Distribution and abundance of Spirochaetes in full-scale anaerobic digesters

Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems

Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance1. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.

External ceramic membrane contactor for in-situ H2 assisted biogas upgrading

Biological H2-assisted biogas upgrading has gained significant attention as an environmentally friendly substitute to common physico-chemical upgrading techniques, but is largely limited by the low solubility of H2. This study evaluated the design of a ceramic membrane contactor module for H2 injection. H2 dissolution was maintained at high efficiency by controlling gas supply and sludge recirculation rate, achieving a biogas quality of average 98.8% CH4 during the stable operation phase with a 108% increase in the CH4 production rate. This also outperforms conventional H2 injection using diffuser sparging which could only achieve a biogas quality of 84% CH4 content. Microbial community analysis found high Methanobacterium spp. abundance within the archaea at 95.2% at the end of the operation, allowing the dominance of the hydrogenotrophic methanogenesis pathway for high upgrading efficiencies. The system is a high-performance external membrane connector module coupled to common anaerobic digestion systems for biogas upgrading.

Bioelectrochemically-assisted ammonia recovery from dairy manure

The sustainability of direct land application of dairy manure is challenged by significant nutrient losses. Bioelectrochemical systems for ammonia recovery offer a manure management strategy that can recover both ammoniacal and organic nitrogen as a stable ammonia fertilizer. In this research, a microbial fuel cell (MFC) was used to treat two types of dairy manure under a variety of imposed anode compartment conditions. The system achieved a maximum coulombic efficiency of 20 ± 18 % and exhibited both COD and total nitrogen removals of approximately 60 %. Furthermore, the MFC showed a maximum organic nitrogen removal of 73.8 ± 12.1 %, and no differences in organic nitrogen (orgN) removal were detected among different conditions tested. Decreasing concentrations of anolyte ammonia nitrogen coupled with the observed orgN removal from the anolyte indicate that the MFC is effective at recovering orgN in dairy manure as ammoniacal nitrogen in the catholyte. Additionally, ion competition between NH4+ and other relevant cations (Na+, K+, and Mg2+) for transport across the CEM was investigated, with only K+ showing minor competitive effects. Based on the results of this research, we propose three key processes and two sub-processes that contribute to the successful operation of the MFC for nitrogen recovery from dairy manure. Bioelectrochemical systems for nitrogen recovery from dairy manure offer a novel, robust technology for producing a valuable ammonia nitrogen fertilizer, a thus far untapped resource in dairy manure streams.

Soil microbial communities' contributions to soil ecosystem multifunctionality in the natural restoration of abandoned metal mines

On a global scale, the restoration of metal mine ecosystem functions is urgently required, and soil microorganisms play an important role in this process. Conventional studies frequently focused on the relationship between individual functions and their drivers; however, ecosystem functions are multidimensional, and considering any given function in isolation ignores the trade-offs and interconnectedness between functions, which complicates obtaining a comprehensive understanding of ecosystem functions. To elucidate the relationships between soil microorganisms and the ecosystem multifunctionality (EMF) of metal mines, this study investigated natural restoration of metal mines, evaluated the EMF, and used high-throughput sequencing to explore the bacterial and fungal communities as well as their influence on EMF. Bacterial community diversity and composition were more sensitive to mine restoration than fungal community. Bacterial diversity exhibited redundancy in improving N-P-K-S multifunctionality; however, rare bacterial taxa including Dependentiae, Spirochaetes, and WPS-2 were important for metal multifunctionality. Although no clear relationship between fungal diversity and EMF was observed, the abundance of Glomeromycota had a significant effect on the three EMF categories (N-P-K-S, carbon, and metal multifunctionality). Previous studies confirmed a pronounced positive association between microbial diversity and multifunctionality; however, the relationship between microbial diversity and multifunctionality differs among functions' categories. In contrast, the presence of critical microbial taxa exerted stronger effects on mine multifunctionality.

Recent advances in co-digestion conjugates for anaerobic digestion of food waste

Anaerobic digestion (AD) is a biological process that breaks down organic waste materials, such as food waste (FW) that produces biogas and digestate. The biogas can be utilized as biofuel, and digestate could be applied as fertilizer. However, AD of FW alone has limitations on optimal degradation, digester stability and biogas yield. Co-digestion of FW along with other organic wastes such as animal manure, agricultural residue, sewage sludge and industrial organic waste, has shown substantial improvement in degradation process with increased biogas yield. The inadequacies in FW for optimum AD, like low carbon-to-nitrogen ratio (C/N ratio), lack of trace elements and irregular particle sizes, can be nullified by adding appropriate co-digestion conjugates. This review aims to describe the characteristic inadequacies of FW and examines the effect on mesophilic co-digestion of FW with animal manure, waste sludge and agricultural wastes for biogas production optimization. A critical review on the impact of pretreatment and co-digestion to enrich the methane (CH4) content in biogas has been performed. The review also examines the microbial community shift due to co-digestion, which is critical for the stability of an anaerobic digester. Finally, it discusses the prospects and challenges for the widespread application of the co-digestion technique as an effective organic waste management practice.

Microbiome Diversity of Anaerobic Digesters Is Enhanced by Microaeration and Low Frequency Sound

Biogas is produced by a consortium of bacteria and archaea. We studied how the microbiome of poultry litter digestate was affected by time and treatments that enhanced biogas production. The microbiome was analyzed at six, 23, and 42 weeks of incubation. Starting at week seven, the digesters underwent four treatments: control, microaeration with 6 mL air L-1 digestate per day, treatment with a 1000 Hz sine wave, or treatment with the sound wave and microaeration. Both microaeration and sound enhanced biogas production relative to the control, while their combination was not as effective as microaeration alone. At week six, over 80% of the microbiome of the four digesters was composed of the three phyla Actinobacteria, Proteobacteria, and Firmicutes, with less than 10% Euryarchaeota and Bacteroidetes. At week 23, the digester microbiomes were more diverse with the phyla Spirochaetes, Synergistetes, and Verrucomicrobia increasing in proportion and the abundance of Actinobacteria decreasing. At week 42, Firmicutes, Bacteroidetes, Euryarchaeota, and Actinobacteria were the most dominant phyla, comprising 27.8%, 21.4%, 17.6%, and 12.3% of the microbiome. Other than the relative proportions of Firmicutes being increased and proportions of Bacteroidetes being decreased by the treatments, no systematic shifts in the microbiomes were observed due to treatment. Rather, microbial diversity was enhanced relative to the control. Given that both air and sound treatment increased biogas production, it is likely that they improved poultry litter breakdown to promote microbial growth.

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.

Retention and recycling of granules in continuous flow-through system to accomplish denitrification and perchlorate reduction

This study employed a completely anoxic reactor and a gravity-settling design for continuously separating from flocculated biomass and hydraulically recycling granules back to the main reactor. The average chemical oxygen demand (COD) removal in the reactor was 98 %. Average nitrate (NO₃^--N) and perchlorate (ClO₄^-) removal efficiencies of 99 % and 74 ± 19 % were observed, respectively. Preferential utilization of NO₃^- over ClO₄^- led to COD limiting conditions, which resulted in ClO₄^- in the effluent. The average granule diameter in continuous flow-through bubble-column (CFB) anoxic granular sludge (AxGS) bioreactor was 6325 ± 2434 µm, and the average SVI₃₀/SVI₁ was > 90% throughout its operation. 16s rDNA amplicon sequencing revealed Proteobacteria (68.53% - 88.57%) and Dechloromonas (10.46% - 54.77%) to be the most abundant phylum and genus present in reactor sludge representing the denitrifying and ClO₄^- reducing microbial community. This work represents a pioneering development of CFB-AxGS bioreactor.

