Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation

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 ASDtreated soils.

Analysis of Environmental Variables and Carbon Input on Soil Microbiome, Metabolome and Disease Control Efficacy in Strawberry Attributable to Anaerobic Soil Disinfestation

“…However, Bacillus spp., which initially represented the dominant component of the Firmicutes community, was displaced as ASD progressed by anaerobic Clostridia, namely Clostridium intestinale and Clostridium roseum . Similar trends in ASD-induced changes to the composition of Firmicute populations over the incubation period were initially reported by [ 20 ] and have subsequently been documented in additional studies on ASD [ 57 ]. An additional, notable shift in microbiome composition was observed during soil aeration between days 21 and 31.…”

Two Distinct Soil Disinfestations Differently Modify the Bacterial Communities in a Tomato Field

“…Indeed, the relative abundances of some groups belonging to the bacterial order Sphingobacteriales and fungal order Sordariales also increased by RSD, which were negatively correlated with disease incidence [60]. In addition to the pathogenic control effect, the abundances of the nitrogenase and ammonia monooxygenase genes related to nitrification increased in RSD-treated soil [68,72], suggesting the improvement of nutritional availability by RSD. Recently, SS was reported to induce organic nitrogen to increase plant growth [34].…”

Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management of Verticillium dahliae in Tomatoes

“…Supplementary Materials: The following are available online at http://www.mdpi.com/2223-7747/9/11/1622/s1, Table S1: Disease compatibility of specific combinations of race-specific secreted effectors (Ave1 and V2) on resistant cultivars of tomatoes containing different combinations of the race 1 (Ve1) and race 2 (V2) resistance phenotypes, Table S2: Biocontrol agents (BCAs) and biologicals with biocontrol activity against Verticillium dahliae, Table S3: Some examples of organic amendments (OAs) with suppressiveness against Verticillium dahliae, Table S4: Examples of sources of carbon from recent studies for anaerobic soil disinfestation of soil-borne pathogens including Verticillium dahliae. References [137,140,[153][154][155][156][157][158][159][160][161]163,164,166,167,169,174,175,224, are cited in the supplementary materials. Funding: This research was funded by a USDA-NIFA Specialty Crop Research Initiative (SCRI) under award number 2016-51181-25404.…”

“…ASD treatments also induced changes in soil microbial communities and increased the soil microbial activity, and the populations of Bacteroidales, Clostridiales, Selenomonadales, Enterobacteriales, Sphingobacteriales, Bacillales, and Burkholderiales that antagonize plant pathogens [ 137 , 169 , 174 ]. The change in the bacterial communities and composition increased denitrification and nitrogen fixation and produced organic acids that influenced disease suppressiveness [ 175 ]. Optimizing the carbon source for ASD can improve the effectiveness of ASD and affordability for growers [ 169 ].…”

“…The following are available online at , Table S1: Disease compatibility of specific combinations of race-specific secreted effectors (Ave1 and V2) on resistant cultivars of tomatoes containing different combinations of the race 1 (Ve1) and race 2 (V2) resistance phenotypes, Table S2: Biocontrol agents (BCAs) and biologicals with biocontrol activity against Verticillium dahliae , Table S3: Some examples of organic amendments (OAs) with suppressiveness against Verticillium dahliae , Table S4: Examples of sources of carbon from recent studies for anaerobic soil disinfestation of soil-borne pathogens including Verticillium dahliae . References [ 137 , 140 , 153 , 154 , 155 , 156 , 157 , 158 , 159 , 160 , 161 , 163 , 164 , 166 , 167 , 169 , 174 , 175 , 224 , 249 , 250 , 251 , 252 , 253 , 254 , 255 , 256 , 257 , 258 , 259 , 260 , 261 , 262 , 263 , 264 , 265 , 266 , 267 , 268 , 269 , 270 , 271 , 272 , 273 , 274 , 275 ...…”