Members of the uncultured bacterial candidate division WWE1 are implicated in anaerobic digestion of cellulose

Magnetite Alters the Metabolic Interaction between Methanogens and Sulfate-Reducing Bacteria

It is known that the presence of sulfate decreases the methane yield in the anaerobic digestion systems. Sulfate-reducing bacteria can convert sulfate to hydrogen sulfide competing with methanogens for substrates such as H2 and acetate. The present work aims to elucidate the microbial interactions in biogas production and assess the effectiveness of electron-conductive materials in restoring methane production after exposure to high sulfate concentrations. The addition of magnetite led to a higher methane content in the biogas and a sharp decrease in the level of hydrogen sulfide, indicating its beneficial effects. Furthermore, the rate of volatile fatty acid consumption increased, especially for butyrate, propionate, and acetate. Genome-centric metagenomics was performed to explore the main microbial interactions. The interaction between methanogens and sulfate-reducing bacteria was found to be both competitive and cooperative, depending on the methanogenic class. Microbial species assigned to the Methanosarcina genus increased in relative abundance after magnetite addition together with the butyrate oxidizing syntrophic partners, in particular belonging to the Syntrophomonas genus. Additionally, Ruminococcus sp. DTU98 and other species assigned to the Chloroflexi phylum were positively correlated to the presence of sulfate-reducing bacteria, suggesting DIET-based interactions. In conclusion, this study provides new insights into the application of magnetite to enhance the anaerobic digestion performance by removing hydrogen sulfide, fostering DIET-based syntrophic microbial interactions, and unraveling the intricate interplay of competitive and cooperative interactions between methanogens and sulfate-reducing bacteria, influenced by the specific methanogenic group.

Effects of functional membrane coverings on carbon and nitrogen evolution during aerobic composting: Insight into the succession of bacterial and fungal communities

Carbon and nitrogen evolution and bacteria and fungi succession in two functional membrane-covered aerobic composting (FMCAC) systems and a conventional aerobic composting system were investigated. The micro-positive pressure in each FMCAC system altered the composting microenvironment, significantly increased the oxygen uptake rates of microbes (p < 0.05), and increased the abundance of cellulose- and hemicellulose-degrading microorganisms. Bacteria and fungi together influenced the conversion between carbon and nitrogen forms. FMCAC made the systems less anaerobic and decreased CH₄ production and emissions by 22.16 %-23.37 % and N₂O production and emissions by 41.34 %-45.37 % but increased organic matter degradation and NH₃ production and emissions by 16.91 %-90.13 %. FMCAC decreased carbon losses, nitrogen losses, and the global warming potential by 7.97 %-11.24 %, 15.43 %-34.00 %, and 39.45 %-42.16 %, respectively. The functional membrane properties (pore size distribution and air permeability) affected fermentation process and gaseous emissions. A comprehensive assessment indicated that FMCAC has excellent prospects for application.

Dynamics of microbial community in response to co-feedstock composition in anaerobic digestion

To enable the utilization of seasonal biomasses in e.g., farm-scale biogas plants, the process should be flexible and ensure stable gas production. However, information about microbial community dynamics in long-term co-digestion with versatile co-feedstocks is lacking. This study investigated the effects of co-feedstock changes on the performance and evolution of microbial consortia during 428-day anaerobic digestion of cow slurry. Co-feedstocks consisted of hydrocarbon-, protein- and lipid-rich materials. A high throughput 16S ribosomal RNA gene sequencing was used to analyze the taxonomic profile of microbial communities. Due to the low loading rate, the changes were subtle in bacteria, but a shift on archaeal genera in response to different and changing feedstock compositions was observed. Despite drastic changes in co-feedstock composition, stable and flexible anaerobic digestion with relatively constant core microbiome can be achieved with cautious operation of the process.

Response of antibiotic resistance genes and microbial niches to dissolved oxygen in an oxygen-based membrane biofilm reactor during greywater treatment

Linear alkylbenzene sulfonates (LAS) in greywater (GW) will simulate antibiotic resistance genes (ARGs) production in the biofilm-based system. Our study emphasizes the dissolved oxygen (DO)-dependent ARGs accumulation and microbial niches succession in an oxygen-based membrane biofilm reactor (O₂-MBfR) treating GW, as well as revealing the key roles of EPS. Changing DO concentrations led to significant differences in ARGs production, EPS secretion and microbial communities, as well as the organics and nitrogen removal efficiency. Increasing DO concentration from 0.2 to 0.4 mg/L led to improved organics (> 90%) and nitrogen removal, as well as less EPS (especially for proteins and carbohydrates) and ARGs accumulation (e.g., intI-1, korB and sul-2) in the biofilm; the high-DO-concentration accumulated microbial niches, including Flavobacteriaceae and Cyanobacteria that revealed by LEfSe analysis, contributed to both nitrogen reduction and organics biodegradation. While, the inefficient electron acceptor at low DO conditions (0.2 mg/L) reduced the organics and nitrogen removal efficiency, as well as the improved accumulation of EPS in biofilm; high EPS enabled the capture of residual LAS from the liquid phase, which stimulated the production of ARGs by the distinct microbial community compositions. These findings suggested the DO-based ARGs reduction regulation strategy in the O₂-MBfR treating GW.

Propagation of antibiotic resistance genes during anaerobic digestion of thermally hydrolyzed sludge and their correlation with extracellular polymeric substances

The positive impact of the thermal hydrolysis process (THP) of sewage sludge on antibiotic resistance genes (ARGs) removal during anaerobic digestion (AD) has been reported in the literature. However, little information is available on how changes in different extracellular polymeric substances (EPS) due to THP can influence ARG propagation during AD. This study focused on systematically correlating EPS components and ARG abundance in AD of sewage sludge pretreated with THP (80 °C, 110 °C, 140 °C, 170 °C). THP under different conditions improved sludge solubilization followed by improved methane yields in the biochemical methane potential (BMP) test. The highest methane yield of 275 ± 11.5 ml CH₄/g COD was observed for THP-140 °C, which was 40.5 ± 2.5% higher than the control. Increasing THP operating temperatures showed a non-linear response of ARG propagation in AD due to the rebound effect. The highest ARGs removal in AD was achieved with THP at 140 °C. The multivariate analysis showed that EPS polysaccharides positively correlated with most ARGs and integrons, except for macrolides resistance genes. In contrast, EPS protein was only strongly correlated with β-lactam resistance genes. These results suggest that manipulating THP operating conditions targeting specific EPS components will be critical to effectively mitigating the dissemination of particular ARG types in AD.

Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity

Background

The horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fibre diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community.

Results

We performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes.

Conclusions

Our metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.

Biogas production from high solids digestion of Pennisetum purpureum x Pennisetum typhoideum: Suitable conditions and microbial communities

Effects of organic loading rates (OLRs), temperatures and effluent recirculation rates on biogas production from Giant Juncao Grass (GJG) using pilot-scale semi-continuously fed CSTRs were investigated. Thermophilic reactors could be stably operated at OLR up to 5.0 kg VS m^-3 d^-1, while damaged process stability was detected in mesophilic reactors at OLR of 4.0 kg VS m^-3 d^-1. Higher effluent recirculation rate (3:1) helped lessen negative effects of system being over-loaded, especially for mesophilic reactors. Microbial community analysis revealed that temperatures had the highest effect on bacterial community structure. Firmicutes were the dominant bacterial phyla found under high temperatures, while majority of archaea in all reactors belonged to the phylum Bathyarchaeota. Changes of microbial communities could partly explain system performance under different operating conditions. This study was the first to show GJG as a superior biogas feedstock to other energy crops thanks to its higher methane yields per planting area.

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.

Shedding Light on Microbial "Dark Matter": Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial "dark matter" taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.

Microbiome signature and diversity regulates the level of energy production under anaerobic condition

The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH₄%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH₄, respectively. The physicochemical analysis revealed that level of energy production (CH₄%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O₂ level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH₄ concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH₄ producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH₄ concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.

A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone

Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors controlling their activities. Here, we determined the active heterotrophic prokaryotic community in the sulphidic water column of the Black Sea, an ideal model system, where a tight coupling between carbon, nitrogen and sulphur cycles is expected. Active microorganisms degrading both dissolved organic matter (DOM) and protein extracts were determined using quantitative DNA stable isotope probing incubation experiments. These results were compared with the metabolic potential of metagenome-assembled genomes obtained from the water column. Organic matter incubations showed that groups like Cloacimonetes and Marinimicrobia are generalists degrading DOM. Based on metagenomic profiles the degradation proceeds in a potential interaction with members of the Deltaproteobacteria and Chloroflexi Dehalococcoidia. On the other hand, microbes with small genomes like the bacterial phyla Parcubacteria, Omnitrophica and of the archaeal phylum Woesearchaeota, were the most active, especially in protein-amended incubations, revealing the potential advantage of streamlined microorganisms in highly reduced conditions.

Evaluation of acidogenesis products' effect on biogas production performed with metagenomics and isotopic approaches

BACKGROUND

During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system.

RESULTS

Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%-67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities.

CONCLUSIONS

In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.

Effects of micro-aeration on microbial niches and antimicrobial resistances in blackwater anaerobic digesters

Anaerobic digestion (AD) of source-diverted blackwater (toilet flush) at ambient room temperature presents challenges for fast hydrolysis of particulate matters. This study investigated the effect of different micro-aeration dosages for blackwater AD. Sequencing batch reactors were operated at ambient room temperature (22 ± 1°C) with micro-aeration (0, 5, 10, 50, and 150 mg O₂ g^-1 COD_feed per cycle) and gradually reduced hydraulic retention times from 5 d to 2 d. The methanogenesis efficiencies were greater at low oxygen dosages (i.e., 0, 5, 10) while the volatile fatty acids (VFAs) accumulated more at high oxygen dosages (i.e., 50, 150). Microbial communities were significantly different under different oxygen dosages (p<0.05), with segregation of microbial ecological niches in low and high oxygen dosage communities. The low-oxygen-dosage niche (0, 5, and 10 mg g^-1 COD_feed) was inhabited by fermenting and syntrophic bacteria (e.g., Cytophaga, Syntrophomonas) and methanogens (e.g., Methanobacterium, Methanolinea, Methanosaeta). The high-oxygen-dosage niche (50 and 150 mg g^-1 COD_feed) had significantly (p<0.05) more facultative anaerobic bacteria (Ignavibacteriales and Cloacamonales), and aerobic bacteria (Rhodocyclales). Moreover, blackwater can be a source of antimicrobial resistance genes (ARGs), which are affected by different oxygen dosages. The ARG variation correlated with the microbial community composition (p<0.05). Low-oxygen-dosage communities contained a higher prevalence of mobile gene elements (intI1 and korB) and tetM, ermB, sul1, sul2, and blaCTX-M than the high-oxygen-dosage communities, indicating that oxygen dosage influenced the prevalence of populations carrying ARGs. These findings suggest that application of micro-aeration to AD can be used to control ARG profiles.

The Effect of Antibiotics on Mesophilic Anaerobic Digestion Process of Cattle Manure

This study explored the effect of eight antimicrobials on the efficiency of biogas production in the anaerobic digestion (AD) process of cattle manure. The microbiome involved in AD, presence and number of genes mcrA, MSC and MST specific for Archaea, and antibiotic resistance genes (ARGs) concentration in digestate (D) were examined. Supplementation of antibiotics to substrate significantly lowered biogas production. Amoxicillin caused a 75% decrease in CH4 production in comparison with the control samples. Enrofloxacin, tetracycline, oxytetracycline, and chlortetracycline reduced the amount of biogas produced by 36, 39, 45 and 53%, respectively. High-throughput sequencing of 16S rRNA results revealed that bacteria dominated the Archaea microorganisms in all samples. Moreover, antibiotics led to a decrease in the abundance of the genes mcrA, MSC, MST, and induced an increase in the number of tetracyclines resistance genes. Antibiotics decreased the efficiency of the AD process and lowered the quantity of CH4 obtained, while stimulating an increase in the number of ARGs in D. This work reveals how antimicrobials affect the cattle manure AD process and changes in microbial biodiversity, number of functional genes and ARGs in the digestate due to drugs exposure. It also, provides useful, practical information about the AD process.