Exposure to cadmium induced gut antibiotic resistance genes (ARGs) and microbiota alternations of Babylonia areolata

Cadmium (Cd) is widely distributed in aquatic environments and has multiple adverse effects on aquatic organisms such as the ivory shell (Babylonia areolata). However, its effects on antibiotic resistance genes (ARGs) and gut microbiota of B. areolata remain unclear. In this study, we explored the effects of different concentrations (0, 0.03, 0.18 and 1.08 mg/L) of Cd on intestinal microbial communities and ARGs in B. areolata through 16S rRNA gene sequencing and high-throughput quantitative PCR. The results showed that the structure and diversity of ARGs and microbiota in B. areolata gut were altered upon Cd exposure. Tetracycline, Vancomycin and Macrolide-Lincosamide-Streptogramin B (MLSB) resistance genes were identified as the major ARGs in B. areolata gut. The absolute abundance and alpha diversity of ARGs in B. areolata gut increased with the rise of cadmium concentration. The microbial communities at genus level were enriched in the low and medium Cd concentration groups, while decreased in the high Cd concentration group compared to the control groups. In addition, the influence of microbiota on the ARG profile was more significant than that of Cd concentration and MGEs in B. areolata gut. Null model analysis demonstrated that stochastic processes dominated ARG assembly in the Cd-exposed groups and were enhanced with the increasing Cd concentrations. Four opportunistic bacterial pathogens (Bacteroides, Legionella, Acinetobacter and Escherichia) detected in B. areolata gut maybe the potential hosts of ARGs. Our findings provide references for the hazards assessment of environmental Cd exposure of gut microbiome in aquatic animals.

Promoting the overall energy profit through using the liquid hydrolysate during microwave hydrothermal pretreatment of wheat straw as co-substrate for anaerobic digestion

Liquid hydrolysate (LH) derived from the microwave hydrothermal pretreatment (MHP) of wheat straw (WS) was anaerobically digested together with the solid residual to promote the overall energy profit. Different MHP temperatures (90, 120, 150, 180 °C) and retention times (10, 20, 40 min) were investigated. Increased MHP intensity generated plenty of VFAs (mainly acetate) and phenols in the LH, implying the double-side effect of LH on AD. The highest methane production of 227.92 mL CH₄·gVS^-1 Raw was obtained with MHP at 120 °C for 10 min, 21.53 % higher than the control. While, MHP at 180 °C for 40 min exhibited 29.02 % lower methane production (113.13 mL CH₄·gVS^-1 Raw) and 115.86 % longer lag phase (3.13 days) than the control. Butyrate fermentation endowed the treatment groups of 180 °C with resilience from the overload and inhibition. Methanosarcina was largely enriched by the abundant acetate in LH on the early stage of anaerobic digestion (AD), especially when with high MHP intensity. Increased abundance of Methanosaeta and Methanobacterium played a crucial role in maintaining methane production at the middle and later stage. The high number of species and evenness in methanogens community were beneficial for the startup of batch AD. Although negative net energy was obtained, the lower ratio of energy input and output compared with the most researches using the solid residual after MHP as the sole substrate for AD demonstrated the contribution of LH to the overall energy profit.

Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor

Introduction

The expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated.

Methods

Here, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year.

Results

We observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p <0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p <0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p <0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p <0.05).

Discussion

Our work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.

Seasonal characterization of the prokaryotic microbiota of full-scale anaerobic UASB reactors treating domestic sewage in southern Brazil

Upflow Anaerobic Sludge Blanket (UASB) reactors are alternatives in the anaerobic treatment of sanitary sewage in different parts of the world; however, in temperate environments, they are subject to strong seasonal influence. Understanding the dynamics of the microbial community in these systems is essential to propose operational alternatives, improve projects and increase the quality of treated effluents. In this study, for one year, high-performance sequencing, associated with bioinformatics tools for taxonomic annotation and functional prediction was used to characterize the microbial community present in the sludge of biodigesters on full-scale, treating domestic sewage at ambient temperature. Among the most representative phyla stood out Desulfobacterota (20.21-28.64%), Proteobacteria (7.48-24.90%), Bacteroidota (10.05-18.37%), Caldisericota (9.49-17.20%), and Halobacterota (3.23-6.55%). By performing a Canonical Correspondence Analysis (CCA), Methanolinea was correlated to the efficiency in removing Chemical Oxygen Demand (COD), Bacteroidetes_VadinHA17 to the production of volatile fatty acids (VFAs), and CI75cm.2.12 at temperature. On the other hand, Desulfovibrio, Spirochaetaceae_uncultured, Methanosaeta, Lentimicrobiaceae_unclassified, and ADurb.Bin063-1 were relevant in shaping the microbial community in a co-occurrence network. Diversity analyses showed greater richness and evenness for the colder seasons, possibly, due to the lesser influence of dominant taxa. Among the principal metabolic functions associated with the community, the metabolism of proteins and amino acids stood out (7.74-8.00%), and the genes related to the synthesis of VFAs presented higher relative abundance for the autumn and winter. Despite the differences in diversity and taxonomic composition, no significant changes were observed in the efficiency of the biodigesters.

Enrichment of sulfur-oxidizing bacteria using S-doped NiFe2O4 nanosheets as the anode in microbial fuel cell enhances power production and sulfur recovery

Microbial fuel cells (MFCs) have great promise for power generation by oxidizing organic wastewater, yet the challenge to realize high efficiency in simultaneous energy production and resource recovery remains. In this study, we designed a novel MFC anode by synthesizing S-doped NiFe₂O₄ nanosheet arrays on carbon cloth (S10-NiFe₂O₄@CC) to build a three-dimensional (3D) hierarchically porous structure, with the aim to regulate the microbial community of sulfur-cycling microbes in order to enhance power production and elemental sulfur (S⁰) recovery. The S10-NiFe₂O₄@CC anode obtained a faster start-up time of 2 d and the highest power density of 4.5 W/m² in acetate-fed and mixed bacteria-based MFCs. More importantly, sulfide removal efficiency (98.3 %) (initial concentration of 50 mg/L S^2-) could be achieved within 3 d and sulfur (S₈) could be produced. Microbial community analysis revealed that the S10-NiFe₂O₄@CC anode markedly enriched sulfur-oxidizing bacteria (SOB) and promoted enrichment of SOB and sulfate-reducing bacteria (SRB) in the bulk solution as well, leading to the enhancement of power generation and S⁰ recovery. This study shows how carefully designing and optimizing the composition and structure of the anode can lead to the enrichment of a multifunctional microbiota with excellent potential for sulfide removal and resource recovery.

Combining high pressure homogenization with free nitrous acid pretreatment to improve anaerobic digestion of sewage sludge

Single pretreatment of sewage sludge, either physical, chemical or biological, has its own drawbacks in term of poor sanitization, energy intensity and high operational and capital cost. To tackle these drawbacks, combined high pressure homogenization (HPH) and free nitrous acid (FNA) pretreatment for sludge solubilization and further biodegradation in anaerobic digestion was investigated. Synergistic effect of combined HPH (40 MPa) and FNA (2.49 mg/L) pretreatment (HPH-FNA) for improving anaerobic digestion was evaluated, and its effect on archaeal and bacterial community structure was analyzed. Compared with single HPH and FNA pretreatments, HPH-FNA pretreatment efficiently solubilized wasted activated sludge (WAS), subsequently improved anaerobic digestion. Cumulative biogas production from sewage sludge pretreated with HPH-FNA was 154%, 108% and 284% more than that with single pretreatment of FNA, HPH and raw sludge, respectively. In addition, volumetric biogas production of combined pretreatment system (815 ml) was more than the sum from single pretreatment (710 ml). Methane content in biogas for raw sludge, FNA, HPH and HPH-FNA pretreated sludge was 45%, 51%, 55% and 65%, respectively. Illumina MiSeq sequencing analysis revealed that HPH-FNA pretreatment promoted bacterial growth of phyla Bacteroidetes, Firmicutes and Synergistetes and archaeal genera Methanospirillum and Methanosaeta. Overall, combined HPH-FNA pretreatment of sewage sludge, prior to anaerobic digestion, is an environmentally-friendly and potentially economic technology.

