1
|
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.
Collapse
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
| |
Collapse
|
2
|
Camuel A, Teulet A, Carcagno M, Haq F, Pacquit V, Gully D, Pervent M, Chaintreuil C, Fardoux J, Horta-Araujo N, Okazaki S, Ratu STN, Gueye F, Zilli J, Nouwen N, Arrighi JF, Luo H, Mergaert P, Deslandes L, Giraud E. Widespread Bradyrhizobium distribution of diverse Type III effectors that trigger legume nodulation in the absence of Nod factor. THE ISME JOURNAL 2023; 17:1416-1429. [PMID: 37355742 PMCID: PMC10432411 DOI: 10.1038/s41396-023-01458-1] [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: 04/24/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023]
Abstract
The establishment of the rhizobium-legume symbiosis is generally based on plant perception of Nod factors (NFs) synthesized by the bacteria. However, some Bradyrhizobium strains can nodulate certain legume species, such as Aeschynomene spp. or Glycine max, independently of NFs, and via two different processes that are distinguished by the necessity or not of a type III secretion system (T3SS). ErnA is the first known type III effector (T3E) triggering nodulation in Aeschynomene indica. In this study, a collection of 196 sequenced Bradyrhizobium strains was tested on A. indica. Only strains belonging to the photosynthetic supergroup can develop a NF-T3SS-independent symbiosis, while the ability to use a T3SS-dependent process is found in multiple supergroups. Of these, 14 strains lacking ernA were tested by mutagenesis to identify new T3Es triggering nodulation. We discovered a novel T3E, Sup3, a putative SUMO-protease without similarity to ErnA. Its mutation in Bradyrhizobium strains NAS96.2 and WSM1744 abolishes nodulation and its introduction in an ernA mutant of strain ORS3257 restores nodulation. Moreover, ectopic expression of sup3 in A. indica roots led to the formation of spontaneous nodules. We also report three other new T3Es, Ubi1, Ubi2 and Ubi3, which each contribute to the nodulation capacity of strain LMTR13. These T3Es have no homology to known proteins but share with ErnA three motifs necessary for ErnA activity. Together, our results highlight an unsuspected distribution and diversity of T3Es within the Bradyrhizobium genus that may contribute to their symbiotic efficiency by participating in triggering legume nodulation.
Collapse
Affiliation(s)
- Alicia Camuel
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Albin Teulet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- University of Cambridge, Sainsbury Laboratory (SLCU), Cambridge, CB2 1LR, UK
| | - Mélanie Carcagno
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Fazal Haq
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Valérie Pacquit
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Marjorie Pervent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Natasha Horta-Araujo
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Shin Okazaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Safirah Tasa Nerves Ratu
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Fatou Gueye
- Carrefour International, Bureau Régional Afrique de l'Ouest, Dakar, Sénégal
| | - Jerri Zilli
- Embrapa Agrobiologia, Bairro Ecologia, Seropedica, Rio de Janeiro, Brazil
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Haiwei Luo
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Laurent Deslandes
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France.
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
| |
Collapse
|
3
|
Avontuur JR, Wilken PM, Palmer M, Coetzee MPA, Stępkowski T, Venter SN, Steenkamp ET. Complex evolutionary history of photosynthesis in Bradyrhizobium. Microb Genom 2023; 9:001105. [PMID: 37676703 PMCID: PMC10569730 DOI: 10.1099/mgen.0.001105] [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: 05/16/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Bradyrhizobium comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of substantial debate. Therefore, our aim here was to investigate the distribution and evolution of photosynthesis in Bradyrhizobium using comparative genomics and representative genomes from closely related taxa in the families Nitrobacteraceae, Methylobacteriaceae, Boseaceae and Paracoccaceae . We identified photosynthesis gene clusters (PGCs) in 25 genomes belonging to three different Bradyrhizobium lineages, notably the so-called Photosynthetic, B. japonicum and B. elkanii supergroups. Also, two different PGC architectures were observed. One of these, PGC1, was present in genomes from the Photosynthetic supergroup and in three genomes from a species in the B. japonicum supergroup. The second cluster, PGC2, was also present in some strains from the B. japonicum supergroup, as well as in those from the B. elkanii supergroup. PGC2 was largely syntenic to the cluster found in Rhodopseudomonas palustris and Tardiphaga . Bayesian ancestral state reconstruction unambiguously showed that the ancestor of Bradyrhizobium lacked a PGC and that it was acquired horizontally by various lineages. Maximum-likelihood phylogenetic analyses of individual photosynthesis genes also suggested multiple acquisitions through horizontal gene transfer, followed by vertical inheritance and gene losses within the different lineages. Overall, our findings add to the existing body of knowledge on Bradyrhizobium ’s evolution and provide a meaningful basis from which to explore how these PGCs and the photosynthesis itself impact the physiology and ecology of these bacteria.
