessions of T. fragiferum, a rare crop wild relative legume species, from their native rhizobia as well as additional nitrogen fertilization in controlled conditions. Asymbiotically cultivated, mineral-fertilized T. fragiferum plants gradually showed signs of nitrogen deficiency, appearing as a decrease in leaf chlorophyll concentration, leaf senescence, and a decrease in growth rate. The addition of nitrogen, and the inoculation with native rhizobia, or both treatments significantly prevented the onset of these symptoms, leading to both increase in plant shoot biomass as well as an increase in tissue concentration of N. The actual degree of each type of response was genotype-specific. Accessions showed a relatively similar degree of dependence on nitrogen (70–95% increase in shoot dry mass) but the increase in shoot dry mass by inoculation with native rhizobia ranged from 27 to 85%. In general, there was no correlation between growth stimulation and an increase in tissue N concentration by the treatments. The addition of N or rhizobial inoculant affected mineral nutrition at the level of both macronutrient and micronutrient concentration in different plant parts. In conclusion, native rhizobial strains associated with geographically isolated accessions of T. fragiferum at the northern range of distribution of the species represent a valuable resource for further studies aimed at the identification of salinity-tolerant N2-fixing bacteria for the needs of sustainable agriculture, as well as in a view of understanding ecosystem functioning at the level of plant-microorganism interactions.
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15
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Warrington S, Ellis AG, Keet JH, Le Roux JJ. How does familiarity in rhizobial interactions impact the performance of invasive and native legumes? NEOBIOTA 2022. [DOI: 10.3897/neobiota.72.79620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mutualisms can be disrupted when non-native plants are introduced into novel environments, potentially impacting their establishment success. Introduced species can reassemble mutualisms by forming novel associations with resident biota or by maintaining familiar associations when they are co-introduced with their mutualists. Invasive Australian Acacia species in South Africa have formed nitrogen-fixing rhizobium mutualisms using both pathways.
Here we examined the contributions of novel vs familiar rhizobial associations to the performance of Acacia saligna across different soils within South Africa’s Core Cape Subregion (CCR), and the concomitant impacts of exotic rhizobia on the endemic legume, Psoralea pinnata. We grew each legume with and without Australian Bradyrhizobium strains across various CCR soil types in a glasshouse. We identified root nodule rhizobium communities associating with seedlings grown in each treatment combination using next-generation sequencing (NGS) techniques.
Our results show that different CCR soils affected growth performances of seedlings for both species while the addition of Australian bradyrhizobia affected growth performances of A. saligna, but not P. pinnata. NGS data revealed that each legume associated mostly with their familiar rhizobial partners, regardless of soil conditions or inoculum treatment. Acacia saligna predominantly associated with Australian bradyrhizobia, even when grown in soils without inoculum, while P. pinnata largely associated with native South African Mesorhizobium strains.
Our study suggests that exotic Australian bradyrhizobia are already present and widespread in pristine CCR soils, and that mutualist limitation is not an impediment to further acacia invasion in the region. The ability of P. pinnata to sanction Australian Bradyrhizobium strains suggests that this species may be a good candidate for restoration efforts following the removal of acacias in CCR habitats.
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16
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Invasional meltdown via horizontal gene transfer of a European symbiosis island variant in North American nodule symbionts of Cytisus scoparius. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02776-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Mavima L, Beukes CW, Palmer M, De Meyer SE, James EK, Maluk M, Muasya MA, Avontuur JR, Yin Chan W, Venter SN, Steenkamp ET. Delineation of Paraburkholderia tuberum sensu stricto and description of Paraburkholderia podalyriae sp. nov. nodulating the South African legume Podalyria calyptrata. Syst Appl Microbiol 2022; 45:126316. [DOI: 10.1016/j.syapm.2022.126316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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18
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Avontuur JR, Palmer M, Beukes CW, Chan WY, Tasiya T, van Zyl E, Coetzee MPA, Stepkowski T, Venter SN, Steenkamp ET. Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns. Mol Phylogenet Evol 2021; 167:107338. [PMID: 34757168 DOI: 10.1016/j.ympev.2021.107338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/22/2021] [Accepted: 10/27/2021] [Indexed: 10/20/2022]
Abstract
Africa is known for its rich legume diversity with a significant number of endemic species originating in South Africa. Many of these legumes associate with rhizobial symbionts of the genus Bradyrhizobium, of which most represent new species. Yet, none of the Bradyrhizobium species from South Africa have been described. In this study, phylogenetic analysis of 16S rRNA gene sequences of fourteen strains isolated in southern Africa from root nodules of diverse legumes (i.e., from the tribes Crotalarieae, Acacieae, Genisteae, Phaseoleae and Cassieae) revealed that they belong to the Bradyrhizobium elkanii supergroup. The taxonomic position and possible novelty of these strains were further interrogated using genealogical concordance of five housekeeping genes (atpD, dnaK, glnII, gyrB and rpoB). These phylogenies consistently recovered four monophyletic groups and one singleton within Bradyrhizobium. Of these groups, two were conspecific with Bradyrhizobium brasilense UFLA 03-321T and Bradyrhizobium ivorense CI-1BT, while the remaining three represented novel taxa. Their existence was further supported with genome data, as well as metabolic and physiological traits. Analysis of nodA gene sequences further showed that the evolution of these bacteria likely involved adapting to local legume hosts and environmental conditions through the acquisition, via horizontal gene transfer, of optimal symbiotic loci. We accordingly propose the following names Bradyrhizobium acaciae sp. nov. 10BBT (SARCC 730T = LMG 31409T), Bradyrhizobium oropedii sp. nov. Pear76T (SARCC 731T = LMG 31408T), and Bradyrhizobium altum sp. nov. Pear77T (SARCC 754T = LMG 31407T) to accommodate three novel species, all of which are symbionts of legumes in South Africa.
