Deep (Meta)genomics and (Meta)transcriptome Analyses of Fungal and Bacteria Consortia From Aircraft Tanks and Kerosene Identify Key Genes in Fuel and Tank Corrosion.

Ines Krohn,Christian Siry,Tim Lübcke,Lutgardis Bergmann,Yuchen Han,Birgit Hägele,Minyue Qi,Malik Alawi,Daniela Indenbirken,Wolfgang R Streit,Pablo Perez-Garcia,Elena Katzowitsch,Ralf Riemann

doi:10.3389/fmicb.2021.722259

Abstract

Microbial contamination of fuels, associated with a wide variety of bacteria and fungi, leads to decreased product quality and can compromise equipment performance by biofouling or microbiologically influenced corrosion. Detection and quantification of microorganisms are critical in monitoring fuel systems for an early detection of microbial contaminations. To address these challenges, we have analyzed six metagenomes, one transcriptome, and more than 1,200 fluid and swab samples taken from fuel tanks or kerosene. Our deep metagenome sequencing and binning approaches in combination with RNA-seq data and qPCR methods implied a metabolic symbiosis between fungi and bacteria. The most abundant bacteria were affiliated with α-, β-, and γ-Proteobacteria and the filamentous fungi Amorphotheca. We identified a high number of genes, which are related to kerosene degradation and biofilm formation. Surprisingly, a large number of genes coded enzymes involved in polymer degradation and potential bio-corrosion processes. Thereby, the transcriptionally most active microorganisms were affiliated with the genera Methylobacteria, Pseudomonas, Kocuria, Amorpotheka, Aspergillus, Fusarium, and Penicillium. Many not yet cultured bacteria and fungi appeared to contribute to the biofilm transcriptional activities. The largest numbers of transcripts were observed for dehydrogenase, oxygenase, and exopolysaccharide production, attachment and pili/flagella-associated proteins, efflux pumps, and secretion systems as well as lipase and esterase activity.

Highlights

Microbial contamination of fuels is a phenomenon widely reported in the literature
Fuel products are subject to microbial degradation, which affects mostly kerosene and diesel fuels
We addressed the following questions in the current study: Can we identify specific bacterial communities associated with fungi in different aircraft habitats and fuel-containing biofilms? What are the most active genes in these communities, and do they give any hints on biofouling of kerosene and bio-corrosion processes? To answer these questions, we first systematically characterized the microbiomes of six biofilms grown directly in aircraft tanks

Summary

Introduction

Microbial contamination of fuels is a phenomenon widely reported in the literature. Microbiological analyses showed that fuel systems like aviation fuel and storage tanks are often contaminated by a variety of microorganisms with a rather low diversity (Gaylarde et al, 1999; Rauch et al, 2006; Yemashova et al, 2007). Previous studies implied that the bacteria–fungi microbial communities can form tightly attached biofilms on various surfaces. These studies identified mainly microorganisms associated with the bacterial genera Methylobacterium, Bacillus, Pseudomonas, Serratia, Sphingomonas, Variovorax, Flavobacterium, Arthrobacter, and Alcaligenes, as well as a limited number of fungal isolates linked to Amorphotheca ( known as Cladosporium and Hormoconis), Aspergillus, and Fusarium; no archaea were reported (Beech and Sunner, 2004; Beale et al, 2014; Khan et al, 2015). Thereby, microbial alkane degradation is important for the bioremediation of petroleum-contaminated environments as well as for microbial enhanced oil recovery (Gaylarde et al, 1999; Brown et al, 2010)

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Conclusion