Comparative Analysis of Brucepastera parasyntrophica gen. nov., sp. nov. and Teretinema zuelzerae gen. nov., comb. nov. (Treponemataceae) Reveals the Importance of Interspecies Hydrogen Transfer in the Energy Metabolism of Spirochetes

Most members of the family Treponemataceae (Spirochaetales) are associated with vertebrate hosts. However, a diverse clade of uncultured, putatively free-living treponemes comprising several genus-level lineages is present in other anoxic environments. The only cultivated representative to date is Treponema zuelzerae, isolated from freshwater mud. Here, we describe the isolation of strain RmG11 from the intestinal tract of cockroaches. The strain represents a novel genus-level lineage of Treponemataceae and is metabolically distinct from T. zuelzerae. While T. zuelzerae grows well on various sugars, forming acetate and H₂ as major fermentation products, strain RmG11 grew poorly on glucose, maltose, and starch, forming mainly ethanol and only small amounts of acetate and H₂. In contrast to the growth of T. zuelzerae, that of strain RmG11 was strongly inhibited at high H₂ partial pressures but improved considerably when H₂ was removed from the headspace. Cocultures of strain RmG11 with the H₂-consuming Methanospirillum hungatei produced acetate and methane but no ethanol. Comparative genomic analysis revealed that strain RmG11 possesses only a single, electron-confurcating hydrogenase that forms H₂ from NADH and reduced ferredoxin, whereas T. zuelzerae also possesses a second, ferredoxin-dependent hydrogenase that allows the thermodynamically more favorable formation of H₂ from ferredoxin via the Rnf complex. In addition, we found that T. zuelzerae utilizes xylan and possesses the genomic potential to degrade other plant polysaccharides. Based on phenotypic and phylogenomic evidence, we describe strain RmG11 as Brucepastera parasyntrophica gen. nov., sp. nov. and Treponema zuelzerae as Teretinema zuelzerae gen. nov., comb. nov. IMPORTANCE Spirochetes are widely distributed in various anoxic environments and commonly form molecular hydrogen as a major fermentation product. Here, we show that two closely related members of the family Treponemataceae differ strongly in their sensitivity to high hydrogen partial pressure, and we explain the metabolic mechanisms that cause these differences by comparative genome analysis. We demonstrate a strong boost in the growth of the hydrogen-sensitive strain and a shift in its fermentation products to acetate during cocultivation with a H₂-utilizing methanogen. Our results add a hitherto unrecognized facet to the fermentative metabolism of spirochetes and also underscore the importance of interspecies hydrogen transfer in not-obligately-syntrophic interactions among fermentative and hydrogenotrophic guilds in anoxic environments.

Microbial community development during syngas methanation in a trickle bed reactor with various nutrient sources

Microbial community development within an anaerobic trickle bed reactor (TBR) during methanation of syngas (56% H₂, 30% CO, 14% CO₂) was investigated using three different nutrient media: defined nutrient medium (241 days), diluted digestate from a thermophilic co-digestion plant operating with food waste (200 days) and reject water from dewatered digested sewage sludge at a wastewater treatment plant (220 days). Different TBR operating periods showed slightly different performance that was not clearly linked to the nutrient medium, as all proved suitable for the methanation process. During operation, maximum syngas load was 5.33 L per L packed bed volume (pbv) & day and methane (CH₄) production was 1.26 L CH₄/L_pbv/d. Microbial community analysis with Illumina Miseq targeting 16S rDNA revealed high relative abundance (20-40%) of several potential syngas and acetate consumers within the genera Sporomusa, Spirochaetaceae, Rikenellaceae and Acetobacterium during the process. These were the dominant taxa except in a period with high flow rate of digestate from the food waste plant. The dominant methanogen in all periods was a member of the genus Methanobacterium, while Methanosarcina was also observed in the carrier community. As in reactor effluent, the dominant bacterial genus in the carrier was Sporomusa. These results show that syngas methanation in TBR can proceed well with different nutrient sources, including undefined medium of different origins. Moreover, the dominant syngas community remained the same over time even when non-sterilised digestates were used as nutrient medium. KEY POINTS: • Independent of nutrient source, syngas methanation above 1 L/L_pbv/D was achieved. • Methanobacterium and Sporomusa were dominant genera throughout the process. • Acetate conversion proceeded via both methanogenesis and syntrophic acetate oxidation.

Mechanisms of allicin exposure for the sludge fermentation enhancement: Focusing on the fermentation processes and microbial metabolic traits

As a frequently used product with antimicrobial activity, consumed allicin might be discharged and concentrated in waste-activated sludge (WAS). However, the influence of allicin (as an exogenous pollutant) on WAS fermentation has not been clearly revealed. This study aimed to disclose the impacts of allicin on volatile fatty acid (VFA) generation during WAS fermentation. The results showed that the appropriate presence of allicin (10 mg/g TSS) significantly enhanced the VFA yield (1894 versus 575 mg COD/L in the control) with increased acetate proportion (24.3%). Further exploration found that allicin promoted WAS solubilization, hydrolysis and acidification simultaneously. Metagenomic analysis revealed that the key genes involved in extracellular hydrolysis metabolism (i.e., CAZymes), membrane transport (i.e., gtsA and ytfT), substrate metabolism (i.e., yhdR and pfkC) and fatty acid synthesis (i.e., accA and accD) were all highly expressed. Allicin also induced the bacteria to produce more signalling molecules and regulate cellular functions, thereby enhancing the microbial adaptive and regulatory capacity to the unfavourable environment. Moreover, the variations in fermentative microbes and their contributions to the upregulation of functional genes (i.e., ytfR, gltL, INV, iolD and pflD) for VFA generation were disclosed. Overall, the simultaneous stimulation of functional microbial abundances and metabolic activities contributed to VFA production in allicin-conditioned reactors.

Mesophilic and Thermophilic Anaerobic Digestion of Wheat Straw in a CSTR System with 'Synthetic Manure': Impact of Nickel and Tungsten on Methane Yields, Cell Count, and Microbiome

Lignocellulosic residues, such as straw, are currently considered as candidates for biogas production. Therefore, straw fermentations were performed to quantitatively estimate methane yields and cell counts, as well as to qualitatively determine the microbiome. Six fully automated, continuously stirred biogas reactors were used: three mesophilic (41 °C) and three thermophilic (58 °C). They were fed every 8 h with milled wheat straw suspension in a defined, buffered salt solution, called 'synthetic manure'. Total reflection X-ray fluorescence spectrometry analyses showed nickel and tungsten deficiency in the straw suspension. Supplementation of nickel and subsequently tungsten, or with an increasing combined dosage of both elements, resulted in a final concentration of approximately 0.1 mg/L active, dissolved tungsten ions, which caused an increase of the specific methane production, up to 63% under mesophilic and 31% under thermophilic conditions. That is the same optimal range for pure cultures of methanogens or bacteria found in literature. A simultaneous decrease of volatile fatty acids occurred. The Ni/W effect occurred with all three organic loading rates, being 4.5, 7.5, and 9.0 g volatile solids per litre and day, with a concomitant hydraulic retention time of 18, 10, or 8 days, respectively. A maximum specific methane production of 0.254 m³ CH₄, under standard temperature and pressure per kg volatile solids (almost 90% degradation), was obtained. After the final supplementation of tungsten, the cell counts of methanogens increased by 300%, while the total microbial cell counts increased by only 3-62%. The mesophilic methanogenic microflora was shifted from the acetotrophic Methanosaeta to the hydrogenotrophic Methanoculleus (85%) by tungsten, whereas the H₂-CO₂-converter, Methanothermobacter, always dominated in the thermophilic fermenters.

