Transition of microbial communities during the adaption to anaerobic digestion of carrot waste

Enhanced hydrolysis of waste activated sludge and recovery of volatile fatty acids: Performance and mechanistic analysis of synergistic treatment with sodium citrate and calcium oxide

Anaerobic fermentation has emerged as a promising method of transforming waste activated sludge into high-value products (e.g., volatile fatty acids (VFAs)). This work developed sodium citrate (SC)-calcium oxide (CaO) pretreatment to accelerate the production of VFAs by enhancing sludge solubilization and disintegration of extracellular polymeric substances. The results showed that co-pretreatment with 0.25 g/g TSS of SC and 0.05 g/g TSS of CaO effectively boosted VFAs accumulation (5823.3 mg COD/L), which was 12.2 times higher than the Control group. SC-CaO pretreatment enhanced hydrolysis and acidogenesis by providing ample organic substrates, thereby promoting the growth of hydrolytic and acidogenic bacteria. Additionally, the fermentation broth resulting from co-pretreatment exhibited lower phosphorus concentration and higher biodegradability. Economic analysis confirmed that the combined pretreatment is cost-effective. This work provides a viable strategy for enhancing high-value product recovery from sludge.

Study on the mechanism of action of methane production by co-fermentation of sludge and lignite

To improve the methanogenic efficiency of lignite anaerobic fermentation and explore innovative approaches to sludge utilization, a co-fermentation technique involving lignite and sludge was employed for converting biomass into biomethane. Volatile suspended solids were introduced as a native enrichment of the sludge and mixed with lignite for fermentation. The synergistic fermentation mechanism between sludge and lignite for biomethane production was analyzed through biochemical methane potential experiments, measurement of various parameters pre- and post-fermentation, observation of bacterial population changes during the peak of reaction, carbon migration assessment, and evaluation of rheological characteristics. The results showed that the addition of sludge in the anaerobic fermentation process improved the microorganisms' ability to degrade lignite and bolstered biomethane production. Notably, the maximum methane production recorded was 215.52 mL/g-volatile suspended solids, achieved at a sludge to coal ratio of 3:1, with a synergistic growth rate of 25.37%. Furthermore, the removal rates of total suspended solids, and total chemical oxygen demand exhibited an upward trend with an increasing percentage of sludge in the mixture. The relative abundance and activity of the methanogens population were found to increase with an appropriate ratio of sludge to lignite. This observation confirmed the migration of carbon between the solid-liquid-gas phases, promoting enhanced system affinity. Additionally, the changes in solid-liquid phase parameters before and after the reaction indicated that the addition of sludge improved the system's degradation capacity. The results of the study hold significant implications in realizing the resource utilization of sludge and lignite while contributing to environmental protection endeavors.

Enhancement of anaerobic digestion of high salinity food waste by magnetite and potassium ions: Digestor performance, microbial and metabolomic analyses

The study investigated the effectiveness of magnetite and potassium ions (K+) in enhancing anaerobic digestion of high salinity food waste. Results indicated that both magnetite and K+ improved anaerobic digestion in high-salt environments, and their combination yielded even better results. The combination of magnetite and K+ promoted microorganism activity, and resulted in increased abundance of DMER64, Halobacteria and Methanosaeta. Metabolomic analysis revealed that magnetite mainly influenced quorum sensing, while K+ mainly stimulated the synthesis of compatible solutes, aiding in maintaining osmotic balance. The combined additives regulated pathways such as ATP binding cassette transport, methane metabolism, and inhibitory substance metabolism, enabling cells to resist environmental stress and maintain normal metabolic activity. Overall, this study demonstrated the potential of magnetite and K+ to enhance food waste anaerobic digestion in high salt conditions and provided valuable insights into the molecular mechanism.

A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester

Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.

Bacterial composition of a competitive exclusion product and its correlation with product efficacy at reducing Salmonella in poultry

The mature intestinal microbiome is a formidable barrier to pathogen colonization. Day-old chicks seeded with cecal contents of adult hens are resistant to colonization with Salmonella, the basis of competitive exclusion. Competitive exclusion products can include individual microbes but are commonly undefined intestinal communities taken from adult animals and in commercial production is amplified in fermentator and sold commercially in freeze dried lots. While superior to single and multiple species probiotics, reducing Salmonella colonization by multiple logs, undefined products have limited acceptance because of their uncharacterized status. In this study, the bacterial composition of the master stock, preproduction seed stocks and commercial lots of a poultry competitive exclusion product, was defined by 16S rRNA sequence analysis, targeting the 16S rRNA variable region (V1-V3). The samples contained a diversity of genera (22-52 distinct genera) however, the commercial lots displayed less diversity compared to the seeds and the master stock. Community composition varied between seeds and the master stock and was not a good predictor of potency, in terms of log₁₀ reduction in Salmonella abundance. While there was significant correlation in composition between seeds and their commercial lots, this too was a not a good predictor of potency. There was linear correlation between unclassified Actinobacteria, Peptococcus, and unclassified Erysipelotrichaceae, and Salmonella abundance (r ² > .75) for commercial seeds. However, upon review of the literature, these three genera were not consistently observed across studies or between trials that examined the correlation between intestinal community composition and Salmonella prevalence or abundance.

