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

Publication date: Available online 30 January 2019Source: Soil Biology and BiochemistryAuthor(s): Rehab Z. Abdallah, Carl-Eric Wegner, Werner LiesackAbstractDrainage is an important mitigation strategy to reduce methane emission from rice paddies. Here, we investigated how drainage shapes structure and functioning of the paddy soil microbial community. Soil microcosms were pre-incubated for 28 days under flooded conditions followed by nine days' drainage. Upon sampling, metatranscriptome libraries were generated from flooded and drained soils. With drainage, oxygen concentration increased from suboxic (1.6 μmol/l) to near-atmospheric (240 μmol/l) levels. Concurrently, water potential decreased to −0.87 MPa (corresponding to 11% soil moisture content). Drainage did not affect the absolute (RT-qPCR) SSU rRNA abundance of Bacteria and Archaea, but changed significantly their community composition. Firmicutes (Clostridiaceae, Ruminococcaceae, and Lachnospiraceae) decreased in relative abundance, while Actinobacteria (Nocardioidaceae) and Proteobacteria (Comamonadaceae) increased. These taxon-specific dynamics were observed on rRNA and mRNA levels. Methanogen SSU rRNA was stable, but methanogen mRNA significantly decreased. This coincided with complete inhibition of the methane production potential in drained soil. Among Eukarya, protists and Amoebozoa thrived in flooded soil, while Fungi proliferated with drainage. In particular, Pezizomycotina (Ascomycota) and Agaricom...
Source: Soil Biology and Biochemistry - Category: Biology Source Type: research