Community transcriptomics reveals drainage effects on paddy soil microbiome across the three domains of life

Methane is a potent greenhouse gas that plays a major role in global climate change. Biogenic methane is produced solely by methanogens thriving in anoxic soil such as wetland rice fields. The wide use of rice straw as an organic fertiliser makes rice farming one of the major global sources of methane emission. It contributes approx. 10% to the total methane budget. The microbial communities in the rice field soil (paddy soil) are able to efficiently degrade rice straw under anoxic conditions. Bio-polymer breakdown is the rate-limiting step for methanogenesis. Drainage is a common practice in rice farming, and it serves as an important mitigation strategy to reduce methane emission from rice paddies. Moreover, it enhances soil health and productivity by increasing soil organic matter (SOM) decomposition and mineralization. The focus of my thesis research was to (i) elucidate how drainage shapes the structure and function of paddy soil microbial communities across all three domains of life and (ii) understand how the paddy soil microbial communities hydrolyse bio-polymers during drainage. Initially, paddy soil microcosms amended with rice straw were pre-incubated for 7 or 28 days under flooded conditions, followed by 9 days of drainage. The analysis showed that except for saprophytic fungi and methanotrophic bacteria, the duration of the pre-incubation period had only a minor effect on the microbial community response to drainage. Therefore, I focused my research on microcosms pre-incubated for 28 days under flooded conditions. During the flooding and drainage periods, the change in soil physical and chemical parameters was measured. The soil was sampled from flooded and drained microcosms, and the response of paddy soil bacterial, archaeal and eukaryotic communities was assessed using metatranscriptomics. With drainage, the oxygen concentration increased from suboxic (~1.6 μmol/l) to near-atmospheric (~240 μmol/l) levels. Concurrently, the moisture content decreased to ~ 11% and the water potential decreased to -0.87 MPa. The changes in soil physical and chemical characteristics did not affect the absolute SSU rRNA transcript abundances of bacteria and archaea, while those of fungi increased with drainage. However, drainage induced significant changes in their taxonomic composition. Firmicutes (Clostridiaceae, Ruminococcaceae, and Lachnospiraceae) decreased in relative abundance, while Actinobacteria (Nocardioidaceae), Proteobacteria (Comamonadaceae) increased. These ii taxon-specific dynamics were consistently observed on rRNA and mRNA levels. Significant increase of Planctomycetes abundance (Planctomycetaceae) was primarily observed on mRNA level. The abundance of methanogen mRNA significantly decreased with drainage, coinciding with complete inhibition of the methane production potential in dry soil. Among Eukarya, protists and Amoebozoa were prevalent under flooded conditions, while fungal rRNA and mRNA abundances were significantly increased upon drainage. In particular, Pezizomycotina (Ascomycota) and Agaricomycotina (Basidiomycota) were the most abundant fungal groups in dry soil. Taking the level of mRNA expression as a proxy, the overall microbiota activity was not severely affected by the decrease in water potential. The proportion of microbial mRNA in total RNA was 1.7% under flooded conditions and 2% upon drainage. Moreover, transcripts affiliated with transcription and translation were enriched with drainage. The mRNA proportion in total RNA combined with stable or increased SSU rRNA abundances indicates that drainage did not have a detrimental effect but induced the development of a community well adapted to oxic and dry soil conditions. This microbial community was characterized by an increase in the relative abundance of transcripts involved in lignin degradation, peptidoglycan lysis and had the capacity to metabolize storage molecules such as glycogen. Under flooded conditions, the microbial community expressed a higher level of glycoside hydrolase transcripts involved in cellulose and chitin degradation.