Deep insights into the anaerobic co-digestion of waste activated sludge with concentrated leachate under different salinity stresses

Treatment of high-salinity organic wastewater (e.g., concentrated leachate) is a major challenge. Anaerobic co-digestion can effectively treat high-salinity organic wastewater and recover energy. In this study, the concentrated landfill leachate and waste activated sludge (WAS) were anaerobic co-digested in the lab-scale continuous stirred tank reactors (CSTR) to understand their co-digestion performance under different salinity stresses. As revealed by the results, when the salinity was low (<10 g/L), the removal ratio of organic matter in the digester was kept at a high level (>91.3%), and the concentration of total volatile fatty acids (TVFAs) was low (<100 mg COD/L), indicating that the digester could operate efficiently and stably. However, when the salinity level was elevated from 10 g/L to 30 g/L, the removal ratio of organic matter in the digester decreased from ~91.3% to ~64.5%, the TVFAs continued to accumulate, the yields of biogas and methane also dropped sharply, and the performance of the digester decreased gradually. The results of microbial community and diversity analysis showed that there is limited adaptability of microbial community to high salinity in such process. Salinity could cause significant changes in the microbial community and diversity, thereby affecting the digestive performance. Metagenomic analysis showed that under high salinity conditions, the content of genes encoding hydrolase and methanogenic enzyme decreased, whereas the pathway of acetotrophic methanogenesis was weakened. Mechanism study showed that with the increase of salinity, the activity of microbial cells decreased, the structure of sludge flocs was damaged more significantly, and the extracellular polymeric substances (EPS) secreted by microbe increased continuously, which was used to resist the toxic effects of salinity stresses on microorganisms. The results of this study could provide certain theoretical guidance for anaerobic digestion under salinity stresses.

Strength Lies in Diversity: How Community Diversity Limits Salmonella Abundance in the Chicken Intestine

The transfer of the intestinal microbiota from adult to juvenile animals reduces Salmonella prevalence and abundance. The mechanism behind this exclusion is unknown, however, certain member species may exclude or promote pathogen colonization and Salmonella abundance in chickens correlates with intestinal community composition. In this study, newly hatched chicks were colonized with Salmonella Typhimurium and 16S rRNA libraries were generated from the cecal bacterial community at 21, 28, 35, and 42 days of age. Salmonella was quantified by real-time PCR. Operational taxonomic units (OTUs) were assigned, and taxonomic assignments were made, using the Ribosomal Database Project. Bacterial diversity was inversely proportional to the Salmonella abundance in the chicken cecum (p < 0.01). In addition, cecal communities with no detectable Salmonella (exclusive community) displayed an increase in the abundance of OTUs related to specific clostridial families (Ruminococcaceae, Eubacteriaceae, and Oscillospiraceae), genera (Faecalibacterium and Turicibacter) and member species (Ethanoligenens harbinense, Oscillibacter ruminantium, and Faecalibacterium prausnitzii). For cecal communities with high Salmonella abundance (permissive community), there was a positive correlation with the presence of unclassified Lachnospiraceae, clostridial genera Blautia and clostridial species Roseburia hominis, Eubacterium biforme, and Robinsoniella peoriensis. These findings strongly support the link between the intestinal bacterial species diversity and the presence of specific member species with Salmonella abundance in the chicken ceca. Exclusive bacterial species could prove effective as direct-fed microbials for reducing Salmonella in poultry while permissive species could be used to predict which birds will be super-shedders.

