Cargando…
Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition
The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understan...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8669749/ https://www.ncbi.nlm.nih.gov/pubmed/34917042 http://dx.doi.org/10.3389/fmicb.2021.675352 |
_version_ | 1784614841442369536 |
---|---|
author | Bandara, Ananda Y. Weerasooriya, Dilooshi K. Trexler, Ryan V. Bell, Terrence H. Esker, Paul D. |
author_facet | Bandara, Ananda Y. Weerasooriya, Dilooshi K. Trexler, Ryan V. Bell, Terrence H. Esker, Paul D. |
author_sort | Bandara, Ananda Y. |
collection | PubMed |
description | The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS). We extracted DNA extracted from collected samples and performed high-throughput sequencing of PCR amplicons from both the fungal ITS and prokaryotic 16S rRNA gene regions. Sequences were then grouped into amplicon sequence variants (ASVs) and subjected to network analysis. Based on both ITS and 16S rRNA gene data, a greater network size and edges were observed for all sample types from H-sites compared to L-sites at both SGS. Network analysis suggested that the number of potential microbial interactions/associations were greater in samples from H-sites compared to L-sites. Diversity analyses indicated that site-type was not a main driver of alpha and beta diversity in soybean-associated microbial communities. L-sites contained a greater percentage of fungal phytopathogens (ex: Fusarium, Macrophomina, Septoria), while H-sites contained a greater percentage of mycoparasitic (ex: Trichoderma) and entomopathogenic (ex: Metarhizium) fungal genera. Furthermore, roots from H-sites possessed a greater percentage of Bradyrhizobium and genera known to contain plant growth promoting bacteria (ex: Flavobacterium, Duganella). Overall, our results revealed that there were differences in microbial composition in soil and roots from H- and L-sites across a variety of soybean farms. Based on our findings, we hypothesize that differences in microbial composition could have a causative relationship with observed within-farm variability in soybean yield. |
format | Online Article Text |
id | pubmed-8669749 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-86697492021-12-15 Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition Bandara, Ananda Y. Weerasooriya, Dilooshi K. Trexler, Ryan V. Bell, Terrence H. Esker, Paul D. Front Microbiol Microbiology The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS). We extracted DNA extracted from collected samples and performed high-throughput sequencing of PCR amplicons from both the fungal ITS and prokaryotic 16S rRNA gene regions. Sequences were then grouped into amplicon sequence variants (ASVs) and subjected to network analysis. Based on both ITS and 16S rRNA gene data, a greater network size and edges were observed for all sample types from H-sites compared to L-sites at both SGS. Network analysis suggested that the number of potential microbial interactions/associations were greater in samples from H-sites compared to L-sites. Diversity analyses indicated that site-type was not a main driver of alpha and beta diversity in soybean-associated microbial communities. L-sites contained a greater percentage of fungal phytopathogens (ex: Fusarium, Macrophomina, Septoria), while H-sites contained a greater percentage of mycoparasitic (ex: Trichoderma) and entomopathogenic (ex: Metarhizium) fungal genera. Furthermore, roots from H-sites possessed a greater percentage of Bradyrhizobium and genera known to contain plant growth promoting bacteria (ex: Flavobacterium, Duganella). Overall, our results revealed that there were differences in microbial composition in soil and roots from H- and L-sites across a variety of soybean farms. Based on our findings, we hypothesize that differences in microbial composition could have a causative relationship with observed within-farm variability in soybean yield. Frontiers Media S.A. 2021-11-30 /pmc/articles/PMC8669749/ /pubmed/34917042 http://dx.doi.org/10.3389/fmicb.2021.675352 Text en Copyright © 2021 Bandara, Weerasooriya, Trexler, Bell and Esker. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Bandara, Ananda Y. Weerasooriya, Dilooshi K. Trexler, Ryan V. Bell, Terrence H. Esker, Paul D. Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition |
title | Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition |
title_full | Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition |
title_fullStr | Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition |
title_full_unstemmed | Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition |
title_short | Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition |
title_sort | soybean roots and soil from high- and low-yielding field sites have different microbiome composition |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8669749/ https://www.ncbi.nlm.nih.gov/pubmed/34917042 http://dx.doi.org/10.3389/fmicb.2021.675352 |
work_keys_str_mv | AT bandaraananday soybeanrootsandsoilfromhighandlowyieldingfieldsiteshavedifferentmicrobiomecomposition AT weerasooriyadilooshik soybeanrootsandsoilfromhighandlowyieldingfieldsiteshavedifferentmicrobiomecomposition AT trexlerryanv soybeanrootsandsoilfromhighandlowyieldingfieldsiteshavedifferentmicrobiomecomposition AT bellterrenceh soybeanrootsandsoilfromhighandlowyieldingfieldsiteshavedifferentmicrobiomecomposition AT eskerpauld soybeanrootsandsoilfromhighandlowyieldingfieldsiteshavedifferentmicrobiomecomposition |