Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

Abstract

Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.

Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants

“…inputs and tillage have been shown to shape bulk soil microbial communities and functions across spatial and temporal scales (1)(2)(3)(4). Comparisons of bulk soil under different management strategies, i.e., organic (nutrients provided from sources other than synthetic inputs) versus conventional management, have revealed effects on soil properties that, in turn, drive variation in microbial communities at small and intermediate scales (5)(6)(7)(8).…”

Functional Diversity of Soil Bacteria from Organic Agro Ecosystem

“…In the past, researchers have reported increased soil bacterial biomass, activity and bacterial functional and taxonomic richness and diversity in organic farm (Gardner et al, 2011;Lopes et al, 2011;Das and Dkhar, 2011;Grantina et al, 2011;Schmid et al, 2011;Wang et al, 2012;Stockdale et al, 2013;Hartmann et al, 2014;Lupatini et al, 2017). These workers have also reported higher population of microorganisms in organic farm in comparison to conventional farms.…”

Effect of long‐term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce

“…Long-term soil fertilization strategies play a significant role in the alteration of soil biological properties, and thus may affect soil functioning and quality (Bünemann et al, 2018). Several studies showed that soil microbial communities are influenced by long-term fertilization strategies (Hartmann et al, 2015;Francioli et al, 2016;Lupatini et al, 2017). The use of mineral fertilizers in conventional agriculture has contributed to increased crop productivity over the last decades (Robertson and Vitousek, 2009).…”