Soil-Derived Inocula Enhance Methane Production and Counteract Common Process Failures During Anaerobic Digestion

Although soil-borne methanogens are known to be highly diverse and adapted to extreme environments, their application as potential (anaerobic) inocula to improve anaerobic digestion has not been investigated until now. The present study aimed at evaluating if soil-derived communities can be beneficial for biogas (methane, CH₄) production and endure unfavorable conditions commonly associated with digestion failure. Nine study sites were chosen and tested for suitability as inoculation sources to improve biogas production via in situ measurements (CH₄ fluxes, physical and chemical soil properties, and abundance of methanogens) and during a series of anaerobic digestions with (a) combinations of both sterile or unsterile soil and diluted fermenter sludge, and (b) pH-, acetate-, propionate-, and ammonium-induced disturbance. Amplicon sequencing was performed to assess key microbial communities pivotal for successful biogas production. Four out of nine tested soil inocula exerted sufficient methanogenic activity and repeatedly allowed satisfactory CH₄/biogas production even under deteriorated conditions. Remarkably, the significantly highest CH₄ production was observed using unsterile soil combined with sterile sludge, which coincided with both a higher relative abundance of methanogens and predicted genes involved in CH₄ metabolism in these variants. Different bacterial and archaeal community patterns depending on the soil/sludge combinations and disturbance variations were established and these patterns significantly impacted CH₄ production. Methanosarcina spp. seemed to play a key role in CH₄ formation and prevailed even under stressed conditions. Overall, the results provided evidence that soil-borne methanogens can be effective in enhancing digestion performance and stability and, thus, harbor vast potential for further exploitation.

Hydrolase activity and microbial community dynamic shift related to the lack in multivalent cations during cation exchange resin-enhanced anaerobic fermentation of waste activated sludge

The correlation of the lack in multivalent cations with hydrolase activity and microbial community in anaerobic fermentation of waste activated sludge was investigated in this study. It was demonstrated that considerable solid phase reduction of 41 % (7.87 g/L) was achievable through a cation exchange resin-enhanced anaerobic fermentation of 4 days. The protease and α-glucosidase, especially α-glucosidase, were easily influenced by a lack in multivalent cations. Furthermore, species abundance and diversity of microbial community gradually decreased. Meanwhile, the bacteria community structure presented obvious dynamic shifts. Ruminococcaceae_UCG_009, Bacteroides and Macellibacteroides responsible for organic matter biodegradation and SCFAs production became dominant bacteria in cation exchange resin-enhanced anaerobic fermentation, which was less influenced by the lack in multivalent cations, while the SCFA consumers (e.g. methanogens) were inhibited with reduced abundances due to their susceptibility to the lack in multivalent cations. Redundancy analysis revealed that the lack in multivalent cations were responsible for the microbial community evolution, which was proved by the high Grey relational coefficients (0.747-0.820) and significant negative Spearman coefficients (-0.5798 to -0.9429) between multivalent cation and microbial community. Obviously, the cation exchange resin-induced removal of multivalent cations reduced enzyme activity and modified microbial community structure, which created a beneficial environment for enhancing anaerobic fermentation.

Effect of NaCl Concentration on Microbiological Properties in NaCl Assistant Anaerobic Fermentation: Hydrolase Activity and Microbial Community Distribution

Previous studies have demonstrated that sludge hydrolysis and short-chain fatty acids (SCFAs) production were improved through NaCl assistant anaerobic fermentation. However, the effect of NaCl concentrations on hydrolase activity and microbial community structure was rarely reported. In this study, it was found that α-glucosidase activity and some carbohydrate-degrading bacteria were inhibited in NaCl tests, owing to their vulnerability to high NaCl concentration. Correspondingly, the microbial community richness and diversity were reduced compared with the control test, while the evenness was not affected by NaCl concentration. By contrast, the protease activity was increased in the presence of NaCl and reached the highest activity at the NaCl concentration of 20 g/L. The protein-degrading and SCFAs-producing bacteria (e.g., Clostridium algidicarnis and Proteiniclasticum) were enriched in the presence of NaCl, which were salt-tolerant.

A full-scale study of high-rate anaerobic bioreactors for whiskey distillery wastewater treatment with size fractionation and metagenomic analysis of granular sludge

Two full-scale high-rate bioreactors, i.e. external circulation sludge bed (ECSB) and expanded granular sludge bed (EGSB), were monitored for three years. Their performances for treating wastewater in a whiskey distillery were compared in terms of COD, pH, alkalinity and VFA. Even though feed flowrate highly fluctuated, COD removals of ECSB and EGSB were both excellent (95.7 ± 1.3% and 94.8 ± 3.0%, respectively). The influent and effluent characteristics of ECSB reactor were profiled and urea and urethane were also detected. High-strength properties of raw spent wash were exhibited in TOC, soluble COD and BOD5,20°C of 13500, 37750, and 1950 mg·L-1, respectively and characterized by GC-MS. Anaerobic granular sludge sampled from different heights of ECSB reactor were fractionated for demonstrating vertical size distributions. Moreover, major species found by next-generation sequencing technique were archaea, i.e. Methanosaeta and Methanolinea, while major bacteria were Bacteroidetes with minor Nitrospiraceae. This metagenomic analysis provided an insight of anaerobic microbial consortium.