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Affiliation(s)
- Juanita R Avontuur
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, United States
| | - Chrizelle W Beukes
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa; National Institute for Communicable Disease, National Health Laboratory Service, Johannesburg, South Africa
| | - Taponeswa Tasiya
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Elritha van Zyl
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tomasz Stepkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Poland
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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19
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Piedra-García D, Struck C. Lupin Root Weevils ( Charagmus spp., Curculionidae: Sitonini), a Lupin Pest: A Review of Their Distribution, Biology, and Challenges in Integrated Pest Management. INSECTS 2021; 12:insects12100950. [PMID: 34680719 PMCID: PMC8540778 DOI: 10.3390/insects12100950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022]
Abstract
Lupins (Lupinus spp.) are an ancient yet important legume crop. In Europe, the protein-rich seeds serve as livestock feed and have the potential to be a healthy vegetarian component of human diets. In some regions in north-eastern Europe, lupins are heavily damaged by two Curculionidae species, the lupin root weevils (LRWs) Charagmus gressorius (syn. Sitona gressorius) and Ch. griseus (syn. S. griseus). Narrow-leaved lupins (L. angustifolius) and white lupins (L. albus) are most affected. The weevils feed on lupin leaves, whereas their larvae feed on root nodules. Therefore, the larvae cause major root damage by creating lacerations that allow soil-borne plant pathogens to enter the plant tissue. These infestations lead to considerable yield losses and markedly reduced N-fixation of the root nodules. This review summarises the current knowledge on the origin, geographical distribution, and biology of these rarely described weevils. It focuses on management strategies, including preconceived insecticide use and potential ecological management methods, as key components of an integrated pest management programme against LRWs in Europe.
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20
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Zhao YX, Guo L, Wang L, Jiang ND, Chen KX, Dai YJ. Biodegradation of the pyridinecarboxamide insecticide flonicamid by Microvirga flocculans and characterization of two novel amidases involved. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112384. [PMID: 34091185 DOI: 10.1016/j.ecoenv.2021.112384] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/11/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
Flonicamid (N-cyanomethyl-4-trifluoromethylnicotinamide, FLO) is a new type of pyridinecarboxamide insecticide that exhibits particularly good efficacy in pest control. However, the extensive use of FLO in agricultural production poses environmental risks. Hence, its environmental behavior and degradation mechanism have received increasing attention. Microvirga flocculans CGMCC 1.16731 rapidly degrades FLO to produce the intermediate N-(4-trifluoromethylnicotinoyl) glycinamide (TFNG-AM) and the end acid metabolite 4-(trifluoromethyl) nicotinol glycine (TFNG). This bioconversion is mediated by the nitrile hydratase/amidase system; however, the amidase that is responsible for the conversion of TFNG-AM to TFNG has not yet been reported. Here, gene cloning, overexpression in Escherichia coli and characterization of pure enzymes showed that two amidases-AmiA and AmiB-hydrolyzed TFNG-AM to TFNG. AmiA and AmiB showed only 20-30% identity to experimentally characterized amidase signature family members, and represent novel amidases. Compared with AmiA, AmiB was more sensitive to silver and copper ions but more resistant to organic solvents. Both enzymes demonstrated good pH tolerance and exhibited broad amide substrate specificity. Homology modeling suggested that residues Asp191 and Ser195 may strongly affect the catalytic activity of AmiA and AmiB, respectively. The present study furthers our understanding of the enzymatic mechanisms of biodegradation of nitrile-containing insecticides and may aid in the development of a bioremediation agent for FLO.
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Affiliation(s)
- Yun-Xiu Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Ling Guo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Li Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Neng-Dang Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Ke-Xin Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Yi-Jun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
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21
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Gnangui SLE, Fossou RK, Ebou A, Amon CER, Koua DK, Kouadjo CGZ, Cowan DA, Zézé A. The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire. Microorganisms 2021; 9:microorganisms9091842. [PMID: 34576737 PMCID: PMC8472840 DOI: 10.3390/microorganisms9091842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/17/2021] [Accepted: 08/21/2021] [Indexed: 01/04/2023] Open
Abstract
Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.