Collapse
Affiliation(s)
- Juanita R. Avontuur
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - P. Markus Wilken
- 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, Las Vegas, NV, USA
| | - Martin P. A. Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warszawa, 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
| |
Collapse
|
4
|
Provorov NA, Andronov EE, Kimeklis AK, Onishchuk OP, Igolkina AA, Karasev ES. Microevolution, speciation and macroevolution in rhizobia: Genomic mechanisms and selective patterns. FRONTIERS IN PLANT SCIENCE 2022; 13:1026943. [PMID: 36388581 PMCID: PMC9640933 DOI: 10.3389/fpls.2022.1026943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Nodule bacteria (rhizobia), N2-fixing symbionts of leguminous plants, represent an excellent model to study the fundamental issues of evolutionary biology, including the tradeoff between microevolution, speciation, and macroevolution, which remains poorly understood for free-living organisms. Taxonomically, rhizobia are extremely diverse: they are represented by nearly a dozen families of α-proteobacteria (Rhizobiales) and by some β-proteobacteria. Their genomes are composed of core parts, including house-keeping genes (hkg), and of accessory parts, including symbiotically specialized (sym) genes. In multipartite genomes of evolutionary advanced fast-growing species (Rhizobiaceae), sym genes are clustered on extra-chromosomal replicons (megaplasmids, chromids), facilitating gene transfer in plant-associated microbial communities. In this review, we demonstrate that in rhizobia, microevolution and speciation involve different genomic and ecological mechanisms: the first one is based on the diversification of sym genes occurring under the impacts of host-induced natural selection (including its disruptive, frequency-dependent and group forms); the second one-on the diversification of hkgs under the impacts of unknown factors. By contrast, macroevolution represents the polyphyletic origin of super-species taxa, which are dependent on the transfer of sym genes from rhizobia to various soil-borne bacteria. Since the expression of newly acquired sym genes on foreign genomic backgrounds is usually restricted, conversion of resulted recombinants into the novel rhizobia species involves post-transfer genetic changes. They are presumably supported by host-induced selective processes resulting in the sequential derepression of nod genes responsible for nodulation and of nif/fix genes responsible for symbiotic N2 fixation.
Collapse
Affiliation(s)
- Nikolay A. Provorov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Evgeny E. Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
- Laboratory of Soil Biology and Biochemistry, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
| | - Anastasiia K. Kimeklis
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia
| | - Olga P. Onishchuk
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| | - Anna A. Igolkina
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Evgeny S. Karasev
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia
| |
Collapse
|
5
|
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]
|
6
|
|
7
|
Khokhani D, Carrera Carriel C, Vayla S, Irving TB, Stonoha-Arther C, Keller NP, Ané JM. Deciphering the Chitin Code in Plant Symbiosis, Defense, and Microbial Networks. Annu Rev Microbiol 2021; 75:583-607. [PMID: 34623896 DOI: 10.1146/annurev-micro-051921-114809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chitin is a structural polymer in many eukaryotes. Many organisms can degrade chitin to defend against chitinous pathogens or use chitin oligomers as food. Beneficial microorganisms like nitrogen-fixing symbiotic rhizobia and mycorrhizal fungi produce chitin-based signal molecules called lipo-chitooligosaccharides (LCOs) and short chitin oligomers to initiate a symbiotic relationship with their compatible hosts and exchange nutrients. A recent study revealed that a broad range of fungi produce LCOs and chitooligosaccharides (COs), suggesting that these signaling molecules are not limited to beneficial microbes. The fungal LCOs also affect fungal growth and development, indicating that the roles of LCOs beyond symbiosis and LCO production may predate mycorrhizal symbiosis. This review describes the diverse structures of chitin; their perception by eukaryotes and prokaryotes; and their roles in symbiotic interactions, defense, and microbe-microbe interactions. We also discuss potential strategies of fungi to synthesize LCOs and their roles in fungi with different lifestyles.