Stability and nutrients removal performance of a Phanerochaete chrysosporium-based aerobic granular sludge process by step-feeding and multi A/O conditions

A Phanerochaete chrysosporium-based aerobic granular sludge (PC-AGS) was developed by inoculating fungal mycelial pellets into a lab-scale aerobic granular sequencing batch reactor (AGSBR). A strategy using step-anaerobic feeding coupled with multi A/O conditions was adopted. The results showed that the removal efficiencies for total phosphorus (TP) and total inorganic nitrogen (TIN) were 94.56 ± 2.92% and 75.20 ± 7.74%, respectively, under relatively low aeration time. Compared with original AGS, the content of extracellular proteins for PC-AGS obviously increased from 18.61 to 41.44 mg/g MLSS by the end of phase I. Moreover, the mature granules had a larger size and better stability during the 100 days operation. Furthermore, the analysis of microbial diversity detected many key functional groups in PC-AGS granules that were beneficial to nutrients removal. This work demonstrated that the addition of fungal pellets not only enhanced the removal performance, but also improved the stability of the AGS system.

Influence of initial pH on the production of volatile fatty acids and hydrogen during dark fermentation of kitchen waste

The purpose of this work was to determine the effect of initial pH on the production of volatile fatty acids (VFA) and hydrogen (H₂) in the dark fermentation processes of kitchen waste. The study was conducted in batch bioreactors of working volume 1 L for different initial pH in the range from 5.5 to 9.0. The dark fermentation processes were carried out for 4 days at 37°C. Initial organic load of the kitchen waste in all bioreactors amounted to 25.5 gVS/L. Buffering of pH during the fermentation process was carried out with the use of ammonia contained mainly in digested sludge. The optimal conditions for the production of VFA and H₂ were achieved at the initial pH of 8. Production of VFA and H₂ in these conditions was, respectively, 13.9 g/L and 72.4 mL/gVS. The main produced components of VFA were acetic and butyric acids. The production of ethanol and lactic acid was at very low levels due to the high ratio of the volatile fatty acids to total organic content of 0.86. With the optimal initial pH of 8 the yield of CO₂ production was 0.30 gC/gC. High initial pH value (above 8) extended the lag phase duration in the course of H₂ production. The dominant groups of micro-organisms at the most favourable initial pH of 8 for the production of VFA and H₂ were Bacteroidetes, Firmicutes, Spirochaetes and Waste Water of Evry 1 (WWE1) at the phylum level.

Microbiota-Macroalgal Relationships at a Hawaiian Intertidal Bench Are Influenced by Macroalgal Phyla and Associated Thallus Complexity

The ocean represents the largest biome on earth; however, we have only begun to understand the diversity and function of the marine microbial inhabitants and their interactions with macroalgal species. Macroalgae play an integral role in overall ocean biome health and serve both as major primary producers and foundation species in the ecosystem. Previous studies have been limited, focusing on the microbiome of a single algal species or its interaction with selected microbes. This project aimed to understand overall biodiversity of microbial communities associated with five common macroalgal species and to determine the drivers of these communities at 'Ewa Beach, O'ahu, HI. Representative species of Chlorophyta (green), Ochrophyta (brown), and Rhodophyta (red) algae, each species having various levels of calcification, thallus complexity, and status as native or invasive species, were collected from an intertidal bench in May 2019. A portion of the V3-V4 variable region of the small-subunit rRNA gene was amplified for high-throughput sequencing using universal bacterial primers to elucidate the core and variable algal microbiome. Significant differences in bacterial community composition were only partially explained by host species, whether the host was native or invasive, and thallus complexity. Macroalgal phylum explained the most variation in associated microbial communities at 'Ewa Beach. This study advances our understanding of microbial-macroalgal interactions and their connectivity by producing insight into factors that influence the community structure of macroalga-associated microbiota. IMPORTANCE Generally, most eukaryotic organisms form relationships with microbes that are important in mediating host organismal health. Macroalgae are a diverse group of photosynthetic eukaryotic organisms that serve as primary producers and foundational species in many ecosystems. However, little is known about their microbial counterparts across a wide range of macroalgal morphologies, phylogenies, and calcification levels. Thus, to further understand the factors involved in bacterial community composition associated with macroalgal species at one point in time, representative samples were collected across phyla. Here, we show that both host macroalga phyla and morphology influenced the associated microbial community. Additionally, we show that the invasive species Avrainvillea lacerata does not have a unique microbial community on this intertidal bench, further supporting the idea that host phylum strongly influences microbial community composition.

Variations of antibiotic resistome in swine wastewater during full-scale anaerobic digestion treatment

Anaerobic digesters have been widely used to treat wastewaters in livestock farms. With the increasing risk of antibiotic resistance originated from livestock husbandry, removal of antibiotics and antibiotic resistance genes (ARGs) via anaerobic digesters deserved more attention. Here we investigated the removal of antibiotics and ARGs in swine wastewater by three on-farm full-scale anaerobic digesters, including buried biogas digester (BBD), up-flow anaerobic sludge blanket (UASB) and high density polyethylene covered biogas digester (HDPE-BD). Variations of antibiotic resistome in swine wastewater were further revealed by metagenomic sequencing. Results showed the removal efficiencies for antibiotics, ARGs and mobile genetic elements (MGEs) varied in the three digesters, ranging from 65.1% to 98.1%, 3.5%-71.0% and 26.9%-77.2%, respectively. In general, UASB and HDPE-BD showed better removal efficiencies than BBD. However, enrichment of metal resistance genes (MRGs) was noted in UASB. Pathogens could not be effectively removed by all of the three digesters. What's more, accumulation of pathogens was found in UASB (removal efficiencies: -8.5%-13.6%). Bacterial community succession, horizontal genetic transfer and biocide and metal resistance genes (BMRGs) profiles jointly structured the variation of antibiotic resistome during anaerobic digestion. A total of 334 high-quality bins were identified from swine wastewater, 96 of which belonged to phylum of Firmicutes, Bacteroidetes and Proteobacteria carried ARGs. Proteobacteria was the dominant multi-drug resistant flora. Meanwhile, ARG-carrying pathogens (Bacteroides and Mycolicibacter) were found in the swine wastewater, suggesting a potential threat to human and animal health. The findings from this study showed that HDPE-BD is the most eco-friendly and effective anaerobic digester in controlling risks from antibiotic resistance determinants in swine wastewater.

Resilience of Faecal Microbiota in Stabled Thoroughbred Horses Following Abrupt Dietary Transition between Freshly Cut Pasture and Three Forage-Based Diets

The management of competition horses in New Zealand often involves rotations of short periods of stall confinement and concentrate feeding, with periods of time at pasture. Under these systems, horses may undergo abrupt dietary changes, with the incorporation of grains or concentrate feeds to the diet to meet performance needs, or sudden changes in the type of forage fed in response to a lack of fresh or conserved forage. Abrupt changes in dietary management are a risk factor for gastrointestinal (GI) disturbances, potentially due to the negative effects observed on the population of GI microbiota. In the present study, the faecal microbiota of horses was investigated to determine how quickly the bacterial communities; (1) responded to dietary change, and (2) stabilised following abrupt dietary transition. Six Thoroughbred mares were stabled for six weeks, consuming freshly cut pasture (weeks 1, 3 and 5), before being abruptly transitioned to conserved forage-based diets, both offered ad libitum. Intestinal markers were administered to measure digesta transit time immediately before each diet change. The conserved forage-based diets were fed according to a 3 × 3 Latin square design (weeks 2, 4 and 6), and comprised a chopped ensiled forage fed exclusively (Diet FE) or with whole oats (Diet FE + O), and perennial ryegrass hay fed with whole oats (Diet H + O). Faecal samples were collected at regular intervals from each horse following the diet changes. High throughput 16S rRNA gene sequencing was used to evaluate the faecal microbiota. There were significant differences in alpha diversity across diets (p < 0.001), and a significant effect of diet on the beta diversity (ANOSIM, p = 0.001), with clustering of samples observed by diet group. There were differences in the bacterial phyla across diets (p < 0.003), with the highest relative abundances observed for Firmicutes (62-64%) in the two diets containing chopped ensiled forage, Bacteroidetes (32-38%) in the pasture diets, and Spirochaetes (17%) in the diet containing hay. Major changes in relative abundances of faecal bacteria appeared to correspond with the cumulative percentage of intestinal markers retrieved in the faeces as the increasing amounts of digesta from each new diet transited the animals. A stable faecal microbiota profile was observed in the samples from 96 h after abrupt transition to the treatment diets containing ensiled chopped forage. The present study confirmed that the diversity and community structure of the faecal bacteria in horses is diet-specific and resilient following dietary transition and emphasised the need to have modern horse feeding management that reflects the ecological niche, particularly by incorporating large proportions of forage into equine diets.

