Meta-omics analyses of dual substrate enrichment culturing of nitrous oxide respiring bacteria suggest that attachment and complex polysaccharide utilisation contributed to the ability of Cloacibacterium strains to reach dominance

Abstract

Bioengineering soil metabolism by inoculation is an emerging approach to enhance plant growth and strengthen specific functions such as N2O reduction in order to reduce climate forcing. The use of organic wastes as substrates and carriers of microbial biomass has proven to be a viable approach to improving effectiveness and economic viability. A key factor in the success of this approach lies in selection of microbes capable of growth and survival in both organic wastes as well as soils, and which are tolerant of the rapid environmental fluctuations such fertilisations involve. A dual substrate, N2O-enrichment experiment, switching between soil and organic waste as substrates has yielded Cloacibacterium isolates which grow well in organic wastes and retain significant N2O reduction capacity when applied to soils. However, an understanding of the genetic and phenotypic characteristics utilised by these enrichment winners to dominate under such conditions remains unexplored. Here we have performed a multi-omics examination of the enrichment cultures, using both metagenomics and metaproteomics to probe the genetic basis and expressed proteins which may contribute to the success of Cloacibacterium in the enrichments, and their survival in soil. These omics results show an increase in complex carbohydrate metabolism, chemotaxis and motility genes throughout the enrichment as well as the expression of gliding motility proteins and polysaccharide utilization loci proteins by Cloacibacterium organisms. Taken together this suggests that attachment and complex polysaccharide utilisation may be key processes allowing Cloacibacterium to tolerate the stresses of a changing environment during transfers between digestate and soil.