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Affiliation(s)
- Sara Laetitia Elphège Gnangui
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
| | - Romain Kouakou Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
- Correspondence:
| | - Anicet Ebou
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
- Équipe Bioinformatique, Département de Formation et de Recherche Agriculture et Ressources Animales, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro 1313, Côte d’Ivoire;
| | - Chiguié Estelle Raïssa Amon
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
| | - Dominique Kadio Koua
- Équipe Bioinformatique, Département de Formation et de Recherche Agriculture et Ressources Animales, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro 1313, Côte d’Ivoire;
| | - Claude Ghislaine Zaka Kouadjo
- Laboratoire Central de Biotechnologies, Centre National de la Recherche Agronomique, 01 Abidjan 1740, Côte d’Ivoire;
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
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22
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Zhao YX, Wang L, Chen KX, Jiang ND, Sun SL, Ge F, Dai YJ. Biodegradation of flonicamid by Ensifer adhaerens CGMCC 6315 and enzymatic characterization of the nitrile hydratases involved. Microb Cell Fact 2021; 20:133. [PMID: 34256737 PMCID: PMC8278588 DOI: 10.1186/s12934-021-01620-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flonicamid (N-cyanomethyl-4-trifluoromethylnicotinamide, FLO) is a new type of pyridinamide insecticide that regulates insect growth. Because of its wide application in agricultural production and high solubility in water, it poses potential risks to aquatic environments and food chain. RESULTS In the present study, Ensifer adhaerens CGMCC 6315 was shown to efficiently transform FLO into N-(4-trifluoromethylnicotinoyl) glycinamide (TFNG-AM) via a hydration pathway mediated by two nitrile hydratases, PnhA and CnhA. In pure culture, resting cells of E. adhaerens CGMCC 6315 degraded 92% of 0.87 mmol/L FLO within 24 h at 30 °C (half-life 7.4 h). Both free and immobilized (by gel beads, using calcium alginate as a carrier) E. adhaerens CGMCC 6315 cells effectively degraded FLO in surface water. PnhA has, to our knowledge, the highest reported degradation activity toward FLO, Vmax = 88.7 U/mg (Km = 2.96 mmol/L). Addition of copper ions could increase the enzyme activity of CnhA toward FLO by 4.2-fold. Structural homology modeling indicated that residue β-Glu56 may be important for the observed significant difference in enzyme activity between PnhA and CnhA. CONCLUSIONS Application of E. adhaerens may be a good strategy for bioremediation of FLO in surface water. This work furthers our understanding of the enzymatic mechanisms of biodegradation of nitrile-containing insecticides and provides effective transformation strategies for microbial remediation of FLO contamination.
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Affiliation(s)
- Yun-Xiu Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Li Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Ke-Xin Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Neng-Dang Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China
| | - Shi-Lei Sun
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou, 221116, People's Republic of China
| | - Feng Ge
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing, 210042, People's Republic of China.
| | - Yi-Jun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, 210023, People's Republic of China.
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23
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Culture-independent assessment of the diazotrophic Bradyrhizobium communities in the Pampa and Atlantic Forest Biomes localities in southern Brazil. Syst Appl Microbiol 2021; 44:126228. [PMID: 34265499 DOI: 10.1016/j.syapm.2021.126228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023]
Abstract
The isolation of rhizobial strains from the root and stem nodules remains a commonly used method despite its limitations as it enables the identification of mainly dominant symbiotic groups within rhizobial communities. To overcome these limitations, we used genus-specific nifD primers in a culture-independent assessment of Bradyrhizobium communities inhabiting soils in southern Brazil. The majority of nifD sequences were generated from DNA isolated from tropical-lowland pasture soils, although some soil samples originated from the Campos de Cima da Serra volcanic plateau. In the nifD tree, all the bradyrhizobial sequences comprised 38 clades, including 18 new clades. The sequences generated in this study were resolved into 22 clades and 21 singletons. The nifD bradyrhizobial assemblage contained Azorhizobium and α-proteobacterial methylotrophic genera, suggesting that these genera may have acquired their nif loci from Bradyrhizobium donors. The most common in the lowland pasture soils subclade III.3D branch comprises the isolates of mainly an American origin. On the other hand, subclade III.4, which was earlier detected in Brazil among Bradyrhizobium isolates nodulating native lupins, appears more common in the Campos de Cima da Serra soils. The second-largest group, Clade XXXVIII, has not yet been reported in culture-dependent studies, while another common group called Clade I represents a symbiovar predominating in Australia. The identification of the diverse nifD Clade I haplotypes in the tropical-lowland pastures infested by Australian Acacia spp implies that the introduction of these legumes to southern Brazil has resulted in the dissemination of their bradyrhizobial symbionts.