Geochemical stability of zero-valent iron modified raw wheat straw innovatively applicated to in situ permeable reactive barrier: N2 selectivity and long-term denitrification

The zero-valent iron (ZVI) modified wheat straw materials are widely used for treating groundwater by permeable reactive barrier (PRB). We report the performance of a field-scale PRB filled with ZVI modified wheat straw materials for nitrate (NO3-)-contaminated groundwater. In lab-scale PRB filled with ZVI modified wheat straw material, NO3- concentration entering the PRB was varied (27.80-59.86 mg L-1) according to the in situ NO3- contamination. A stable NO3- removal rate of 90% was achieved at a controlled hydraulic retention time of 22 days, together with a proportion of denitrifying bacteria up to 34.37%. The field-scale PRB filled with ZVI modified wheat straw material was successful at removing NO3- from groundwater (removal percentages ≥60%) at a groundwater flow rate of 0.01 m3 d-1. Monitoring of groundwater within this PRB provided evidences that the nitrogen gas (N2) selectivity increased with lower ammonia (NH4+) generated from ZVI reduction of NO3-, and few emission of NO2- present due to denitrification capacity in this PRB. The results are finally compared with the few others reported existing PRBs for nitrate-contaminated groundwater worldwide, and demonstrated that the ZVI modified wheat straw material would be an effective fillings for field PRB to remediate groundwater.

Density profile modeling for real-time estimation of liquid level in anaerobic digester using multiple pressure meters

The liquid level of a bioreactor is an important operating parameter governing the hydraulic retention time. In this study, a novel method is proposed to estimate the liquid level of anaerobic digesters. The proposed method has an advantage over typical differential pressure measurement as it considers the heterogeneity of the digestate along the level using multiple pressure meters. The real-time measurement generates a model to fit the densities at different liquid columns, predicts the density of the surface layer and determines the overall liquid level. A pilot-scale (0.33 m³ working volume; 1.2 m liquid level) digester, equipped with seven pressure meters, was operated to test the methodology. The performance of the digester was confirmed stable during a long-term (175 d) operation. A set of density-pressure models was developed and were validated using the long-term experimental data. The new method employing cubic model showed significantly better estimation of the reactor level (mean error rate of 1.31%) with improved CDF, as compared with the traditional differential pressure method (mean error rate of 5.71%). The methodology proposed in this study is simple, robust, and cost-effective and can be used to provide additional insights into the operation of an anaerobic digester such as assessing the mixing efficiency.

High efficiency in-situ biogas upgrading in a bioelectrochemical system with low energy input

Biogas produced from anaerobic digestion usually contains 30%-50% CO_2, much of which must be removed, before utilization. Bioelectrochemical biogas upgrading approaches show promise, however, they have not yet been optimized for practical applications. In this study, a bioelectrochemical system with low energy input (applied cathode potential of -0.5 V vs. standard hydrogen electrode, SHE) was used for in-situ biogas upgrading. High efficiency CO₂ conversion (318.5 mol/d/m²) was achieved when the system was operated with an organic load of 1.7 kgCOD/(m³ d). Methane content in the upgraded biogas was 97.0% and CO₂ concentrations stayed below 3%, which is comparable to biogas upgraded with more expensive and less sustainable physiochemical approaches. The high efficiency of this approach could likely be attributed to a significant enrichment of Methanothrix (92.7%) species on the cathode surface that were expressing genes involved in both acetogenic methanogenesis and direct electron transfer (DET). Electromethanogenesis by these organisms also increased proton consumption and created a higher pH that increased the solubility of CO₂ in the bioreactor. In addition, CO₂ removal from the biogas was likely further enhanced by an enrichment of Actinobacillus species known to be capable of CO₂ fixation. Artificial neural network (ANN) models were also used to estimate CH₄ production under different loading conditions. The ANN architecture with 10 neurons at hidden layers fit best with a mean square error of 6.06 × 10^-3 and R² of 0.99.

Carbon-based conductive materials accelerated methane production in anaerobic digestion of waste fat, oil and grease

Little is known about the effect of carbon-based conductive material (CM) addition on the anaerobic co-digestion of fat, oil and grease (FOG) and waste activated sludge (WAS). In this study, three types of carbon-based CMs (nano-graphite (NG), granular activated carbon (GAC), and carbon cloth (CC)) and nine dosages were evaluated for their influences on co-digestion performance. The best dosage was achieved at 0.2 g/L NG, 10 g/L GAC, and 1 cm × 5 cm CC with 13-22% incremental methane production, 25-55% increased VS removal and 28-32% enhanced COD conversion efficiency compared to the control. The highest total amount of bacteria/archaea was found in CC (1 cm × 5 cm), followed by GAC at 10 g/L and NG at 0.2 g/L, which were all higher than those of the control. Microbial community analysis revealed that direct interspecies electron transfer (DIET)-mediated syntrophic acetate oxidation (SAO) enabling faster acetate conversion might be responsible for the enhancement of methane production.

Integrating microbial electrolysis cell based on electrochemical carbon dioxide reduction into anaerobic osmosis membrane reactor for biogas upgrading

It has been reported that anaerobic osmosis membrane bioreactors have the potential for energy recovery since dissolved methane was almost rejected by commercial forward osmosis membranes. Notwithstanding, upgraded biogas has to be achieved by removing as much carbon dioxide as possible. In this study, a novel anaerobic osmotic membrane bioreactor-microbial electrolysis cell (AnOMBR-MEC) system was developed for simultaneous biogas upgrading and wastewater treatment. The AnOMBR-MEC elicited an excellent and stable soluble chemical oxygen demand and phosphorus removal. As the experiment progressed, unwanted carbon dioxide produced from biogas was reduced to formate using a SnO₂ nanoparticles electrocatalytic cathode in an electrocatalytic-assisted MEC, with the highest faradic efficiency of formate being 85% at 1.2V. Compared to AnOMBR, the methane content increased from 55% to 90% at the end of operation and methane yield experienced a1.6-fold increment in the AnOMBR-MEC. Microbial community analysis revealed that hydrogenotrophic methanogens (e.g. Methanobacterium and Methanobrevibacter) converted the produced H₂ and formate to methane at saline conditions. These results have demonstrated an efficient strategy based on the integration of an electrocatalytic-assisted MEC into AnOMBR for upgrading biogas, enhancing methane yield and wastewater treatment.

