Genome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion Sludge

Metagenomic insights into the toxicity of carbamazepine to functional microorganisms in sludge anaerobic digestion

Contaminants of emerging concern (CECs) contained in sludge, such as carbamazepine, may be toxic to microorganisms and affect the biogenesis of methane during anaerobic digestion. In this study, different scales of anaerobic digesters were constructed to investigate the inhibitory effect of carbamazepine. Results showed that carbamazepine reduced methane production by 11.3 % and 62.1 % at concentrations of 0.4 and 2 mg/g TS, respectively. Carbamazepine hindered the dissolution of organic matter and the degradation of protein. Carbamazepine inhibited some fermentative bacteria, especially uncultured Aminicenantales, whose abundance decreased by 9.5-93.4 % under carbamazepine stress. It is worth noting that most prior studies investigated the effects of CECs only based on well-known microorganisms, ignoring the metabolisms of uncultured microorganisms. Genome-predicted metabolic potential suggested that 54 uncultured metagenome-assembled genomes (MAGs) associated with acidogenesis or acetogenesis. Therein, uncultured Aminicenantales related MAGs were proved to be acetogenic fermenters, their significant reduction may be an important reason for the decrease of methane production under carbamazepine stress. The toxicity of carbamazepine to microorganisms was mainly related to the overproduction of reactive oxygen species. This study elucidates the inhibition mechanism of carbamazepine and emphasizes the indispensable role of uncultured microorganisms in anaerobic digestion.

BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis

Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.

Alkaline fermentation of refinery waste activated sludge mediated by refinery spent caustic for volatile fatty acids production

Volatile fatty acids (VFA), produced from waste activated sludge (WAS), provide unique opportunities for resource recovery in wastewater treatment plants. This study investigates the potential of refinery spent caustic (RSC) on VFA production during refinery WAS (RWAS) alkaline fermentation. The highest VFA yield was 196.3 mg/g-VS at a sludge retention time of 6 days. Amplicon sequencing revealed the enrichment of Soehngenia (20.21%), Bacilli (11.86%), and Brassicibacter (4.17%), which was associated with improved activities of protease (626%) and α-glucosidase (715%). Function prediction analysis confirmed that acetyl-CoA production and fatty acid biosynthesis were enhanced, while fatty acid degradation was inhibited. Accordingly, hydrolysis, acidogenesis, and acetogenesis were improved by 6.87%, 10.67%, and 28.50%, respectively; whereas methanogenesis was inhibited by 28.87%. The sulfate and free ammonia in RSC likely contributed to increased acetic acid production. This study showcases that RWAS alkaline fermentation mediated by RSC for VFA production is the practicable approach.

Comprehensive insights into the impact of pretreatment on anaerobic digestion of waste active sludge from perspectives of organic matter composition, thermodynamics, and multi-omics

Although various pretreatments have been applied to promote the anaerobic digestion of waste active sludge (WAS), the mechanisms regarding the impact of pretreatment on anaerobic digestion have not been well addressed. In this study, the effects of acid, alkali, and thermal pretreatments on anaerobic digestion of WAS were comprehensively investigated from the perspectives of organic matter composition, thermodynamics, and multi-omics. Results showed acid, alkali, and thermal pretreatments increased the methane production potential of WAS by 53.7%, 98.2%, and 101.8%, respectively, compared with the control. The protein secondary structure was disrupted after pretreatment, with a shift from α-helix and β-sheet to random coil and antiparallel β-sheet/aggregated strands. Thermodynamically, the WAS flocculation process was controlled by the short-range interfacial interactions described by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory, which was positively correlated (R = 0.97, p < 0.05) with the organic matter solubilization of the WAS. After pretreatment, the flocculation energy barrier of pretreated WAS was 4.1 (acid), 7.0 (alkali) and 7.1 (thermal) times higher than that of the control group, respectively. Multi-omics analysis confirmed that pretreatment promoted amino acids (tryptophan, tyrosine, phenylalanine, aspartate, glutamate) metabolism, energy metabolism (ABC transporters) and vitamin metabolism. Moreover, the comparison of upregulated differentially expressed proteins (DEPs) revealed that for amino acid metabolism, thermal treatment had the best promotion effect; for carbohydrate metabolism, alkali treatment had the best promotion effect; and for lipid metabolism, acid treatment was more advantageous, resulting in different anaerobic digestion efficiencies. This study provides an in-depth understanding of the impact of different pretreatments on WAS anaerobic digestion and has practical implication for the choice of proper pretreatment technology for biosolids.

Impact of substrate digestibility on microbial community stability in methanogenic digestors: The mechanism and solution

This study investigated the temporal dynamics of digestion efficiency and community stability in digesters fed with waste activated sludge (WAS), straw (STR-AD), food waste (FW-AD) and mixture of straw-and-food waste (STR-FW-AD). Results showed that carbon removals of recalcitrant substrates (i.e., 48.2 ± 3.9% in WAS-AD and 57.8 ± 4.9% in STR-AD) were lower than that of labile substrates (i.e., 70.7 ± 4.0% in FW-AD). Nonetheless, carbon removal of recalcitrant substrates was largely improved through co-digestion (70.3 ± 3.2% in STR-FW-AD). In contrast to monopoly communities (e.g., the highly enriched Paludibacter) fed with the labile substrates, recalcitrant substrates supported highly diverse communities. Accordingly, the medians of negative/positive cohesions of communities in WAS-AD, STR-AD, STR-FW-AD and FW-AD decreased from 0.86 to 0.63, suggesting their decreasing community stability. Microbial source tracking analyses showed the major contribution of the STR-AD community to the co-digestion community. This study provided unprecedented mechanistic insight into stability improvement of substrate co-digestion on the methanogenic digestion microbiome.

Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system

Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.

Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions

BACKGROUND

Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process.

RESULTS

Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions.

CONCLUSIONS

The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.