The core populations and co-occurrence patterns of prokaryotic communities in household biogas digesters

Abstract

BackgroundHousehold biogas digesters are widely used to harvest energy in rural areas of developing countries. Understanding core prokaryotic communities, their co-occurrence patterns, and their relationships to environmental factors is important to manage these small-scale anaerobic digestion systems effectively. In this study, 43 household biogas digesters were collected across eight provinces in China. Prokaryotic communities were investigated using 454 pyrosequencing of 16S rRNA genes.ResultsFourteen core genera and ten core OTUs were identified in household biogas digesters. They were mainly affiliated with the phylum Firmicutes, Synergistetes, Actinobacteria, Chloroflexi, and Spirochaetes. Core prokaryotic genera were mainly composed of Clostridium, Clostridium XI, Syntrophomonas, Cloacibacillus, Sedimentibacter, and Turicibacter. Prokaryotic communities in the 43 samples were clearly divided into two clusters. Cluster I was dominated by Clostridium, while Cluster II was dominated by members of Spirochaetes, Bacteroidales, Clostridia, and abundant syntrophs and methanogens. NH4+-N and COD contributed significantly to the assembly of the prokaryotic community in Cluster I, while NH4+-N, pH, and phosphate contributed significantly to Cluster II. Correlation-based network analysis showed that the prokaryotic communities in the biogas digesters were dominated by some functional modules. Cluster I was dominated by acetotrophic methanogenic modules and the Clostridium-driven primary fermentation module, while the network of Cluster II was dominated by hydrogenotrophic and acetogenic methanogenesis modules and multi-group-driven (Spirochaetes, Bacteroidales, and Clostridia) primary fermentation modules. The network of Cluster II was more complex and functionally redundant.ConclusionsProkaryotic communities identified in the household biogas digesters varied significantly and were affected by environmental factors, such as NH4+-N, pH, and COD. However, core prokaryotic communities existed, and most of them were also dominant populations. Cosmopolitan OTUs tended to co-occur. Prokaryotic communities in biogas digesters were well organized by some functional modules. The modular structure of the prokaryotic community, which has functional redundancy, enhances the resistance against environmental stress and maintains digestion efficiency in the anaerobic digestion process.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0339-3) contains supplementary material, which is available to authorized users.

Temperature affects microbial abundance, activity and interactions in anaerobic digestion

“…The function of each module in pMENs can be derived from the microbial composition and their known physiological functions, and PICRUSt prediction (Rui et al, 2015). The module R1, mainly composed of Firmicutes (65.5%) and Bacteroidetes (13.8%) (Supplementary Table S6), was predicted to conduct fermentation.…”

“…Efficient interactions among functional taxa or microbial consortia are required to sustain the process chain in AD systems to prevent accumulation of hydrogen or excessive acidification (Rui et al, 2015). As such, an AD system can be considered an artificial microbial ecosystem with high diversity and complexity.…”

Seasonal Microbial Population Shifts in a Bioremediation System Treating Metal and Sulfate-Rich Seepage

“…Representative sequences for the Spirochaetes C-2 and OP11 classified OTUs were not closely related to any isolates or cultured species. Members within the Spirochaetes are core to anaerobic digesters [53] and are known to be syntrophic with methanogens and can outcompete other fermenters, such as Clostridium species [54]. The first environmental clone for OP11 was isolated from the Obsidian Pool in Yellow Stone National Park that is an environment rich in metals and sulfur compounds [55].…”

Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity

“…A clear difference has been observed in both phylogenetic and metabolic characteristics between the only two presently known genera able to use the acetoclastic methanogenic pathway ( i.e., Methanosaeta and Methanosarcina ), which explains their differential niche selection in AD (Conklin et al ., ; De Vrieze et al ., ; Walter et al ., ; Regueiro et al ., ). Second, a core community involved in the AD process has been identified (Riviere et al ., ; Lee et al ., ; St‐Pierre and Wright, ; Li et al ., ; Rui et al ., ). The influence of important operational parameters, mainly temperature and (total) ammonia concentration, and feed composition on microbial community composition has been shown (Sundberg et al ., ; Zhang et al ., ; De Vrieze et al ., ; Li et al ., ).…”