Zeolite favours propionate syntrophic degradation during anaerobic digestion of food waste under low ammonia stress

Zeolite addition has been widely suggested for its ability to overcome ammonia stress occurring during anaerobic digestion. However little is known regarding the underlying mechanisms of mitigation and especially how zeolite influences the microbial structuration. The aim of this study was to bring new contributions on the effect of zeolite on the microbial community arrangement under a low ammonia stress. Replicated batch experiments were conducted. The microbial population was characterised with 16S sequencing. Methanogenic pathways were identified with methane isotopic fractionation. In presence of ammonia, zeolite mitigated the decrease of biogas production rate. Zeolite induced the development of Izimaplasmatales order and preserved Peptococcaceae family members, known as propionate degraders. Moreover methane isotopic fractionation showed that hydrogenotrophic methanogenesis was maintained in presence of zeolite under ammonia low stress. Our results put forward the benefit of zeolite to improve the bacteria-archaea syntrophy needed for propionate degradation and methane production under a low ammonia stress.

Impact of oxytetracycline on anaerobic wastewater treatment and mitigation using enhanced hydrolysis pretreatment

In this study, two parallel-operated up-flow anaerobic sludge bed reactors, one used to treat synthetic wastewater spiked with oxytetracycline and the other used to treat the same wastewater after enhanced hydrolysis, were used to evaluate the impact of oxytetracycline on anaerobic digestion and resistance development and the efficacy of enhanced hydrolysis pretreatment on the elimination of adverse effects. The reactors were operated under a constant organic-loading rate (10 g/L/d) with increasing oxytetracycline doses (0 mg/L to 200 mg/L) over a period of 15 months. For the reactor without pretreatment, the chemical oxygen demand removal reached up to 89.5%%at oxytetracycline doses ranging from 0 mg/L to 100 mg/L, which collapsed at higher oxytetracycline doses. Miseq sequencing showed that a diverse hydrolysis/fermentation/acetogenesis bacterial community was maintained as the oxytetracycline dose was increased from 0 mg/L to 100 mg/L, while extreme dominance of Macellibacteroides (65.70%%- 71.56%) was found to occur at higher oxytetracycline doses. The total abundance of antibiotic resistance genes increased from 1.3 × 10^-1 copies per cell to 2.6 × 10^-1 copies per cell with increasing oxytetracycline dose from 0 mg/L to 5 mg/L, remained unchanged at oxytetracycline doses ranging from 25 mg/L to 100 mg/L, and then increased to 4.8 × 10^-1 copies per cell and 1.3 copies per cell at oxytetracycline doses of 150 mg/L and 200 mg/L, respectively. Multidrug resistance developed in response to oxytetracycline treatment at 200 mg/L. Poor chemical oxygen demand removal and a marked enrichment in antibiotic resistance genes was validated using a full-scale up-flow anaerobic sludge bed system fed with an influent oxytetracycline concentration of approximately 200 mg/L. For the reactor treating wastewater pretreated with enhanced hydrolysis (85 °C for 6 h), the chemical oxygen demand removal rate and antibiotic resistance genes level over the whole oxytetracycline dose range were found to be similar to those achieved with zero oxytetracycline treatment. These results demonstrated that the control of conventional pollutants and ARGs could be achieved simultaneously in the UASB reactor by employing enhanced hydrolysis pretreatment.

Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol

Anaerobic digestion (AD) is a process that can efficiently degrade organic waste into renewable energies. AD failure is however common as the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds. Sequencing technologies enable the identification of microbial indicators of digesters inhibition, but existing studies are limited. They used different inocula, substrates, sites and types of reactors and reported different or contradictory indicators. Our aim was to identify a robust signature of microbial indicators of phenol and ammonia inhibitions across four independent AD microbial studies. To identify such signature, we applied an original multivariate integrative method on two in-house studies, then validated our approach by predicting the inhibitory status of samples from two other studies with more than 90% accuracy. Our approach shows how we can efficiently leverage on existing studies to extract reproducible microbial community patterns and predict AD inhibition to improve AD microbial management.

Anaerobic digestion of spectinomycin mycelial residues pretreated by thermal hydrolysis: removal of spectinomycin and enhancement of biogas production

Anaerobic digestion (AD) is an effective technology to dispose antibiotic mycelial residues, but biogas production is influenced by hydrolysis rates and antibiotic residue. Herein, the effects of thermal hydrolysis pretreatment for AD of spectinomycin mycelial residues (SMRs) were investigated. The results showed that the removal ratio of spectinomycin was increased while the temperature of pretreatment was escalating. Meanwhile, thermal hydrolysis facilitated the dissolution of organic matters. However, non-biodegradable substances measured by fluorescence excitation-emission matrix accumulated and thus had an adverse influence on biogas production. Based on batch assays, the optimal pretreatment temperature for SMRs was 120 °C. The removal of spectinomycin was benefit for biogas production (increasing by 7.6%), and the overall biogas production increased by 27.6% compared with 289.90 mL gVS^-1 of untreated SMRs. The microbial community analysis revealed that spectinomycin (265 mg L^-1) might influence bacteria in the early stage of AD (first 5 days), while redundancy analysis showed that spectinomycin had a non-significant influence on community succession over the 32 days of fermentation.

Coupling biogas recirculation with FeCl3 addition in anaerobic digestion system for simultaneous biogas upgrading, phosphorus conservation and sludge conditioning

The high costs involved in sewage sludge treatment and disposal in wastewater treatment plants (WWTPs) not only bring about improper sludge disposal and thus environmental pollutions, but also limit the investment on construction of WWTPs, especially in rural areas or low-income regions. This comparative study examined the effect of biogas recirculation coupled with chemical addition in a semi-continuous anaerobic digester for sludge treatment, which was proven to achieve biogas upgrading, phosphorus conservation and sludge conditioning simultaneously, largely reducing the sludge treatment cost. Results show that FeCl₃ addition coupling biogas recirculation can improve sludge dewaterability by 94% in comparison to 75% by equivalent MgCl₂ addition, and 97% phosphorus in digestate can be conserved in solid with formation of vivianite-like crystals. Biogas recirculation can enhance CH₄ yield and content by 13% and 11%, respectively, likely attributable to the increased relative abundances of both hydrogenotrophic Methanomicrobiales and acetoclastic Methanosarcinales.

Enhancing anaerobic digestion for rural wastewater treatment with granular activated carbon (GAC) supplementation

Notwithstanding many efforts to increase the efficiency of anaerobic digestion at low-temperature (winter) conditions, a cost-effective and efficient method is lacking. This study proposes a low-cost method of low-temperature (<35 °C) anaerobic digestion of wastewater, involving supplementation with granular activated carbon (GAC). Supplementation with GAC was found to reduce the lag time by 29.8% (from 15.1 to 10.6 days) and increase the maximum methane production rate by 23.4% (from 6.4 to 7.9 mL/day) at 25 °C. Network analysis demonstrated a strong co-occurrence of Syntrophobacteriales and hydrogenotrophic methanogens (Methanobacteriaceae; WSA2; Methanoregulaceae). GAC supplementation can drastically reduce the time required for organic matter decomposition and methane production, thereby increase the efficiency of wastewater treatment.

Intensified simultaneous nitrification and denitrification performance in integrated packed bed bioreactors using PHBV with different dosing methods

To explore an effective approach of simultaneous nitrification and denitrification in wastewater with low C/N ratios, integrated packed bed bioreactors based on poly(3-hydroxybutyrate-hydroxyvalerate) (PHBV) with different dosing methods were designed. The removal efficiency of NH₄⁺-N in bioreactor with aeration was 88.62%, and higher NO₃^--N removal efficiency was observed in bioreactor filled with grainy PHBV (95.21%) than bioreactor filled with strip PHBV (93.34%). Microbial study indicated that microbes harboring amoA and nirS genes preferred to attach on the surface of ceramsite, and significant differences in microbial community compositions at phylum and genus levels were observed. To summarize, it is feasible to utilize grainy PHBV for simultaneous and efficient removal of NH₄⁺-N and NO₃^--N from wastewater with low C/N ratios.

