The mechanisms of pH regulation on promoting volatile fatty acids production from kitchen waste

The anaerobic acid production experiments were conducted with the pretreated kitchen waste under pH adjustment. The results showed that pH 8 was considered to be the most suitable condition for acid production, especially for the formation of acetic acid and propionic acid. The average value of total volatile fatty acid at pH 8 was 8814 mg COD/L, 1.5 times of that under blank condition. The average yield of acetic acid and propionic acid was 3302 mg COD/L and 2891 mg COD/L, respectively. The activities of key functional enzymes such as phosphotransacetylase, acetokinase, oxaloacetate transcarboxylase and succinyl-coA transferase were all enhanced. To further explore the regulatory mechanisms within the system, the distribution of microorganisms at different levels in the fermentation system was obtained by microbial sequencing, results indicating that the relative abundances of Clostridiales, Bacteroidales, Chloroflexi, Clostridium, Bacteroidetes and Propionibacteriales, which were great contributors for the hydrolysis and acidification, increased rapidly at pH 8 compared with the blank group. Besides, the proportion of genes encoding key enzymes was generally increased, which further verified the mechanism of hydrolytic acidification and acetic acid production of organic matter under pH regulation.

Identification and cultivation of anaerobic bacterial scavengers of dead cells

The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.

Mitigation of N2O emissions via enhanced denitrification in a biological landfill leachate treatment using external carbon from fermented sludge

The effects of an external carbon source (C-source) on the mitigation of N₂O gas (N₂O_(g)) emissions from landfill leachate were investigated via enhanced denitrification using anaerobically fermented sewage sludge. Anaerobic fermentation of sewage sludge was conducted under thermophilic conditions with progressively increasing organic loading rates (OLR). Optimal conditions for fermentation were determined based on the efficiency of hydrolysis and the concentrations of sCOD and volatile fatty acids (VFAs) as follows: at an OLR of 40.48 ± 0.77 g COD/L·d with 1.5 days of solid retention time (SRT), 14.68 ± 0.59% of efficiency of hydrolysis, 14.42 ± 0.30 g sCOD/L and 7.85 ± 0.18 g COD/L of VFAs. Analysis of the microbial community in the anaerobic fermentation reactor revealed that degradation of sewage sludge might be potentially affected by proteolytic microorganisms producing VFAs from proteinaceous materials. Sludge-fermentate (SF) retrieved from the anaerobic fermentation reactor was used as the external C-source for denitrification testing. The specific nitrate removal rate (K_NR) of the SF-added condition was 7.54 mg NO₃^-N/g VSS·hr, which was 5.42 and 2.43 times higher than that of raw landfill leachate (LL) and a methanol-added condition, respectively. In the N₂O_(g) emission test, the liquid phase N₂O (N₂O-^N_(l)) of 20.15 mg N/L was emitted as N₂O_(g) of 19.64 ppmv under only LL-added condition. On the other hand, SF led to the specific N₂O_(l) reduction rate (K_N2O) of 6.70 mg N/g VSS hr, resulting in mitigation of 1.72 times the N₂O_(g) emission compared to under the only-LL-added condition. The present study revealed that N₂O_(g) emissions from biological landfill leachate treatment plants can be attenuated by simultaneous reduction of NO₃^-N and N₂O_(l) during enhanced denitrification via a stable supply of an external C-source retrieved from anaerobically fermented organic waste.

Using heat-activated persulfate to accelerate short-chain fatty acids production from waste activated sludge fermentation triggered by sulfate-reducing microbial consortium

Persulfate has been applied extensively for waste activated sludge (WAS) decomposition due to the strong oxidizing sulfate radical generated as a product. However, the efficiency is not improved without activation to produce free radicals. In this study, a novel coupling strategy of heat-activated persulfate (Heat_PS) pretreatment and sulfate-reducing bacteria (SRB) triggering was explored to enhance short-chain fatty acids (SCFAs) produced by WAS fermentation. The remaining sulfate acts as an essential acceptor of electrons for the metabolism of synergistic SRB, thereby boosting WAS acidification by energetic cooperation with anaerobic fermenters. The results showed that SCFAs yield in the Heat_PS + SRB group peaked at 431.89 mg COD/gVSS, with the proportion of acetate reaching 57.8 %. This was 6.33 and 1.75 times higher than that in raw and single Heat_PS treated WAS, respectively. Carbon balance revealed a conversion rate of 26.1 % of carbon content in WAS to SCFAs, with 4.5 % lower CO₂ equivalents emitted than that in raw WAS fermentation by the assessments of environmental impacts. This was partially attributed to the strong decomposition of WAS by SO₄^•- and ^•OH oxidation from heat-activated PS and the SRB trigger. In addition, the synergistic relationship among acidogenic/fermentative bacteria and SRB consortia was further verified by the positive correlation among Desulfovibrio, the hydrolytic Escherichia-Shigella, Morganella and the fermetative Macellibacteroides and Bacteroides, as revealed by molecular ecological networks (MENs) analysis. The results of this study may highlight the cooperation of the synergistic micribial consortia as an additional perspective for the recovery of value-added biological metabolites from complex biotransformation.

