Alpha-, gamma- and beta-proteobacteria detected in legume nodules in Latvia, using full-length 16S rRNA gene sequencing

ABSTRACT

Rhizobia are soil bacteria that form nodules on legumes and fix atmospheric nitrogen, reducing the need for chemical fertilisers. In most studies rhizobia are described as alpha-proteobacteria and have been studied extensively for several decades. However, in recent years an increasing number of studies present beta- and gamma-proteobacteria strains as potential rhizobia-like bacteria. In this study we identify bacteria isolated from nodules of various legumes grown in Latvia, using a full-length 16S rRNA gene sequence, used for more precision, compared with a partial sequence of the gene. Bacterial strains in this study have been isolated from 1962–2019, part of which are rhizobia strains from a unique historical collection. This is the first time bacterial strains isolated from nodules in Latvian soils have been identified with molecular biology methods. A wide taxonomic diversity was detected – bacteria species from α-, β-, γ-proteobacteria classes and Paenibacillus polymyxa strains from the Bacilli class. P. polymyxa strains were detected only in the historical collection, while β- and γ-proteobacteria strains were obtained only from the newly isolated specimens, uncovering new potential strains for a commercial legume seed inoculum. Soil samples were collected, and phosphorus levels were determined. Several strains indicate phosphate solubilising properties.

KEYWORDS:

• Legume nodules
• non-rhizobia endophytes
• phosphate-solubilising bacteria
• rhizobia
• rhizosphere diversity

Acknowledgements

We thank the personnel at the LBTU, Institute of Soil and Plant Sciences for their assistance in sample collection. We thank LBTU Research Laboratory of Biotechnology, The Division of Molecular Biology and Microbiology for the provided laboratory space and molecular biology equipment.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data Availability Statement

Sequencing data presented in this study are openly available in GenBank database referring to the accession numbers provided in Table S2.

Author contribution

The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Notes

1 EU Common Agricultural Policy: https://bit.ly/2t0GM1E.

2 European Green Deal: https://bit.ly/418wRpY.

Additional information

Funding

This research was funded by FP7 Research Project EUROLEGUME (Enhancing of legumes growing in Europe through sustainable cropping for protein supply for food and feed) [Grant agreement ID: 613781] and SusCrop- ERA-NET project LegumeGap (Increasing productivity and sustainability of European plant protein production by closing the grain legume yield gap.

Notes on contributors

A. Klūga

A. Klūga is a PhD degree candidate at the Latvia University of Life Sciences and Technologies (LBTU), Faculty of Agriculture. She received a master's degree in biology from the University of Amsterdam in Amsterdam, Netherlands. She is currently working in LBTU Faculty of Agriculture as a lecturer and as a researcher in various research projects concerning legumes. She is interested in legume-rhizobia interactions as well as rhizobia and other soil microorganism role in sustainable agriculture.

L. Dubova

Dr. L. Dubova is a docent and lead scientist at the Latvia University of Life Sciences and Technologies (LBTU), Institute of Soil and Plant Sciences. Dr. Dubova has received her Ph.D. degree in agriculture from LBTU, Faculty of Agriculture, Jelgava, Latvia. Laila Dubova is currently working at LBTU Institute of Soil and Plant Sciences as a lecturer and as a researcher in various projects. She is interested in soil microbiology and the beneficial effects of mycorrhiza and rhizobia bacteria in sustainable agriculture.

I. Alsiņa

Dr. I. Alsiņa has received her Ph.D. degree in biology from University of Latvia, Faculty of Biology, Riga, Latvia. She is currently a professor and lead scientist at the Latvia University of Life Sciences and Technologies, Institute of Soil and Plant Sciences (Jelgava, Latvia), working as a lecturer, as well as a researcher in various projects. Her scientific interests include plant physiological and horticultural topics, such as non-destructive methods; greenhouse light quality; legume-rhizobia interactions; sustainable agriculture.

N. Rostoks

Dr. N. Rostoks is professor and program director at the Faculty of Biology, University of Latvia, Riga, Latvia. Dr. Rostoks has over 20 years of experience in plant genetics, genomics, genetic engineering, and biotechnology. He is currently the director of Latvian Biomedical Research and Study Centre (Riga, Latvia). He also has 8 years of experience in the European Food Safety Authority GMO Panel that authorizes GMOs for food and feed uses, and cultivation in the EU.