In this paper we review the influence of various soil factors on the legume–Rhizobium symbiotic relationship. Abiotic factors such as extremes in soil pH (highly acidic or alkaline soils), salinity, tillage, high soil temperature and chemical residues, all of which can occur in crop and pasture systems in southern Australia, generally reduce populations of Rhizobium in the soil. Naturally occurring Rhizobium populations, although often found in high numbers, are generally poor in their ability to fix nitrogen and can compete strongly with introduced Rhizobium inoculant. The introduction of new legume genera as a continuing and essential part of change in farming systems usually requires the need to identify new and specific inoculant Rhizobium strains not found in the soil, but necessary for optimum nitrogen fixation. It is therefore necessary to characterise the specific requirements or limitations in the soil for establishing Rhizobium populations to ensure optimal nitrogen fixation following inoculation of legumes. The ability of the introduced Rhizobium to form effective nodules is rarely linked to a single soil attribute; therefore the study of rhizobial ecology requires an understanding of many soil and environmental factors. This paper reviews current knowledge of the influence of soil factors on rhizobial survival, the nodulation process, and nitrogen fixation by legumes.

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Background: The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production. Results: This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65-87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3-24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.

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The current dissatisfaction with low productivity of annual medic (Medicago spp.) pastures has highlighted the need to seek alternative legumes to provide efficient N2 fixation in low rainfall, alkaline soil environments of southern Australia. Clover species adapted to these environments will have limited N2 fixation if effective rhizobia are not present in sufficient quantities. A survey of 61 sites was conducted across South Australia to determine the size, distribution and effectiveness of Rhizobium leguminosarum bv. trifolii (clover rhizobia) populations resident in these low rainfall, alkaline soil environments. Clover rhizobia were detected at 56 of the sites, with a median density of 230–920 rhizobia/g soil. Most rhizobial populations were poor in their capacity to fix nitrogen. Rhizobial populations from fields provided 11–89% and 10–85% of the shoot biomass of commercial reference strains when inoculated onto host legumes T. purpureum (purple clover) and T. resupinatum (persian clover), respectively. Rhizobial population size was correlated negatively to pH and the percentage of CaCO3 in the soil, and was significantly increased in the rhizospheres of naturalised clover, found at 17 sites. Management options for rhizobial populations to improve legume diversity and productivity are discussed in terms of rhizobial population dynamics and likely soil constraints to successful rhizobial colonisation.