Deciphering the role of microplastic size on anaerobic sludge digestion: Changes of dissolved organic matter, leaching compounds and microbial community

Here the role of microplastic size on dissolved organic matter, leaching compounds and microbial community during anaerobic sludge digestion was evaluated. Compared to that without the addition of polyvinyl chloride (PVC), during the 30 days' incubation, the anaerobic sludge digestion by adding PVC at the size of 75 μm and the concentration of 2.4 g/g volatile solids (VS) showed a 8.5% lower cumulative methane production, while a 17.9% higher cumulative methane production was noted by adding PVC at the size of 3000 μm and the concentration of 2.4 g/g VS. A long-term fed-batch laboratory-scale fermenter test for 147 days further testified, that higher removal efficiencies of total solids, volatile solids, and total chemical oxygen demand, and higher methane production were noted by adding PVC (2.4 g/g VS, 3000 μm) into the fermenter. More interestingly, higher concentrations of proteins, polysaccharides, volatile fatty acids, and soluble microbial by-products component were noted in the liquid phase of sludge drawn from the fermenter added with PVC since the biomass therein showed higher efficiencies of solubilization, hydrolysis, acidification, and methanogenesis. Moreover, as identified from the fermenter added with PVC, dibutyl phthalate (DBP) was the most predominant leaching phthalates compound, although the biomass therein showed a 93.4% anaerobic biodegradability of DBP. The leaching of DBP drove the predominance of microbial community towards Synergistota and Methanosaeta. More irregular elliptical shallow dimples were noted on the PVC surface after 147 days' incubation, accompanied with abundances of Proteobacteria, Actinobacteriota, Chloroflexi, Methanosaeta and Methanobacterium. The results from this study showed that the size of microplastic was a crucial factor in evaluating its impact on anaerobic sludge digestion.

Archaeal and Bacterial Content in a Two-Stage Anaerobic System for Efficient Energy Production from Agricultural Wastes

Anaerobic digestion (AD) is a microbially-driven process enabling energy production. Microorganisms are the core of anaerobic digesters and play an important role in the succession of hydrolysis, acidogenesis, acetogenesis, and methanogenesis processes. The diversity of participating microbial communities can provide new information on digester performance for biomass valorization and biofuel production. In this study anaerobic systems were used, operating under mesophilic conditions that realized biodegradation processes of waste wheat straw pretreated with NaOH-a renewable source for hydrogen and methane production. These processes could be managed and optimized for hydrogen and methane separately but combining them in a two-stage system can lead to higher yields and a positive energy balance. The aim of the study was to depict a process of biohydrogen production from lignocellulosic waste followed by a second one leading to the production of biomethane. Archaeal and bacterial consortia in a two-stage system operating with wheat straw were identified for the first time and the role of the most important representatives was elucidated. The mixed cultures were identified by the molecular-biological methods of metagenomics. The results showed that biohydrogen generation is most probably due to the presence of Proteiniphilum saccharofermentans, which was 28.2% to 45.4% of the microbial community in the first and the second bioreactor, respectively. Archaeal representatives belonging to Methanobacterium formicicum (0.71% of the community), Methanosarcina spelaei (0.03%), Methanothrix soehngenii (0.012%), and Methanobacterium beijingense (0.01%) were proven in the methane-generating reactor. The correlation between substrate degradation and biogas accumulation was calculated, together with the profile of fatty acids as intermediates produced during the processes. The hydrogen concentration in the biogas reached 14.43%, and the Methane concentration was 69%. Calculations of the energy yield during the two-stage process showed 1195.89 kWh·t-1 compared to a 361.62 kWh·t-1 cumulative yield of energy carrier for a one-stage process.

Long-term performance, membrane fouling behaviors and microbial community in a hollow fiber anaerobic membrane bioreactor (HF-AnMBR) treating synthetic terephthalic acid-containing wastewater

Purified terephthalic acid (PTA) wastewater with properties of poor biodegradation and high toxicity is produced from refining and synthesis of petrochemical products. In this study, a lab-scale hollow fiber membrane bioreactor (HF-AnMBR) fed with synthetic PTA wastewater was operated over 200 days with stepwise decreased hydraulic retention time (HRT) to investigate the long-term performance, membrane fouling mechanism and microbial community evolution. Results showed that a stable chemical oxygen demand (COD) removal rate of 65.8 ± 4.1% was achieved at organic loading rate of 3.1 ± 0.3 g-COD/L-reactor/d and HRT 24 h, under which the methane production rate reached 0.33 ± 0.02 L/L-reactor/d. Further shortening HRT, however, led to the decreased COD removal efficiency and low methane bioconversion. A mild membrane fouling occurred due to the production of colloidal biopolymers and the interaction between increased colloidal substances secreted/cracked by microorganisms and membrane interface. Further 16S rRNA analysis indicated that microbial diversity and richness had changed with the variation of HRT while Methanosaeta, and Methanolinea species were always the dominant methanogens responsible for methane production. The results verify that HF-AnMBR is an alternative technology for PTA wastewater treatment along with energy harvesting, and provide a new avenue toward sustainable petrochemical wastewater management.

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.

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.

