Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members

Abstract

In the present study, RNA-sequencing was used to elucidate the change of anaerobic digestion metatranscriptome after long chain fatty acids (oleate) exposure. To explore the general transcriptional behavior of the microbiome, the analysis was first performed on shotgun reads without considering a reference metagenome. As a second step, RNA reads were aligned on the genes encoded by the microbial community, revealing the expression of more than 51 000 different transcripts. The present study is the first research which was able to dissect the transcriptional behavior at a single species level by considering the 106 microbial genomes previously identified. The exploration of the metabolic pathways confirmed the importance of Syntrophomonas species in fatty acids degradation, and also highlighted the presence of protective mechanisms toward the long chain fatty acid effects in bacteria belonging to Clostridiales, Rykenellaceae, and in species of the genera Halothermothrix and Anaerobaculum. Additionally, an interesting transcriptional activation of the chemotaxis genes was evidenced in seven species belonging to Clostridia, Halothermothrix, and Tepidanaerobacter. Surprisingly, methanogens revealed a very versatile behavior different from each other, even among similar species of the Methanoculleus genus, while a strong increase of the expression level in Methanosarcina sp. was evidenced after oleate addition.

Non-autotrophic methanogens dominate in anaerobic digesters

“…6), indicating that methanogenesis by these methanogens were active under both conditions. The abundant expression of these genes under methanogenic conditions has also been reported in previous studies 65–68 . The mrtBDGA operon, which encodes methyl-coenzyme M reductase II (MRII) found in Mt .…”

Inhibition of anaerobic digestion processes: Applications of molecular tools

“…Thermodynamically, LCFA fermentation is both endothermic and nonspontaneous . Therefore, LCFA degradation to acetate and hydrogen is made possible through β-oxidation and syntrophy with hydrogenotrophic or acetoclastic methanogens Treu et al, 2016;Ziels et al, 2017).…”

“…Relative to methanogens, syntrophic bacteria better tolerate high VFA and ammonia . In fact, high VFA could initially promote the growth of syntrophic bacteria Treu et al, 2016). However, inhibition of hydrogenotrophic methanogens, their syntrophic partners, at elevated VFA concentrations destabilizes syntrophy, eventually leading to increased hydrogen partial pressure and a decrease in thermodynamic favorability of the reaction .…”

“…Differences in microbial community structure make it particularly challenging to compare inhibition in AD. The majority of studies to date have only applied DNA-based methods to study microbial community structure during AD inhibition (de Jonge et al, 2017;Li et al, 2015;Ma et al, 2015;Treu et al, 2016;Ziels et al, 2016). However, DNA-based methods are relatively insensitive, particularly in anaerobic communities with low biomass yields.…”

“…We can also couple highthroughput sequencing with isotope tracing (i.e., DNA-and RNA-stable isotope probing (SIP)) to link substrate uptake with specific microbial populations (Werner et al, 2014). Using advanced molecular tools, we now know that syntrophic acetate oxidation (SAO), a thermodynamically unfavorable reaction (De Vrieze and Verstraete, 2016), is possible by more diverse microbial populations than originally assumed (Lee et al, 2015;Treu et al, 2016;Werner et al, 2014). However, we continue to struggle with connecting community structure and function in AD systems (Carballa et al, 2015;De Vrieze and Verstraete, 2016) and have not yet unraveled the 'black-box' microbial ecology of AD (Nobu et al, 2015).…”