Collapse
Affiliation(s)
- Devanshi Khokhani
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , , .,Current affiliation: Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108, USA;
| | - Cristobal Carrera Carriel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Shivangi Vayla
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Thomas B Irving
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Christina Stonoha-Arther
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , , .,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , , .,Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| |
Collapse
|
8
|
Ma F, Wang Y, Yang J, Guo H, Su D, Yu L. Degradation of 1,4-Dioxane by Xanthobacter sp. YN2. Curr Microbiol 2021; 78:992-1005. [PMID: 33547937 DOI: 10.1007/s00284-021-02347-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/10/2021] [Indexed: 12/28/2022]
Abstract
1,4-Dioxane is a highly toxic and carcinogenic pollutant found worldwide in groundwater and soil environments. Several microorganisms have been isolated by their ability to grow on 1,4-dioxane; however, low 1,4-dioxane tolerance and slow degradation kinetics remain obstacles for their use in 1,4-dioxane bioremediation. We report here the isolation and characterization of a new strain, Xanthobacter sp. YN2, capable of highly efficient 1,4-dioxane degradation. High degradation efficiency and high tolerance to 1,4-dioxane make this new strain an ideal candidate for the biodegradation of 1,4-dioxane in various treatment facilities. The maximum degradation rate of 1,4-dioxane was found to be 1.10 mg-1,4-dioxane/h mg-protein. Furthermore, Xanthobacter sp. YN2 was shown to grow in the presence of higher than 3000 mg/L 1,4-dioxane with little to no degradation inhibition. In addition, Xanthobacter sp. YN2 could grow on and degrade 1,4-dioxane at pH ranges 5 to 8 and temperatures between 20 and 40 °C. Xanthobacter sp. YN2 was also found to be able to grow on a variety of other substrates including several analogs of 1,4-dioxane. Genome sequence analyses revealed the presence of two soluble di-iron monooxygenase (SDIMO) gene clusters, and regulation studies determined that all of the genes in these two clusters were upregulated in the presence of 1,4-dioxane. This study provides insights into the bacterial stress response and the highly efficient biodegradation of 1,4-dioxane as well as the identification of a novel Group-2 SDIMO.
Collapse
Affiliation(s)
- Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China.
| | - Yingning Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Haijuan Guo
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, China
| | - Delin Su
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Lan Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| |
Collapse
|
9
|
Safronova VI, Guro PV, Sazanova AL, Kuznetsova IG, Belimov AA, Yakubov VV, Chirak ER, Afonin AМ, Gogolev YV, Andronov EE, Tikhonovich IA. Rhizobial Microsymbionts of Kamchatka Oxytropis Species Possess Genes of the Type III and VI Secretion Systems, Which Can Affect the Development of Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1232-1241. [PMID: 32686981 DOI: 10.1094/mpmi-05-20-0114-r] [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
A collection of rhizobial strains isolated from root nodules of the narrowly endemic legume species Oxytropis erecta, O. anadyrensis, O. kamtschatica, and O. pumilio originating from the Kamchatka Peninsula (Russian Federation) was obtained. Analysis of the 16S ribosomal RNA gene sequence showed a significant diversity of isolates belonging to families Rhizobiaceae (genus Rhizobium), Phyllobacteriaceae (genera Mesorhizobium, Phyllobacterium), and Bradyrhizobiaceae (genera Bosea, Tardiphaga). A plant nodulation assay showed that only strains belonging to genus Mesorhizobium could form nitrogen-fixing nodules on Oxytropis plants. The strains M. loti 582 and M. huakuii 583, in addition to symbiotic clusters, possessed genes of the type III and type VI secretion systems (T3SS and T6SS, respectively), which can influence the host specificity of strains. These strains formed nodules of two types (elongated and rounded) on O. kamtschatica roots. We suggest this phenomenon may result from Nod factor-dependent and -independent nodulation strategies. The obtained strains are of interest for further study of the T3SS and T6SS gene function and their role in the development of rhizobium-legume symbiosis. The prospects of using rhizobia having both gene systems related to symbiotic and nonsymbiotic nodulation strategies to enhance the efficiency of plant-microbe interactions by expanding the host specificity and increasing nodulation efficiency are discussed.