Co-digestion of cheese whey with sewage sludge for caproic acid production: Role of microbiome and polyhydroxyalkanoates potential production

The main aim of this work was to evaluate the efficiency of producing caproic acid and other volatile fatty acids using a co-digestion between cheese whey and sewage sludge in a continuous reactor. The effect of two different feeding regimes (one and two per day) and three hydraulic retention times (HRT) (15, 10 and 6 days) on the organic acids production were studied. The optimal conditions for the process were 10 days HRT, 2 feeding cycles per day, reaching a maximum degree of acidification of 44%. Under these conditions, the most abundant organic acid was caproic acid. The analysis of the microbial community dynamics in the reactor during the HRT changes revealed a microbiome enriched in organisms involved in caproic acid production. Additionally, the production of polyhydroxyalkanoates using the organic acids stream as feeding was verified in a fed-batch experiment obtaining a copolymer formed by hydroxybutyrate, hydroxyvalerate and hydroxyhexanoate.

Anaerobic and Microaerobic Pretreatment for Improving Methane Production From Paper Waste in Anaerobic Digestion

Having been generated with a tremendous amount annually, paper waste (PW) represents a large proportion in municipal solid waste (MSW) and also a potential source of renewable energy production through the application of anaerobic digestion (AD). However, the recalcitrant lignocellulosic structure poses obstacles to efficient utilization in this way. Recently, anaerobic and microaerobic pretreatment have attracted attention as approaches to overcome the obstacles of biogas production. This study was set out to present a systematic comparison and assessment of anaerobic and microaerobic pretreatment of PW with different oxygen loadings by five microbial agents: composting inoculum (CI), straw-decomposing inoculum (SI), cow manure (CM), sheep manure (SM), and digestate effluent (DE). The hints of microbial community evolution during the pretreatment and AD were tracked by 16S rRNA high-throughput sequencing. The results demonstrated that PW pretreated by DE with an oxygen loading of 15 ml/gVS showed the highest cumulative methane yield (CMY) of 343.2 ml/gVS, with a BD of 79.3%. In addition to DE, SI and SM were also regarded as outstanding microbial agents for pretreatment because of the acceleration of methane production at the early stage of AD. The microbial community analysis showed that Clostridium sensu stricto 1 and Clostridium sensu stricto 10 possessed high relative abundance after anaerobic pretreatment by SI, while Bacteroides and Macellibacteroides were enriched after microaerobic pretreatment by SM, which were all contributable to the cellulose degradation. Besides, aerobic Bacillus in SI and Acinetobacter in SM and DE probably promoted lignin degradation only under microaerobic conditions. During AD, VadinBC27, Ruminococcaceae Incertae Sedis, Clostridium sensu stricto 1, Fastidiosipila, and Caldicoprobacter were the crucial bacteria that facilitated the biodegradation of PW. By comparing the groups with same microbial agent, it could be found that changing the oxygen loading might result in the alternation between hydrogenotrophic and acetoclastic methanogens, which possibly affected the methanogenesis stage. This study not only devised a promising tactic for making full use of PW but also provided a greater understanding of the evolution of microbial community in the pretreatment and AD processes, targeting the efficient utilization of lignocellulosic biomass in full-scale applications.

Cellulases: From Bioactivity to a Variety of Industrial Applications

Utilization of microbial enzymes has been widely reported for centuries, but the commercial use of enzymes has been recently adopted. Particularly, cellulases have been utilized in various commercial sectors including agriculture, brewing, laundry, pulp and paper and textile industry. Cellulases of microbial origin have shown their potential application in various commercial sectors including textile, pulp and paper, laundry, brewing, agriculture and biofuel. Cellulases have diversified applications in the food industry, food service, food supply and its preservation. Indeed, cellulases can tenderize fruits, clarify the fruit juices, reduce roughage in dough, hydrolyze the roasted coffee, extract tea polyphenols and essential oils from olives and can increase aroma and taste in food items. However, their role in food industries has by and large remained neglected. The use of immobilized cellulases has further expanded their application in fruit and vegetable processing as it potentiates the catalytic power and reduces the cost of process. Technological and scientific developments will further expand their potential usage in the food industry.

Pilot-scale fermentation of urban food waste for volatile fatty acids production: The importance of pH

Here, a pilot-scale volatile fatty acids (VFAs) production system was established using food waste (FW) as feedstock under acidic conditions. The effects of pH (uncontrolled, 4.5, 5.5, and 6.5) on the FW acidification system were investigated. The results showed that VFAs concentration increased from 8419 to 15048 mg COD/L with pH level increasing from 4.5 to 6.5, and the highest VFA production yield (0.79 mgCOD/mgCOD) was obtained at a pH of 6.5. A larger proportion of butyric acid (52.9%) was observed, accompanied by a 23% decrease of acetic acid when pH was elevated to 6.5. Microbial analysis showed that Clostridium sensu stricto 1, Sporanaerobacter, and Proteiniphilum were dominant, which not only positively influence the hydrolysis and acidogenesis processes but also play an essential role in the conversion of acetic acid to butyric acid. In summary, this study provides a valuable reference for large-scale FW treatment to recover valuable resources.

