Novel hydrocarbon-utilizing soil mycobacteria synthesize unique mycocerosic acids at a Sicilian everlasting fire

Mira Holzheimer,Fausto Grassa,Nadine T Smit,Laura Villanueva,Jaap S Sinninghe Damsté,Darci Rush,Caitlyn R Witkowski,Adriaan J Minnaard,Stefan Schouten

doi:10.5194/bg-18-1463-2021

Abstract

Abstract. Soil bacteria rank among the most diverse groups of organisms on Earth and actively impact global processes of carbon cycling, especially in the emission of greenhouse gases like methane, CO2 and higher gaseous hydrocarbons. An abundant group of soil bacteria are the mycobacteria, which colonize various terrestrial, marine and anthropogenic environments due to their impermeable cell envelope that contains remarkable lipids. These bacteria have been found to be highly abundant at petroleum and gas seep areas, where they might utilize the released hydrocarbons. However, the function and the lipid biomarker inventory of these soil mycobacteria are poorly studied. Here, soils from the Fuoco di Censo seep, an everlasting fire (gas seep) in Sicily, Italy, were investigated for the presence of mycobacteria via 16S rRNA gene sequencing and fatty acid profiling. The soils contained high relative abundances (up to 34 % of reads assigned) of mycobacteria, phylogenetically close to the Mycobacterium simiae complex and more distant from the well-studied M. tuberculosis and hydrocarbon-utilizing M. paraffinicum. The soils showed decreasing abundances of mycocerosic acids (MAs), fatty acids unique for mycobacteria, with increasing distance from the seep. The major MAs at this seep were tentatively identified as 2,4,6,8-tetramethyl tetracosanoic acid and 2,4,6,8,10-pentamethyl hexacosanoic acid. Unusual MAs with mid-chain methyl branches at positions C-12 and C-16 (i.e., 2,12-dimethyl eicosanoic acid and 2,4,6,8,16-pentamethyl tetracosanoic acid) were also present. The molecular structures of the Fuoco di Censo MAs are different from those of the well-studied mycobacteria like M. tuberculosis or M. bovis and have relatively δ13C-depleted values (−38 ‰ to −48 ‰), suggesting a direct or indirect utilization of the released seep gases like methane or ethane. The structurally unique MAs in combination with their depleted δ13C values identified at the Fuoco di Censo seep offer a new tool to study the role of soil mycobacteria as hydrocarbon gas consumers in the carbon cycle.

Highlights

Soils harbor the largest diversity of microorganisms on our planet and have a large influence on the Earth’s ecosystem as they actively impact nutrient and carbon cycling, plant production and the emissions of greenhouse gases (Tiedje et al, 1999; Bardgett and van der Putten, 2014; DelgadoBaquerizo et al, 2018)
This analysis showed a high relative abundance of 16S ribosomal RNA (rRNA) gene reads attributed to Mycobacteriaceae ranging from 0.7 % to 34.1 % of assigned bacterial plus archaeal reads in the soils with relative abundances increasing with decreasing distance from the seep (Table 1)
Described cultivated mycobacteria of the M. simiae complex are slow-growing mycobacterium species isolated from environmental niches and associated with infections in humans as opportunistic pathogens (Lévy-Frébault et al, 1987; Heap, 1989; Bouam et al, 2018)

Summary

Introduction

Soils harbor the largest diversity of microorganisms on our planet and have a large influence on the Earth’s ecosystem as they actively impact nutrient and carbon cycling, plant production and the emissions of greenhouse gases (Tiedje et al, 1999; Bardgett and van der Putten, 2014; DelgadoBaquerizo et al, 2018). Soil bacteria rank among the most diverse and abundant groups of organisms on Earth. Numerous studies suggest that most of their function and diversity in our ecosystems are still undescribed (Tiedje et al, 1999; Bardgett and van der Putten, 2014). Besides the use of DNA-based techniques, lipid biomarkers offer an additional tool to investigate soil bacterial communities, such as branched glycerol dialky glycerol tetraether (brGDGTs) believed to derive from soil acidobacteria (Weijers et al, 2009; Peterse et al, 2010; Sinninghe Damsté et al, 2018) or lipids derived from methanotrophic bacteria like certain fatty acids (Bull et al, 2000; Bodelier et al, 2009), specific bacteriohopanepolyols (van Winden et al, 2012; Talbot et al, 2016) or 13C-depleted hopanoids (Inglis et al, 2019; van Winden et al, 2020)

Methods

Results

Conclusion