Utilizing the soil microbiome for sustainable agriculture in the UK: Drawing from rhizobial inoculants and farmer knowledge

The soil microbial community provides many soil functions such as plant growth stimulation and resistance. Modern intensive agricultural practices depend on industrial inputs such as inorganic fertilisers, which weaken the soil microbe-plant interactions. In the light of multiple challenges associated with the use of chemicals in agriculture, it is thus, crucial to make a transition to more sustainable practices and techniques by using and enhancing the functions of the soil microbiome itself. In this thesis, I investigate the use of rhizobial inoculants – nitrogen-fixing bacteria that form symbiotic associations with legumes, used as biofertilizers/inoculants in agriculture - to make this transition.
My thesis approaches this question from two very different approaches – firstly, through classical hypothesis - driven biological research, and secondly, through hypothesis - generating social science.
Temperate phages are naturally occurring symbiotic viruses that can provide beneficial traits to their bacteria including increased competitiveness. I explore the relationship between phages and rhizobia to see if this could ‘naturally’ enhance potential inoculant strains. In chapter 2, I analyzed the impact of temperate phage carriage on rhizobia performance by measuring gene expression data from within clover nodules and host plant growth. RNA sequencing results show that the same phage has different effects on the gene expression of different rhizobial strains. However, this does not affect the symbiotic efficiency of rhizobia-clover symbiosis i.e. the dry weight of plants and total nitrogen of eight week plants. In chapter 3, I investigated if phage carriage increases the fitness of host rhizobia in competition with other diverse rhizobia. No competitive fitness benefits were observed in vitro and in plantae in different rhizobia strains, regardless of their susceptibility to phage infection and killing, except a susceptible strain that couldn’t be lysogenized by the phage. This non-lysogenized strain increased its competitive fitness by 72% in vitro and by 21% in the plant root environment. These results show that phage mediated competitive fitness effects depend on the spatial structure and competitor's susceptibility to phage infection and killing. In chapter 4, I took an entirely different approach to this same question. I interviewed UK legume farmers and urban growers to explore the existing soil microbiome and soil inoculant perceptions and practices. The social science chapter shows that farmers had different perceptions about the soil microbiome and soil inoculants. They followed different practices and soil assessment techniques to take care of the soil microbiome and assess their presence as well as functioning. There is thus diverse and fragmentary knowledge of soil inoculants in the growing community. The importance of experiential knowledge to people’s perceptions of soil inoculants and understanding of the soil microbiome suggests that future research needs to involve the growing community more strongly in product development and testing.