Role of organic matter and microbial communities in mercury retention and methylation in sediments near run-of-river hydroelectric dams

Run-of-river power plants (RoRs) are expected to triple in number over the next decades in Canada. These structures are not anticipated to considerably promote the mobilization and transport of mercury (Hg) and its subsequent microbial transformation to methylmercury (MeHg), a neurotoxin able to biomagnify in food webs up to humans. To test whether construction of RoRs had an effect on Hg transport and transformation, we studied Hg and MeHg concentrations, organic matter contents and methylating microbial community abundance and composition in the sediments of a section of the St. Maurice River (Quebec, Canada). This river section has been affected by the construction of two RoR dams and its watershed has been disturbed by a forest fire, logging, and the construction of wetlands. Higher total Hg (THg) and MeHg concentrations were observed in the surface sediments of the flooded sites upstream of the RoRs. These peaks in THg and MeHg were correlated with organic matter proportions in the sediments (r² = 0.87 and 0.82, respectively). In contrast, the proportion of MeHg, a proxy for methylation potential, was best explained by the carbon to nitrogen ratio suggesting the importance of terrigenous organic matter as labile substrate for Hg methylation in this system. Metagenomic analysis of Hg-methylating communities based on the hgcA functional gene marker indicated an abundance of methanogens, sulfate reducers and fermenters, suggesting that these metabolic guilds may be primary Hg methylators in these surface sediments. We propose that RoR pondages act as traps for sediments, organic matter and Hg, and that this retention can be amplified by other disturbances of the watershed such as forest fire and logging. RoR flooded sites can be conducive to Hg methylation in sediments and may act as gateways for bioaccumulation and biomagnification of MeHg along food webs, particularly in disturbed watersheds.

Production of Volatile Fatty Acids in a Semi-Continuous Dark Fermentation of Kitchen Waste: Impact of Organic Loading Rate and Hydraulic Retention Time

The aim of the study was to evaluate the possibility of using the process of dark fermentation to convert kitchen waste into valuable volatile fatty acids in a semi-continuous process at different values of the organic loading rate (2.5 and 5.0 gVS/(L × d)) and hydraulic retention time (5 and 10 d) using anaerobic mixed microbial consortia. The experiments were performed in a bioreactor of working volume 8L with pH control. The maximum volatile fatty acids yield in a steady state (22.3 g/L) was achieved at the organic loading rate of 5.0 gVS/(L × d) and HRT of 10 days. The main products of dark fermentation were acetic and butyric acids, constituting, respectively, 35.2–47.7% and 24.1–30.0% of all identified volatile fatty acids. Additionally, at the beginning of the fermentation and in a steady-state condition, the microbial population analysis (16S rDNA) of the fermentation mixture with the most effective volatile fatty acids generation has been performed to monitor the DF microflora development. The dominant microorganisms at a phylum level in a steady state were Firmicutes (44.9%) and Bacteroidetes (30.1%), which indicate the main role of those phyla in the volatile fatty acids synthesis.

Roles of intestinal bacteroides in human health and diseases

Bacteroides, an abundant genus in the intestines of mammals, has been recently considered as the next generation probiotics (NGP) candidate due to its potential role in promoting host health. However, the role of Bacteroides in the development of intestinal dysfunctions such as diarrhea, inflammatory bowel disease, and colorectal cancer should not be overlooked. In the present study, we focused on nine most widely occurred and abundant Bacteroides species and discussed their roles in host immunity, glucose and lipid metabolism and the prevention or induction of diseases. Besides, we also discussed the current methods used in the safety evaluation of Bacteroides species and key opinions about the concerns of these strains for the future use.

Food selectivity of anaerobic protists and direct evidence for methane production using carbon from prey bacteria by endosymbiotic methanogen

Anaerobic protists are major predators of prokaryotes in anaerobic ecosystems. However, little is known about the predation behavior of anaerobic protists because almost none have been cultured. In particular, these characteristics of anaerobic protists in the phyla Metamonada and Cercozoa have not been reported previously. In this study, we isolated three anaerobic protists, Cyclidium sp., Trichomitus sp., and Paracercomonas sp., from anaerobic granular sludge in an up-flow anaerobic sludge blanket reactor used to treat domestic sewage. Ingestion and digestion of food bacteria by anaerobic protists with or without endosymbiotic methanogens were demonstrated using tracer experiments with green fluorescent protein and a stable carbon isotope. These tracer experiments also demonstrated that Cyclidium sp. supplied CO₂ and hydrogen to endosymbiotic methanogens. While Cyclidium sp. and Trichomitus sp. ingested both Gram-negative and -positive bacteria, Paracercomonas sp. could only take up Gram-negative bacteria. Archaeal cells such as Methanobacterium beijingense and Methanospirillum hungatei did not support the growth of these protists. Metabolite patterns of all three protists differed and were influenced by food bacterial species. These reported growth rates, ingestion rates, food selectivity, and metabolite patterns provide important insights into the ecological roles of these protists in anaerobic ecosystems.