Collapse
Affiliation(s)
- Vera I Safronova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Polina V Guro
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Anna L Sazanova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Irina G Kuznetsova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Andrey A Belimov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Valentin V Yakubov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the RAS, 690022, Vladivostok, Ave. 100-let Vladivostoka 159, Russian Federation
| | - Elizaveta R Chirak
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Alexey М Afonin
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Yuri V Gogolev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky St., Kazan 420111, Russian Federation
| | - Evgeny E Andronov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Igor A Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
- Saint Petersburg State University, Department of Genetics and Biotechnology, 199034, St.-Petersburg, Universitetskaya Emb. 7/9, Russian Federation
| |
Collapse
|
10
|
Cui C, Lin H, Pu W, Guo C, Liu Y, Pei XQ, Wu ZL. Asymmetric Epoxidation and Sulfoxidation Catalyzed by a New Styrene Monooxygenase from Bradyrhizobium. Appl Biochem Biotechnol 2020; 193:65-78. [PMID: 32808246 DOI: 10.1007/s12010-020-03413-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
Asymmetric epoxidation catalyzed with styrene monooxygenase (SMO) is a powerful enzymatic process producing enantiopure styrene epoxide derivatives. To establish a more diversified reservoir of SMOs, a new SMO from Bradyrhizobium sp. ORS 375, named BrSMO, was mined from the database and characterized. BrSMO was constituted of an epoxygenase component of 415 amino acid residues and an NADH-dependent flavin reductase component of 175 residues. BrSMO catalyzed the epoxidation of styrene and 7 more styrene derivatives, yielding the corresponding (S)-epoxides with excellent enantiomeric excesses (95- > 99% ee), with the highest activity achieved for styrene. BrSMO also catalyzed the asymmetric sulfoxidation of 7 sulfides, producing the corresponding (R)-sulfoxides (20-90% ee) with good yields.
Collapse
Affiliation(s)
- Can Cui
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Lin
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.
| | - Wei Pu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Guo
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiao-Qiong Pei
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhong-Liu Wu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| |
Collapse
|
11
|
Provorov NA, Andronov EE, Kimeklis AK, Chirak ER, Karasev ES, Aksenova TS, Kopat VV. Evolutionary Geography of Root Nodule Bacteria: Speciation Directed by the Host Plants. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Safronova VI, Belimov AA, Sazanova AL, Chirak ER, Verkhozina AV, Kuznetsova IG, Andronov EE, Puhalsky JV, Tikhonovich IA. Taxonomically Different Co-Microsymbionts of a Relict Legume, Oxytropis popoviana, Have Complementary Sets of Symbiotic Genes and Together Increase the Efficiency of Plant Nodulation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:833-841. [PMID: 29498565 DOI: 10.1094/mpmi-01-18-0011-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ten rhizobial strains were isolated from root nodules of a relict legume Oxytropis popoviana Peschkova. For identification of the isolates, sequencing of rrs, the internal transcribed spacer region, and housekeeping genes recA, glnII, and rpoB was used. Nine fast-growing isolates were Mesorhizobium-related; eight strains were identified as M. japonicum and one isolate belonged to M. kowhaii. The only slow-growing isolate was identified as a Bradyrhizobium sp. Two strains, M. japonicum Opo-242 and Bradyrhizobium sp. strain Opo-243, were isolated from the same nodule. Symbiotic genes of these isolates were searched throughout the whole-genome sequences. The common nodABC genes and other symbiotic genes required for plant nodulation and nitrogen fixation were present in the isolate Opo-242. Strain Opo-243 did not contain the principal nod, nif, and fix genes; however, five genes (nodP, nodQ, nifL, nolK, and noeL) affecting the specificity of plant-rhizobia interactions but absent in isolate Opo-242 were detected. Strain Opo-243 could not induce nodules but significantly accelerated the root nodule formation after coinoculation with isolate Opo-242. Thus, we demonstrated that taxonomically different strains of the archaic symbiotic system can be co-microsymbionts infecting the same nodule and promoting the nodulation process due to complementary sets of symbiotic genes.
