Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil
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Abstract
Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium, as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium, closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium. All the isolates lacked nod and nif symbiotic genes but contained a repABC replication / maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. These repABC sequences were related, but not identical, to repABC sequences found in symbiotic plasmids from N. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members of Neorhizobium from soil.
Cite this as
2018. Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil. PeerJ Preprints 6:e26724v1 https://doi.org/10.7287/peerj.preprints.26724v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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Supplemental Information
Schematic representation of the semi-selective enrichment procedure to isolate fast-growing Rhizobia from the Tomejil soil
PCR amplification of a genomic DNA band from Tomejil Neorhizobium sp. strains with fnrN primers
(A) Agarose gel electrophoresis separation of PCR products. (B) Schematic representation of the genomic region amplified by fnrN primers in Tomejil Neorhizobium sp. strains (see text).
GenBank IDs of DNA sequences obtained or used in this work
Pairwise Average Nucleotide Identities (ANIb) between representative Neorhizobium sp. Tomejil isolates and Neorhyzobium sp. type strains
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Amalia Soenens conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Juan Imperial conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
The 16S rDNA and rpoB sequences described here were deposited in GenBank under accession numbers MG957216 to MG957235, and MG966473 toMG966492, respectively. Genome sequences were deposited in GenBank under Bioprojects
Data Deposition
The following information was supplied regarding data availability:
No raw data / code was generated
Funding
This work was supported by the CONSOLIDER-INGENIO program (CSD2009-00006) and by project LUPIGEN (CGL2011-26932), both from the Spanish Plan Nacional de Investigación Científica y Técnica. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
