Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents

Abstract

Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.

Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management

“…Both DNA and RNA were simultaneously extracted from soil samples (2 g each), using a lab-made protocol based on phenolchloroform-isoamylalcohol extraction (Harkes et al, 2019). Quality and quantity of the obtained RNA and DNA was measured with a Nanodrop and Qubit.…”

“…The variable V4 region of bacterial 16S rRNA gene was utilized as target for the analyses of Illumina 16S rDNA sequencing and the V9, V7-V8, V5-V7 regions were utilized as targets for protozoa, fungi, and metazoan 18S rDNA sequencing, respectively. To prepare the samples for sequencing, a two-step PCR procedure was followed as described in (Harkes et al, 2019). In short, locus-specific primer combinations extended with an Illumina read area and the appropriate adapter were used to produce primary amplicons.…”

“…Ribosomal RNA is frequently used to map the active microbial fractions (Ofek et al, 2014;De Vrieze et al, 2016). By the molecular characterization of both the resident and the active fractions of the bacterial, fungal, protist, and metazoan community, it is possible to assess the impact of soil management regimes on the soil food web (Harkes et al, 2019).…”

Contrasting responses of protistan plant parasites and phagotrophs to ecosystems, land management and soil properties

“…The importance of soil type is corroborated by significant effects of soil physico-chemical parameters (soil pH, clay content, soil organic matter content) on the regional scale (Table S5 & Figure S5). Soil types, with their specific physical and chemical properties, are considered to be strong environmental filters for the assembly of microbial communities, sometimes more influential than plant species (Garbeva et al, 2004;Harkes et al, 2019). Importantly, soil types may contribute to explain regional differences in microbial community composition.…”

“…A study under controlled greenhouse conditions showed a reduction of the relative abundance of plant pathogenic protists was reduced by organic fertilizer amendments, while bacterivores and omnivores increased (Xiong et al, 2018). However, in a field study, plant parasites were favoured by organic fertilization (Harkes et al, 2019). Thus, currently a global and coherent picture of the responses of protistan plant pathogens to fertilization and other anthropogenic changes cannot be inferred.…”