Shifts in Soil Bacterial Communities as a Function of Carbon Source Used During Anaerobic Soil Disinfestation

Poret-Peterson, Amisha T.; Albu, Sebastian; McClean, Ali E.; Kluepfel, Daniel A.

doi:10.3389/fenvs.2018.00160

Cited by 38 publications

(56 citation statements)

References 62 publications

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“…This study showed RB amendment induces turnover in the microbial community by linking changes in the microbiome and metabolome of ASD-treated soils. RB and TP communities tended to cluster together on all sampling days, similar to previous observations in field trials with these same carbon substrates [15]. RGP communities largely grouped separately from RB and TP communities.…”

Section: Changes In Microbial Communities Over Time In Soil Mesocosmssupporting

confidence: 85%

“…Microbial communities that develop in ASD-treated soils are shaped, to varying degrees, by the type of carbon substrate used to initiate the process [7,15,33,34]. In replicated field trials of ASD stimulated with different agricultural byproducts (RB, TP, molasses, or mustard seed meal), we found ASD carbon input explained a small amount of the variance in community composition (10 and 22%), but resulted in communities with much higher group dispersions than in untreated soils after 4 and 5 weeks of treatment [15]. We posited that the microbial communities would be more strongly structured by ASD carbon substrates and exhibit lower group dispersions following initiation of the process and the onset of anaerobic soil conditions.…”

Section: Changes In Microbial Communities Over Time In Soil Mesocosmsmentioning

confidence: 99%

“…ASD not only causes turnover in microbial communities but also reduces alpha diversity in many studies of the process [7,12,15,34]. Alpha diversity is often negatively correlated with oxygen availability in marine ecosystems due to constraints on energy sources available to fuel microbial metabolism [37,38].…”

Section: Changes In Microbial Communities Over Time In Soil Mesocosmsmentioning

confidence: 99%

“…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 also 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 reduce costs of the process and increase its adoption as a management tool [15]. Despite the carbon source used, ASD-mediated pathogen control has been found to involve the products of microbial fermentation (i.e., volatile fatty acids, acetate, butyrate, etc.…”

Section: Introductionmentioning

confidence: 99%

“…ASD is also a disturbance to the soil ecosystem and offers opportunities to examine the response of soil microbes to the imposition of anaerobic conditions, input of organic carbon, and the re-assembly of the soil microbiome [19]. Previously, we reported that ASD implemented with different agricultural by-products did not yield communities that were strongly structured as a function of carbon substrate after 4 and 5 weeks of ASD treatment [15]. Instead, ASD resulted in communities consisting of a core group of taxa belonging to the Firmicutes classes Clostridiales and Selenomonadales.…”

Section: Introductionmentioning

confidence: 99%

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Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation

et al. 2019

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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.

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Section: Changes In Microbial Communities Over Time In Soil Mesocosmssupporting

confidence: 85%

Section: Changes In Microbial Communities Over Time In Soil Mesocosmsmentioning

confidence: 99%

Section: Changes In Microbial Communities Over Time In Soil Mesocosmsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation

et al. 2019

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The macroecology of butyrate‐producing bacteria via metagenomic assessment of butyrate production capacity

Brame,

Liddicoat,

Abbott

et al. 2024

Ecology and Evolution

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Butyrate‐producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short‐chain fatty acid butyrate. However, the macroecological influences on their biogeographical distribution remain poorly resolved. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n = 13,078) and Australia‐wide soil 16S rRNA (n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest median BPC scores were found in anoxic and fermentative environments, including the human (BPC = 2.99) and non‐human animal gut (BPC = 2.91), and in some plant–soil systems (BPC = 2.33). Within plant–soil systems, roots (BPC = 2.50) and rhizospheres (BPC = 2.34) had the highest median BPC scores. Among soil samples, geographical and climatic variables had the strongest overall effects on BPC scores (variable importance score range = 0.30–0.03), with human population density also making a notable contribution (variable importance score = 0.20). Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas and sites with moderate‐to‐high soil iron concentrations. Abundances of butyrate‐producing bacteria in outdoor soils followed complex ecological patterns influenced by geography, climate, soil chemistry and hydrological fluctuations. These new macroecological insights further our understanding of the ecological patterns of outdoor butyrate‐producing bacteria, with implications for emerging microbially focused ecological and human health policies.

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