Microbial Processes and Microbial Communities in the Water Column of the Polar Meromictic Lake Bol'shie Khruslomeny at the White Sea Coast

Microbiological, molecular ecological, biogeochemical, and isotope geochemical research was carried out at the polar Lake Bol'shie Khruslomeny at the coast of the Kandalaksha Bay, White Sea in March and September 2017. The uppermost mixolimnion was oxic, with low salinity (3-5%). The lower chemocline layer was brown-green colored, with very high content of particulate organic matter (up to 11.8 mg C L-1). The lowermost monimolimnion had marine salinity (22-24%) and very high concentrations of sulfide (up to 18 mmol L-1) and CH4 (up to 1.8 mmol L-1). In the chemocline, total microbial abundance and the rate of anoxygenic photosynthesis were 8.8 × 106 cells mL-1 and 34.4 μmol C L-1 day-1, respectively. Both in March and September, sulfate reduction rate increased with depth, peaking (up to 0.6-1.1 μmol S L-1 day-1) in the lower chemocline. Methane oxidation rates in the chemocline were up to 85 and 180 nmol CH4 L-1 day-1 in March and September, respectively; stimulation of this process by light was observed in September. The percentages of cyanobacteria and methanotrophs in the layer where light-induced methane oxidation occurred were similar, ∼2.5% of the microbial community. Light did not stimulate methane oxidation in deeper layers. The carbon isotope composition of particulate organic matter (δ13C-Corg), dissolved carbonates (δ13C-DIC), and methane (δ13C- CH4) indicated high microbial activity in the chemocline. Analysis of the 16S rRNA gene sequences revealed predominance of Cyanobium cyanobacteria (order Synechococcales) in the mixolimnion. Green sulfur bacteria Chlorobium phaeovibrioides capable of anoxygenic photosynthesis constituted ∼20% of the chemocline community both in March and in September. Methyloprofundus gammaptoteobacteria (family Methylomonaceae) were present in the upper chemocline, where active methane oxidation occurred. During winter, cyanobacteria were less abundant in the chemocline, while methanotrophs occurred in higher horizons, including the under-ice layer. Chemolithotrophic gammaproteobacteria of the genus Thiomicrorhabdus, oxidizing reduced sulfur compounds at low oxygen concentrations, were revealed in the chemocline in March. Both in March and September archaea constituted up to 50% of all microorganisms in the hypolimnion. The percentage of putative methanogens in the archaeal community was low, and they occurred mainly in near-bottom horizons.

Dynamics of Clostridium genus and hard-cheese spoiling Clostridium species in anaerobic digesters treating agricultural biomass

Biogas plants are a widespread renewable energy technology. However, the use of digestate for agronomic purposes has often been a matter of concern. It is controversial whether biogas plants might harbor some pathogenic clostridial species, which represent a biological risk. Moreover, the inhabitance of Clostridium hard-cheese spoiling species in anaerobic digesters can be problematic for hard-cheese manufacturing industries, due to the issue of cheese blowing defects. This study investigated the effect of mesophilic anaerobic digestion processes on the Clostridium consortia distribution over time. Specifically, three lab-scale CSTRs treating agricultural biomass were characterized by considering both the whole microbial community and the cultivable clostridial spores. It is assessed an overall reduction of the Clostridium genus during the anaerobic digestion process. Moreover, it was evidenced a slight, but steady decrease of the cultivable clostridial spores, mainly represented by two pathogenic species, C. perfringens and C. bifermentans, and one hard-cheese spoiling species, C. butyricum. Thus, it is revealed an overall reduction of the clostridial population abundance after the mesophilic anaerobic digestion treatment of agricultural biomass.

Microbial communities in anaerobic digesters change over time and sampling depth

Anaerobic digestion (AD) is a process resulting from the anaerobic metabolism of specific microorganisms that produce an eco-friendly type of energy and a stabilized soil fertilizer. We described the microbial communities and their changes in three depths of BioKöhler® biodigester, fed with cattle manure for 18 days, under anaerobic incubation at the psychrophilic temperature range (~ 20 °C). During the experiment, the maximum methane content in the raw biogas was 79.9%. Non-metric multidimensional scaling (MDS) showed significant differences among microbial communities in the bottom, medium, and upper depths. Considering all the periods of incubation, the microbial communities changed until the eighth day, and they remained stable from eighth to seventeenth days. Bacteroidetes, Firmicutes, and Synergistetes were the most abundant phyla in samples, representing approximately 41% of the total OTUs. The relative abundance of the phyla Euryarchaeota, Actinobacteria, Firmicutes, and Verrucomicrobia changed from bottom to medium sampling points. Moreover, Crenarchaeota differed in frequencies from medium to upper, and Acidobacteria from bottom to upper samples. Lentisphaerae, Chloroflexi, and LD1 were different solely at the bottom, whereas OP9 and Tenericutes only in the medium. Psychrophilic AD performed in this work removed pathogens like Salmonella and Escherichia, as observed at the digestate analyzed. This type of treatment of raw manure besides producing eco-friendly energy efficiently also generates a stabilized and safe biomass that can be used as fertilizer in soils.

Uncovering Viable Microbiome in Anaerobic Sludge Digesters by Propidium Monoazide (PMA)-PCR

Use of anaerobic sludge digester is a common practice around the world for solids digestion and methane generation from municipal sewage sludge. Understanding microbial community structure is vital to get better insight into the anaerobic digestion process and to gain better process control. However, selective analysis of viable microorganisms is limited by DNA-based assays. In this study, propidium monoazide (PMA)-PCR with 16S rRNA gene sequencing analysis was used to distinguish live and dead microorganisms based on cell membrane integrity. Microbial community structures of PMA-treated and PMA-untreated anaerobic digester sludge samples were compared. Quantitative PCR revealed that 5-30% of the rRNA genes were derived from inactive or dead cells in anaerobic sludge digesters. This caused a significant decrease in the numbers of operational taxonomic units and Chao1 and Shannon indices compared with that of the PMA-untreated sludge. Microbial community analysis showed that majority of the viable microbiome consisted of Euryarchaeota, Bacteroidetes, Deltaproteobacteria, Chloroflexi, Firmicutes, WWE1, Spirochaetes, Synergistetes, and Caldiserica. On the other hand, after the PMA treatment, numbers of Alphaproteobacteria and Betaproteobacteria declined. These were considered residual microbial members. The network analysis also revealed a relationship among the OTUs belonging to WWE1 and Bacteroidales. PMA-PCR-based 16S rRNA gene sequencing analysis is an effective tool for uncovering viable microbiome in complex environmental samples.