Collapse
Affiliation(s)
- Vera I Safronova
- 1 All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, sh. Podbelskogo 3, Russian Federation
| | - Andrey A Belimov
- 1 All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, sh. Podbelskogo 3, Russian Federation
| | - Anna L Sazanova
- 1 All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, sh. Podbelskogo 3, Russian Federation
| | - Elizaveta R Chirak
- 1 All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, sh. Podbelskogo 3, Russian Federation
| | - Alla V Verkhozina
- 2 Siberian Institute of Plant Physiology and Biochemistry (SIPPB), 664033, Irkutsk, P.O.Box 1243, Russian Federation; and
| | - Irina G Kuznetsova
- 1 All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, sh. Podbelskogo 3, Russian Federation
| | - Evgeny E Andronov
- 1 All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, sh. Podbelskogo 3, Russian Federation
| | - Jan V Puhalsky
- 1 All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, sh. Podbelskogo 3, Russian Federation
| | - Igor A Tikhonovich
- 1 All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, sh. Podbelskogo 3, Russian Federation
- 3 Saint Petersburg State University, Department of Genetics and Biotechnology, 199034, St. Petersburg, Universitetskaya Emb. 7/9, Russian Federation
| |
Collapse
|
14
|
Barrière Q, Guefrachi I, Gully D, Lamouche F, Pierre O, Fardoux J, Chaintreuil C, Alunni B, Timchenko T, Giraud E, Mergaert P. Integrated roles of BclA and DD-carboxypeptidase 1 in Bradyrhizobium differentiation within NCR-producing and NCR-lacking root nodules. Sci Rep 2017; 7:9063. [PMID: 28831061 PMCID: PMC5567381 DOI: 10.1038/s41598-017-08830-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022] Open
Abstract
Legumes harbor in their symbiotic nodule organs nitrogen fixing rhizobium bacteria called bacteroids. Some legumes produce Nodule-specific Cysteine-Rich (NCR) peptides in the nodule cells to control the intracellular bacterial population. NCR peptides have antimicrobial activity and drive bacteroids toward terminal differentiation. Other legumes do not produce NCR peptides and their bacteroids are not differentiated. Bradyrhizobia, infecting NCR-producing Aeschynomene plants, require the peptide uptake transporter BclA to cope with the NCR peptides as well as a specific peptidoglycan-modifying DD-carboxypeptidase, DD-CPase1. We show that Bradyrhizobium diazoefficiens strain USDA110 forms undifferentiated bacteroids in NCR-lacking soybean nodules. Unexpectedly, in Aeschynomene afraspera nodules the nitrogen fixing USDA110 bacteroids are hardly differentiated despite the fact that this host produces NCR peptides, suggesting that USDA110 is insensitive to the host peptide effectors and that nitrogen fixation can be uncoupled from differentiation. In agreement with the absence of bacteroid differentiation, USDA110 does not require its bclA gene for nitrogen fixing symbiosis with these two host plants. Furthermore, we show that the BclA and DD-CPase1 act independently in the NCR-induced morphological differentiation of bacteroids. Our results suggest that BclA is required to protect the rhizobia against the NCR stress but not to induce the terminal differentiation pathway.