Full-scale anaerobic reactor samples would be more suitable than lab-scale anaerobic reactor and natural samples to inoculate the wheat straw batch anaerobic digesters

This study evaluated the effects of the inocula from natural wetland, lab-scale and full-scale anaerobic reactors on wheat straw anaerobic digestion. Three replicate batch reactors were constructed for each inoculum to investigate the reactor performances and microbial communities. Reactors seeded with full-scale reactor samples were started up most rapidly, achieved the highest methane production, and were recognized as the higher efficient reactors. The dominance of acetoclastic methanogens, including Methanosaeta and Methanoscrina, was crucial for the higher efficient reactors, whereas hydrogenotrophic methanogens were dominant in other reactors. Genus Treponema, which could enhance the cellulose degradation and conduct homoacetogenesis, was first reported to be dominant in the bacterial communities of high efficient reactors. Inoculum sources and process conditions were suggested to be the deterministic factors in shaping the microbial communities in the higher efficient reactors. These findings contribute to the startup of new anaerobic reactors.

Enrichment and Characterisation of a Mixed-Source Ethanologenic Community Degrading the Organic Fraction of Municipal Solid Waste Under Minimal Environmental Control

The utilisation of the organic fraction of municipal solid waste as feedstock for bioethanol production could reduce the need for disposal of the ever-increasing amounts of municipal solid waste, especially in developing countries, and fits with the integrated goals of climate change mitigation and transport energy security. Mixed culture fermentation represents a suitable approach to handle the complexity and variability of such waste, avoiding expensive and vulnerable closed-control operational conditions. It is widely accepted that the control of pH in these systems can direct the fermentation process toward a desired fermentation product, however, little empirical evidence has been provided in respect of lignocellulosic waste substrates and different environmental inocula sources. We evaluated ethanol production from the organic fraction of municipal solid waste using five different inocula sources where lignocellulose degradation putatively occurs, namely, compost, woodland soil, rumen, cow faeces and anaerobic granular sludge, when incubated in batch microcosms at either initially neutral or acidic pH and under initially aerobic or anaerobic conditions. Although ethanol was produced by all the inocula tested, their performance was different in response to the imposed experimental conditions. Rumen and anaerobic granular sludge produced significantly the highest ethanol concentrations (∼30 mM) under initially neutral and acidic pH, respectively. A mixed-source community formed by mixing rumen and sludge (R + S) was then tested over a range of initial pH. In contrast to the differences observed for the individual inocula, the maximal ethanol production of the mixed community was not significantly different at initial pH of 5.5 and 7. Consistent with this broader functionality, the microbial community analyses confirmed the R + S community enriched comprised bacterial taxa representative of both original inocula. It was demonstrated that the interaction of initial pH and inocula source dictated ethanologenic activity from the organic fraction of municipal solid waste. Furthermore, the ethanologenic mixed-source community enriched, was comprised of taxa belonging to the two original inocula sources (rumen and sludge) and had a broader functionality. This information is relevant when diverse inocula sources are combined for mix culture fermentation studies as it experimentally demonstrates the benefits of diversity and function assembled from different inocula.

Ammonia stress on a resilient mesophilic anaerobic inoculum: Methane production, microbial community, and putative metabolic pathways

Short term inhibition tests, 16S rRNA tag sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), were employed to visualise the effects of increasing total ammoniacal nitrogen (TAN) concentration (3400-10166 ppm TAN) on microbial community structure and metabolic pathways for acetate degradation. The rate of methane production on acetate was significantly reduced by TAN concentrations above 6133 ppm; however, methane continued to be produced, even at 10166 ppm TAN (0.026 ± 0.0003 gCOD.gVS^-1_inoculum.day^-1). Hydrogenotrophic methanogenesis with syntrophic acetate oxidation (SAO) was identified as the dominant pathway for methane production. A shift towards SAO pathways at higher TAN concentrations and a decrease in the number of 'gene hits' for key genes in specific methanogenesis pathways was observed. Overall, the results highlighted potential for inhibition activity testing to be used together with PICRUSt, to estimate changes in microbial metabolism and to better understand microbial resilience in industrial AD facilities.