Grazing Management Influences Gut Microbial Diversity of Livestock in the Same Area

The composition of gut microbiota is closely related to health and nutrition of livestock. Research on the interaction between gut microbiota in livestock and grazing management strategies is unfortunately sparse. By studying the compositions of gut microbiota in sheep and goats in a single, mixed grazing population under the control of herdsman, as well as those of free-range camels in the same area of Qaidam Basin, we found that the composition of gut microbiota between sheep and goats showed no significant difference. However, there were significant differences between mixed group and camels at α- and β-diversities. We speculate that grazing management can shape gut microbial diversity indirectly. Mixed grazing under the control of herdsman lead to similarities in the diversity of gut microbiota among different species and limit their diversities of gut microbiota, which is not conducive to healthy growth of the host. On the contrary, free-range grazing is better for the diversity of gut microbiota. In order to sustainably manage populations of livestock, gut microbiota analysis may prove to be an important indicator for evaluating the merits of different grazing management strategies. Our results lay a foundation to improve the health of livestock and grazing management.

Effects of Italian Ryegrass (IRG) Supplementation on Animal Performance, Gut Microbial Compositions and Odor Emission from Manure in Growing Pigs

Fermentable carbohydrate (FC) is a promising material to reduce odor emission from pig manure. This study was conducted to investigate the impact of diets containing Italian ryegrass (IRG), as a FC, on animal performance, odorous chemical and bacterial composition of manure. Pigs were weighed and fed diets containing various levels of IRG powder (0%, 0.5%, 1.0% and 1.5%) for 28 days. At the end of the trial, manure was collected to analyze the chemical composition, odorous compounds and bacterial community structure. As dietary IRG levels increased, concentrations of phenols and indoles were decreased by 12% and 37% compared with control, respectively, without changes in growth performance. IRG treatment increased the relative abundances of genera belong to the family Lachnospiraceae, Ruminococcaceae, Veillonellaceae, Peptostreptococcaceae and Lactobacillaceae, in order Clostridiales of phylum Firmicutes, but decreased the relative abundances of genus Sphaerochaeta in phylum Spirochaetes and genus AB243818_g of family Porphyromonadaceae in phylum Bacteroidetes when compared with control. Results from the current study demonstrate that IRG supplemented diets had a beneficial effect of reducing the odorous compounds in manure, possibly by altering the bacterial community structure towards predominantly carbohydrate utilizing microorganisms in the large intestine.

Identification of Novel Butyrate- and Acetate-Oxidizing Bacteria in Butyrate-Fed Mesophilic Anaerobic Chemostats by DNA-Based Stable Isotope Probing

Butyrate is one of the most important intermediates during anaerobic digestion of protein wastewater, and its oxidization is considered as a rate-limiting step during methane production. However, information on syntrophic butyrate-oxidizing bacteria (SBOB) is limited due to the difficulty in isolation of pure cultures. In this study, two anaerobic chemostats fed with butyrate as the sole carbon source were operated at different dilution rates (0.01/day and 0.05/day). Butyrate- and acetate-oxidizing bacteria in both chemostats were investigated, combining DNA-Stable Isotope Probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing. The results showed that, in addition to known SBOB, Syntrophomonas, other species of unclassified Syntrophomonadaceae were putative butyrate-oxidizing bacteria. Species of Mesotoga, Aminivibrio, Acetivibrio, Desulfovibrio, Petrimonas, Sedimentibacter, unclassified Anaerolineae, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria may contribute to acetate oxidation from butyrate metabolism. Among them, the ability of butyrate oxidation was unclear for species of Sedimentibacter, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria. These results suggested that more unknown species participated in the degradation of butyrate. However, the corresponding function and pathway for butyrate or acetate oxidization of these labeled species need to be further investigated.

Long-Term Mesophilic Anaerobic Co-Digestion of Swine Manure with Corn Stover and Microbial Community Analysis

Long-term anaerobic co-digestion of swine manure (SM) and corn stover (CS) was conducted using semi-continuously loaded digesters under mesophilic conditions. A preliminary test was first conducted to test the effects of loading rates, and results indicated the 3 g-VS L⁻¹ d⁻¹ was the optimal loading rate. Based on the preliminary results, a verification replicated test was conducted with 3 g-VS L⁻¹ d⁻¹ loading rate and different SM/CS ratios (1:1, 2:1 and 1:2). Results showed that a SM/CS ratio of 2/1 was optimal, based on maximum observed methane-VS_des generation and carbon conversion efficiency (72.56 ± 3.40 mL g⁻¹ and 40.59%, respectively). Amplicon sequencing analysis suggested that microbial diversity was increased with CS loading. Amino-acid-degrading bacteria were abundant in the treatment groups. Archaea Methanoculleus could enhance biogas and methane productions.

Enhanced biogas production from municipal solid waste via co-digestion with sewage sludge and metabolic pathway analysis

The present study intends to evaluate the potential of co-digestion for utilizing Organic fraction of Municipal Solid Waste (OFMSW) and sewage sludge (SS) for enhanced biogas production. Metagenomic analysis was performed to identify the dominant bacteria, archaea and fungi, changes in their communities with time and their functional roles during the course of anaerobic digestion (AD). The cumulative biogas yield of 586.2 mL biogas/gVS with the highest methane concentration of 69.5% was observed under an optimum ratio of OFMSW:SS (40:60 w/w). Bacteria and fungi were found to be majorly involved in hydrolysis and initial stages of AD. Probably, the most common archaea Methanosarsina sp. primarily followed the acetoclastic pathway. The hydrogenotrophic pathway was less followed as indicated by the reduction in abundance of syntrophic acetate oxidizers. An adequate understanding of microbial communities is important to manipulate and inoculate the specific microbial consortia to maximize CH₄ production through AD.

Using DNA-based stable isotope probing to reveal novel propionate- and acetate-oxidizing bacteria in propionate-fed mesophilic anaerobic chemostats

Propionate is one of the most important intermediates of anaerobic fermentation. Its oxidation performed by syntrophic propionate-oxidizing bacteria coupled with hydrogenotrophic methanogens is considered to be a rate-limiting step for methane production. However, the current understanding of SPOB is limited due to the difficulty of pure culture isolation. In the present study, two anaerobic chemostats fed with propionate as the sole carbon source were operated at different dilution rates (0.05 d^-1 and 0.15 d^-1). The propionate- and acetate-oxidizing bacteria in the two methanogenic chemostats were investigated combining DNA-stable isotope probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing. The results of DNA-SIP with ¹³C-propionate/acetate suggested that, Smithella, Syntrophobacter, Cryptanaerobacter, and unclassified Rhodospirillaceae may be putative propionate-oxidizing bacteria; unclassified Spirochaetaceae, unclassified Synergistaceae, unclassified Elusimicrobia, Mesotoga, and Gracilibacter may contribute to acetate oxidation; unclassified Syntrophaceae and Syntrophomonas may be butyrate oxidizers. By DNA-SIP, unclassified OTUs with 16S rRNA gene abundance higher than 62% of total Bacteria in the PL chemostat and 38% in the PH chemostat were revealed to be related to the degradation of propionate. These results suggest that a variety of uncultured bacteria contribute to propionate degradation during anaerobic digestion. The functions and metabolic characteristics of these bacteria require further investigation.

Anaerobic digestion of aqueous phase from pyrolysis of biomass: Reducing toxicity and improving microbial tolerance

Among the products of pyrolysis is an aqueous phase (AP), which contains a significant fraction of carbon but is too dilute to make recovery of this organic content cost-effectively. This study was to explore the use of AP for anaerobic digestion. Different treatment methods including overliming, Fenton's reagent oxidation, bleaching and activated carbon adsorption were investigated to reduce toxicity of AP. Overliming treatment increased biogas production up to 32-fold compared to non-treated AP. Enhancing the tolerance of the bacterial and archaeal community to the AP toxicity was also attempted with a directed evolution method, resulting the microbes' tolerance to AP from 5% to 14%. Directed evolution resulted a major bacterial taxa as Cloacimonetes, Firmicutes, and Chloroflexi, while shifted the predominant archaea shifted from acetoclastic to hydrogenotrophic methanogens. Collectively, the results demonstrated that combining feedstock treatment and directed evolution of the microbial community is an effective way for AP anaerobic digestion.

