Abstract
Root nodule bacteria (RNB) or “rhizobia” are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic association and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogenetic distribution patterns and sequence signatures based on known precepts of symbiotic- and host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. These analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.
Highlights
The use of plant growth promoting bacteria to enhance crop yield and control disease is gaining worldwide acceptance as a sustainable agricultural practice, while reducing costs by supplanting the use of expensive agrochemicals
Root nodule bacteria (RNB) play a role in the production of biofuel crops–Millettia pinnata, for example, is a leguminous tree nodulated by Bradyrhizobium and Rhizobium spp. that produces biodiesel, starch, ethanol and biogas[8]
A more recent paper surveyed the occurrence of known plant growth promotion genes in all available proteobacterial genomes[12], and clearly many RNB were found to possess plant growth promotion traits beyond nitrogen fixation, but little had been done to explore novel effectors of plant growth or even the accessory factors mediating RNB-plant interactions
Summary
The use of plant growth promoting bacteria to enhance crop yield and control disease is gaining worldwide acceptance as a sustainable agricultural practice, while reducing costs by supplanting the use of expensive (and polluting) agrochemicals. With a burgeoning world population and increasing food demands, harnessing the innate potential of RNB to improve sustainable agricultural productivity is of paramount importance Despite these significant environmental and economic incentives, only a few genomes of a phylogenetically restricted group of model RNB strains had been sequenced at the inception of this study. The primary objective of our study was to (i) increase the repertoire of available RNB genomes in terms of their phylogenetic, biogeographic and host legume diversity, and (ii) identify novel microbial effectors of symbiosis, and plant growth and productivity, beyond what is currently known about nodulation and nitrogen fixation. These data provide a resource and conceptual framework for studying RNB-legume interactions, but our results highlight many new potential plant beneficial genes that could be targeted to improve legume productivity around the globe
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