Valuable Compound Extraction, Anaerobic Digestion, and Composting: A Leading Biorefinery Approach for Agricultural Wastes

In a society where the environmental conscience is gaining attention, it is necessary to evaluate the potential valorization options for agricultural biomass to create a change in the perception of the waste agricultural biomass from waste to resource. In that sense, the biorefinery approach has been proposed as the roadway to increase profit of the agricultural sector and, at the same time, ensure environmental sustainability. The biorefinery approach integrates biomass conversion processes to produce fuels, power, and chemicals from biomass. The present review is focused on the extraction of value-added compounds, anaerobic digestion, and composting of agricultural waste as the biorefinery approach. This biorefinery approach is, nevertheless, seen as a less innovative configuration compared to other biorefinery configurations, such as bioethanol production or white biotechnology. However, any of these processes has been widely proposed as a single operation unit for agricultural waste valorization, and a thoughtful review on possible single or joint application has not been available in the literature up to now. The aim is to review the previous and current literature about the potential valorization of agricultural waste biomass, focusing on valuable compound extraction, anaerobic digestion, and composting of agricultural waste, whether they are not, partially, or fully integrated.

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.

Proposal for the reclassification of obligately purine-fermenting bacteria Clostridium acidurici (Barker 1938) and Clostridium purinilyticum (Dürre et al. 1981) as Gottschalkia acidurici gen. nov. comb. nov. and Gottschalkiapurinilytica comb. nov. and of Eubacterium angustum (Beuscher and Andreesen 1985) as Andreesenia angusta gen. nov. comb. nov. in the family Gottschalkiaceae fam. nov

Several strictly anaerobic bacteria that are Gram-stain-positive have the ability to use uric acid as the sole source of carbon and energy. The phylogeny of three such species, Clostridium acidurici, Clostridium purinilyticum, and Eubacterium angustum, members of the Clostridium cluster XII that ferment purines, but not most amino acids or carbohydrates, has been re-examined, taking advantage of their recently sequenced genomes. Phylogenetic analyses, based on 16S rRNA gene sequences, protein sequences of RpoB and GyrB, and on a concatenated alignment of 50 ribosomal proteins, revealed tight clustering of C. acidurici and C. purinilyticum. Eubacterium angustum showed consistent association with C. acidurici and C. purinilyticum , but differed from these two in terms of the genome size, G+C content of its chromosomal DNA and its inability to form spores. We propose reassigning C. acidurici and C. purinilyticum to the novel genus Gottschalkia as Gottschalkia acidurici gen. nov. comb. nov. (the type species of the genus) and Gottschalkia purinilytica comb. nov., respectively. Eubacterium angustum is proposed to be reclassified as Andreesenia angusta gen. nov. comb. nov. Furthermore, based on the phylogenetic data and similar metabolic properties, we propose assigning genera Gottschalkia and Andreesenia to the novel family Gottschalkiaceae. Metagenomic sequencing data indicate the widespread distibution of organisms falling within the radiation of the proposed family Gottschalkiaceae in terrestrial and aquatic habitats from upstate New York to Antarctica, most likely due to their ability to metabolize avian-produced uric acid.

Diversity and Distribution of Freshwater Aerobic Anoxygenic Phototrophic Bacteria across a Wide Latitudinal Gradient

Aerobic anoxygenic phototrophs (AAPs) have been shown to exist in numerous marine and brackish environments where they are hypothesized to play important ecological roles. Despite their potential significance, the study of freshwater AAPs is in its infancy and limited to local investigations. Here, we explore the occurrence, diversity and distribution of AAPs in lakes covering a wide latitudinal gradient: Mongolian and German lakes located in temperate regions of Eurasia, tropical Great East African lakes, and polar permanently ice-covered Antarctic lakes. Our results show a widespread distribution of AAPs in lakes with contrasting environmental conditions and confirm that this group is composed of different members of the Alpha- and Betaproteobacteria. While latitude does not seem to strongly influence AAP abundance, clear patterns of community structure and composition along geographic regions were observed as indicated by a strong macro-geographical signal in the taxonomical composition of AAPs. Overall, our results suggest that the distribution patterns of freshwater AAPs are likely driven by a combination of small-scale environmental conditions (specific of each lake and region) and large-scale geographic factors (climatic regions across a latitudinal gradient).

Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions

Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH4/g volatile solids (VS) and 246.1 ± 11 mL CH4/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities.

[Agroindustrial wastes methanization and bacterial composition in anaerobic digestion]

The tons of organic waste that are annually generated by agro-industry, can be used as raw material for methane production. For this reason, it is important to previously perform biodegradability tests to organic wastes for their full scale methanization. This paper addresses biodegradability, methane production and the behavior of populations of eubacteria and archaeabacteria during anaerobic digestion of banana, mango and papaya agroindustrial wastes. Mango and banana wastes had higher organic matter content than papaya in terms of their volatile solids and total solid rate (94 and 75% respectively). After 63 days of treatment, the highest methane production was observed in banana waste anaerobic digestion: 63.89ml CH4/per gram of chemical oxygen demand of the waste. In the PCR-DGGE molecular analysis, different genomic footprints with oligonucleotides for eubacteria and archeobacteria were found. Biochemical methane potential results proved that banana wastes have the best potential to be used as raw material for methane production. The result of a PCR- DGGE analysis using specific oligonucleotides enabled to identify the behavior of populations of eubacteria and archaeabacteria present during the anaerobic digestion of agroindustrial wastes throughout the process.