Comparative study of industrial-scale high-solid biogas production from food waste: Process operation and microbiology

Anaerobic high-solid treatment (HST) for processing food waste and biogas production is a viable technology with considerable commercial potential. In this study, we examined and compared mesophilic and thermophilic industrial-scale plug-flow digesters. The HSTs demonstrated reasonable biogas yields from food waste (0.4-0.6 Nm³ CH₄/kg volatile solids). However, during operation at thermophilic conditions ammonia inhibition (~2 g NH₃-N/L) and acid accumulation (6-14 g/L) caused severe process disturbance. Microbial community structures diverged between the processes, with temperature appearing to be a strong driver. A unique feature of the thermophilic HSTs was high abundance of the uncultivated Clostridia group MBA03 and temperature fluctuations in one mesophilic HST were linked to drastically decreased abundance of methanogens and relative abundance of Cloacimonetes. The process data obtained in this study clearly demonstrate both potential and challenges in HST of food waste but also possibilities for management approaches to tackle process imbalance and restore process function.

Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments

Degradation of amino acids is an important process in methanogenic environments. Early studies in the 1980s focused on isolated clostridia species to study the degradation behaviours. However, it is now well-recognized that isolated species may not represent those with important roles in situ. This study conducted a continuous enrichment experiment with focus on the comparison of the microbial communities after short-term enrichment (SE) and long-term enrichment (LE). Individual amino acids were used as the substrate, and two different anaerobic digester sludge were used as the inoculum. Based on 16S rRNA and 16S rRNA gene, a clear community shift was observed during a time course of 18 months. The SE communities were dominated by microbial populations such as an uncultured Bacteroidales that was different from known fermenters. In the LE communities, known amino acids fermenters were consistently observed with high abundance, including Peptoclostridium acidaminophilum, Acidaminobacter hydrogenoformans and Propionivibrio pelophilus. The community structures could be classified into four types depending on the diversity of fermenters and syntrophs. A culturability index was developed to compare the SE and LE community and revealed that long-term enrichment tended to select microbial populations closely related to species that has been cultivated whereas larger fractions of the inoculum and SE communities remained uncultured.

Increased loading stress leads to convergence of microbial communities and high methane yields in adapted anaerobic co-digesters

Enhancing biogas production, while avoiding inhibition of methanogenesis during co-digestion of grease interceptor waste (GIW), can help water resource recovery facilities reduce their carbon footprint. Here we used pre-adapted and non-adapted digesters to link microbial community structure to digester function. Before disturbance, the pre-adapted and non-adapted digesters showed similar methane production and microbial community diversity but dissimilar community composition. When exposed to an identical disturbance, the pre-adapted digester achieved better performance, while the non-adapted digester was inhibited. When re-exposed to disturbance after recovery, communities and performance of both digesters converged, regardless of the temporal variations. Co-digestion of up to 75% GIW added on a volatile solids (VS) basis was achieved, increasing methane yield by 336% from 0.180 to 0.785 l-methane/g-VS-added, the highest methane yield reported to date for lipid-rich waste. Progressive perturbation substantially enriched fatty acid-degrading Syntrophomonas from less than 1% to 24.6% of total 16S rRNA gene sequences, acetoclastic Methanosaeta from 2.3% to 11.9%, and hydrogenotrophic Methanospirillum from less than 1% to 6.6% in the pre-adapted digester. Specific hydrolytic and fermentative populations also increased. These ecological insights demonstrated how progressive perturbation can be strategically used to influence methanogenic microbiomes and improve co-digestion of GIW.

Spatio-temporal insights into microbiology of the freshwater-to-hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake

Ursu Lake is located in the Middle Miocene salt deposit of Central Romania. It is stratified, and the water column has three distinct water masses: an upper freshwater-to-moderately saline stratum (0-3 m), an intermediate stratum exhibiting a steep halocline (3-3.5 m), and a lower hypersaline stratum (4 m and below) that is euxinic (i.e. anoxic and sulphidic). Recent studies have characterized the lake's microbial taxonomy and given rise to intriguing ecological questions. Here, we explore whether the communities are dynamic or stable in relation to taxonomic composition, geochemistry, biophysics, and ecophysiological functions during the annual cycle. We found: (i) seasonally fluctuating, light-dependent communities in the upper layer (≥0.987-0.990 water-activity), a stable but phylogenetically diverse population of heterotrophs in the hypersaline stratum (water activities down to 0.762) and a persistent plate of green sulphur bacteria that connects these two (0.958-0.956 water activity) at 3-3.5 to 4 m; (ii) communities that might be involved in carbon- and sulphur-cycling between and within the lake's three main water masses; (iii) uncultured lineages including Acetothermia (OP1), Cloacimonetes (WWE1), Marinimicrobia (SAR406), Omnitrophicaeota (OP3), Parcubacteria (OD1) and other Candidate Phyla Radiation bacteria, and SR1 in the hypersaline stratum (likely involved in the anaerobic steps of carbon- and sulphur-cycling); and (iv) that species richness and habitat stability are associated with high redox-potentials. Ursu Lake has a unique and complex ecology, at the same time exhibiting dynamic fluctuations and stability, and can be used as a modern analogue for ancient euxinic water bodies and comparator system for other stratified hypersaline systems.

The microbiome driving anaerobic digestion and microbial analysis

The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.

A novel insight into the influence of thermal pretreatment temperature on the anaerobic digestion performance of floatable oil-recovered food waste: Intrinsic transformation of materials and microbial response

The intrinsic reason determining digestion performance of 100-160 °C preheated food waste after recovering floatable oil (FO-recovered FW) was investigated using two-dimensional correlated infrared spectroscopy, three-dimensional fluorescence spectroscopy and high-throughput 16S rRNA amplicon sequencing. The results indicated that thermal temperature significantly affected CH₄ production of FO-recovered FW due to different structural alteration degree of starch, protein, cellulose and lipid components. Fragmentation of starch mainly occurred at 100 °C. The hydrolytic and acidogenic rate of starch was promoted and accordingly induced rapid growth of carbohydrate-fermenting bacteria, which resulted in severe acidification. Protein hydrolysis and cellulose H-bonds cleavage occurring at 120-160 °C accelerated the accessible sites interacting with microbial hydrolytic enzymes, and growth of Cloacimonetes and Syntrophomonas enhanced CH₄ production. Non-degradable humic acid-like organics remarkably formed at 160 °C caused a carbon loss and digestion inhibiting/deteriorating. Pretreatment at 120 °C was feasible for promoted methane production based on energy assessment.

Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1

Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.

Interaction Between Conservation Tillage and Nitrogen Fertilization Shapes Prokaryotic and Fungal Diversity at Different Soil Depths: Evidence From a 23-Year Field Experiment in the Mediterranean Area

Soil biodiversity accomplishes key roles in agro-ecosystem services consisting in preserving and enhancing soil fertility and nutrient cycling, crop productivity and environmental protection. Thus, the improvement of knowledge on the effect of conservation practices, related to tillage and N fertilization, on soil microbial communities is critical to better understand the role and function of microorganisms in regulating agro-ecosystems. In the Mediterranean area, vulnerable to climate change and suffering for management-induced losses of soil fertility, the impact of conservation practices on soil microbial communities is of special interest for building mitigation and adaptation strategies to climate change. A long-term experiment, originally designed to investigate the effect of tillage and N fertilization on crop yield and soil organic carbon, was utilized to understand the effect of these management practices on soil prokaryotic and fungal community diversity. The majority of prokaryotic and fungal taxa were common to all treatments at both soil depths, whereas few bacterial taxa (Cloacimonates, Spirochaetia and Berkelbacteria) and a larger number of fungal taxa (i.e., Coniphoraceae, Debaryomycetaceae, Geastraceae, Cordicypitaceae and Steccherinaceae) were unique to specific management practices. Soil prokaryotic and fungal structure was heavily influenced by the interaction of tillage and N fertilization: the prokaryotic community structure of the fertilized conventional tillage system was remarkably different respect to the unfertilized conservation and conventional systems in the surface layer. In addition, the effect of N fertilization in shaping the fungal community structure of the surface layer was higher under conservation tillage systems than under conventional tillage systems. Soil microbial community was shaped by soil depth irrespective of the effect of plowing and N addition. Finally, chemical and enzymatic parameters of soil and crop yields were significantly related to fungal community structure along the soil profile. The findings of this study gave new insights on the identification of management practices supporting and suppressing beneficial and detrimental taxa, respectively. This highlights the importance of managing soil microbial diversity through agro-ecological intensified systems in the Mediterranean area.

Carbohydrate Hydrolytic Potential and Redundancy of an Anaerobic Digestion Microbiome Exposed to Acidosis, as Uncovered by Metagenomics

Increased hydrolysis of easily digestible biomass may lead to acidosis of anaerobic reactors and decreased methane production. Previously, it was shown that the structure of microbial communities changed during acidosis; however, once the conditions are back to optimal, biogas (initially CO2) production quickly restarts. This suggests the retention of the community functional redundancy during the process failure. In this study, with the use of metagenomics and downstream bioinformatics analyses, we characterize the carbohydrate hydrolytic potential of the microbial community, with a special focus on acidosis. To that purpose, carbohydrate-active enzymes were identified, and to further link the community hydrolytic potential with key microbes, bacterial genomes were reconstructed. In addition, we characterized biochemically the specificity and activity of selected enzymes, thus verifying the accuracy of the in silico predictions. The results confirm the retention of the community hydrolytic potential during acidosis and indicate Bacteroidetes to be largely involved in biomass degradation. Bacteroidetes showed higher diversity and genomic content of carbohydrate hydrolytic enzymes that might favor the dominance of this phylum over other bacteria in some anaerobic reactors. The combination of bioinformatic analyses and activity tests enabled us to propose a model of acetylated glucomannan degradation by BacteroidetesIMPORTANCE The enzymatic hydrolysis of lignocellulosic biomass is mainly driven by the action of carbohydrate-active enzymes. By characterizing the gene profiles at the different stages of the anaerobic digestion experiment, we showed that the microbiome retains its hydrolytic functional redundancy even during severe acidosis, despite significant changes in taxonomic composition. By analyzing reconstructed bacterial genomes, we demonstrate that Bacteroidetes hydrolytic gene diversity likely favors the abundance of this phylum in some anaerobic digestion systems. Further, we observe genetic redundancy within the Bacteroidetes group, which accounts for the preserved hydrolytic potential during acidosis. This work also uncovers new polysaccharide utilization loci involved in the deconstruction of various biomasses and proposes the model of acetylated glucomannan degradation by Bacteroidetes Acetylated glucomannan-enriched biomass is a common substrate for many industries, including pulp and paper production. Using naturally evolved cocktails of enzymes for biomass pretreatment could be an interesting alternative to the commonly used chemical pretreatments.

System performance and microbial community in ethanol-fed anaerobic reactors acclimated with different organic carbon to sulfate ratios

Sulfate influences the organics removal and methanogenic performance during anaerobic wastewater treatment. System performance, microbial community and metabolic pathways in ethanol-fed anaerobic reactors were investigated under different COD/SO₄^2- ratios (2, 1 and 0.67) and control without sulfate addition. The sulfate removal percentages declined (99%, 60% and 49%) with decreasing COD/SO₄^2- ratios, and methanogenesis was completely inhibited. Acetate accumulated to 903-734 mg/L, though propionate was constantly lower than 30 mg/L. Without sulfate, acetate and propionate did not accumulate, despite the extended time for propionate degradation. Incomplete oxidizing sulfate reducing bacteria (Desulfobulbus and Desulfomicrobium) and hydrolysis-acidification genera (Treponema and Bacteroidales) predominated but could not degrade acetate. Desulfobulbus was the key genus for propionate degradation through the pyruvate & propanoate metabolism pathway. Pseudomonas and Desulfobulbus, possessing genes encoding Type IV pili and cytochrome c6 OmcF, respectively, potentially participated in the direct interspecies electron transfer in sulfate-rich conditions.

Exploring the roles of and interactions among microbes in dry co-digestion of food waste and pig manure using high-throughput 16S rRNA gene amplicon sequencing

BACKGROUND

With the increasing global population and increasing demand for food, the generation of food waste and animal manure increases. Anaerobic digestion is one of the best available technologies for food waste and pig manure management by producing methane-rich biogas. Dry co-digestion of food waste and pig manure can significantly reduce the reactor volume, capital cost, heating energy consumption and the cost of digestate liquid management. It is advantageous over mono-digestion of food waste or pig manure due to the balanced carbon/nitrogen ratio, high pH buffering capacity, and provision of trace elements. However, few studies have been carried out to study the roles of and interactions among microbes in dry anaerobic co-digestion systems. Therefore, this study aimed to assess the effects of different inocula (finished digestate and anaerobic sludge taken from wastewater treatment plants) and substrate compositions (food waste to pig manure ratios of 50:50 and 75:25 in terms of volatile solids) on the microbial community structure in food waste and pig manure dry co-digestion systems, and to examine the possible roles of the previously poorly described bacteria and the interactions among dry co-digestion-associated microbes.

