Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation

Amisha T Poret-Peterson,Nada Sayed,Enid T González-Orta,Daniel A Kluepfel,Nathaniel Glyzewski,Holly Forbes

doi:10.1007/s00248-019-01477-6

Abstract

Anaerobic soil disinfestation (ASD) is an organic amendment-based management tool for controlling soil-borne plant diseases and is increasingly used in a variety of crops. ASD results in a marked decrease in soil redox potential and other physicochemical changes, and a turnover in the composition of the soil microbiome. Mechanisms of ASD-mediated pathogen control are not fully understood, but appear to depend on the carbon source used to initiate the process and involve a combination of biological (i.e., release of volatile organic compounds) and abiotic (i.e., lowered pH, release of metal ions) factors. In this study, we examined how the soil microbiome changes over time in response to ASD initiated with rice bran, tomato pomace, or red grape pomace as amendments using growth chamber mesocosms that replicate ASD-induced field soil redox conditions. Within 2 days, the soil microbiome rapidly shifted from a diverse assemblage of taxa to being dominated by members of the Firmicutes for all ASD treatments, whereas control mesocosms maintained diverse and more evenly distributed communities. Rice bran and tomato pomace amendments resulted in microbial communities with similar compositions and trajectories that were different from red grape pomace communities. Quantitative PCR showed nitrogenase gene abundances were higher in ASD communities and tended to increase over time, suggesting the potential for altering soil nitrogen availability. These results highlight the need for temporal and functional studies to understand how pathogen suppressive microbial communities assemble and function in ASD-treated soils.

Highlights

Anaerobic soil disinfestation (ASD) is an organic amendmentbased pre-plant treatment for the control of plant pathogens in a variety of cropping systems [1,2,3,4]
ASD using different carbon substrates has been shown to be effective at controlling plant parasitic nematodes [9] and several microbial plant pathogens: Agrobacterium tumefaciens, Fusarium oxysporum, Ralstonia solanacearum, Rhizoctonia solani, Pythium spp., and Verticillium dahliae [5, 6, 10,11,12,13]
Treatments consisted of four replicates of a no carbon control (NCC) and ASD using rice bran (RB), red grape pomace (RGP), or tomato pomace (TP) as the carbon sources

Summary

Introduction

Anaerobic soil disinfestation (ASD) is an organic amendmentbased pre-plant treatment for the control of plant pathogens in a variety of cropping systems [1,2,3,4]. ASD using different carbon substrates has been shown to be effective at controlling plant parasitic nematodes [9] and several microbial plant pathogens: Agrobacterium tumefaciens, Fusarium oxysporum, Ralstonia solanacearum, Rhizoctonia solani, Pythium spp., and Verticillium dahliae [5, 6, 10,11,12,13]. Carbon substrates used to initiate ASD include agricultural by-products (e.g., ethanol, molasses, rice bran, seed meals, and wheat bran), cruciferous cover crops, and composted poultry litter [2, 3, 14]. Other agricultural byproducts are being examined for their effectiveness as ASD substrates, including tomato pomace, red grape pomace, nuts and shells from almond, walnut, and pistachio in order to

Methods

Results

Conclusion