Effects of phosphate addition on methane fermentation in the batch and upflow anaerobic sludge blanket (UASB) reactors

Ammonia inhibition of methane fermentation is one of the leading causes of failure of anaerobic digestion reactors. In a batch anaerobic digestion reactor with 429 mM NH3-N/L of ammonia, the addition of 25 mM phosphate resulted in an increase in methane production rate. Similar results were obtained with the addition of disodium phosphate in continuous anaerobic digestion using an upflow anaerobic sludge blanket (UASB) reactor. While methane content and production rate decreased in the presence of more than 143 mM NH3-N/L of ammonium chloride in UASB, the addition of 5 mM disodium phosphate suppressed ammonia inhibition at 214 mM NH3-N/L of ammonium chloride. The addition prevented acetate/propionate accumulation, which might be one of the effects of the phosphate on the ammonia inhibition. The effects on the microbial community in the UASB reactor was also assessed, which was composed of Bacteria involved in hydrolysis, acidogenesis, acetogenesis, and dehydrogenation, as well as Archaea carrying out methanogenesis. The change in the microbial community was observed by ammonia inhibition and the addition of phosphate. The change indicates that the suppression of ammonia inhibition by disodium phosphate addition could stimulate the activity of methanogens, reduce shift in bacterial community, and enhance hydrogen-producing bacteria. The addition of phosphate will be an important treatment for future studies of methane fermentation.

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.

Effect of solids retention time on membrane fouling intensity in two-stage submerged anaerobic membrane bioreactors treating palm oil mill effluent

Submerged anaerobic membrane bioreactors (SAnMBRs) treating palm oil mill effluent were analysed in terms of membrane fouling dynamics when working at three different sludge retention times (SRTs of 15, 30 and 60 d). The average permeate flux was fixed at 2.4 L x m(-2) x h(-1). During operation, the membrane was regenerated by using two steps: membrane wiping during each experiment as soon as trans-membrane pressure reached 125-130 mbars, and complete membrane cleaning including backwash and chemical cleaning at the end of each experiment when analysing the membrane surface and foulant material. Whatever the SRT, the cake formation was the dominant effect on membrane fouling dynamics. The concentration of suspended solids in the SAnMBRs, depending on the SRT, was then a determining criterion. Scanning electron microscopy, energy dispersive X-ray spectroscopy, atomic force microscopy, Fourier transform infrared spectroscopy indicated that fouled membrane surfaces were covered with a cake layer containing organic and inorganic elements whose concentrations were higher when working at a higher SRT; the higher concentrations of such elements gave to the cake layer a denser and more compact structure. In these experiments, the soluble fractions played a secondary role because of the dominant effect of cake layer structuring.

Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants

This study applied Illumina high-throughput sequencing to explore the microbial communities and functions in anaerobic digestion sludge (ADS) from two wastewater treatment plants based on a metagenomic view. Taxonomic analysis using SILVA SSU database indicated that Proteobacteria (9.52-13.50 %), Bacteroidetes (7.18 %-10.65 %) and Firmicutes (7.53 %-9.46 %) were the most abundant phyla in the ADS. Differences of microbial communities between the two types of ADS were identified. Genera of Methanosaeta and Methanosarcina were the major methanogens. Functional analysis by SEED subsystems showed that the basic metabolic functions of metagenomes in the four ADS samples had no significant difference among them, but they were different from other microbial communities from activated sludge, human faeces, ocean and soil. Abundances of genes in methanogenesis pathway were also quantified using a methanogenesis genes database extracted from KEGG. Results showed that acetotrophic was the major methanogenic pathway in the anaerobic sludge digestion.

