Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams

Silas H W Vick,Paul Greenfield,David J Midgley,Ian T Paulsen,Sasha G Tetu

doi:10.1038/s41598-019-52846-7

Silas H W Vick, Paul Greenfield + Show 3 more

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https://doi.org/10.1038/s41598-019-52846-7

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Abstract

Microbes in subsurface coal seams are responsible for the conversion of the organic matter in coal to methane, resulting in vast reserves of coal seam gas. This process is important from both environmental and economic perspectives as coal seam gas is rapidly becoming a popular fuel source worldwide and is a less carbon intensive fuel than coal. Despite the importance of this process, little is known about the roles of individual bacterial taxa in the microbial communities carrying out this process. Of particular interest is the role of members of the genus Pseudomonas, a typically aerobic taxa which is ubiquitous in coal seam microbial communities worldwide and which has been shown to be abundant at early time points in studies of ecological succession on coal. The current study performed aerobic isolations of coal seam microbial taxa generating ten facultative anaerobic isolates from three coal seam formation waters across eastern Australia. Subsequent genomic sequencing and phenotypic analysis revealed a range of ecological strategies and roles for these facultative anaerobes in biomass recycling, suggesting that this group of organisms is involved in the degradation of accumulated biomass in coal seams, funnelling nutrients back into the microbial communities degrading coal to methane.

Highlights

Microbes in subsurface coal seams are responsible for the conversion of the organic matter in coal to methane, resulting in vast reserves of coal seam gas
With the discovery that significant portions of the worlds coal seam gas (CSG) are produced through microbial degradation of the organic matter in coal to methane, has come an increasing interest in understanding the microbial communities involved in this process, with the aim of stimulating CSG production from coal reserves[3,4]
One of the highly abundant OTUs (Operational Taxonomic Unit) observed in this 16S rRNA amplicon sequence based study was taxonomically identified as a pseudomonad (OTU_9), and its presence during early colonisation suggested it may play some role in degrading organic matter in coal

Summary

Introduction

Microbes in subsurface coal seams are responsible for the conversion of the organic matter in coal to methane, resulting in vast reserves of coal seam gas. Efforts to understand the process of biological coal degradation have focussed primarily on either (1) understanding what nutrients to add to stimulate microbial communities to degrade organic matter in coal to methane, and/or; (2) characterising the microbial community compositions on coal and associated formation waters either in situ on or in laboratory grown microcosms (reviewed in Ritter et al, 2015) These studies have typically used 16S rRNA gene based community profiling. In order to try to assign functions to these coal-associated pseudomonads, and functionally related facultative aerobic taxa, a culturing effort was undertaken to bring facultatively aerobic organisms, including that corresponding to OTU_9, into axenic culture This isolation was followed by genomic and phenotypic characterisation to uncover the metabolic and ecological roles played by these organisms in coal seams. As these organisms are facultative aerobes, the present study employed oxic conditions and a complex medium to obtain axenic cultures

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