Microbiome Diversity and Community-Level Change Points within Manure-based small Biogas Plants

Abstract

Efforts to integrate biogas plants into bioeconomy concepts will lead to an expansion of manure-based (small) biogas plants, while their operation is challenging due to critical characteristics of some types of livestock manure. For a better process understanding, in this study, three manure-based small biogas plants were investigated with emphasis on microbiome diversity. Due to varying digester types, feedstocks, and process conditions, 16S rRNA gene amplicon sequencing showed differences in the taxonomic composition. Dynamic variations of each investigated biogas plant microbiome over time were analyzed by terminal restriction fragment length polymorphism (TRFLP), whereby nonmetric multidimensional scaling (NMDS) revealed two well-running systems, one of them with a high share of chicken manure, and one unstable system. By using Threshold Indicator Taxa Analysis (TITAN), community-level change points at ammonium and ammonia concentrations of 2.25 g L-1 and 193 mg L-1 or volatile fatty acid concentrations of 0.75 g L-1were reliably identified which are lower than the commonly reported thresholds for critical process stages based on chemical parameters. Although a change in the microbiome structure does not necessarily indicate an upcoming critical process stage, the recorded community-level change points might be a first indication to carefully observe the process.

Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants

“…For the archaeal community, the genus Methanosaeta was identified as an indicative taxon with a relative abundance of 6.3% ± 2.9% (Figure 5, Table S4). This is partly in accordance with previously published results by Theuerl et al [29,31], where the occurrence of members from the bacterial phyla Bacteroidetes and Cloacimonetes and the archaeal genus Methanosaeta (syn. Methanothrix) were related to unstressed anaerobic digestion systems with low concentrations of potential process inhibitory factors.…”

Microbiome dysbiosis regulates the level of energy production under anaerobic condition

“…However, at the very beginning of the twentieth century more than 150 species of microorganisms have been identified from the anaerobic bioreactors through the application modern genomic approaches [19]. The current accelerated pace of genomic technology and the rapid incorporation of biotechnological techniques allowed us the rapid identification and characterization microorganisms such as Clostridium bornimense, Herbinix hemicellulosilytica, Herbinix luporum, Herbivorax saccincola, Proteiniphilum saccharofermentans, Petrimonas mucosa, Fermentimonas caenicola, and Proteiniborus indolifex or even their genomic features for the increased production of biogas [9,13,17,[19][20][21]. The conventional culture-based techniques [22,23] for characterization of the microbiotas in different niches including controlled anaerobic chambers [11,24] has been replaced during the last decade by the rapid advances in high-throughput NGS technology and bioinformatics tools [25,26].…”

“…Methane rich biogas (typically 50 – 70% methane, 30–50% CO 2 , with traces of H 2 S and other gases) is a clean, efficient, and renewable source of energy, which offers a multipurpose carrier of energy, and can be used as a substitute for other fuels [12]. Though biogas (CH 4 ) is directly influenced by the composition of the AD microbiomes [9,13], the genomic potentials of the microbiomes favoring anaerobic metabolism to control the level of CH 4 production is thermodynamically dependent on environmental parameters of the AD [14]. Diverse microbial communities are associated with biomass decomposition and CH 4 production through the metabolic activities of substrate hydrolysis, acidogenesis, acetogenesis and methanogenesis [15].…”

“…Diverse microbial communities are associated with biomass decomposition and CH 4 production through the metabolic activities of substrate hydrolysis, acidogenesis, acetogenesis and methanogenesis [15]. The environmental and internal factors such as substrate ingredients, temperature, pH, level of CO 2 , O 2 and H 2 S, and mixing or the geometry of the AD can be achieved through microbial selection or manipulation [9,13,16]. Therefore, a clear understanding of the structure, composition and diversity of the multifarious microbial community involved in biogas production is crucial for the optimization of their performance and stable operational process of the AD.…”

“…Moreover, a detailed insight into relevant microbial metabolic pathways involved in CH 4 synthesis and syntropy is essential to upsurge the yield of biogas. To reveal the dynamic changes of the exceedingly diverse and unified networks of AD microbiomes, few studies focused on the taxonomic and functional characterization of microbiomes originating from both laboratory-scale [9] and full-scale [9,17] biogas reactors under different prevailing ecological conditions [13,18]. Initially, AD microbiomes characterization mainly relied on conventional microbiology approaches.…”