RESULTS

The dry co-digestion experiment lasted for 120 days. The microbial profile during different anaerobic digestion stages was explored using high-throughput 16S rRNA gene amplicon sequencing. It was found that the inoculum factor was more significant in determining the microbial community structure than the substrate composition factor. Significant correlation was observed between the relative abundance of specific microbial taxa and digesters' physicochemical parameters. Hydrogenotrophic methanogens dominated in dry co-digestion systems.

CONCLUSIONS

The possible roles of specific microbial taxa were explored by correlation analysis, which were consistent with the literature. Based on this, the anaerobic digestion-associated roles of 11 bacteria, which were previously poorly understood, were estimated here for the first time. The inoculum played a more important role in determining the microbial community structure than substrate composition in dry co-digestion systems. Hydrogenotrophic methanogenesis was a significant methane production pathway in dry co-digestion systems.

Feeding frequency influences process performance and microbial community composition in anaerobic digesters treating steam exploded food waste

In anaerobic digestion, studies of feeding frequency have produced conflicting results. Hence, the effect of feeding frequency on process variables and microbial community structure was investigated by comparing a laboratory-scale digester fed steam exploded food waste 10 times daily vs. one fed an equivalent amount once daily. The Frequently Fed Digester (FFD) produced on average 20% more methane and had lower effluent concentrations of long-chain fatty acids. Greater daily fluctuations in acetate, pH and biogas production rate could explain the lower specific methane yield and β-oxidation. Feeding frequency also influenced the microbial community whereby Tenericutes (42%) dominated in FFD but Firmicutes (31%) was most abundant in the Daily Fed Digester (DFD). Feeding frequency effects are therefore postulated to occur more often in digesters fed labile feedstocks at high organic loading rates.

Simultaneous biogas upgrading and biochemicals production using anaerobic bacterial mixed cultures

A novel biological process to upgrade biogas was developed and optimised during the current study. In this process, CO₂ in the biogas and externally provided H₂ were fermented under mesophilic conditions to volatile fatty acids (VFAs), which are building blocks of higher-value biofuels. Meanwhile, the biogas was upgraded to biomethane (CH₄ >95%), which can be used as a vehicle fuel or injected into the natural gas grid. To establish an efficient fermentative microbial platform, a thermal (at two different temperatures of 70 °C and 90 °C) and a chemical pretreatment method using 2-bromoethanesulfonate were investigated initially to inhibit methanogenesis and enrich the acetogenic bacterial inoculum. Subsequently, the effect of different H₂:CO₂ ratios on the efficiency of biogas upgrading and production of VFAs were further explored. The composition of the microbial community under different treatment methods and gas ratios has also been unravelled using 16S rRNA analysis. The chemical treatment of the inoculum had successfully blocked the activity of methanogens and enhanced the VFAs production, especially acetate. The chemical treatment led to a significantly better acetate production (291 mg HAc/L) compared to the thermal treatment. Based upon 16S rRNA gene sequencing, it was found that H₂-utilizing methanogens were the dominant species in the thermally treated inoculum, while a significantly lower abundance of methanogens was observed in the chemically treated inoculum. The highest biogas content (96% (v/v)) and acetate production were achieved for 2H₂:1CO₂ ratio (v/v), with Acetoanaerobium noterae, as the dominant homoacetogenic hydrogen scavenger. Results from the present study can pave the way towards more development with respect to microorganisms and conditions for high efficient VFAs production and biogas upgrading.

Marker microbiome clusters are determined by operational parameters and specific key taxa combinations in anaerobic digestion

In this study, microbiomes of 36 full-scale anaerobic digesters originated from 22 different biogas plants were compared by terminal restriction fragment length polymorphism (TRFLP) analysis. Regarding the differences in microbial community composition, a weighting of the environmental parameters could be derived from higher to lower importance as follows: (i) temperature, (ii) TAN and NH₃ concentrations and conductivity, and (iii) the chemical composition of the supplied feedstocks. Biotic interactions between specific bacterial and archaeal community arrangements were revealed, whereby members of the phyla Bacteroidetes and Cloacimonetes combined with the archaeal genus Methanothrix dominated the conversion of homogeneous feedstocks, such as waste water sludge or industrial waste. As most of the detected TRFs were only found in a certain number of anaerobic digestion plants, each plant develops its unique microbiome. The putative rare species, the specialists, are potentially hidden drivers of microbiome functioning as they provide necessary traits under, e.g., process-inconvenient conditions.

Effect of long residence time and high temperature over anaerobic biodegradation of Scenedesmus microalgae grown in wastewater

Anaerobic digestion of indigenous Scenedesmus spp. microalgae was studied in continuous lab-scale anaerobic reactors at different temperatures (35 °C and 55 °C), and sludge retention time - SRT (50 and 70 days). Mesophilic digestion was performed in a continuous stirred-tank reactor (CSTR) and in an anaerobic membrane bioreactor (AnMBR). Mesophilic CSTR operated at 50 days SRT only achieved 11.9% of anaerobic biodegradability whereas in the AnMBR at 70 days SRT and 50 days HRT reached 39.5%, which is even higher than the biodegradability achieved in the thermophilic CSTR at 50 days SRT (30.4%). Microbial analysis revealed a high abundance of cellulose-degraders in both reactors, AnMBR (mainly composed of 9.4% Bacteroidetes, 10.1% Chloroflexi, 8.0% Firmicutes and 13.2% Thermotogae) and thermophilic CSTR (dominated by 23.8% Chloroflexi and 12.9% Firmicutes). However, higher microbial diversity was found in the AnMBR compared to the thermophilic CSTR which is related to the SRT. since high SRT promoted low growth-rate microorganisms, increasing the hydrolytic potential of the system. These results present the membrane technology as a promising approach to revalue microalgal biomass, suggesting that microalgae biodegradability and consequently the methane production could be improved operating at higher SRT.

