Syntroph diversity and abundance in anaerobic digestion revealed through a comparative core microbiome approach

MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.

Enhancement of triclocarban biodegradation: Metabolic division of labor in co-culture of Rhodococcus sp. BX2 and Pseudomonas sp. LY-1

Triclocarban (TCC) and its metabolite, 3,4-dichloroaniline (DCA), are classified as emerging organic contaminants (EOCs). Significant concerns arise from water and soil contamination with TCC and its metabolites. These concerns are especially pronounced at high concentrations of up to approximately 20 mg/kg dry weight, as observed in wastewater treatment plants (WWTPs). Here, a TCC-degrading co-culture system comprising Rhodococcus rhodochrous BX2 and Pseudomonas sp. LY-1 was utilized to degrade TCC (14.5 mg/L) by 85.9% in 7 days, showing improved degradation efficiency compared with monocultures. A combination of high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR) was performed. Meanwhile, through the combination of further experiments involving heterologous expression and gene knockout, we proposed three TCC metabolic pathways and identified four key genes (tccG, tccS, phB, phL) involved in the TCC degradation process. Moreover, we revealed the internal labor division patterns and connections in the co-culture system, indicating that TCC hydrolysis products were exchanged between co-cultured strains. Additionally, mutualistic cooperation between BX2 and LY-1 enhances TCC degradation efficiency. Finally, phytotoxicity assays confirmed a significant reduction in the plant toxicity of TCC following synergistic degradation by two strains. The in-depth understanding of the TCC biotransformation mechanisms and microbial interactions provides useful information for elucidating the mechanism of the collaborative biodegradation of various contaminants.

Integrative biohydrogen- and biomethane-producing bioprocesses for comprehensive production of biohythane

The production of biohythane, a combination of energy-dense hydrogen and methane, from the anaerobic digestion of low-cost organic wastes has attracted attention as a potential candidate for the transition to a sustainable circular economy. Substantial research has been initiated to upscale the process engineering to establish a hythane-based economy by addressing major challenges associated with the process and product upgrading. This review provides an overview of the feasibility of biohythane production in various anaerobic digestion systems (single-stage, dual-stage) and possible technologies to upgrade biohythane to hydrogen-enriched renewable natural gas. The main goal of this review is to promote research in biohythane production technology by outlining critical needs, including meta-omics and metabolic engineering approaches for the advancements in biohythane production technology.

Identification of key steps and associated microbial populations for efficient anaerobic digestion under high ammonium or salinity conditions

Ammonium (NH₄⁺) and salinity are major inhibitors of CH₄ production in anaerobic digestion. This study evaluated their inhibitory effects on CH₄ production and explored the key populations for efficient CH₄ production under high NH₄⁺ and NaCl concentrations to understand their inhibition mechanisms. Comparative batch experiments for mesophilic anaerobic digestion were conducted using three seeding sludges under different concentrations of NH₄⁺ (1-5 gNH₄-N/L) and NaCl (10-30 g/L). Although all sludges tolerated 3 gNH₄-N/L and 10 g/L NaCl, NH₄⁺ or NaCl concentrations higher than these substantially reduced CH₄ production, depending on the seeding sludge, primarily by impairing the initial hydrolysis and methanogenesis steps. In addition, propionate was found to be a deterministic factor affecting CH₄ production. Based on microbial community analysis, Candidatus Brevefilum was identified as a potential syntrophic propionate-oxidizing bacterium that facilitates the mitigation of propionate accumulation, allowing the maintenance of unaffected CH₄ production under high inhibitory conditions.

Alleviating "inhibited steady-state" in anaerobic digestion of poultry manure by bentonite amendment: Performance evaluation and microbial mechanism

This study systematically evaluated the effects of bentonite as a possible additive to alleviate the "inhibited steady-state" induced by ammonia and acid accumulation during anaerobic digestion. Continuous stirred tank reactors fed with poultry manure were operated at 35 ± 1 °C either with bentonite or not. The results demonstrate that bentonite amendment increased average specific methane production by 35% as suffered from steady-state at an organic loading rate of 6.25 g VS/L·d. 16S rRNA gene amplicon sequencing revealed that the relative abundance of electron-donating Sedimentibacter and Syntrophomonas, and electrophilic Methanosarcina was increased by 110%, 91%, and 49%, respectively. The genera were identified as crucial for alleviating "inhibited steady-state", through establishment of a more robust syntrophic pathway of methanogenic acetate degradation. The enhancement might result from the accelerated electron transfer by bentonite, which is qualified for serving as an exogenetic electron mediator due to containing abundant redox-active metal elements.

Modification of hydrochar increased the capacity to promote anaerobic digestion

Hydrochar has been demonstrated to increase methane production rate during anaerobic digestion (AD) of organic wastes/wastewater by facilitating direct interspecies electron transfer (DIET). The present study compared the hydrochars prepared at different conditions (260 °C-1 h, 260 °C-8 h, 320 °C-1 h and 320 °C-8 h) on AD of glucose. Hydrochar prepared at lower temperature and residence time (260 °C-1 h) resulted in the highest methane production rate, which was 237% higher of control experiment without hydrochar. Modification of hydrochar (260 °C-1 h) by ball-milling further increased the capacity to increase methane production rate. Hydrothermal liquefaction (HTL) conditions affected the surface oxygen-containing functional groups that related with DIET, and hydrochar (260 °C-1 h) had higher peaks relating with C-O and O-H functional groups. Ball-milling enhanced the formation of such groups. Microbial analysis showed hydrochar (260 °C-1 h) by ball-milling resulted in the formation of different microbial communities as compared with control experiments, and Azospira and Methanosarcina were enriched, which might be involved in DIET.