Agroindustrial waste as a resource for volatile fatty acids production via anaerobic fermentation

This study evaluated the feasibility of the anaerobic digestion as a sustainable valorisation strategy for volatile fatty acids production from agroindustrial waste (cucumber, tomato and lettuce). High bioconversion efficiencies were reached by operating the reactors at 25 °C, 3 g VS·d^-1·L^-1 with pH adjustment. Cucumber fermentation achieved the highest bioconversion (52.6%), whereas tomato degradation was the least efficient bioprocess (40.1%) due to the low pH (5.6) that partially inhibited the hydrolytic and acidogenic activities. In all cases, carboxylic acid profiles were mainly composed of volatile fatty acids with even carbon number. The developed microbial community exhibited high hydrolytic and acidogenic activities associated to carbohydrates degradation. This microbial population was dominated by Firmicutes phylum and showed a lack of acetogenic bacteria related with CH₄ production, resulting in a remarkably high VFAs accumulation.

Impact of Organic Loading Rate in Volatile Fatty Acids Production and Population Dynamics Using Microalgae Biomass as Substrate

Volatile fatty acids (VFAs) are regarded as building blocks with a wide range of applications, including biofuel production. The traditional anaerobic digestion used for biogas production can be alternatively employed for VFAs production. The present study aimed at maximizing VFAs productions from Chlorella vulgaris through anaerobic digestion by assessing the effect of stepwise organic loading rates (OLR) increases (3, 6, 9, 12 and 15 g COD L^-1 d^-1). The biological system was proven to be robust as organic matter conversion efficiency into VFAs increased from 0.30 ± 0.02 COD-VFAs/COD_in at 3 g COD L^-1 d^-1 to 0.37 ± 0.02 COD-VFAs/COD_in at 12 g COD L^-1d^-1. Even though, the hydrolytic step was similar for all studied scenario sCOD/tCOD = 0.52-0.58), the highest OLR (15 g COD L^-1 d^-1) did not show any further increase in VFAs conversion (0.29 ± 0.01 COD-VFAs/COD_in). This fact suggested acidogenesis inhibition at 15 g COD L^-1d^-1. Butyric (23-32%), acetic (19-26%) and propionic acids (11-17%) were the most abundant bioproducts. Population dynamics analysis revealed microbial specialization, with a high presence of Firmicutes followed by Bacteroidetes. In addition, this investigation showed the microbial adaptation of Euryarchaeota species at the highest OLR (15 g COD L^-1d^-1), evidencing one of the main challenges in VFAs production (out-competition of archaea community to avoid product consumption). Stepwise OLR increase can be regarded as a tool to promote VFAs productions. However, acidogenic inhibition was reported at the highest OLR instead of the traditional hydrolytic barriers. The operational conditions imposed together with the high VFAs and ammonium concentrations might have affected the system yields. The relative abundance of Firmicutes (74%) and Bacteroidetes (20%), as main phyla, together with the reduction of Euryarchaeota phylum (0.5%) were found the best combination to promote organic matter conversion into VFAs.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Comparative analysis of the composition and function of fecal-gut bacteria in captive juvenile Crocodylus siamensis between healthy and anorexic individuals

The Siamese crocodile (Crocodylus siamensis) is a freshwater, endangered crocodile with high economic value in the farming industry. Gut microflora plays an essential role in host physiological activity, and it contributes significantly to both the health and diseased states of animals. However, thus far, no study has focused on the correlation between diseases and intestinal bacterial communities in crocodilians. Here, we first compared the composition and function of gut microbial communities in captive juvenile C. siamensis suffering from anorexia and healthy crocodile controls using deep amplicon sequencing. The gut microbial diversity of anorexic crocodiles was much lower than the healthy individuals. Obvious changes in gut microbial composition were observed between sick and healthy crocodiles, except for Cetobacterium somerae of phylum Fusobacteria. In particular, the abundance of Bacteroides luti, Clostridium disporicum, Plesiomonas shigelloides, and Odoribacter sp. in the gut flora of healthy crocodiles was distinctly higher than the diseased group. Conversely, the species Edwardsiella tarda was overrepresented in the gut of anorexic crocodiles compared to the healthy group. Furthermore, in anorexic crocodiles, the predicted microbial functions that were related to amino acid metabolism, biosynthesis of other secondary metabolites, nucleotide metabolism, replication and repair, and translation were significantly reduced, while signal transduction was significantly enriched. These findings of the present study provide a reference to enrich the field of gut microorganism studies in crocodilians and suggest that alterations in the composition and function of gut bacteria in C. siamensis juveniles may be associated with anorexia in crocodiles.

First Insights Into Bacterial Gastrointestinal Tract Communities of the Eurasian Beaver (Castor fiber)

The Eurasian or European beaver (Castor fiber) is the second-largest living rodent after the capybara. It is a semi-aquatic animal known for building dams and lodges. They strictly feed on lignocellulose-rich plants and correspondingly harbor cellulolytic microbial communities in their digestive tract. In this study, the bacterial community composition, diversity, and functional profile of different gut compartments ranging from stomach to colon have been explored. A total of 277 bacterial operational taxonomic units (OTUs) at species level were obtained from the gut systems of two males (juvenile and subadult) and one subadult female beaver. In general, cecum and colon are dominated by Firmicutes and Actinobacteria. High abundance of Bacteroidetes was observed only in male juvenile beaver cecum and colon, suggesting that the bacterial composition changes with age. Within the cecum and colon, members of known cellulase-producing bacterial taxa including the families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae 1 were detected. The presence of putative genes encoding cellulolytic and carbohydrate-degrading enzymes indicated also the degradation of recalcitrant plant material in both gut compartments. The bacterial community in the gut systems of the Eurasian beaver differed from that of the North American beaver. Higher abundance of Actinobacteria and lower abundances of Bacteroidetes were recorded in the Eurasian beaver. Similar differences were obtained to bacterial communities of termites and herbivorous animals such as bovine. The data presented in this study provides the first insight into bacterial communities in the gut system of the Eurasian beaver.

