Network analysis reveals distinct bacterial and fungal co-occurrence patterns in soils with different organic amendments in a seven-year-old field experiment

The living soil harbors a significant number and diversity of bacteria and fungi. Studies working on soil microorganisms often focus on either bacteria or fungi, ignoring potential interrelationships between kingdoms. In this work, we investigated the long-term influence of amelioration of the soil with organic amendments (compost and bokashi) in a seven-year-old field experiment on bacterial and fungal co-occurrence patterns in soil networks, extending community analyses beyond the exploration of taxonomic diversity and individual functions of one kingdom. We observed that organic amendments changed the co-occurrence patterns of bacteria and fungi, and this occurred in a dose-independent manner. Distinctive network modules were also observed in soil receiving different types and doses of organic amendments, and these distinctive modules were potentially shaped by physico-chemical properties of soil (dissolved organic carbon and nutrients). We also found that organic amendments reduced potential completion among microorganisms for resources and potential nutritional interactions between inter-kingdoms due to increased levels of nutrients. Our work provides valuable insights into whether and how co-occurrence patterns of bacteria and fungi in soil respond to commonly applied organic amendments.