First proof of concept for full-scale, direct, low-temperature anaerobic treatment of municipal wastewater

Municipal wastewater constitutes the largest fraction of wastewater, and yet treatment processes are largely removal-based. High-rate anaerobic digestion (AD) has revolutionised the sustainability of industrial wastewater treatment and could additionally provide an alternative for municipal wastewater. While AD of dilute municipal wastewater is common in tropical regions, the low temperatures of temperate climates has resulted in slow uptake. Here, we demonstrate for the first time, direct, high-rate, low-temperature AD of low-strength municipal wastewater at full-scale. An 88 m³ hybrid reactor was installed at the municipal wastewater treatment plant in Builth Wells, UK and operated for 290 days. Ambient temperatures ranged from 2 to 18 °C, but remained below 15 °C for > 100 days. Influent BOD fluctuated between 2 and 200 mg L^-1. However, BOD removal often reached > 85%. 16S rRNA amplicon sequencing of DNA from the biomass revealed a highly adaptable core microbiome. These findings could provide the basis for the next-generation of municipal wastewater treatment.

Microbiome taxonomic and functional profiles of two domestic sewage treatment systems

Anaerobic systems for domestic sewage treatment, like septic tanks and anaerobic filters, are used in developing countries due to favorable economic and functional features. The anaerobic filter is used for the treatment of the septic tank effluent, to improve the COD removal efficiency of the system. The microbial composition and diversity of the microbiome from two wastewater treatment systems (factory and rural school) were compared through 16S rRNA gene sequencing using MiSeq 2 × 250 bp Illumina sequencing platform. Additionally, 16S rRNA data were used to predict the functional profile of the microbial communities using PICRUSt2. Results indicated that hydrogenotrophic methanogens, like Methanobacterium, were found in higher abundance in both systems compared to acetotrophic methanogens belonging to Methanosaeta genus. Also, important syntrophic microorganisms (Smithella, Syntrophus, Syntrophobacter) were found in the factory and rural school wastewater treatment systems. Microbial communities were also compared between stages (septic tank and anaerobic filter) of each wastewater treatment stage, revealing that, in the case of the rural school, both microbial communities were quite similar most likely due to hydraulic short-circuit issues. Meanwhile, in the factory, microbial communities from the septic tank and anaerobic filter were different. The school system showed lower COD removal rates (2-30%), which were probably related to a higher abundance of Firmicutes members in addition to the hydraulic short-circuit and low abundance of Chloroflexi members. On the other hand, the fiberglass factory presented higher COD removal rates (60-83%), harboring phyla reported as the core microbiome of anaerobic digesters (Bacteroidetes, Chloroflexi, and Proteobacteria phyla). The knowledge of the structure and composition of wastewater treatment systems may provide support for the improvement of the pollutant removal in anaerobic process.

Sludge pre-treatments change performance and microbiome in methanogenic sludge digesters by releasing different sludge organic matter

In this study, temporal impacts of thermal, alkaline/acid and thermal-alkaline sludge pre-treatments on digestion performance and microbiome were investigated and compared in methanogenic sludge digesters. Results showed that thermal and alkaline/acid pre-treatments were efficient in releasing intracellular and EPS organic matter, respectively. The thermal-alkaline pre-treatment showed synergistic impacts of both thermal and alkaline/acid pre-treatments by releasing the major portion of sludge organic matter from solid- to liquid-phase, which result in 60-65% organic carbon removal in subsequent sludge digestion and further optimizing digestion temperature had negligible improvement. The 16S rRNA gene-based analyses suggested that organic matter released from sludge pre-treatments is a major deterministic parameter in shaping sludge microbiome. Pre-treatment specific lineages were identified in different sludge digesters, whereas several taxa were identified as common functionally active populations in sludge digestion. This study provided mechanistic insights into impacts of pre-treatments on digestion performance and microbiome in methanogenic sludge digesters.

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum

Bacterial hydrolysis of polysaccharides is an important step for the production of sustainable energy, for example during the conversion of plant biomass to methane-rich biogas. Previously, Hungateiclostridium thermocellum was identified as cellulolytic key player in thermophilic biogas microbiomes with a great frequency as an accompanying organism. The aim of this study was to physiologically characterize a recently isolated co-culture of H. thermocellum and the saccharolytic bacterium Defluviitalea raffinosedens from a laboratory-scale biogas fermenter. The characterization focused on cellulose breakdown by applying the measurement of cellulose hydrolysis, production of metabolites, and the activity of secreted enzymes. Substrate degradation and the production of volatile metabolites was considerably enhanced when both organisms acted synergistically. The metabolic properties of H. thermocellum have been studied well in the past. To predict the role of D. raffinosedens in this bacterial duet, the genome of D. raffinosedens was sequenced for the first time. Concomitantly, to deduce the prevalence of D. raffinosedens in anaerobic digestion, taxonomic composition and transcriptional activity of different biogas microbiomes were analyzed in detail. Defluviitalea was abundant and metabolically active in reactor operating at highly efficient process conditions, supporting the importance of this organism for the hydrolysis of the raw substrate.