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

Anaerobic digestion is an important biotechnology treatment process for conversion of waste to energy. In this study, a comparative core microbiome approach, i.e., determining taxa that are shared in functioning digesters but not shared in non-functioning digesters, was used to determine microbial taxa that could play key roles for effective anaerobic digestion. Anaerobic digester functions were impaired by adding the broad-spectrum antimicrobial triclosan (TCS) or triclocarban (TCC) at different concentrations, and the core microbiomes in both functioning and non-functioning anaerobic digesters were compared. Digesters treated with high (2500 mg/kg) or medium (450 mg/kg) TCS and high (850 mg/kg) TCC concentrations lost their function, i.e., methane production decreased, effluent volatile fatty acid concentrations increased, and pH decreased. Changes in microbial community diversity and compositions were assessed using 16S rRNA gene amplicon sequencing. Microbial richness decreased significantly in non-functioning digesters (p < 0.001). Microbial community compositions in non-functioning digesters significantly differed from those in functioning digesters (p = 0.001, ANOSIM). Microbes identified as potentially key taxa included previously known fatty acid-degrading syntrophs and amino acid-degrading syntrophs. A diverse group of syntrophs detected in this study had low relative abundance in functioning digesters, suggesting the importance of rare microbes in anaerobic digester operation. The comparative microbiome approach used in this study can be applied to other microbial systems where a community-driven biological phenomena can be observed directly.

Organic overloading affects the microbial interactions during anaerobic digestion in sewage sludge reactors

There is still a lack of information about microbial interactions of anaerobic digestion microbiome during process disturbance which limits our ability to predict the mechanisms that drive community dynamics on these events. This paper aims to determine how an organic overloading affects these interactions and to characterize in detail the microbiome structure and diversity in sewage sludge anaerobic reactors during an acidosis event. Two identical sewage sludge anaerobic reactors were subjected to an organic loading shock by adding glycerol waste. As consequence, volatile fatty acids accumulated after only 24 h (up to 2.5 g/L) while Bacteroidales and Methanomicrobiales became displaced by Firmicutes and Methanosaeta sp, showing that reactor acidosis can occur without an immediate decline of this methanogen. Network analysis revealed 9 clusters of co-occurring microorganisms with different behaviors during overloading. At first, Veillonellaceae family, the main glycerol degrading, associated with Candidatus Cloacimonetes, volatile fatty acids fermenters, increased their relative abundance in detriment of the syntrophic bacteria; although as conditions become more acidic, these groups were displaced by other fermenters like Porphyromonadaceae and Chitinophagaceae. Eventually, the methanogenesis failed 72 h after organic overloading, when pH reached values lower than 6. Overall, our results showed a succession of functionally redundant microorganisms, most likely because of niche specialization during organic overloading. The detailed temporal analysis elucidated the processes governing the dynamics anaerobic digestion microbiome, a knowledge required to develop anaerobic digestion management strategies based on its microbiome during process disturbances.

Pretreatment of spiramycin fermentation residue using hyperthermophilic digestion: quick startup and performance

This study aimed to evaluate the feasibility of hyperthermophilic anaerobic digestion at 70 °C in the pretreatment of spiramycin fermentation residue. By feeding municipal excess sludge under a solid retention time of 5 days, the hyperthermophilic digester was successfully started up within 3 days from mesophilic digestion by a one-step temperature increase from 35 to 70 °C. MiSeq sequencing showed the fast establishment of thermophilic fermenting bacterial communities in 3 days immediately after the temperature increase, with increases in abundance of Coprothermobacter, Spirochaetaceae_uncultured and Fervidobacterium from <0.001%, 1.06% and <0.001% to 33.77%, 11.65% and 3.42%, respectively. The feasibility of hyperthermophilic digestion for spiramycin residue was evaluated in batch experiments for 7 days. Hyperthermophilic digestion considerably reduced antibiotic concentrations, with removal efficiencies of 55.3% and 99.0% for the spiramycin residue alone and its mixture with hyperthermophilic sludge, respectively. At the same time, the abundances of four macrolide-lincosamide-streptogramin resistance genes were also reduced within 7 days, due to the decrease of their corresponding hosts. These results suggest that hyperthermophilic digestion could easily be started up from mesophilic digestion and might be a suitable pretreatment approach for spiramycin residue.

Evaluation of phase separation in a single-stage vertical anaerobic reactor: Performance and microbial composition analysis

In order to explore whether the acidogenic phase and methanogenic phase could be separated vertically into a single-stage anaerobic reactor, a controlled double circulation (CDC) anaerobic reactor was proposed for treating traditional Chinese medicine (TCM) wastewater in this study. The results showed that most of the organic pollutants and refractory were removed in the first reaction area where most of the amount of sludge existed. The organic acids were accumulated in the first reaction area, and larger specific methanogenic activity (SMA) and coenzyme F₄₂₀ values were found in the second reaction area. Bacterial and archaeal community structures in the two reaction areas of the CDC reactor were analyzed by Illumina MiSeq Sequencing, which revealed that the archaeal community showed larger difference compared with the bacterial community. Differences in the performance and microbial composition of the two reaction areas confirmed that phase separation was implemented in the CDC reactor.

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor

A lab-scale anaerobic membrane bioreactor (AnMBR) with a side stream tubular membrane was developed to treat synthetic domestic sewage to evaluate its performance and the dynamic shift of bacterial and archaeal communities during the start-up, steady-state, overloading and recovery periods of operation at mesophilic temperatures. During the start-up period, the bacterial and archaeal communities changed drastically, and Proteobacteria and Bacteroidetes predominated. During the steady-state period, the AnMBR exhibited excellent COD removal above 91%, and COD of the effluent was below 50 mg/L. High-throughput sequencing analysis results revealed that bacterial and archaeal communities shifted significantly from the start-up to the steady-state period, and that the Proteobacteria phylum predominated on days 140, 162 and 190, and the archaea community hydrogenotrophic methanogen genus Methanolinea (1.5–6.64%) predominated over the aceticlastic methanogen genus Methanothrix (1.35–3.07%). During the overloading period, significant changes occurred in microbial community on day 210, e.g., the phyla Bacteroidetes (30%), Proteobacteria (23%) and Firmicutes (18%) predominated and the archaeal community was completely suppressed, and Methanobrevibacter (0.7%) was the only methanogen genus that emerged in the overloading period. After a shock loading period, the microbial communities exhibited significant changes within the ranks of methanogens and shifted to dominance of the aceticlastic methanogen pathway. In addition, the TVFAs to alkalinity ratio in this study was suitable as an indicator of monitoring performance in the AnMBR operation.

Enhancement of methane production in anaerobic digestion of sewage sludge by thermal hydrolysis pretreatment

This study was performed to optimize thermal hydrolysis pretreatment (THP) of sewage sludge for enhanced anaerobic digestion (AD). Using the response surface methodology (RSM), the optimal conditions were found 180 °C of reaction temperature and 76 min of reaction time. Through THP under optimal conditions, high molecular substances in sewage sludge such as soluble microbial by-products (SMPs) and extracellular polymeric substances (EPSs) were hydrolyzed into low molecular ones without the generation of refractory compounds. The microbial community analysis revealed that relative abundances of Methanomicrobia such as Methanosarcina, Methanosaeta (acetoclastic methanogens), and Methanoculleus (hydrogenotrophic methanogens) in AD with THP were higher than those in conventional AD.