Structural changes in bacterial and fungal soil microbiome components during biosolarization as related to volatile fatty acid accumulation

Yigal Achmon; Joshua T. Claypool; Jesús D. Fernández-Bayo; Katie Hernandez; Dlinka G. McCurry; Duff R. Harrold; Joey Su; Blake A. Simmons; Steven W. Singer; Ruth M. Dahlquist-Willard; James J. Stapleton; Jean S. VanderGheynst; Christopher W. Simmons

doi:10.1016/j.apsoil.2020.103602

Structural changes in bacterial and fungal soil microbiome components during biosolarization as related to volatile fatty acid accumulation

Yigal Achmon^*, Joshua T. Claypool, Jesús D. Fernández-Bayo, Katie Hernandez, Dlinka G. McCurry, Duff R. Harrold, Joey Su, Blake A. Simmons, Steven W. Singer, Ruth M. Dahlquist-Willard, James J. Stapleton, Jean S. VanderGheynst, Christopher W. Simmons

^*Corresponding author for this work

Biotechnology and Food Engineering

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

Abstract

Biosolarization is an integrated pest management strategy that combines soil solarization with organic amendment application. In the present study, soil samples were taken after biosolarization using tomato pomace and green waste compost (GWC) amendments and analyzed to elucidate changes to the soil microbiome, including both fungal and bacterial communities. Following a field trial wherein soil mesocosms were biosolarized for 8 days, the effects of soil depth and soil amendments were assessed via sequencing and bioinformatic analysis of 16S rRNA gene and ITS2 amplicons generated from soil microbial genomic DNA. Structural and network analyses were used to quantify differences in microbiota between treatments and these results were correlated with measured levels of volatile fatty acids in the soils. The results showed that biosolarization had a stronger impact on the bacterial community relative abundance profile than on the fungal community at the phylum and order levels. However, at the operational taxonomic units (OTUs) level, biosolarization treatment had a significant impact on both fungal and bacterial communities, across soil depth and GWC addition. Co-occurrence microbial network analysis revealed a unique circular network consisting of 8 discrete clusters. Correlation between the clusters and soil volatile fatty acid (VFA) production suggested that the bacterial Clostridium, Weissella and Acetobacter genera tolerate, and perhaps drive, VFA accumulation. Notable fungal community effects included significantly reduced relative abundance within genera known to contain plant pathogenic members, such as Gibberella, Haematonectria, Fusarium, Aspergillus and Alternaria.

Original language	English
Article number	103602
Journal	Applied Soil Ecology
Volume	153
DOIs	https://doi.org/10.1016/j.apsoil.2020.103602
State	Published - Sep 2020

Keywords

Anaerobic soil disinfestation
Co-occurrence networks
Fungal pathogens
Integrated pest management
Soil microbiome
Soil solarization

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10.1016/j.apsoil.2020.103602

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Achmon, Y., Claypool, J. T., Fernández-Bayo, J. D., Hernandez, K., McCurry, D. G., Harrold, D. R., Su, J., Simmons, B. A., Singer, S. W., Dahlquist-Willard, R. M., Stapleton, J. J., VanderGheynst, J. S., & Simmons, C. W. (2020). Structural changes in bacterial and fungal soil microbiome components during biosolarization as related to volatile fatty acid accumulation. Applied Soil Ecology, 153, Article 103602. https://doi.org/10.1016/j.apsoil.2020.103602

@article{3f77ea7f6c334c22ad01f3cf731c88f9,

title = "Structural changes in bacterial and fungal soil microbiome components during biosolarization as related to volatile fatty acid accumulation",

abstract = "Biosolarization is an integrated pest management strategy that combines soil solarization with organic amendment application. In the present study, soil samples were taken after biosolarization using tomato pomace and green waste compost (GWC) amendments and analyzed to elucidate changes to the soil microbiome, including both fungal and bacterial communities. Following a field trial wherein soil mesocosms were biosolarized for 8 days, the effects of soil depth and soil amendments were assessed via sequencing and bioinformatic analysis of 16S rRNA gene and ITS2 amplicons generated from soil microbial genomic DNA. Structural and network analyses were used to quantify differences in microbiota between treatments and these results were correlated with measured levels of volatile fatty acids in the soils. The results showed that biosolarization had a stronger impact on the bacterial community relative abundance profile than on the fungal community at the phylum and order levels. However, at the operational taxonomic units (OTUs) level, biosolarization treatment had a significant impact on both fungal and bacterial communities, across soil depth and GWC addition. Co-occurrence microbial network analysis revealed a unique circular network consisting of 8 discrete clusters. Correlation between the clusters and soil volatile fatty acid (VFA) production suggested that the bacterial Clostridium, Weissella and Acetobacter genera tolerate, and perhaps drive, VFA accumulation. Notable fungal community effects included significantly reduced relative abundance within genera known to contain plant pathogenic members, such as Gibberella, Haematonectria, Fusarium, Aspergillus and Alternaria.",

keywords = "Anaerobic soil disinfestation, Co-occurrence networks, Fungal pathogens, Integrated pest management, Soil microbiome, Soil solarization",

