Organic soil amendment with Spent Mushroom Substrate results in fungal colonisation, alters bacterial-fungal co-occurrence patterns and improves plant productivity

Abstract

16In agricultural systems based on organic fertilisers, the activity of prokaryotes and fungi is 17 essential for degradation of complex substrates and release of nutrients for plant uptake. Understanding 18 the dynamics of microbial communities in these systems is, therefore, desirable for designing successful 19 management strategies aiming to optimise nutrient availability and to improve plant productivity. Of 20 particular interest is how the microbial inoculum provided by an organic substrate persists in the soil 21 and interacts with soil and plant microbiomes, as these processes may affect the long-term benefits of 22 organic amendments. We aimed to investigate how these dynamics occurred in soil treated with 23 stabilised spent mushroom substrate (SMS), a soil amendment rich in nutrients and complex organic 24 matter. We carried out a 14 weeks soil trial to assess the plant growth promoting properties of the SMS 25 and to monitor the successional processes of the resulting SMS-soil communities compared to a mineral 26 amended control. Bacterial and fungal communities were analysed by high-throughput sequencing at 27 both DNA and RNA (cDNA) levels. Using a combination of computational tools, including SourceTracker and Network analysis, we assessed the persistence of SMS-derived taxa in soil, and the 29 changes in co-occurrence patterns and microbial community structure over time. Prokaryotic and fungal 30 communities presented remarkably distinct trajectories following SMS treatment. The soil prokaryotic 31 communities displayed higher levels of resilience to the changes introduced by SMS treatment and 32 rapidly tended toward a soil-like profile, with low persistence of SMS-derived prokaryotes. In contrast, 33 the SMS fungal community had greater success in soil colonisation during the time monitored. SMS 34 treatment promoted an increase in the participation of fungi in the highly connected fraction of the 35 active community, including fungal taxa of SMS origin. We observed the presence of highly connected 36 microbial guilds, composed by fungal and bacterial taxa with reported capabilities of complex organic 37matter degradation. Many of these taxa were also significantly correlated with the organic matter 38 content and plant yield, suggesting that these highly connected taxa may play key roles not only in the 39 community structure, but also in the plant-soil system under organic fertilisation.