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24
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Banasiewicz J, Granada CE, Lisboa BB, Grzesiuk M, Matuśkiewicz W, Bałka M, Schlindwein G, Vargas LK, Passaglia LMP, Stępkowski T. Diversity and phylogenetic affinities of Bradyrhizobium isolates from Pampa and Atlantic Forest Biomes. Syst Appl Microbiol 2021; 44:126203. [PMID: 33857759 DOI: 10.1016/j.syapm.2021.126203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
In this work, we investigated Bradyrhizobium strains isolated from soils collected from the rhizosphere of native and exotic legumes species inhabiting two ecoclimatic zones - asubtropical-lowland pasture (Pampa Biome) and a volcanic plateau covered by Araucaria Moist Forests (Atlantic Forest Biome). The rhizobial strains were isolated from the nodules of seven native and one exotic legume species used as rhizobium traps. Single-gene (recA, glnII, dnaK) and combined-gene MLSA analyses (dnaK-glnII-gyrB-recA-rpoB) revealed that nearly 85% of the isolates clustered in B. elkanii supergroup, while the remaining (except for two isolates) in B. japonicum supergroup, albeit, in most cases, separately from the type strains of Bradyrhizobium species. As a symbiotic gene marker, a portion of nifD gene was sequenced for 194 strains. In the nifD-tree, an American branch III.3D (104 isolates), was the most numerous among the isolates. A significant portion of the isolates clustered in American groups; subclade III.4 (40 strains), Clade VII (3 strains), and a new Clade XX (4 strains). Most of the remaining strains belonged to a pantropical III.3C branch (39 isolates). On the other hand, identification of isolates belonging, respectively, to Clade I and Clade II may result of spreading of the Australian (Clade I) and European (Clade II) bradyrhizobia following the introduction of their legume hosts. Our study indicated that the American groups predominated in the symbiotic Bradyrhizobium communities in southern Brazil. However, there is a significant component of exotic lineages, resulting from the dispersal of pantropical Fabaceae taxa and the introduction of exotic legumes.
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Affiliation(s)
- Joanna Banasiewicz
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Camille E Granada
- Universidade do Vale do Taquari - UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil
| | - Bruno B Lisboa
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060 Porto Alegre, RS, Brazil
| | - Małgorzata Grzesiuk
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Weronika Matuśkiewicz
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Mateusz Bałka
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Gilson Schlindwein
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060 Porto Alegre, RS, Brazil
| | - Luciano K Vargas
- Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Rua Gonçalves Dias 570, 90130-060 Porto Alegre, RS, Brazil
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul., Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil
| | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
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25
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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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26
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Losi A, Gärtner W. A light life together: photosensing in the plant microbiota. Photochem Photobiol Sci 2021; 20:451-473. [PMID: 33721277 DOI: 10.1007/s43630-021-00029-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022]
Abstract
Bacteria and fungi of the plant microbiota can be phytopathogens, parasites or symbionts that establish mutually advantageous relationships with plants. They are often rich in photoreceptors for UVA-Visible light, and in many cases, they exhibit light regulation of growth patterns, infectivity or virulence, reproductive traits, and production of pigments and of metabolites. In addition to the light-driven effects, often demonstrated via the generation of photoreceptor gene knock-outs, microbial photoreceptors can exert effects also in the dark. Interestingly, some fungi switch their attitude towards plants in dependence of illumination or dark conditions in as much as they may be symbiotic or pathogenic. This review summarizes the current knowledge about the roles of light and photoreceptors in plant-associated bacteria and fungi aiming at the identification of common traits and general working ideas. Still, reports on light-driven infection of plants are often restricted to the description of macroscopically observable phenomena, whereas detailed information on the molecular level, e.g., protein-protein interaction during signal transduction or induction mechanisms of infectivity/virulence initiation remains sparse. As it becomes apparent from still only few molecular studies, photoreceptors, often from the red- and the blue light sensitive groups interact and mutually modulate their individual effects. The topic is of great relevance, even in economic terms, referring to plant-pathogen or plant-symbionts interactions, considering the increasing usage of artificial illumination in greenhouses, the possible light-regulation of the synthesis of plant-growth stimulating substances or herbicides by certain symbionts, and the biocontrol of pests by selected fungi and bacteria in a sustainable agriculture.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy.
