The impact of crop rotation on soil microbial diversity: A meta-analysis

• Meta-analysis reveals increased microbial richness and diversity with crop rotation.
• This effect differed significantly between methods of microbial analysis.
• Longer rotation trials produced stronger positive effects on microbial richness.
• The associated effect on agroecosystem functioning needs clarification through next generation sequencing.

Agricultural intensification can involve the simplification of agroecosystems to crop monocultures while the practices of crop rotation, intercropping and companion planting maintain some crop diversity over time and space. It is generally postulated that reduced diversity can have an impact on ecosystem function. Here we determine whether decreased aboveground crop diversity affects belowground microbial biodiversity by conducting a meta-analysis of studies comparing monocultures and crop rotations. We based taxonomic richness and diversity indices on both molecular and biochemical fingerprinting methods. Soils under a higher diversity of crops in rotation produced higher microbial richness (+15.11%, n = 26) and diversity (+3.36%, n = 43) scores. This effect was significantly influenced by the proxy and methodology used where pyrosequencing produced higher richness scores compared to fingerprinting methods. Longer study trials produced larger increases in microbial richness, although the opposite was true for microbial diversity. The addition of legumes to rotation had no consistent effects on microbial diversity or richness. Whether the overall rotation-effect on microbial diversity promotes ecosystem functioning in terms of nutrient cycling and resilience to stress remains unclear. Future studies that incorporate next-generation sequencing techniques will help to elucidate complex microbial community structures and specific functional niches in agroecosystems.