Ecogenomics-Based Mass Balance Model Reveals the Effects of Fermentation Conditions on Microbial Activity

Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor

To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.

Enhanced bio-electrochemical performance of microbially catalysed anode and cathode in a microbial electrosynthesis system

Most bio-electrochemical systems (BESs) use biotic/abiotic electrode combinations, with platinum-based abiotic electrodes being the most common. However, the non-renewability, cost, and poisonous nature of such electrode systems based on noble metals are major bottlenecks in BES commercialisation. Microbial electrosynthesis (MES), which is a sustainable energy platform that simultaneously treats wastewater and produces chemical commodities, also faces the same problem. In this study, a dual bio-catalysed MES system with a biotic anode and cathode (MES-D) was tested and compared with a biotic cathode/abiotic anode system (MES-S). Different bio-electrochemical tests revealed improved BES performance in MES-D, with a 3.9-fold improvement in current density compared to that of MES-S. Volatile fatty acid (VFA) generation also increased 3.2-, 4.1-, and 1.8-fold in MES-D compared with that in MES-S for acetate, propionate, and butyrate, respectively. The improved performance of MES-D could be attributed to the microbial metabolism at the bioanode, which generated additional electrons, as well as accumulative VFA production by both the bioanode and biocathode chambers. Microbial community analysis revealed the enrichment of electroactive bacteria such as Proteobacteria (60%), Bacteroidetes (67%), and Firmicutes + Proteobacteria + Bacteroidetes (75%) on the MES-S cathode and MES-D cathode and anode, respectively. These results signify the potential of combined bioanode/biocathode BESs such as MES for application in improving energy and chemical commodity production.

Role of polyamide microplastic in altering microbial consortium and carbon and nitrogen cycles in a simulated agricultural soil microcosm

Microplastics (MPs) are persistent organic pollutants globally, with a continuous increase in MP wastes near and away from the regions of human activities. Studies to date aimed to explore the impact of MPs on ecosystems, but the area of research could not go beyond environmental pollution caused by MPs. To address the menace of MPs, scientists need to pay enough attention to the biogeochemical cycles, microbial communities, and functional microorganisms. Hence, this study aimed to evaluate the impact of adding 0.3% (mass ratio) [low-concentration (LC) group] and 1% [high-concentration (HC) group] of polyamide (PA) MP to the soil microenvironment with regard to the aforementioned parameters. PA MP decreased the soil microbial diversity (Shannon and Simpson indices, P < 0.05). At the phylum level, PA MP increased the abundance of Acidobacteria, Firmicutes, and Crenarchaeota (P < 0.05); at the genus level, it enhanced that of Geobacter, Thiobacillus, Pseudomonas, and Bradyrhizobium (P < 0.01) while decreased that of Bacillus, Flavisolibacter, Geothrix, and Pseudarthrobacter (P < 0.05). PA MP affected the carbon (C) cycle. PA MP accelerated the soil C fixation by enhancing the abundance of the genes accA and pccA. The LC PA MP accelerated organic C degradation and methane metabolism by changing the abundance of mnp, chiA, mcrA, pmoA, and mmoX genes, while the HC PA MP inhibited them with increasing the experimental time. Regarding the effects of PA on the nitrogen (N) cycle, the PA MP promoted N assimilation and ammonification by increasing the abundance of the genes gdh and ureC, the impact of PA MP on N fixation and denitrification depended on its concentration and treating time. This study showed that PA MP impacted the microbial consortium, it also affected the C and N cycles and its effect depended on its concentration and the treating time.

Meta-Omics-Supervised Characterization of Respiration Activities Associated with Microbial Immigrants in Anaerobic Sludge Digesters

Immigration has been recently recognized as an important ecological process that affects the microbial community structure in diverse ecosystems. However, the fate of microbial immigrants in the new environment and their involvement in the local biochemical network remain unclear. In this study, we performed meta-omics-supervised characterization of immigrants' activities in anaerobic sludge digesters. Metagenomic analyses revealed that immigrants from the feed sludge accounted for the majority of populations capable of anaerobic respiration in a digester. Electron acceptors that were predicted to be respired, including nitrate, nitrite, sulfate, and elemental sulfur, were added to digester sludge in batch tests. Consumption of up to 91% of the added electron acceptors was observed within the experiment period. 16S rRNA sequencing detected populations that were stimulated by the electron acceptors, largely overlapping with respiration-capable immigrants identified by metagenomic analysis. Metatranscriptomic analysis of the batch tests provided additional evidence for upregulated expression of respiration genes and concomitant suppressed expression of methanogenesis. Anaerobic respiration activity was further evaluated in full-scale digesters in nine wastewater treatment plants. Although nitrate and sulfate respiration were ubiquitous, the expression level of respiration genes was generally 2-3 orders of magnitude lower than the expression of methanogenesis in most digesters, suggesting marginal ecological roles by immigrants in full-scale digester ecosystems.