Soil bacterial community succession during long-term ecosystem development

The physicochemical and biological gradients of soil and vegetative succession along the Franz Josef chrono sequence in New Zealand were used to test whether bacterial communities show patterns of change associated with long-term ecosystem development. Pyrosequencing was conducted on soil-derived 16S rRNA genes at nine stages of ecosystem progression and retrogression, ranging in age from 60 to c. 120 000 years since glacial retreat. Bray–Curtis ordination indicated that the bacterial communities showed clear patterns of change that were closely aligned with ecosystem development, pedogenesis and vegetative succession (Mantel test; r = 0.58; P < 0.001). Eighty per cent (80%) of the explained variability in bacterial community structure was observed during the first c.1000 years of development, when bacterial richness (Simpson's 1/D) declined from 130 to 30. The relatively high turnover of soil bacterial communities corresponded with an integrative 'plant–microbial successional feedback' model that predicts primarily negative feedbacks between plants and soil bacterial communities during progression and early pedogenesis. Positive feedbacks, similar to those of the plant community, could explain the long periods of community stability during later retrogressive stages of ecosystem development. This hypothesized model provides a consistent description linking below ground communities to ecosystem development and succession. The research, using deep sequencing technology, provides the first evidence for soil bacterial community change associated with the process of long-term ecosystem development. How these bacterial community changes are linked to the processes of primary ecosystem succession is not known and needs further investigation.

Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters

While the use of anaerobic digestion to generate methane as a source of bioenergy is increasing worldwide, our knowledge of the microbial communities that perform biomethanation is very limited. Using next-generation sequencing, bacterial population profiles were determined in three full-scale mesophilic anaerobic digesters operated on dairy farms in the state of Vermont (USA). To our knowledge, this is the first report of a metagenomic analysis on the bacterial population of anaerobic digesters using dairy manure as their main substrate. A total of 20,366 non-chimeric sequence reads, covering the V1-V2 hypervariable regions of the bacterial 16S rRNA gene, were assigned to 2,176 operational taxonomic units (OTUs) at a genetic distance cutoff value of 5 %. Based on their limited sequence identity to validly characterized species, the majority of OTUs identified in our study likely represented novel bacterial species. Using a naïve Bayesian classifier, 1,624 anaerobic digester OTUs could be assigned to 16 bacterial phyla, while 552 OTUs could not be classified and may belong to novel bacterial taxonomic groups that have yet to be described. Firmicutes, Bacteroidetes, and Chloroflexi were the most highly represented bacteria overall, with Bacteroidetes and Chloroflexi showing the least and the most variation in abundance between digesters, respectively. All digesters shared 132 OTUs, which as a "core" group represented 65.4 to 70.6 % of sequences in individual digesters. Our results show that bacterial populations from microbial communities of anaerobic manure digesters can display high levels of diversity despite sharing a common core substrate.

Anaerobic digestion of municipal solid waste composed of food waste, wastepaper, and plastic in a single-stage system: performance and microbial community structure characterization

The performance of municipal organic solid waste anaerobic digestion was investigated using a single-stage bioreactor, and the microbial community structures were characterized during the digestion. The results showed that the biogas and methane production rates were 592.4 and 370.1L/kg with volatile solid added at the ratio of 2:1:1 for food waste, wastepaper, and plastic based on dry weight. The methane volume concentration fluctuated between 44.3% and 75.4% at steady stage. Acetic acid, propionic acid, and butyric acid were the major volatile fatty acids produced during the digestion process. The anaerobic process was not inhibited by the accumulation of ammonia and free ammonia. The bacterial community was found to consist of at least 21 bands of bacteria and 12 bands of archaea at the steady state. All of the results indicated that the mixture of food waste, wastepaper, and plastic could be efficiently co-digested using the anaerobic digestion system.

Can probiotics improve the environmental microbiome and resistome of commercial poultry production?

Food animal production systems have become more consolidated and integrated, producing large, concentrated animal populations and significant amounts of fecal waste. Increasing use of manure and litter as a more "natural" and affordable source of fertilizer may be contributing to contamination of fruits and vegetables with foodborne pathogens. In addition, human and animal manure have been identified as a significant source of antibiotic resistance genes thereby serving as a disseminator of resistance to soil and waterways. Therefore, identifying methods to remediate human and animal waste is critical in developing strategies to improve food safety and minimize the dissemination of antibiotic resistant bacteria. In this study, we sought to determine whether withdrawing antibiotic growth promoters or using alternatives to antibiotics would reduce the abundance of antibiotic resistance genes or prevalence of pathogens in poultry litter. Terminal restriction fragment length polymorphism (T-RFLP) paired with high throughput sequencing was used to evaluate the bacterial community composition of litter from broiler chickens that were treated with streptogramin growth-promoting antibiotics, probiotics, or prebiotics. The prevalence of resistance genes and pathogens was determined from sequencing results or PCR screens of litter community DNA. Streptogramin antibiotic usage did not elicit statistically significant differences in Shannon diversity indices or correlation coefficients among the flocks. However, T-RFLP revealed that there were inter-farm differences in the litter composition that was independent of antibiotic usage. The litter from all farms, regardless of antibiotic usage, contained streptogramin resistance genes (vatA, vatB, and vatE), macrolide-lincosamide-streptogramin B resistance genes (ermA and ermB), the tetracycline resistance gene tetM and class 1 integrons. There was inter-farm variability in the distribution of vatA and vatE with no statistically significant differences with regards to usage. Bacterial diversity was higher in litter when probiotics or prebiotics were administered to flocks but as the litter aged, diversity decreased. No statistically significant differences were detected in the abundance of class 1 integrons where 3%-5% of the community was estimated to harbor a copy. Abundance of pathogenic Clostridium species increased in aging litter despite the treatment while the abundance of tetracycline-resistant coliforms was unaffected by treatment. However some treatments decreased the prevalence of Salmonella. These findings suggest that withdrawing antibiotics or administering alternatives to antibiotics can change the litter bacterial community and reduce the prevalence of some pathogenic bacteria, but may not immediately impact the prevalence of antibiotic resistance.