Collapse
Affiliation(s)
- Quentin Barrière
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Ibtissem Guefrachi
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.,Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès University, Erriadh-Zrig, 6072, Gabès, Tunisia.,Université de Pau et des Pays de l'Adour, Pau, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Florian Lamouche
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Olivier Pierre
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.,Institut Sophia AgroBiotech, Sophia-Antipolis, France
| | - Joël Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Benoît Alunni
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Tatiana Timchenko
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Peter Mergaert
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.
| |
Collapse
|
15
|
Provorov NA, Andronov EE. Evolution of root nodule bacteria: Reconstruction of the speciation processes resulting from genomic rearrangements in a symbiotic system. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716020156] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
16
|
Ancient Evolution and Recent Evolution Converge for the Biodegradation of Cyanuric Acid and Related Triazines. Appl Environ Microbiol 2016; 82:1638-1645. [PMID: 26729715 DOI: 10.1128/aem.03594-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanuric acid was likely present on prebiotic Earth, may have been a component of early genetic materials, and is synthesized industrially today on a scale of more than one hundred million pounds per year in the United States. In light of this, it is not surprising that some bacteria and fungi have a metabolic pathway that sequentially hydrolyzes cyanuric acid and its metabolites to release the nitrogen atoms as ammonia to support growth. The initial reaction that opens the s-triazine ring is catalyzed by the unusual enzyme cyanuric acid hydrolase. This enzyme is in a rare protein family that consists of only cyanuric acid hydrolase (CAH) and barbiturase, with barbiturase participating in pyrimidine catabolism by some actinobacterial species. The X-ray structures of two cyanuric acid hydrolase proteins show that this family has a unique protein fold. Phylogenetic, bioinformatic, enzymological, and genetic studies are consistent with the idea that CAH has an ancient protein fold that was rare in microbial populations but is currently becoming more widespread in microbial populations in the wake of anthropogenic synthesis of cyanuric acid and other s-triazine compounds that are metabolized via a cyanuric acid intermediate. The need for the removal of cyanuric acid from swimming pools and spas, where it is used as a disinfectant stabilizer, can potentially be met using an enzyme filtration system. A stable thermophilic cyanuric acid hydrolase from Moorella thermoacetica is being tested for this purpose.
Collapse
|
17
|
Okazaki S, Tittabutr P, Teulet A, Thouin J, Fardoux J, Chaintreuil C, Gully D, Arrighi JF, Furuta N, Miwa H, Yasuda M, Nouwen N, Teaumroong N, Giraud E. Rhizobium-legume symbiosis in the absence of Nod factors: two possible scenarios with or without the T3SS. THE ISME JOURNAL 2016; 10:64-74. [PMID: 26161635 PMCID: PMC4681849 DOI: 10.1038/ismej.2015.103] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/28/2015] [Accepted: 05/08/2015] [Indexed: 02/07/2023]
Abstract
The occurrence of alternative Nod factor (NF)-independent symbiosis between legumes and rhizobia was first demonstrated in some Aeschynomene species that are nodulated by photosynthetic bradyrhizobia lacking the canonical nodABC genes. In this study, we revealed that a large diversity of non-photosynthetic bradyrhizobia, including B. elkanii, was also able to induce nodules on the NF-independent Aeschynomene species, A. indica. Using cytological analysis of the nodules and the nitrogenase enzyme activity as markers, a gradient in the symbiotic interaction between bradyrhizobial strains and A. indica could be distinguished. This ranged from strains that induced nodules that were only infected intercellularly to rhizobial strains that formed nodules in which the host cells were invaded intracellularly and that displayed a weak nitrogenase activity. In all non-photosynthetic bradyrhizobia, the type III secretion system (T3SS) appears required to trigger nodule organogenesis. In contrast, genome sequence analysis revealed that apart from a few exceptions, like the Bradyrhizobium ORS285 strain, photosynthetic bradyrhizobia strains lack a T3SS. Furthermore, analysis of the symbiotic properties of an ORS285 T3SS mutant revealed that the T3SS could have a positive or negative role for the interaction with NF-dependent Aeschynomene species, but that it is dispensable for the interaction with all NF-independent Aeschynomene species tested. Taken together, these data indicate that two NF-independent symbiotic processes are possible between legumes and rhizobia: one dependent on a T3SS and one using a so far unknown mechanism.