Enhancing syntrophic associations among Clostridium butyricum, Syntrophomonas and two types of methanogen by zero valent iron in an anaerobic assay with a high organic loading

The impacts of ZVI on microbial community diversity in an anaerobic assay with high organic loading were investigated. The relative abundance of bacteria, archaea, and the functional methyl coenzyme-M reductase (mcrA) gene were investigated using high-throughput sequencing, and variations in their quantity were determined by qPCR. The results showed that ZVI significantly increased both the relative abundance and quantity of Methanobacteriales and Methanosarcinales during hydrogenotrophic and acetoclastic methanogenesis. The relative abundance of syntrophic Methanobacteriales at the hydrolysis and acidogenesis stages resulted in H₂ partial pressure decrease through an interspecies hydrogen transfer (IHT) network, which further induced butyric conversion to acetic by Syntrophomonas. The primary microbial metabolism then converted to acetoclastic methanogensis in the assay with ZVI addition. The short duration of this process and high relative abundance of Syntrophomonas, Clostridium butyricum and Methanosarcinales potentially indicated the existence of a novelty syntrophic mechanism for extracellular electron transfer, which promoted CH₄ generation.

Do microbial communities in an anaerobic bioreactor change with continuous feeding sludge into a full-scale anaerobic digestion system?

Microbial communities of sludge samples from a full-scale anaerobic digestion (AD) fed with primary sludge (PS) and excess sludge (ES) were analyzed using qPCR and MiSeq. The results showed that the microbial composition of digested sludge remained relatively stable but was partially changed by microbial immigration from feeding sludge. The dominant archaea in the digested sludge were largely the same as those in the feeding sludge, but their abundances differed markedly. The dominant fungal genera in the digested sludge were different from those in PS but were similar to those in ES. Various differences in bacterial community differences between digested sludge and PS/ES were observed. Notably, this study is the first to suggest Verrucomicrobia is the predominant bacterial phylum in the digested sludge, and that numerous unreported microorganisms belonging to the order LD1-PB3 existed in this AD system and potentially played roles in the processes of hydrolysis, fermentation, and acetogenesis.

Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition

Biodegradation of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32) or heavy crude oil (°API = 16). Over the course of 17 months, we conducted routine analytical (GC, GC-MS) and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing) surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella), along with syntrophic bacteria (Syntrophus), methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”). Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems.

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

BACKGROUND

Anaerobic digestion (AD) is a microbe-driven process of biomass decomposition to CH₄ and CO₂. In addition to renewable and cost-effective energy production, AD has emerged in the European Union as an environmentally friendly model of bio-waste valorisation and nutrient recycling. Nevertheless, due to the high diversity of uncharacterised microbes, a typical AD microbiome is still considered as "dark matter".

RESULTS

Using the high-throughput sequencing of small rRNA gene, and a monthly monitoring of the physicochemical parameters for 20 different mesophilic full-scale bioreactors over 1 year, we generated a detailed view of AD microbial ecology towards a better understanding of factors that influence and shape these communities. By studying the broadly distributed OTUs present in over 80% of analysed samples, we identified putatively important core bacteria and archaea to the AD process that accounted for over 70% of the whole microbial community relative abundances. AD reactors localised at the wastewater treatment plants were shown to operate with distinct core microbiomes than the agricultural and bio-waste treating biogas units. We also showed that both the core microbiomes were composed of low (with average community abundance ≤ 1%) and highly abundant microbial populations; the vast majority of which remains yet uncharacterised, e.g. abundant candidate Cloacimonetes. Using non-metric multidimensional scaling, we observed microorganisms grouping into clusters that well reflected the origin of the samples, e.g. wastewater versus agricultural and bio-waste treating biogas units. The calculated diversity patterns differed markedly between the different community clusters, mainly due to the presence of highly diverse and dynamic transient species. Core microbial communities appeared relatively stable over the monitoring period.

CONCLUSIONS

In this study, we characterised microbial communities in different AD systems that were monitored over a 1-year period. Evidences were shown to support the concept of a core community driving the AD process, whereas the vast majority of dominant microorganisms remain yet to be characterised.

Inhibition of anaerobic digestion processes: Applications of molecular tools

Inhibition of anaerobic digestion (AD) due to perturbation caused by substrate composition and/or operating conditions can significantly reduce performance. Such perturbations could be limited by elucidating microbial community response to inhibitors and devising strategies to increase community resilience. To this end, advanced molecular methods are increasingly being applied to study the AD microbiome, a diverse community of microbial populations with complex interactions. This literature review of AD inhibition studies indicates that inhibitory concentrations are highly variable, likely stemming from differences in community structure or activity profile and previous exposure to inhibitors. More recent molecular methods such as 'omics' tools, substrate mapping, and real-time sequencing are helping to unravel the complexity of AD inhibition by elucidating physiological and ecological significance of key microbial populations. The AD community must strive towards developing predictive abilities to avoid system failure (e.g., real-time tracking of an indicator species) to improve resilience of AD systems.

Acclimation to extremely high ammonia levels in continuous biomethanation process and the associated microbial community dynamics

Acclimatized anaerobic communities to high ammonia levels can offer a solution to the ammonia toxicity problem in biogas reactors. In the current study, a stepwise acclimation strategy up to 10g NH₄⁺-N L^-1, was performed in mesophilic (37±1°C) continuously stirred tank reactors. The reactors were co-digesting (20/80 based on volatile solid) cattle slurry and microalgae, a protein-rich, 3rd generation biomass. Throughout the acclimation period, methane production was stable with more than 95% of the uninhibited yield. Next generation 16S rRNA gene sequencing revealed a dramatic microbiome change throughout the ammonia acclimation process. Clostridium ultunense, a syntrophic acetate oxidizing bacteria, increased significantly alongside with hydrogenotrophic methanogen Methanoculleus spp., indicating strong hydrogenotrophic methanogenic activity at extreme ammonia levels (>7g NH₄⁺-N L^-1). Overall, this study demonstrated for the first time that acclimation of methanogenic communities to extreme ammonia levels in continuous AD process is possible, by developing a specialised acclimation AD microbiome.