Distribution of acI-Actinorhodopsin genes in Baltic Sea salinity gradients indicates adaptation of facultative freshwater photoheterotrophs to brackish waters

Knowledge on Actinobacteria rhodopsin gene (actR) diversity and spatial distribution is scarce. The Baltic Sea is characterized by strong salinity gradients leading to the coexistence of marine and freshwater bacteria and hence is an ideal study area to elucidate the dispersion and phylogenetic affiliation of actR in dependence on salinity. ActR DGGE fingerprints in summer 2008 revealed between 3 and 19 distinct bands within a salinity range of 2.4-27 PSU. Environmental actR clone sequences were obtained from stations distributed along the whole salinity gradient. Overall, 20 different actR sequence groups (operational taxonomic units) were found, with up to 11 different ones per station. Phylogenetically, the actR sequences were predominantly (80%) affiliated with freshwater acI-Actinobacteria whose 16S rRNA gene accounted for 2-33% of total 16S rRNA genes in both the Bothnian Sea and central Baltic Sea. However, at salinities above 14 PSU, acI-16S rRNA gene accounted for less than 1%. In contrast, the diversity of actR remained high. Changes in actR gene diversity were significantly correlated with salinity, oxygen, silica or abundance of Synechococcus sp. Our results demonstrate a wide distribution of freshwater actR along the Baltic Sea salinity gradient indicating that some freshwater Actinobacteria might have adapted to higher salinities.

The fate of antagonistic microorganisms and antimicrobial substances during anaerobic digestion of pig and dairy manure

The goals of the present study were to evaluate the suppressive capability of anaerobically digested slurry (ADS) against Phytophthora capsici and to determine the key factors of disease control in ADS. This was achieved by the investigations of the changes in microbial populations and the levels of antimicrobial compound during anaerobic digestion (AD). AD had no significant impact on the numbers of antagonistic fluorescent pseudomonads or Bacillus sp. The contents of total phenolics, volatile fatty acids and sugar fed with the raw slurries to the reactors were decreased by AD. However, the bioreactor effluents had higher concentrations of humic substances and ammonia than the feedstocks. Moreover, AD had a different influence on the content of amino acid in the pig manure compared to the dairy manure. The results obtained indicated that the key inhibitory factors of ADS might be attributed to ammonia and humic substances.

The role of different methanogen groups evaluated by Real-Time qPCR as high-efficiency bioindicators of wet anaerobic co-digestion of organic waste

Methanogen populations and their domains are poorly understood; however, in recent years, research on this topic has emerged. The relevance of this field has also been enhanced by the growing economic interest in methanogen skills, particularly the production of methane from organic substrates. Management attention turned to anaerobic wastes digestion because the volume and environmental impact reductions. Methanogenesis is the biochemically limiting step of the process and the industrially interesting phase because it connects to the amount of biogas production. For this reason, several studies have evaluated the structure of methanogen communities during this process. Currently, it is clear that the methanogen load and diversity depend on the feeding characteristics and the process conditions, but not much data is available. In this study, we apply a Real-Time Polymerase Chain Reaction (RT-PCR) method based on mcrA target to evaluate, by specific probes, some subgroups of methanogens during the mesophilic anaerobic digestion process fed wastewater sludge and organic fraction of the municipal solid waste with two different pre-treatments. The obtained data showed the prevalence of Methanomicrobiales and significantly positive correlation between Methanosarcina and Methanosaetae and the biogas production rate (0.744 p < 0.01 and 0.641 p < 0.05). Methanosarcina detected levels are different during the process after the two pre-treatment of the input materials (T-test p < 0.05). Moreover, a role as diagnostic tool could be suggested in digestion optimisation.