Collapse
Affiliation(s)
- Shin Okazaki
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Panlada Tittabutr
- Institute of Agricultural Technology, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Albin Teulet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Julien Thouin
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Jean- François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Noriyuki Furuta
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hiroki Miwa
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Michiko Yasuda
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Neung Teaumroong
- Institute of Agricultural Technology, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| |
Collapse
|
18
|
Extra-slow-growing Tardiphaga strains isolated from nodules of Vavilovia formosa (Stev.) Fed. Arch Microbiol 2015; 197:889-98. [PMID: 26013968 DOI: 10.1007/s00203-015-1122-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
Abstract
Eleven extra-slow-growing strains were isolated from nodules of the relict legume Vavilovia formosa growing in North Ossetia (Caucasus) and Armenia. All isolates formed a single rrs cluster together with the type strain Tardiphaga robiniae LMG 26467(T), while the sequencing of the 16S-23S rDNA intergenic region (ITS) and housekeeping genes glnII, atpD, dnaK, gyrB, recA and rpoB divided them into three groups. North Ossetian isolates (in contrast to the Armenian ones) were clustered separately from the type strain LMG 26467(T). However, all isolates were classified as T. robiniae because the DNA-DNA relatedness between them and the type strain LMG 26467(T) was 69.6% minimum. Two symbiosis-related genes (nodM and nodT) were amplified in all isolated Tardiphaga strains. It was shown that the nodM gene phylogeny is similar to that of ITS and housekeeping genes. The presence of the other symbiosis-related genes in described Tardiphaga strains, which is recently described genus of rhizobia, as well as their ability to form nodules on any plants are under investigation.
Collapse
|
19
|
Preferential association of endophytic bradyrhizobia with different rice cultivars and its implications for rice endophyte evolution. Appl Environ Microbiol 2015; 81:3049-61. [PMID: 25710371 DOI: 10.1128/aem.04253-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/17/2015] [Indexed: 11/20/2022] Open
Abstract
Plant colonization by bradyrhizobia is found not only in leguminous plants but also in nonleguminous species such as rice. To understand the evolution of the endophytic symbiosis of bradyrhizobia, the effect of the ecosystems of rice plantations on their associations was investigated. Samples were collected from various rice (Oryza sativa) tissues and crop rotational systems. The rice endophytic bradyrhizobia were isolated on the basis of oligotrophic properties, selective medium, and nodulation on siratro (Macroptilium atropurpureum). Six bradyrhizobial strains were obtained exclusively from rice grown in a crop rotational system. The isolates were separated into photosynthetic bradyrhizobia (PB) and nonphotosynthetic bradyrhizobia (non-PB). Thai bradyrhizobial strains promoted rice growth of Thai rice cultivars better than the Japanese bradyrhizobial strains. This implies that the rice cultivars possess characteristics that govern rice-bacterium associations. To examine whether leguminous plants in a rice plantation system support the persistence of rice endophytic bradyrhizobia, isolates were tested for legume nodulation. All PB strains formed symbioses with Aeschynomene indica and Aeschynomene evenia. On the other hand, non-PB strains were able to nodulate Aeschynomene americana, Vigna radiata, and M. atropurpureum but unable to nodulate either A. indica or A. evenia. Interestingly, the nodABC genes of all of these bradyrhizobial strains seem to exhibit low levels of similarity to those of Bradyrhizobium diazoefficiens USDA110 and Bradyrhizobium sp. strain ORS285. From these results, we discuss the evolution of the plant-bradyrhizobium association, including nonlegumes, in terms of photosynthetic lifestyle and nod-independent interactions.