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103, Leipzig, Germany
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27
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Dove R, Wolfe ER, Stewart NU, Ballhorn DJ. Ecoregion—Rather Than Sympatric Legumes—Influences Symbiotic Bradyrhizobium Associations in Invasive Scotch Broom (Cytisus scoparius) in the Pacific Northwest. NORTHWEST SCIENCE 2020. [DOI: 10.3955/046.094.0205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Robyn Dove
- Portland State University, Department of Biology, 1719 SW 10th Avenue, Portland, Oregon 97201
| | - Emily R. Wolfe
- Portland State University, Department of Biology, 1719 SW 10th Avenue, Portland, Oregon 97201
| | - Nathan U. Stewart
- Portland State University, Department of Biology, 1719 SW 10th Avenue, Portland, Oregon 97201
| | - Daniel J. Ballhorn
- Portland State University, Department of Biology, 1719 SW 10th Avenue, Portland, Oregon 97201
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28
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Zhao YX, Yang WL, Guo L, Jiang HY, Cheng X, Dai YJ. Bioinformatics of a Novel Nitrile Hydratase Gene Cluster of the N 2-Fixing Bacterium Microvirga flocculans CGMCC 1.16731 and Characterization of the Enzyme. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9299-9307. [PMID: 32786837 DOI: 10.1021/acs.jafc.0c03702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microvirga flocculans CGMCC 1.16731 can degrade many cyano group-containing neonicotinoid insecticides. Here, its genome was sequenced, and a novel nitrile hydratase gene cluster was discovered in a plasmid. The NHase gene cluster (pnhF) has gene structure β-subunit 1, α-subunit, and β-subunit 2, which is different from previously reported NHase gene structures. Phylogenetic analysis of α-subunits indicated that NHases containing the three subunit (β1αβ2) structure are independent from NHases containing two subunits (αβ). pnhF was successfully expressed in Escherichia coli, and the purified PnhF could convert the nitrile-containing insecticide flonicamid to N-(4-trifluoromethylnicotinoyl)glycinamide. The enzymatic properties of PnhF were investigated using flonicamid as a substrate. Homology models revealed that amino acid residue β1-Glu56 may strongly affect the catalytic activity of PnhF. This study expands our understanding of the structures and functions of NHases and the enzymatic mechanism of the environmental fate of flonicamid.
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Affiliation(s)
- Yun-Xiu Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Wen-Long Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Ling Guo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Huo-Yong Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Xi Cheng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Yi-Jun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
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29
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Pang S, Lin Z, Zhang W, Mishra S, Bhatt P, Chen S. Insights Into the Microbial Degradation and Biochemical Mechanisms of Neonicotinoids. Front Microbiol 2020; 11:868. [PMID: 32508767 PMCID: PMC7248232 DOI: 10.3389/fmicb.2020.00868] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/14/2020] [Indexed: 12/22/2022] Open
Abstract
Neonicotinoids are derivatives of synthetic nicotinoids with better insecticidal capabilities, including imidacloprid, nitenpyram, acetamiprid, thiacloprid, thiamethoxam, clothianidin, and dinotefuran. These are mainly used to control harmful insects and pests to protect crops. Their main targets are nicotinic acetylcholine receptors. In the past two decades, the environmental residues of neonicotinoids have enormously increased due to large-scale applications. More and more neonicotinoids remain in the environment and pose severe toxicity to humans and animals. An increase in toxicological and hazardous pollution due to the introduction of neonicotinoids into the environment causes problems; thus, the systematic remediation of neonicotinoids is essential and in demand. Various technologies have been developed to remove insecticidal residues from soil and water environments. Compared with non-bioremediation methods, bioremediation is a cost-effective and eco-friendly approach for the treatment of pesticide-polluted environments. Certain neonicotinoid-degrading microorganisms, including Bacillus, Mycobacterium, Pseudoxanthomonas, Rhizobium, Rhodococcus, Actinomycetes, and Stenotrophomonas, have been isolated and characterized. These microbes can degrade neonicotinoids under laboratory and field conditions. The microbial degradation pathways of neonicotinoids and the fate of several metabolites have been investigated in the literature. In addition, the neonicotinoid-degrading enzymes and the correlated genes in organisms have been explored. However, few reviews have focused on the neonicotinoid-degrading microorganisms along with metabolic pathways and degradation mechanisms. Therefore, this review aimed to summarize the microbial degradation and biochemical mechanisms of neonicotinoids. The potentials of neonicotinoid-degrading microbes for the bioremediation of contaminated sites were also discussed.
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Affiliation(s)
- Shimei Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ziqiu Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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30
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Symbiotic, phenotypic and genotypic characterization of Bradyrhizobium sp. nodulating Spartium junceum L. from Bejaia, northeastern Algeria. Symbiosis 2020. [DOI: 10.1007/s13199-020-00679-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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31
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The ACC-Deaminase Producing Bacterium Variovorax sp . CT7.15 as a Tool for Improving Calicotome villosa Nodulation and Growth in Arid Regions of Tunisia. Microorganisms 2020; 8:microorganisms8040541. [PMID: 32283666 PMCID: PMC7232455 DOI: 10.3390/microorganisms8040541] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/29/2022] Open
Abstract
Calicotome villosa is a spontaneous Mediterranean legume that can be a good candidate as pioneer plants to limit regression of vegetation cover and loss of biodiversity in Tunisian arid soils. In order to grow legumes in such soils, pairing rhizobia and nodule associated bacteria (NAB) might provide numerous advantages. In this work, cultivable biodiversity of rhizobial symbionts and NAB in nodules of C. villosa plants growing in five arid regions of south Tunisia was characterized. Phylogenetic analysis using 16S rDNA gene, dnak, recA and nodD sequences separated nodule-forming bacteria in six clades associated to genera Ensifer, Neorhizobium, Phyllobacterium and Rhizobium. Among NAB, the strain Variovorax sp. CT7.15 was selected due to its capacity to solubilise phosphate and, more interestingly, its high level of aminocyclopropane-1-carboxylate deaminase (ACC deaminase) activity. C. villosa plants were inoculated with representative rhizobia of each phylogenetic group and co-inoculated with the same rhizobia and strain CT7.15. Compared with single rhizobia inoculation, co-inoculation significantly improved plant growth and nodulation, ameliorated plant physiological state and increased nitrogen content in the plants, independently of the rhizobia used. These results support the benefits of pairing rhizobia and selected NAB to promote legume growth in arid or degraded soils.
