Implications from distinct sulfate-reducing bacteria populations between cattle manure and digestate in the elucidation of H2S production during anaerobic digestion of animal slurry

Comparative Methods for Quantification of Sulfate-Reducing Bacteria in Environmental and Engineered Sludge Samples

This study aimed to compare microscopic counting, culture, and quantitative or real-time PCR (qPCR) to quantify sulfate-reducing bacteria in environmental and engineered sludge samples. Four sets of primers that amplified the dsrA and apsA gene encoding the two key enzymes of the sulfate-reduction pathway were initially tested. qPCR standard curves were constructed using genomic DNA from an SRB suspension and dilutions of an enriched sulfate-reducing sludge. According to specificity and reproducibility, the DSR1F/RH3-dsr-R primer set ensured a good quantification based on dsrA gene amplification; however, it exhibited inconsistencies at low and high levels of SRB concentrations in environmental and sulfate-reducing sludge samples. Ultimately, we conducted a qPCR method normalized to dsrA gene copies, using a synthetic double-stranded DNA fragment as a calibrator. This method fulfilled all validation criteria and proved to be specific, accurate, and precise. The enumeration of metabolically active SRB populations through culture methods differed from dsrA gene copies but showed a plausible positive correlation. Conversely, microscopic counting had limitations due to distinguishing densely clustered organisms, impacting precision. Hence, this study proves that a qPCR-based method optimized with dsrA gene copies as a calibrator is a sensitive molecular tool for the absolute enumeration of SRB populations in engineered and environmental sludge samples.

Emerging Strategies for Enhancing Propionate Conversion in Anaerobic Digestion: A Review

Anaerobic digestion (AD) is a triple-benefit biotechnology for organic waste treatment, renewable production, and carbon emission reduction. In the process of anaerobic digestion, pH, temperature, organic load, ammonia nitrogen, VFAs, and other factors affect fermentation efficiency and stability. The balance between the generation and consumption of volatile fatty acids (VFAs) in the anaerobic digestion process is the key to stable AD operation. However, the accumulation of VFAs frequently occurs, especially propionate, because its oxidation has the highest Gibbs free energy when compared to other VFAs. In order to solve this problem, some strategies, including buffering addition, suspension of feeding, decreased organic loading rate, and so on, have been proposed. Emerging methods, such as bioaugmentation, supplementary trace elements, the addition of electronic receptors, conductive materials, and the degasification of dissolved hydrogen, have been recently researched, presenting promising results. But the efficacy of these methods still requires further studies and tests regarding full-scale application. The main objective of this paper is to provide a comprehensive review of the mechanisms of propionate generation, the metabolic pathways and the influencing factors during the AD process, and the recent literature regarding the experimental research related to the efficacy of various strategies for enhancing propionate biodegradation. In addition, the issues that must be addressed in the future and the focus of future research are identified, and the potential directions for future development are predicted.

Chemical and microbiological characterization of pig manures and digestates

Livestock and poultry breeding modes, feed compositions and manure collection systems have regional characteristics, which can directly affect the composition of livestock and poultry breeding manure, energy production by anaerobic digestion and resource utilization of products. The chemical, heavy metal contents and microbiological characteristics of pig manures and digestates were characterized in five pig farms and biogas plants in Quzhou (Zhejiang Province) in this study. The results showed that hemicellulose and cellulose of pig manures could be partly degraded in anaerobic digestion, but lignin was difficultly degraded and accumulated in digestates. The content of Zn was highest in the pig manure and digestate samples, followed by Cu, Cr, As, Ni, Pb, Cd, T1 and Hg. The As content was 16.09-31.22 mg kg^-1 in the pig manure and digestate samples, which exceeded the standard limitation requirements in fertilizers in China (≤15 mg kg^-1). Bacteroidota, Firmicutes, Proteobacteria and Spirochaetota dominated in the pig manure and digestate samples, with a relative abundance of 73.6%-99.4%. The microbial community structure in the pig manure samples was quite different among the five farms. The pH, contents of lignin, T1 and As had a significant effect on the microbial community structure in the pig manure samples, while the contents of total phosphorus, NO₃^--N, cellulose and Pb could significantly influence the microbial community structure in the digestate samples. These findings can provide a theoretical basis for recycling manure and improving biogas engineering in large-scale pig farms.

Enrichment culture combined with microbial electrochemical enhanced low-temperature anaerobic digestion of cow dung

Enrichment culture combined with the microbial electrochemical system was used to co-enhance the low-temperature (20 °C) anaerobic digestion. The results showed that enrichment culture combined with microbial electrochemical system increased the cumulative methane production in low-temperature anaerobic digestion system by 39.64 % and 133.29 % compared to single and no enrichment culture, respectively. Enrichment culture combined with microbial electrochemical system increased the relative abundance of methanogenic archaea (Methanomassiliicoccus, Methanocorpusculum, unclassified Methanomicrobiaceae, Methanobacterium, Methanoculleus, Methanocalculus) and the relative abundance of cold-tolerant hydrolytic acidifying bacteria (unclassified Bacteroidetes, Treponema). The expressions of specific enzyme genes in the methanogenesis pathway were enhanced, including acetyl-CoA synthetase, formylmethanofuran dehydrogenase, methanol cobalamin methyltransferase, etc. These results indicated that enrichment culture combined with microbial electrochemical system enhanced low-temperature anaerobic digestion methanogenesis by altering microbial communities and stimulating enzyme gene expression to affect volatile fatty acids, pH, redox potential, and reducing sugar parameters.