Enhanced bioconversion of hemicellulosic biomass by microbial consortium for biobutanol production with bioaugmentation strategy

As a renewable and sustainable source for next-generation biofuel production, lignocellulosic biomass can be effectively utilized in environmentally friendly manner. In this study, a stable, xylan-utilizing, anaerobic microbial consortium MC1 enriched from mangrove sediments was established, and it was taxonomically identified that the genera Ruminococcus and Clostridium from this community played a crucial role in the substrate utilization. In addition, a butanol-producing Clostridium sp. strain WST was introduced via the bioaugmentation process, which resulted in the conversion of xylan to biobutanol up to 10.8 g/L, significantly improving the butanol yield up to 0.54 g/g by 98-fold. When this system was further applied to other xylan-rich biomass, 1.09 g/L of butanol could be achieved from 20 g/L of corn cob. These results provide another new method to efficiently convert xylan, the main hemicellulose from lignocellulosic biomass into biofuels through a low-cost and eco-friendly manner.

Highly Specific Sewage-Derived Bacteroides Quantitative PCR Assays Target Sewage-Polluted Waters

The identification of sewage contamination in water has primarily relied on the detection of human-associated Bacteroides using markers within the V2 region of the 16S rRNA gene. Despite the establishment of multiple assays that target the HF183 cluster (i.e., Bacteroides dorei) and other Bacteroides organisms (e.g., Bacteroides thetaiota omicron), the potential for more human-associated markers in this genus has not been explored in depth. We examined the Bacteroides population structure in sewage and animal hosts across the V4V5 and V6 hypervariable regions. Using near-full-length cloned sequences, we identified the sequences in the V4V5 and V6 hypervariable regions that are linked to the HF183 marker in the V2 region and found these sequences were present in multiple animals. In addition, the V4V5 and V6 regions contained human fecal marker sequences for organisms that were independent of the HF183 cluster. The most abundant Bacteroides in untreated sewage was not human associated but pipe derived. Two TaqMan quantitative PCR (qPCR) assays targeting the V4V5 and V6 regions of this organism were developed. Validation studies using fecal samples from seven animal hosts (n = 76) and uncontaminated water samples (n = 30) demonstrated the high specificity of the assays for sewage. Freshwater Bacteroides were also identified in uncontaminated water samples, demonstrating that measures of total Bacteroides do not reflect fecal pollution. A comparison of two previously described human Bacteroides assays (HB and HF183/BacR287) in municipal wastewater influent and sewage-contaminated urban water samples revealed identical results, illustrating the assays target the same organism. The detection of sewage-derived Bacteroides provided an independent measure of sewage-impacted waters.IMPORTANCE Bacteroides are major members of the gut microbiota, and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure of Bacteroides within sewage to contextualize the well-studied HF183 marker for a human-associated Bacteroides The study also delineates host-specific sequence patterns across multiple hypervariable regions of the 16S rRNA gene to improve our ability to use sequence data to assess water quality. Here, we demonstrate that regions downstream of the HF183 marker are nonspecific but other potential human-associated markers are present. Furthermore, we show the most abundant Bacteroides in sewage is free living, rather than host associated, and specifically found in sewage. Quantitative PCR assays that target organisms specific to sewer pipes offer measures that are independent of the human microbiome for identifying sewage pollution in water.

Microbial characteristics in anaerobic digestion process of food waste for methane production-A review

Food waste (FW) is rich in starch, fat, protein and cellulose. It is easy to decay and brings environmental pollution and other social problems. FW shows a high potential to produce methane by anaerobic digestion (AD) due to its high organic content. However, many inhibitors, such as accumulation of ammonia and volatile fatty acids (VFAs), usually result in inefficient performances and even process failure. Microorganisms play an important role in the process of hydrolysis, acidogenesis, acetogenesis and methanogenesis. This review provided a critical summary of microbial characteristics to obtain connects of microbial community structure with operational conditions at various states of AD, such as mesophilic and thermophilic, wet and dry, success and failure, pretreated or not, lab-scale and full-scale. This article emphasizes that it is necessary to analyze changes and mechanisms of microbial communities in unbalanced system and seek efficiency dynamic succession rules of the dominant microorganisms.

The long-term impact of cefalexin on organic substrate degradation and microbial community structure in EGSB system

In order to investigate long-term effect of cefalexin (CFX) on the performance of expanded granular sludge bed (EGSB) system and microbial community structure, two 1.47 L EGSB reactors E1 and E2 were designed and run for 224 days treating with synthetic antibiotic wastewater. For the purpose of comparison, E1 was fed with synthetic antibiotic industry wastewater with CFX added as the test reactor, while, E2 was fed without any CFX added as the control reactor (E2). The addition of CFX resulted in the continual increasing of soluble COD (sCOD) and accumulation of VFAs in the effluent of E1 system. Besides, it was found that the accumulation of CFX by-products D-1, D-2 and D-3 was negative correlation with sCOD removal efficiency. Furthermore, the microbial community structures were also investigated. For the bacterial community, Gelria and Syntrophorhabdus which can ferment propionate and other organic pollutants as their substrate were obviously enriched in E1 system. For the archaea, there was more functional diversity in E1 system than in E2 system. Furthermore, fungi also played an important role on the removal of complex organics in E1 system.