Collapse
|
20
|
Tschaplinski TJ, Plett JM, Engle NL, Deveau A, Cushman KC, Martin MZ, Doktycz MJ, Tuskan GA, Brun A, Kohler A, Martin F. Populus trichocarpa and Populus deltoides exhibit different metabolomic responses to colonization by the symbiotic fungus Laccaria bicolor. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:546-56. [PMID: 24548064 DOI: 10.1094/mpmi-09-13-0286-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Within boreal and temperate forest ecosystems, the majority of trees and shrubs form beneficial relationships with mutualistic ectomycorrhizal (ECM) fungi that support plant health through increased access to nutrients as well as aiding in stress and pest tolerance. The intimate interaction between fungal hyphae and plant roots results in a new symbiotic "organ" called the ECM root tip. Little is understood concerning the metabolic reprogramming that favors the formation of this hybrid tissue in compatible interactions and what prevents the formation of ECM root tips in incompatible interactions. We show here that the metabolic changes during favorable colonization between the ECM fungus Laccaria bicolor and its compatible host, Populus trichocarpa, are characterized by shifts in aromatic acid, organic acid, and fatty acid metabolism. We demonstrate that this extensive metabolic reprogramming is repressed in incompatible interactions and that more defensive compounds are produced or retained. We also demonstrate that L. bicolor can metabolize a number of secreted defensive compounds and that the degradation of some of these compounds produces immune response metabolites (e.g., salicylic acid from salicin). Therefore, our results suggest that the metabolic responsiveness of plant roots to L. bicolor is a determinant factor in fungus-host interactions.
Collapse
|
21
|
Chaintreuil C, Arrighi JF, Giraud E, Miché L, Moulin L, Dreyfus B, Munive-Hernández JA, Villegas-Hernandez MDC, Béna G. Evolution of symbiosis in the legume genus Aeschynomene. THE NEW PHYTOLOGIST 2013; 200:1247-59. [PMID: 23879229 DOI: 10.1111/nph.12424] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 06/24/2013] [Indexed: 05/22/2023]
Abstract
Legumes in the genus Aeschynomene form nitrogen-fixing root nodules in association with Bradyrhizobium strains. Several aquatic and subaquatic species have the additional capacity to form stem nodules, and some of them can symbiotically interact with specific strains that do not produce the common Nod factors synthesized by all other rhizobia. The question of the emergence and evolution of these nodulation characters has been the subject of recent debate. We conducted a molecular phylogenetic analysis of 38 different Aeschynomene species. The phylogeny was reconstructed with both the chloroplast DNA trnL intron and the nuclear ribosomal DNA ITS/5.8S region. We also tested 28 Aeschynomene species for their capacity to form root and stem nodules by inoculating different rhizobial strains, including nodABC-containing strains (ORS285, USDA110) and a nodABC-lacking strain (ORS278). Maximum likelihood analyses resolved four distinct phylogenetic groups of Aeschynomene. We found that stem nodulation may have evolved several times in the genus, and that all Aeschynomene species using a Nod-independent symbiotic process clustered in the same clade. The phylogenetic approach suggested that Nod-independent nodulation has evolved once in this genus, and should be considered as a derived character, and this result is discussed with regard to previous experimental studies.
Collapse
Affiliation(s)
- Clémence Chaintreuil
- IRD/CIRAD/UM2/Supagro, Laboratoire des Symbioses Tropicales et Méditerranéennes, F-34398, Montpellier, France
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Genome analysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica. Appl Environ Microbiol 2013; 79:2542-51. [PMID: 23396330 DOI: 10.1128/aem.00009-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agromonas oligotrophica (Bradyrhizobium oligotrophicum) S58(T) is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lacking nodABC genes and the typical symbiosis island. The genome showed a high level of similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrhizobium sp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant, Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nif and fix) with A. indica were well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with five A. oligotrophica strains (S58, S42, S55, S72, and S80). Surprisingly, all five strains of A. oligotrophica formed effective nitrogen-fixing nodules on the roots and/or stems of A. indica, with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis with A. indica is a common trait of nodABC- and symbiosis island-lacking strains within the members of the photosynthetic Bradyrhizobium clade, including A. oligotrophica.
Collapse
|