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32
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Boudehouche W, Parker MA, Boulila F. Relationships of Bradyrhizobium strains nodulating three Algerian Genista species. Syst Appl Microbiol 2020; 43:126074. [PMID: 32169316 DOI: 10.1016/j.syapm.2020.126074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 11/17/2022]
Abstract
The Mediterranean world is the cradle for the diversification of a large number of plant species, including legumes belonging to the Tribe Genisteae. Nodule bacteria from three species of Genista legumes indigenous to northwestern Africa (G. ferox, G. numidica, G. tricuspidata) were sampled across a 150km region of Algeria in order to investigate symbiotic relationships. Partial 23S rRNA sequences from 107 isolates indicated that Bradyrhizobium was the predominant symbiont genus (96% of isolates), with the remainder belonging to Rhizobium or Mesorhizobium. A multilocus sequence analysis on 46 Bradyrhizobium strains using seven housekeeping (HK) genes showed that strains were differentiated into multiple clades with affinities to seven species: B. canariense (17 isolates), B. japonicum (2), B. ottawaense (2), B. cytisi/B. rifense (9), 'B. valentinum' (5), and B. algeriense (11). Extensive discordance between the HK gene phylogeny and a tree for four loci in the symbiosis island (SI) region implied that horizontal transfer of SI loci has been common. Cases of close symbiont relationship across pairs of legumes hosts were evident, with 33% of isolates having as their closest relative a strain sampled from a different Genista species. Nevertheless, tree permutation tests also showed that there was substantial host-related phylogenetic clustering. Thus, each of the three Genista hosts utilized a measurably different array of bacterial lineages.
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Affiliation(s)
- Wafa Boudehouche
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria.
| | - Matthew A Parker
- Biological Sciences, Binghamton University, Binghamton, NY 13902, USA
| | - Farida Boulila
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria.
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Fossou RK, Pothier JF, Zézé A, Perret X. Bradyrhizobium ivorense sp. nov. as a potential local bioinoculant for Cajanus cajan cultures in Côte d'Ivoire. Int J Syst Evol Microbiol 2020; 70:1421-1430. [PMID: 32122457 PMCID: PMC7397250 DOI: 10.1099/ijsem.0.003931] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For many smallholder farmers of Sub-Saharan Africa, pigeonpea (Cajanus cajan) is an important crop to make ends meet. To ascertain the taxonomic status of pigeonpea isolates of Côte d’Ivoire previously identified as bradyrhizobia, a polyphasic approach was applied to strains CI-1BT, CI-14A, CI-19D and CI-41S. Phylogeny of 16S ribosomal RNA (rRNA) genes placed these nodule isolates in a separate lineage from current species of the B. elkanii super clade. In phylogenetic analyses of single and concatenated partial dnaK, glnII, gyrB, recA and rpoB sequences, the C. cajan isolates again formed a separate lineage, with strain CI-1BT sharing the highest sequence similarity (95.2 %) with B. tropiciagri SEMIA 6148T. Comparative genomic analyses corroborated the novel species status, with 86 % ANIb and 89 % ANIm as the highest average nucleotide identity (ANI) values with B. elkanii USDA 76T. Although CI-1BT, CI-14A, CI-19D and CI-41S shared similar phenotypic and metabolic properties, growth of CI-41S was slower in/on various media. Symbiotic efficacy varied significantly between isolates, with CI-1BT and CI-41S scoring on the C. cajan ‘Light-Brown’ landrace as the most and least proficient bacteria, respectively. Also proficient on Vigna radiata (mung bean), Vigna unguiculata (cowpea, niébé) and additional C. cajan cultivars, CI-1BT represents a potential bioinoculant adapted to local soil conditions and capable of fostering the growth of diverse legume crops in Côte d'Ivoire. Given the data presented here, we propose the 19 C. cajan isolates to belong to a novel species called Bradyrhizobium ivorense sp. nov., with CI-1BT (=CCOS 1862T=CCMM B1296T) as a type strain.