Effects of co-inoculating rice straw with ruminal microbiota and anaerobic sludge: digestion performance and spatial distribution of microbial communities

Ruminal microbiota (RM) were co-inoculated with anaerobic sludge (AS) at different ratios to study the digestion of rice straw in batch experiments. The CH₄ yield reached 273.64 mL/g volatile solid (VS) at a co-inoculum ratio of 1:1. The xylanase and cellulase activities were 198.88-212.88 and 24.51-29.08 U/mL in co-inoculated samples, respectively, and were significantly different compared to the results for single inoculum (p < 0.05). Higher ratios of AS enhanced acetoclastic methanogenesis, and propionate accumulation could be the main reason for the longer lag phase observed in samples with a higher RM ratio. The microbial compositions were clearly altered after digestion. Fibrobacter, Ruminococcus and Butyrivibrio from the rumen did not settle in the co-inoculated system, whereas Clostridiales members became the main polysaccharide degraders. Microbial interactions involving hydrolytic bacteria and acetoclastic methanogens in the residue were considered to be significant for hydrolysis activities and methane production. Syntrophy involving propionate oxidizers with associated methanogens occurred in the liquid phase. Our findings provide a better understanding of the anaerobic digestion of rice straw that is driven by specific microbial populations.

Characterization of biocarbon-source recovery and microbial community shifts from waste activated sludge by conditioning with cornstover: Assessment of cellulosic compositions

Most studies on the production of volatile fatty acids (VFAs) from waste activated sludge (WAS) digestion have focused on operating conditions, pretreatments and characteristic adjustments. Conditioning by extra carbon sources (ECS), normally added in a solid form, has been reported to be an efficient approach. However, this has caused considerable waste of monomeric sugars in the hydrolysate. In this study, the effects of two added forms (pretreated straw (S) and hydrolyzed liquid (L)) of cornstover (CS) on WAS acidification were investigated. To obtain different cellulosic compositions of CS, low-thermal or autoclaved assisted alkaline (TA or AA) pretreatments were conducted. The results showed that AA-L test achieved the highest VFAs value (653 mg COD/g VSS), followed by AA-S (613 mg COD/g VSS). These values were 12% and 28% higher, respectively, than that obtained in the TA-L and TA-S tests. Meanwhile, higher percentages of acetic acid were observed after AA pretreatment (~62% versus ~53% in TA). The added forms of CS played an important role in structuring the innate microbial community in the WAS, as shown by high-throughput sequencing and canonical correspondence analysis. The findings obtained in this work may provide a scientific basis for the potential implementation of co-digesting WAS with ECS simultaneously obtaining energy and high value-added products.

Microbial community dynamics linked to enhanced substrate availability and biogas production of electrokinetically pre-treated waste activated sludge

The restricted hydrolytic degradation rate of complex organic matter presents a considerable challenge in anaerobic digestion of waste activated sludge (WAS). Within this context, application of pre-treatment of digester substrate has potential for improved waste management and enhanced biogas production. Anaerobic degradation of untreated or electrokinetically pre-treated WAS was performed in two pilot-scale digesters for 132days. WAS electrokinetically pre-treated with energy input 0.066kJ/kg sludge was used in a first phase of operation and WAS pre-treated with energy input 0.091kJ/kg sludge was used in a second phase (each phase lasted at least three hydraulic retention times). Substrate characteristics before and after pre-treatment and effects on biogas digester performance were comprehensively analysed. To gain insights into influences of altered substrate characteristics on microbial communities, the dynamics within the bacterial and archaeal communities in the two digesters were investigated using 16S rRNA gene sequencing (pyrosequencing) and quantitative PCR (qPCR). Specific primers targeting dominant operation taxonomic units (OTUs) and members of the candidate phylum Cloacimonetes were designed to further evaluate their abundance and dynamics in the digesters. Electrokinetic pre-treatment significantly improved chemical oxygen demand (COD) and carbohydrate solubility and increased biogas production by 10-11% compared with untreated sludge. Compositional similarity of the bacterial community during initial operation and diversification during later operation indicated gradual adaptation of the community to the higher solubility of organic material in the pre-treated substrate. Further analyses revealed positive correlations between gene abundance of dominant OTUs related to Clostridia and Cloacimonetes and increased substrate availability and biogas production. Among the methanogens, the genus Methanosaeta dominated in both digesters. Overall, the results showed that electrokinetic pre-treatment of WAS increases substrate solubility and biogas production. Changes in bacterial community composition and abundances of dominant bacterial OTUs were observed during anaerobic degradation of pre-treated WAS, whereas the relative abundance of methanogenic community members remained stable.