author = "Yigal Achmon and Claypool, {Joshua T.} and Fern{\'a}ndez-Bayo, {Jes{\'u}s D.} and Katie Hernandez and McCurry, {Dlinka G.} and Harrold, {Duff R.} and Joey Su and Simmons, {Blake A.} and Singer, {Steven W.} and Dahlquist-Willard, {Ruth M.} and Stapleton, {James J.} and VanderGheynst, {Jean S.} and Simmons, {Christopher W.}",

note = "Publisher Copyright: {\textcopyright} 2020 Elsevier B.V.",

year = "2020",

month = sep,

doi = "10.1016/j.apsoil.2020.103602",

language = "英语",

volume = "153",

journal = "Applied Soil Ecology",

issn = "0929-1393",

publisher = "Elsevier",

}

Achmon, Y, Claypool, JT, Fernández-Bayo, JD, Hernandez, K, McCurry, DG, Harrold, DR, Su, J, Simmons, BA, Singer, SW, Dahlquist-Willard, RM, Stapleton, JJ, VanderGheynst, JS & Simmons, CW 2020, 'Structural changes in bacterial and fungal soil microbiome components during biosolarization as related to volatile fatty acid accumulation', Applied Soil Ecology, vol. 153, 103602. https://doi.org/10.1016/j.apsoil.2020.103602

TY - JOUR

T1 - Structural changes in bacterial and fungal soil microbiome components during biosolarization as related to volatile fatty acid accumulation

AU - Achmon, Yigal

AU - Claypool, Joshua T.

AU - Fernández-Bayo, Jesús D.

AU - Hernandez, Katie

AU - McCurry, Dlinka G.

AU - Harrold, Duff R.

AU - Su, Joey

AU - Simmons, Blake A.

AU - Singer, Steven W.

AU - Dahlquist-Willard, Ruth M.

AU - Stapleton, James J.

AU - VanderGheynst, Jean S.

AU - Simmons, Christopher W.

PY - 2020/9

Y1 - 2020/9

N2 - Biosolarization is an integrated pest management strategy that combines soil solarization with organic amendment application. In the present study, soil samples were taken after biosolarization using tomato pomace and green waste compost (GWC) amendments and analyzed to elucidate changes to the soil microbiome, including both fungal and bacterial communities. Following a field trial wherein soil mesocosms were biosolarized for 8 days, the effects of soil depth and soil amendments were assessed via sequencing and bioinformatic analysis of 16S rRNA gene and ITS2 amplicons generated from soil microbial genomic DNA. Structural and network analyses were used to quantify differences in microbiota between treatments and these results were correlated with measured levels of volatile fatty acids in the soils. The results showed that biosolarization had a stronger impact on the bacterial community relative abundance profile than on the fungal community at the phylum and order levels. However, at the operational taxonomic units (OTUs) level, biosolarization treatment had a significant impact on both fungal and bacterial communities, across soil depth and GWC addition. Co-occurrence microbial network analysis revealed a unique circular network consisting of 8 discrete clusters. Correlation between the clusters and soil volatile fatty acid (VFA) production suggested that the bacterial Clostridium, Weissella and Acetobacter genera tolerate, and perhaps drive, VFA accumulation. Notable fungal community effects included significantly reduced relative abundance within genera known to contain plant pathogenic members, such as Gibberella, Haematonectria, Fusarium, Aspergillus and Alternaria.

AB - Biosolarization is an integrated pest management strategy that combines soil solarization with organic amendment application. In the present study, soil samples were taken after biosolarization using tomato pomace and green waste compost (GWC) amendments and analyzed to elucidate changes to the soil microbiome, including both fungal and bacterial communities. Following a field trial wherein soil mesocosms were biosolarized for 8 days, the effects of soil depth and soil amendments were assessed via sequencing and bioinformatic analysis of 16S rRNA gene and ITS2 amplicons generated from soil microbial genomic DNA. Structural and network analyses were used to quantify differences in microbiota between treatments and these results were correlated with measured levels of volatile fatty acids in the soils. The results showed that biosolarization had a stronger impact on the bacterial community relative abundance profile than on the fungal community at the phylum and order levels. However, at the operational taxonomic units (OTUs) level, biosolarization treatment had a significant impact on both fungal and bacterial communities, across soil depth and GWC addition. Co-occurrence microbial network analysis revealed a unique circular network consisting of 8 discrete clusters. Correlation between the clusters and soil volatile fatty acid (VFA) production suggested that the bacterial Clostridium, Weissella and Acetobacter genera tolerate, and perhaps drive, VFA accumulation. Notable fungal community effects included significantly reduced relative abundance within genera known to contain plant pathogenic members, such as Gibberella, Haematonectria, Fusarium, Aspergillus and Alternaria.

KW - Anaerobic soil disinfestation

KW - Co-occurrence networks

KW - Fungal pathogens

KW - Integrated pest management

KW - Soil microbiome

KW - Soil solarization

UR - http://www.scopus.com/inward/record.url?scp=85084993336&partnerID=8YFLogxK

U2 - 10.1016/j.apsoil.2020.103602

DO - 10.1016/j.apsoil.2020.103602

M3 - 文章

AN - SCOPUS:85084993336

SN - 0929-1393

VL - 153

JO - Applied Soil Ecology

JF - Applied Soil Ecology

M1 - 103602

ER -

Structural changes in bacterial and fungal soil microbiome components during biosolarization as related to volatile fatty acid accumulation

Abstract

Keywords

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