Biogas production from food waste via co-digestion and digestion- effects on performance and microbial ecology

In this work, performance and microbial structure of a digestion (food waste-only) and a co-digestion process (mixture of cow manure and food waste) were studied at mesophilic (37 °C) and thermophilic (55 °C) temperatures. The highest methane yield (480 mL/g VS) was observed in the mesophilic digester (MDi) fed with food waste alone. The mesophilic co-digestion of food waste and manure (McoDi) yielded 26% more methane than the sum of individual digestions of manure and food waste. The main volatile fatty acid (VFA) in the mesophilic systems was acetate, averaging 93 and 172 mg/L for McoDi and MDi, respectively. Acetate (2150 mg/L) and propionate (833 mg/L) were the main VFAs in the thermophilic digester (TDi), while propionate (163 mg/L) was the major VFA in the thermophilic co-digester (TcoDi). The dominant bacteria in MDi was Chloroflexi (54%), while Firmicutes was dominant in McoDi (60%). For the mesophilic reactors, the dominant archaea was Methanosaeta in MDi, while Methanobacterium and Methanosaeta had similar abundance in McoDi. In the thermophilic systems, the dominant bacteria were Thermotogae, Firmicutes and Synergistetes in both digesters, however, the relative abundance of these phyla were different. For archaea, the genus Methanothermobacter were entirely dominant in both TDi and TcoDi.

Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm

Biogas production from animal waste is an economically viable way to reduce environmental pollution and produce valuable products, i.e<i>.</i>, methane and a nutrient-rich organic waste product. An anaerobic digestion reactor for biogas production from pig waste was sampled at the entrance, middle (digestion chamber), and exit of a digester, while the bacterial and archaeal community structure was studied by 16S rRNA gene metagenomics. The number of bacterial operational taxonomic units (OTU)-97% was 3-7 times larger than that of archaeal ones. Bacteria and Archaea found in feces of animals (e.g., Clostridiaceae, Lachnospiraceae, Ruminococcaceae, <i>Methanosarcina</i>, <i>Methanolobus</i>, <i>Methanosaeta</i>, and <i>Methanospirillum</i>) dominated the entrance of the digester. The digestion chamber was dominated by anaerobic sugar-fermenting OP9 bacteria and the syntrophic bacteria <i>Candidatus</i> Cloacamonas (Waste Water of Evry 1; WWE1). The methanogens dominant in the digestion chamber were the acetoclastic <i>Methanosaeta</i> and the hydrogenothrophic <i>Methanoculleus</i> and <i>Methanospirillum</i>. Similar bacterial and archaeal groups that dominated in the middle of the digestion chamber were found in the waste that left the digester. Predicted functions associated with degradation of xenobiotic compounds were significantly different between the sampling locations. The microbial community found in an anaerobic digestion reactor loaded with pig manure contained microorganisms with biochemical capacities related to the 4 phases of methane production.

Mainstream upflow nitritation-anammox system with hybrid anaerobic pretreatment: Long-term performance and microbial community dynamics

Mainstream nitritation-anammox is of strong interest to energy- and resource-efficient domestic wastewater treatment. However, there lack in-depth studies of pretreatment, tests of actual wastewater, and examination of long-term performance. Herein, an upflow nitritation-anammox granular reactor has been investigated to treat primary effluent with a hybrid anaerobic reactor (HAR) as pretreatment for more than 300 days. This system achieved 92% of COD removal, 75% of which was accomplished by the HAR, and had an average final effluent COD concentration of 22 mg L^-1. More than 90% of ammonium was removed in the nitritation-anammox reactor, achieving a nitrogen removal rate of 81.0 g N m^-3 d^-1 in the last stage. The accumulation of sulfate-reducing bacteria in the HAR evidenced the effect of sulfate on COD removal and subsequent nitrogen removal. Anammox bacteria (predominantly Ca. Jettenia asiatica) accounted for up to 40.2% of total granular communities, but their abundance decreased over time in the suspended communities. The dynamics of major metabolisms and functional genes involved in nitrogen conversion were predicted by PICRUSt based on the taxonomic data, providing more insights into the functions of the microbial communities. These results have demonstrated the effectiveness and importance of anaerobic pretreatment to successful mainstream nitritation-anammox.

Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome

Anaerobic digester (AD) microbiomes harbor complex, interacting microbial populations to achieve biomass reduction and biogas production, however how they are influenced by operating conditions and feed sludge microorganisms remain unclear. These were addressed by analyzing the microbial communities of 90 full-scale digesters at 51 municipal wastewater treatment plants from five countries. Heterogeneity detected in community structures suggested that no single AD microbiome could be defined. Instead, the AD microbiomes were classified into eight clusters driven by operating conditions (e.g., pretreatment, temperature range, and salinity), whereas geographic location of the digesters did not have significant impacts. Comparing digesters populations with those present in the corresponding feed sludge led to the identification of a hitherto overlooked feed-associated microbial group (i.e., the residue populations). They accounted for up to 21.4% of total sequences in ADs operated at low temperature, presumably due to ineffective digestion, and as low as 0.8% in ADs with pretreatment. Within each cluster, a core microbiome was defined, including methanogens, syntrophic metabolizers, fermenters, and the newly described residue populations. Our work provides insights into the key factors shaping full-scale AD microbiomes in a global scale, and draws attentions to the overlooked residue populations.

The effect of initial organic load of the kitchen waste on the production of VFA and H2 in dark fermentation

Dark fermentation of kitchen wastes was studied in batch bioreactors, with no pH adjustment, to evaluate the effect of the initial organic load on the process performance in terms of volatile fatty acids and H₂ production. Initial organic load of the kitchen wastes ranged from 4.1 to 48.2gVS/L. Acetic and butyric acids were produced in the largest amount. At the initial organic load of 48.2KWgVS/L the highest concentration of volatile fatty acids was 9.81g/L. The maximum production yield of H₂ (76.1mL/gVS) was found for the initial organic load of kitchen wastes at 14.3gVS/L. The carbon balance calculation showed that the maximum CO₂ yield of 0.34 gC/gC was attained in the bioreactor with the initial organic load of 14.3gVS/L. The microbiological analysis revealed that the predominant microorganisms in the dark fermentation process were Bacteroidetes, Firmicutes, Spirochaetes and WWE1 at phyla level.

NanoSIMS for biological applications: Current practices and analyses

Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, the authors provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analyses, and current outlooks. Specifically, the authors offer an overview of SIMS and development of the NanoSIMS. The authors describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, the authors provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, the authors present a perspective on the future of this technology and where they think it will have the greatest impact in near future.