Temperature affects microbial abundance, activity and interactions in anaerobic digestion

Temperature is a major factor determining the performance of the anaerobic digestion process. The microbial abundance, activity and interactional networks were investigated under a temperature gradient from 25°C to 55°C through amplicon sequencing, using 16S ribosomal RNA and 16S rRNA gene-based approaches. Comparative analysis of past accumulative elements presented by 16S rRNA gene-based analysis, and the in-situ conditions presented by 16S rRNA-based analysis, provided new insights concerning the identification of microbial functional roles and interactions. The daily methane production and total biogas production increased with temperature up to 50°C, but decreased at 55°C. Increased methanogenesis and hydrolysis at 50°C were main factors causing higher methane production which was also closely related with more well-defined methanogenic and/or related modules with comprehensive interactions and increased functional orderliness referred to more microorganisms participating in interactions. This research demonstrated the importance of evaluating functional roles and interactions of microbial community.

Optimization and microbial community analysis of anaerobic co-digestion of food waste and sewage sludge based on microwave pretreatment

The effects of microwave pretreatment (MW) on co-digestion of food waste (FW) and sewage sludge (SS) have never been investigated. In this study, a series of mesophilic biochemical methane potential (BMP) tests were conducted to determine the optimized ratio of FW and SS based on MW, and the evolution of bacterial and archaeal community was investigated through high-throughput sequencing method. Results showed that the optimized ratio was 3:2 for co-digestion of FW and SS based on MW, and the methane production was 316.24 and 338.44mLCH4/gVSadded for MW-FW and MW-SS, respectively. The MW-SS was superior for methane production compared to MW-FW, in which accumulation of propionic acid led to the inhibition of methanogenesis. Proteiniborus and Parabacteroides were responsible for proteins and polysaccharides degradation for all, respectively, while Bacteroides only dominated in co-digestion. Methanosphaera dominated in MW-FW at the active methane production phase, while it was Methanosarcina in MW-SS and mono-SS.

The microbial community structure in industrial biogas plants influences the degradation rate of straw and cellulose in batch tests

BACKGROUND

Materials rich in lignocellulose, such as straw, are abundant, cheap and highly interesting for biogas production. However, the complex structure of lignocellulose is difficult for microbial cellulolytic enzymes to access, limiting degradation. The rate of degradation depends on the activity of members of the microbial community, but the knowledge of this community in the biogas process is rather limited. This study, therefore, investigated the degradation rate of cellulose and straw in batch cultivation test initiated with inoculums from four co-digestion biogas plants (CD) and six wastewater treatment plants (WWTP). The results were correlated to the bacterial community by 454-pyrosequencing targeting 16S rRNA gene and by T-RFLP analysis targeting genes of glycoside hydrolase families 5 (cel5) and 48 (cel48), combined with construction of clone libraries.

RESULTS

UniFrac principal coordinate analysis of 16S rRNA gene amplicons revealed a clustering of WWTPs, while the CDs were more separated from each other. Bacteroidetes and Firmicutes dominated the community with a comparably higher abundance of the latter in the processes operating at high ammonia levels. Sequences obtained from the cel5 and cel 48 clone libraries were also mainly related to the phyla Firmicutes and Bacteroidetes and here ammonia was a parameter with a strong impact on the cel5 community. The results from the batch cultivation showed similar degradation pattern for eight of the biogas plants, while two characterised by high ammonia level and low bacterial diversity, showed a clear lower degradation rate. Interestingly, two T-RFs from the cel5 community were positively correlated to high degradation rates of both straw and cellulose. One of the respective partial cel5 sequences shared 100 % identity to Clostridium cellulolyticum.

CONCLUSION

The degradation rate of cellulose and straw varied in the batch tests dependent on the origin of the inoculum and was negatively correlated with the ammonia level. The cellulose-degrading community, targeted by analysis of the glycoside hydrolase families 5 (cel5) and 48 (cel48), showed a dominance of bacteria belonging the Firmicutes and Bacteriodetes, and a positive correlation was found between the cellulose degradation rate of wheat straw with the level of C. cellulolyticum.

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure

Responses of bacterial and archaeal communities to the addition of straw during anaerobic digestion of manure at different temperatures (37°C, 44°C and 52°C) were investigated using five laboratory-scale semi-continuous stirred tank reactors. The results revealed that including straw as co-substrate decreased the species richness for bacteria, whereas increasing the operating temperature decreased the species richness for both archaea and bacteria, and also the evenness of the bacteria. Taxonomic classifications of the archaeal community showed that Methanobrevibacter dominated in the manure samples, while Methanosarcina dominated in all digesters regardless of substrate. Increase of the operating temperature to 52°C led to increased relative abundance of Methanoculleus and Methanobacterium. Among the bacteria, the phyla Firmicutes and Bacteroidetes dominated within all samples. Compared with manure itself, digestion of manure resulted in a higher abundance of an uncultured class WWE1 and lower abundance of Bacilli. Adding straw to the digesters increased the level of Bacteroidia, while increasing the operating temperature decreased the level of this class and instead increased the relative abundance of an uncultured genus affiliated to order MBA08 (Clostridia). A considerable fraction of bacterial sequences could not be allocated to genus level, indicating that novel phylotypes are resident in these communities.