Diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments

The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world's most important crops, constituting over a third of global vegetable oil production. Currently there is...

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Main Authors: Kirkman, Eleanor R., Hilton, Sally, Sethuraman, Gomathy, Elias, Dafydd M. O., Taylor, Andrew, Clarkson, John, Soh, Aik Chin, Bass, David, Ooi, Gin Teng, McNamara, Niall P., Bending, Gary D.
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Published: Frontiers Media Sa 2022
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Online Access:http://eprints.um.edu.my/33362/
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spelling my.um.eprints.333622022-04-22T07:23:26Z http://eprints.um.edu.my/33362/ Diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments Kirkman, Eleanor R. Hilton, Sally Sethuraman, Gomathy Elias, Dafydd M. O. Taylor, Andrew Clarkson, John Soh, Aik Chin Bass, David Ooi, Gin Teng McNamara, Niall P. Bending, Gary D. QR Microbiology The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world's most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome. Frontiers Media Sa 2022-02-11 Article PeerReviewed Kirkman, Eleanor R. and Hilton, Sally and Sethuraman, Gomathy and Elias, Dafydd M. O. and Taylor, Andrew and Clarkson, John and Soh, Aik Chin and Bass, David and Ooi, Gin Teng and McNamara, Niall P. and Bending, Gary D. (2022) Diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments. Frontiers in Microbiology, 13. ISSN 1664-302X, DOI https://doi.org/10.3389/fmicb.2022.792928 <https://doi.org/10.3389/fmicb.2022.792928>. 10.3389/fmicb.2022.792928
institution Universiti Malaya
building UM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaya
content_source UM Research Repository
url_provider http://eprints.um.edu.my/
topic QR Microbiology
spellingShingle QR Microbiology
Kirkman, Eleanor R.
Hilton, Sally
Sethuraman, Gomathy
Elias, Dafydd M. O.
Taylor, Andrew
Clarkson, John
Soh, Aik Chin
Bass, David
Ooi, Gin Teng
McNamara, Niall P.
Bending, Gary D.
Diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments
description The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world's most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.
format Article
author Kirkman, Eleanor R.
Hilton, Sally
Sethuraman, Gomathy
Elias, Dafydd M. O.
Taylor, Andrew
Clarkson, John
Soh, Aik Chin
Bass, David
Ooi, Gin Teng
McNamara, Niall P.
Bending, Gary D.
author_facet Kirkman, Eleanor R.
Hilton, Sally
Sethuraman, Gomathy
Elias, Dafydd M. O.
Taylor, Andrew
Clarkson, John
Soh, Aik Chin
Bass, David
Ooi, Gin Teng
McNamara, Niall P.
Bending, Gary D.
author_sort Kirkman, Eleanor R.
title Diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments
title_short Diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments
title_full Diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments
title_fullStr Diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments
title_full_unstemmed Diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments
title_sort diversity and ecological guild analysis of the oil palm fungal microbiome across root, rhizosphere, and soil compartments
publisher Frontiers Media Sa
publishDate 2022
url http://eprints.um.edu.my/33362/
_version_ 1735409584690954240
score 13.211869