Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation

Ornella Carrión,Huub J M Op Den Camp,Niall P Mcnamara,Terry J Mcgenity,Theo A Van Alen,Dafydd M O Elias,Christina Vimala Supramaniam,J Colin Murrell,Lisa Gibson

doi:10.1186/s40168-020-00860-7

Abstract

BackgroundIsoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding rapidly, are among the highest isoprene-producing trees.ResultsDNA stable isotope probing (DNA-SIP) to study the microbial isoprene-degrading community associated with oil palm trees revealed novel genera of isoprene-utilising bacteria including Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea in both oil palm soils and on leaves. Amplicon sequencing of isoA genes, which encode the α-subunit of the isoprene monooxygenase (IsoMO), a key enzyme in isoprene metabolism, confirmed that oil palm trees harbour a novel diversity of isoA sequences. In addition, metagenome-assembled genomes (MAGs) were reconstructed from oil palm soil and leaf metagenomes and putative isoprene degradation genes were identified. Analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere.ConclusionThis study greatly expands the known diversity of bacteria that can metabolise isoprene and contributes to a better understanding of the biological degradation of this important but neglected climate-active gas.ERQydvN7o3H_e-PFoDphLaVideo abstract.

Highlights

Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane
To better understand the role that microbes play in mitigating the effects of this climate-active gas, it is essential to examine the microbial diversity and abundance of isoprene-degrading bacteria
We show that oil palm harbours a unique and distinct community of isoprene degraders compared to other high isoprene-emitting trees from temperate environments and contains higher numbers of bacteria with the genetic potential to metabolise this climate-active gas, especially soils beneath oil palm trees

Summary

Introduction

Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Isoprene (2-methyl-1,3-butadiene), with atmospheric emissions of 400–600 Tg year−1, is the most abundantly produced biogenic volatile compound (BVOC) on Earth. This is approximately one third of the total volatile organic compound (VOC) emissions and almost equal to (2020) 8:81. While there are some industrial sources of isoprene (0.8 Tg year−1), primarily from the production of synthetic rubber [8], the vast majority of isoprene emissions (~ 90%) originate from terrestrial plants [9, 10], with small contributions from marine algae (0.1–12 Tg year−1), bacteria, fungi and animals [9, 11,12,13,14,15,16]. It has been recently suggested that isoprene may play a role in regulating gene expression in plants [27]

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