Pseudomonas spp. are key players in agricultural biogas substrate degradation

Christian Buettner,Nico Jehmlich,Martin Von Bergen,Matthias Noll

doi:10.1038/s41598-019-49313-8

Abstract

Anaerobic degradation (AD) of heterogeneous agricultural substrates is a complex process involving a diverse microbial community. While microbial community composition of a variety of biogas plants (BPs) is well described, little is known about metabolic processes and microbial interaction patterns. Here, we analyzed 16 large-scale BPs using metaproteomics. All metabolic steps of AD were observed in the metaproteome, and multivariate analyses indicated that they were shaped by temperature, pH, volatile fatty acid content and substrate types. Biogas plants could be subdivided into hydrogenotrophic, acetoclastic or a mixture of both methanogenic pathways based on their process parameters, taxonomic and functional metaproteome. Network analyses showed large differences in metabolic and microbial interaction patterns. Both, number of interactions and interaction partners were highly dependent on the prevalent methanogenic pathway for most species. Nevertheless, we observed a highly conserved metabolism of different abundant Pseudomonas spp. for all BPs indicating a key role during AD in carbohydrate hydrolysis irrespectively of variabilities in substrate input and process parameters. Thus, Pseudomonas spp. are of high importance for robust and versatile AD food webs, which highlight a large variety of downstream metabolic processes for their respective methanogenic pathways.

Highlights

Climate change and rising energy consumption trigger innovation in the global energy market
Mainly species composition and abundances of biogas plants (BPs) were characterized on 16S rRNA gene level[11,12,13,14,15,16], which allows phylogenetic affiliation followed by predicting their potential metabolic functions
Tools for network analyses such as MENA20, SparCC21 or CoNet[22] are frequently used to predict interactions between microorganisms. Such network calculations are mainly based on 16S rRNA gene amplicon abundance data and anaerobic degradation-based findings have to be interpreted with caution, as metabolic functions are difficult to predict

Summary

Introduction

Climate change and rising energy consumption trigger innovation in the global energy market. Microbial communities in BPs have to overcome variations of each process parameter and substrate by metabolic readjustment to enable a stable and high biogas production. Tools for network analyses such as MENA20, SparCC21 or CoNet[22] are frequently used to predict interactions between microorganisms Such network calculations are mainly based on 16S rRNA gene amplicon abundance data and anaerobic degradation-based findings have to be interpreted with caution, as metabolic functions are difficult to predict. Main goals of this study are (i) to identify most important parameters driving the AD on protein level, (ii) to group the BPs according to their metaproteome (taxonomic and functional profiles), (iii) to arrange the BPs corresponding to their prevalent methanogenesis pathway and (iv) to identify microbial key players and their interaction patterns by a metabolic and microbial network analysis. The overall aim was to gain a better understanding of the metabolic processes during AD with a focus on methanogenesis as well as explore possibilities of metaproteomics for practical applications

Methods

Results

Discussion

Conclusion