Genomics of Nitrogen-Fixing Plant Symbiotic Bacteria

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 19869

Special Issue Editors


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Chief Guest Editor
CSIC - Estación Experimental del Zaidín (EEZ), Granada, Spain
Interests: nitrogen-fixing symbiosis; rhizobia; regulation of gene expression; non-coding transcriptome; regulation by RNA; RNA-binding proteins

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Guest Editor
Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
Interests: rhizospheric and endophytic microbiomes; microbial evolution; bacterial genetics and ecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Some soil-dwelling microbes of the α and β classes of proteobacteria, collectively referred to as rhizobia, are well-known for their ability to establish species-specific nitrogen-fixing mutualistic symbioses with legumes. Other diazotrophic bacteria (e.g., Frankia and Cyanobacteria) can also live in symbiosis with a large diversity of non-legume plants. These associations render plant growth independent of the costly and environmentally unfriendly chemical fertilizers, collectively contributing more than half of the combined nitrogen incorporated annually into terrestrial ecosystems. Plant symbiotic diazotrophs have been the focus of intensive research worldwide during recent decades due to their great impact on planet sustainability. Besides, these symbioses represent complex biological experimental models to decipher the underlying fundamental mechanisms of interactions between bacteria and a eukaryotic host. During the last two decades, the development of high-throughput technologies to explore the structure and function of bacterial genomes has revolutionized our understanding of nitrogen-fixing symbioses at a fundamental level, providing new opportunities for a more rational biotechnological exploitation of the different systems. This Special Issue has been conceived to update the most recent insights into the biology of the plant symbiotic nitrogen-fixers from a holistic genomic perspective. The issue will gather review and research articles addressing different aspects of plant symbiotic diazotrophs genomics including but not limited to the following:

  • Structure of genomes and pangenomes of the different species
  • Population and evolutionary genomics
  • Genetic, metabolic and regulatory networks
  • The non-coding transcriptome and regulation of gene expression by RNA
  • Novel functional genomics approaches to understand plant symbioses
  • Genomics-based engineering of bioinoculants and nitrogen-fixation

Dr. José I. Jiménez-Zurdo
Chief Guest Editor
Prof. Dr. Alessio Mengoni
Guest Editors

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Published Papers (3 papers)

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Research

12 pages, 1449 KiB  
Article
Identification of an Exopolysaccharide Biosynthesis Gene in Bradyrhizobium diazoefficiens USDA110
by Chunxia Xu, Huaqin Ruan, Wenjie Cai, Christian Staehelin and Weijun Dai
Microorganisms 2021, 9(12), 2490; https://doi.org/10.3390/microorganisms9122490 - 01 Dec 2021
Cited by 4 | Viewed by 1948
Abstract
Exopolysaccharides (EPS) play critical roles in rhizobium-plant interactions. However, the EPS biosynthesis pathway in Bradyrhizobium diazoefficiens USDA110 remains elusive. Here we used transposon (Tn) mutagenesis with the aim to identify genetic elements required for EPS biosynthesis in B. diazoefficiens USDA110. Phenotypic screening of [...] Read more.
Exopolysaccharides (EPS) play critical roles in rhizobium-plant interactions. However, the EPS biosynthesis pathway in Bradyrhizobium diazoefficiens USDA110 remains elusive. Here we used transposon (Tn) mutagenesis with the aim to identify genetic elements required for EPS biosynthesis in B. diazoefficiens USDA110. Phenotypic screening of Tn5 insertion mutants grown on agar plates led to the identification of a mutant with a transposon insertion site in the blr2358 gene. This gene is predicted to encode a phosphor-glycosyltransferase that transfers a phosphosugar onto a polyprenol phosphate substrate. The disruption of the blr2358 gene resulted in defective EPS synthesis. Accordingly, the blr2358 mutant showed a reduced capacity to induce nodules and stimulate the growth of soybean plants. Glycosyltransferase genes related to blr2358 were found to be well conserved and widely distributed among strains of the Bradyrhizobium genus. In conclusion, our study resulted in identification of a gene involved in EPS biosynthesis and highlights the importance of EPS in the symbiotic interaction between USDA110 and soybeans. Full article
(This article belongs to the Special Issue Genomics of Nitrogen-Fixing Plant Symbiotic Bacteria)
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15 pages, 2484 KiB  
Article
Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022
by Laura Baxter, Proyash Roy, Emma Picot, Jess Watts, Alex Jones, Helen Wilkinson, Patrick Schäfer, Miriam Gifford and Beatriz Lagunas
Microorganisms 2021, 9(12), 2428; https://doi.org/10.3390/microorganisms9122428 - 25 Nov 2021
Cited by 2 | Viewed by 2675
Abstract
Here, we report an improved and complete genome sequence of Sinorhizobium (Ensifer) meliloti strain WSM1022, a microsymbiont of Medicago species, revealing its tripartite structure. This improved genome sequence was generated combining Illumina and Oxford nanopore sequencing technologies to better understand [...] Read more.
Here, we report an improved and complete genome sequence of Sinorhizobium (Ensifer) meliloti strain WSM1022, a microsymbiont of Medicago species, revealing its tripartite structure. This improved genome sequence was generated combining Illumina and Oxford nanopore sequencing technologies to better understand the symbiotic properties of the bacterium. The 6.75 Mb WSM1022 genome consists of three scaffolds, corresponding to a chromosome (3.70 Mb) and the pSymA (1.38 Mb) and pSymB (1.66 Mb) megaplasmids. The assembly has an average GC content of 62.2% and a mean coverage of 77X. Genome annotation of WSM1022 predicted 6058 protein coding sequences (CDSs), 202 pseudogenes, 9 rRNAs (3 each of 5S, 16S, and 23S), 55 tRNAs, and 4 ncRNAs. We compared the genome of WSM1022 to two other rhizobial strains, closely related Sinorhizobium (Ensifer) meliloti Sm1021 and Sinorhizobium (Ensifer) medicae WSM419. Both WSM1022 and WSM419 species are high-efficiency rhizobial strains when in symbiosis with Medicago truncatula, whereas Sm1021 is ineffective. Our findings report significant genomic differences across the three strains with some similarities between the meliloti strains and some others between the high efficiency strains WSM1022 and WSM419. The addition of this high-quality rhizobial genome sequence in conjunction with comparative analyses will help to unravel the features that make a rhizobial symbiont highly efficient for nitrogen fixation. Full article
(This article belongs to the Special Issue Genomics of Nitrogen-Fixing Plant Symbiotic Bacteria)
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17 pages, 3268 KiB  
Article
Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity
by Riccardo Rosselli, Nicola La Porta, Rosella Muresu, Piergiorgio Stevanato, Giuseppe Concheri and Andrea Squartini
Microorganisms 2021, 9(2), 407; https://doi.org/10.3390/microorganisms9020407 - 16 Feb 2021
Cited by 5 | Viewed by 2920
Abstract
Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial [...] Read more.
Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N2 into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions. Full article
(This article belongs to the Special Issue Genomics of Nitrogen-Fixing Plant Symbiotic Bacteria)
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