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Affiliation(s)
- Romain K Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne, Unité Mixte de Recherche et d'Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire.,Department of Botany and Plant Biology, Microbiology Unit, University of Geneva, Sciences III, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, CH-8820 Wädenswil, Switzerland
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, Unité Mixte de Recherche et d'Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Xavier Perret
- Department of Botany and Plant Biology, Microbiology Unit, University of Geneva, Sciences III, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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Abstract
AbstractWe isolated 18 rhizobial strains from root nodules of a leguminous shrub Laburnum anagyroides (common laburnum) grown in Southeast Poland as an exotic plant. With the use of BOX-PCR fingerprinting, the isolates were clustered into 2 main groups and one separate lineage, which was congruent with the ITS-RFLP results. The phylogenetic trees constructed based on 16S rRNA and combined atpD, dnaK, glnA, and recA gene sequence data separated the representative strains into three evolutionary lineages within the Bradyrhizobium jicamae supergroup, with Bradyrhizobium algeriense and Bradyrhizobium valentinum as the closest relatives. The nodA and nifH gene phylogenies proved that the L. anagyroides symbionts carry a symbiotic gene variant known as Clade IV, representing the symbiovar retamae. Phenotypic characteristics of the isolates and reference strains are also reported. Our study of the rhizobia nodulating L. anagyroides growing in Poland complements earlier few findings on the symbiotic associations of this Genisteae species.
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Kalita M, Małek W, Coutinho TA. Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus. Syst Appl Microbiol 2020; 43:126056. [PMID: 31987702 DOI: 10.1016/j.syapm.2020.126056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 10/25/2022]
Abstract
In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89T and Bradyrhizobium valentinum LmjM3T. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887T in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89T, Bradyrhizobium valentinum LmjM3T and Bradyrhizobium retamae Ro19T belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.
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Affiliation(s)
- Michał Kalita
- Department of Genetics and Microbiology, M. Curie-Sklodowska University, Lublin, Poland.
| | - Wanda Małek
- Department of Genetics and Microbiology, M. Curie-Sklodowska University, Lublin, Poland
| | - Teresa A Coutinho
- Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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Zuluaga MYA, Lima Milani KM, Azeredo Gonçalves LS, Martinez de Oliveira AL. Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum. PLoS One 2020; 15:e0227422. [PMID: 31923250 PMCID: PMC6953851 DOI: 10.1371/journal.pone.0227422] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022] Open
Abstract
Studies of the interactions between plants and their microbiome have been conducted worldwide in the search for growth-promoting representative strains for use as biological inputs for agriculture, aiming to achieve more sustainable agriculture practices. With a focus on the isolation of plant growth-promoting (PGP) bacteria with ability to alleviate N stress, representative strains that were found at population densities greater than 104 cells g-1 and that could grow in N-free semisolid media were isolated from soils under different management conditions and from the roots of tomato (Solanum lycopersicum) and lulo (Solanum quitoense) plants that were grown in those soils. A total of 101 bacterial strains were obtained, after which they were phylogenetically categorized and characterized for their basic PGP mechanisms. All strains belonged to the Proteobacteria phylum in the classes Alphaproteobacteria (61% of isolates), Betaproteobacteria (19% of isolates) and Gammaproteobacteria (20% of isolates), with distribution encompassing nine genera, with the predominant genus being Rhizobium (58.4% of isolates). Strains isolated from conventional horticulture (CH) soil composed three bacterial genera, suggesting a lower diversity for the diazotrophs/N scavenger bacterial community than that observed for soils under organic management (ORG) or secondary forest coverture (SF). Conversely, diazotrophs/N scavenger strains from tomato plants grown in CH soil comprised a higher number of bacterial genera than did strains isolated from tomato plants grown in ORG or SF soils. Furthermore, strains isolated from tomato were phylogenetically more diverse than those from lulo. BOX-PCR fingerprinting of all strains revealed a high genetic diversity for several clonal representatives (four Rhizobium species and one Pseudomonas species). Considering the potential PGP mechanisms, 49 strains (48.5% of the total) produced IAA (2.96–193.97 μg IAA mg protein-1), 72 strains (71.3%) solubilized FePO4 (0.40–56.00 mg l-1), 44 strains (43.5%) solubilized AlPO4 (0.62–17.05 mg l-1), and 44 strains produced siderophores (1.06–3.23). Further, 91 isolates (90.1% of total) showed at least one PGP trait, and 68 isolates (67.3%) showed multiple PGP traits. Greenhouse trials using the bacterial collection to inoculate tomato or lulo plants revealed increases in plant biomass (roots, shoots or both plant tissues) elicited by 65 strains (54.5% of the bacterial collection), of which 36 were obtained from the tomato rhizosphere, 15 were obtained from the lulo rhizosphere, and 14 originated from samples of soil that lacked plants. In addition, 18 strains showed positive inoculation effects on both Solanum species, of which 12 were classified as Rhizobium spp. by partial 16S rRNA gene sequencing. Overall, the strategy adopted allowed us to identify the variability in the composition of culturable diazotroph/N-scavenger representatives from soils under different management conditions by using two Solanum species as trap plants. The present results suggest the ability of tomato and lulo plants to enrich their belowground microbiomes with rhizobia representatives and the potential of selected rhizobial strains to promote the growth of Solanum crops under limiting N supply.
