Role of the Bacterial BacA ABC‐Transporter in Chronic Infection of Nodule Cells by<i>Rhizobium</i>Bacteria

Guefrachi, Ibtissem; Verly, Camille; Kondorosi, Éva; Alunni, Benoît; Mergaert, Peter

doi:10.1002/9781119053095.ch31

Cited by 5 publications

(5 citation statements)

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“…In addition, CNPSo 106 may have lost putative nopM and a bacA -like genes. The negative impact of nopM was described above, while bacA and bclA ( bacA -like) encode peptide transporters essential for symbiosis with legumes that produce nodule-specific cysteine-rich (NCR) peptide, but not for symbiosis with legumes such as soybean that do not produce NCR peptides (Glazebrook et al, 1993; Karunakaran et al, 2010; Guefrachi et al, 2015). Interestingly, CNPSo 104, the most competitive and efficient nitrogen-fixer of this group, appears to have lost nine genes encoding five transposases, three hypothetical proteins, a sulfite exporter TauE/SafE family protein, and a sulfurtransferase important to sulfur and carbon cycles, while gaining two hypothetical genes and two putative transposases.…”

Section: Discussionmentioning

confidence: 97%

Comparative genomic analysis ofBradyrhizobiumstrains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions

Klepa,

diCenzo,

Hungria

2024

Preprint

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Bradyrhizobiumis known for its ability to fix atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight putative natural variants ofB. japonicumSEMIA 586 (=CNPSo 17) orB. diazoefficiensSEMIA 566 (=CNPSo 10), previously used as commercial inoculants for soybean crops in Brazil. We aimed to detect genetic variations that might be related to biological nitrogen fixation, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains and used for comparative genomic analyses. The core genome phylogeny revealed that strains of each group are closely related, confirmed by high average nucleotide identity (ANI) values. However, variants accumulated divergences resulting from horizontal gene transfer (HGT), genomic rearrangements, and nucleotide polymorphisms. TheB. japonicumgroup presented a larger pangenome and a higher number of nucleotide polymorphisms than theB. diazoefficiensgroup, probably due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of theB. japonicumgroup carry two plasmids. The genetic variability found in both groups is discussed in light of the observed differences in their nitrogen fixation capacity, competitiveness for nodule occupancy, and environmental adaptation.SIGNIFICANCEThe two main reference strains for soybean inoculation in Brazil,B. japonicumCPAC 15 (=SEMIA 5079) andB. diazoefficiensCPAC 7 (=SEMIA 5080), have been considered highly competitive and highly efficient in nitrogen fixation, respectively. In this study, we obtained and analyzed the genomes of the parental and variant strains. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into evolution ofBradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.

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Section: Discussionmentioning

confidence: 97%

Comparative genomic analysis ofBradyrhizobiumstrains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions

Klepa,

diCenzo,

Hungria

2024

Preprint

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“…In addition, CNPSo 106 may have lost putative nopM and bacA -like genes. The negative impact of nopM was described above, while bacA and bclA ( bacA -like) encode peptide transporters essential for symbiosis with legumes that produce nodule-specific cysteine-rich (NCR) peptide but not for symbiosis with legumes such as soybean that do not produce NCR peptides ( 51 – 53 ). Interestingly, CNPSo 104, the most competitive and efficient nitrogen fixer of this group, appears to have lost nine genes encoding five transposases, three hypothetical proteins, a sulfite exporter TauE/SafE family protein, and a sulfurtransferase important to sulfur and carbon cycles, while gaining two hypothetical genes and two putative transposases.…”

Section: Discussionmentioning

confidence: 97%

Comparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions

Klepa,

diCenzo,

Hungria

2024

Microbiol Spectr

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Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s–1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation. IMPORTANCE Today, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops. As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into the evolution of Bradyrhizobium , and some of the identified differences may be applied as genetic markers to assist strain selection programs.

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“…Additionally, it can foster endocytosis of the cell host, among other functions related to microbial-host interactions 79 . The pSIs identified in Halomonas (LC_1) and Cobetia (LC_6) genomes were rich in TRAP and ABC transporters, which are also important for microbial-host interactions 80 , 81 . Flagellar motility and chemotaxis are also essential for bacterial symbionts to reach and colonize the coral host 82 – 84 .…”

Section: Discussionmentioning

confidence: 99%

Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host

Villela

Modolon

Schultz

et al. 2023

Sci Rep

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Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.

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Role of the Bacterial BacA ABC‐Transporter in Chronic Infection of Nodule Cells byRhizobiumBacteria

Cited by 5 publications

References 74 publications

Comparative genomic analysis ofBradyrhizobiumstrains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions

Comparative genomic analysis ofBradyrhizobiumstrains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions

Comparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions

Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host

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