Diversity and Ecological Guild Analysis of the Oil Palm Fungal Microbiome Across Root, Rhizosphere, and Soil Compartments.

Eleanor R Kirkman,Gin Teng Ooi,Aik Chin Soh,Gomathy Sethuraman,Dafydd M O Elias,Niall P Mcnamara,Gary D Bending,Andrew Taylor,Sally Hilton,David Bass,John Clarkson

doi:10.3389/fmicb.2022.792928

Abstract

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.

Highlights

Palm oil is a versatile vegetable oil derived from the fruit of oil palm trees Elaeis guineensis (Sambanthamurthi et al, 2000), and comprises ≈36% of total worldwide vegetable oil production
Analysis of fungal community composition at the class level revealed that when data from all sites was combined, with progression from bulk soil, through to rhizosphere soil and root there was significant (P < 0.05) enrichment in the relative abundance of Agaricomycetes, Glomeromycetes and Lecanoromycetes and reduced relative abundance of Eurotiomycetes, Geoglossomycetes, and Tremellomycetes (Figure 2B)
Despite the considerable importance of palm oil as a global commodity and the widespread cultivation of oil palm across SouthEast Asia, South America and Africa, little is known about the composition or function of its microbiome

Summary

Introduction

Palm oil is a versatile vegetable oil derived from the fruit of oil palm trees Elaeis guineensis (Sambanthamurthi et al, 2000), and comprises ≈36% of total worldwide vegetable oil production. Malaysia and Indonesia are currently the largest producers of palm oil, encompassing ≈85% of worldwide production (Mukherjee and Sovacool, 2014). Oil palm cultivation areas in Malaysia increased dramatically from 54,000 hectares in 1960 to 5.8 million hectares (Mha) in 2018 (Basiron, 2007; The World Bank, 2020). Soybean oil is the second most consumed vegetable oil worldwide but requires 10 times the land area of oil palm (≈90 Mha) to produce an equivalent oil yield, highlighting the economic and livelihood benefits of oil palm cultivation (Basiron, 2007). Substituting palm oil with alternative vegetable oil crops could create new environmental consequences following land clearance if expanded into other regions of the world (Mejaard et al, 2018). Improving productivity in existing oil palm lands is vital for future sustainable vegetable oil supply

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Conclusion