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Affiliation(s)
| | - Karina Maria Lima Milani
- Departamento de Bioquímica e Biotecnologia, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
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Missbah El Idrissi M, Lamin H, ElFaik S, Tortosa G, Peix A, Bedmar E, Abdelmoumen H. Microvirga
sp. symbiovar mediterranense nodulates
Lupinus cosentinii
grown wild in Morocco. J Appl Microbiol 2019; 128:1109-1118. [DOI: 10.1111/jam.14526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 01/14/2023]
Affiliation(s)
- M. Missbah El Idrissi
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
| | - H. Lamin
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
| | - S. ElFaik
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
| | - G. Tortosa
- Department of Soil Microbiology and Symbiotic Systems Estación Experimental del Zaidín Consejo Superior de Investigaciones Científicas Granada Spain
| | - A. Peix
- Instituto de Recursos Naturales y Agrobiología IRNASA‐CSIC Salamanca Spain
| | - E.J. Bedmar
- Department of Soil Microbiology and Symbiotic Systems Estación Experimental del Zaidín Consejo Superior de Investigaciones Científicas Granada Spain
| | - H. Abdelmoumen
- Centre de Biotechnologie Végétale et Microbienne Faculty of Sciences Mohammed V University Agdal, Rabat Morocco
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Rejili M, Msaddak A, Filali I, Benabderrahim MA, Mars M, Marín M. New chromosomal lineages within Microvirga and Bradyrhizobium genera nodulate Lupinus angustifolius growing on different Tunisian soils. FEMS Microbiol Ecol 2019; 95:5537381. [DOI: 10.1093/femsec/fiz118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
ABSTRACTThirty-one rhizobial isolates nodulating native Lupinus angustifolius (blue lupine) plants growing in Northern Tunisian soils were isolated and analysed using different chromosomal and symbiotic gene markers. Phylogenetic analyses based on recA partial sequences grouped them into at least five groups: four of them within the genus Bradyrhizobium (26 isolates) and one into the genus Microvirga (5 isolates). Representative strains were analysed by multilocus sequence analysis of three housekeeping genes rrs-recA-glnII and rrs-gyrB-dnaK for Bradyrhizobium and Microvirga isolates, respectively. Based on this analysis, eight isolates clustered with the previously described strains Bradyrhizobium lupini USDA3051 and Bradyrhizobium canariense BTA-1. However, five of the isolates clustered separately and may constitute a new species within the Bradyrhizobium genus. The remaining five isolates were closely related to the strain Microvirga sp. LmiM8 and may constitute a new Microvirga species. The analysis of the nodC gene showed that all Bradyrhizobium strains nodulating blue lupine belong to the symbiovar genistearum, whereas the Microvirga isolates are associated with the symbiovar mediterranense. The results of this study support that the L. angustifolius root nodule symbionts isolated in Northern Tunisia belong mostly to the B. canariense/B. lupini lineages. However, new clades of Bradyrhizobium and Microvirga have been identified as L. angustifolius endosymbionts.
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Affiliation(s)
- M Rejili
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - A Msaddak
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - I Filali
- College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, Riyadh PO Box 84428, Saudi Arabia
| | - M A Benabderrahim
- Arid and Oases Cropping Laboratory, Arid Area Institute, Gabes 6051, Tunisia
| | - M Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) – Faculty of Sciences of Gabes, University of Gabes, Erriadh, Zrig 6072, Gabes, Tunisia
| | - M Marín
- Institute of Genetics, Ludwig Maximilians University of Munich (LMU), Grosshaderner Str. 2–4, D-82152 Martinsried, Germany
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Wójcik M, Kalita M, Małek W. Numerical analysis of phenotypic properties, genomic fingerprinting, and multilocus sequence analysis of Bradyrhizobium strains isolated from root nodules of Lembotropis nigricans of the tribe Genisteae. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01491-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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40
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Mellal H, Yacine B, Boukaous L, Khouni S, Benguedouar A, Castellano-Hinojosa A, Bedmar EJ. Phylogenetic diversity of Bradyrhizobium strains isolated from root nodules of Lupinus angustifolius grown wild in the North East of Algeria. Syst Appl Microbiol 2019; 42:397-402. [DOI: 10.1016/j.syapm.2019.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 11/25/2022]
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41
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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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42
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Phylogenetic diversity of Bradyrhizobium strains nodulating Calicotome spinosa in the Northeast of Algeria. Syst Appl Microbiol 2018; 41:452-459. [DOI: 10.1016/j.syapm.2018.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/24/2018] [Accepted: 05/24/2018] [Indexed: 11/20/2022]
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43
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Andrews M, De Meyer S, James EK, Stępkowski T, Hodge S, Simon MF, Young JPW. Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance. Genes (Basel) 2018; 9:E321. [PMID: 29954096 PMCID: PMC6071183 DOI: 10.3390/genes9070321] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/17/2023] Open
Abstract
Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume⁻rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch 6150, Australia.
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium.
| | - Euan K James
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland.
| | - Simon Hodge
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Marcelo F Simon
- Embrapa Genetic Resources and Biotechnology, Brasilia DF 70770-917, Brazil.
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK.
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