The riddle of soil microbial assessments in organic greenhouse horticulture

Soil is a dynamic and living resource and base for the production of food and non-food crops, but also an important player in the global balance of ecosystems and ecosystem functions. The quality and health status of soils are used to describe the sustainability of agroecosystem, its environmental quality and are an indicator for plant, animal and human health. The recently launched EU-legislation for organic farming is explicit about organic cropping systems’ contribution to a high level of biodiversity. Although it mentions various ecosystem services provided through soil, there is no indication on what this means for the soil biota, especially soil microbiota and how this should be monitored, scored and followed up. Various methods may be employed to describe soil microbial attributes and processes in organic greenhouse horticulture. The challenge is to embrace the complexity of interactions to draw adequate conclusions on implementation. In this contribution, we focus on soil-microbe interactions. Recent development of high-throughput methods for culture independent description of microbial community composition, gathering a copious volume of data, increases the level of complexity even more. This article concentrates on methods to assess microbial biomass, abundance, diversity and function. It is based on cases from various national Swedish as well as European, projects on organic greenhouse horticulture.