Effect of Fluoride in Drinking Water on Fecal Microbial Community in Rats

Intestinal nutrition has a close association with the onset and development of fluorosis. Intestinal microbes play a major role in intestinal nutrition. However, the effect of fluoride on intestinal microbes is still not fully understood. This study aimed to evaluate the dose-response of fluoride on fecal microbes as well as the link between fluorosis and fecal microbes. The results showed that fluoride did not significantly alter the diversity of fecal microbiota, but richness estimators (ACE and Chao) increased first, and then decreased with the increase of water fluoride. At the genus level, 150 mg/L fluoride significantly reduced the abundances of Roseburia and Clostridium sensu stricto, and 100 mg/L and 150 mg/L fluoride obviously increased the abundances of Unclassified Ruminococcaceaes and Unclassified Bdellovibrionales, respectively. The correlation analysis showed fluoride exposure had a negative association with Roseburia and Turicibacter and was positively associated with Pelagibacterium, Unclassified Ruminococcaceae, and Unclassified Bdellovibrionales. Dental fluorosis was negatively associated with Clostridium sensu stricto, Roseburia, Turicibacter, and Paenalcaligenes and had a positive association with Pelagibacterium, Unclassified Ruminococcaceae, and Unclassified Bdellovibrionales. In conclusion, this study firstly reports fluoride in drinking water has a remarkable biphasic effect on fecal microbiota in rats, and some bacteria are significantly associated with fluoride exposure and dental fluorosis. These results indicate the gut microbiota may play an important role in fluorosis, and some bacteria are likely to be developed as biomarkers for fluorosis.

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

BACKGROUND

Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing.

RESULTS

Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut.

CONCLUSIONS

The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. Video abstract.

Impact of metallic nanoparticles on anaerobic digestion: A systematic review

Anaerobic digestion (AD) is one of the most energy-efficient waste treatment technologies for biodegradable wastes. Owing to the increasing trend of metallic nanoparticle applications in industry, they are ubiquitous to the waste streams, which may lead to remarkable impacts on the performance of the AD process. This review addresses the knowledge gaps and summarises the findings from the academic articles published from 2010 to 2019 focusing on the influences on both AD processes of biochemical hydrogen-generation and methane-production from selected metallic nano-materials. Both qualitative and quantitative analyses were conducted with selected indicators to evaluate the metallic nanoparticles' influences on the AD process. The selected metallic nanoparticles were grouped in the view of their chemical formulations aiming to point out the possible mechanisms behind their effects on AD processes. In summary, most metallic nanoparticles with trace-element-base (e.g. iron, cobalt, nickel) have positive effects on both AD hydrogen-generation and methane-production processes in terms of gas production, effluent quality, as well as process optimisation. Within an optimum concentration, they serve as key nutrients providers, aid key enzymes and co-enzymes synthesis, and thus stimulate anaerobic microorganism activities. As for the nano-additives without trace-element base, their positive influences are relied on providing active sites for the microorganism, as well as absorbing inhibitory factors. Moreover, comparisons of these nano-additives' impacts on the two gas-production phases were conducted, while methane-production phases are found to be more sensitive to additions of these nanoparticles then hydrogen-production phase. Research perspectives and research gaps in this area are discussed.

Sulfur from biogas desulfurization: Fate of S during storage in manure and after application to plants

Residues from hydrogen sulfide (H₂S) removal in biogas filters contain sulfur (S) in various forms (sulfate, sulfide, elemental S) that, if properly stored, is potentially valuable as crop fertilizer. We investigated 1) the turnover of the S compounds from filter materials during storage in untreated and digested cattle manure (CM), and 2) the S fertilizer replacement value (SFRV) of the filter materials applied in pure form or mixed manure with and without storage. The S filter materials from four H₂S removal processes (biological and physical-chemical) containing mostly sulfate and/or elemental S were added to untreated CM or digested CM and stored at 10 °C for six months. Afterwards, a pot experiment was established to assess the S availability in an oil-seed rape (Brassica napus) crop. Microbial reduction of sulfate into sulfide took place rapidly after 69 days storage of untreated CM. A lower reduction rate was observed in digested CM mixtures. After six months, 68% and 32% of the initial sulfate content were still present in mixtures containing the S filter materials from biological desulfurization with digested CM and untreated CM, respectively. Sulfate reduction was inhibited for 120 days when digested CM was mixed with S saturated solution from an ash filter, probably due to high pH (≥8.2) and redox potential (>-100 mV) levels. Oppositely, elemental S was immediately and simultaneously both reduced and oxidized. Relatively low losses of total S were observed during the present storage conditions. Despite S turnover, the SFRV of CM and digested CM significantly increased from 15-19% (of total S applied) to 56-90% when S filter materials were added. The storage of S filter materials in digested manure reduced the risk of sulfide production and potential S volatilization. The S filter materials were a valuable source of plant-available S.

Screening of Microbes Associated With Swine Growth and Fat Deposition Traits Across the Intestinal Tract

Pigs, as one of the most common livestock species worldwide, are expected to have a fast growth rate and lower subcutaneous fatness but higher intramuscular fat ("marbling meat"). Nowadays, it is believed that not only host genetics but also its gut microbiomes can modulate farm animal phenotypes, however, many of the mechanisms remain elusive. We measured the body weight (BW), average daily gain (ADG), backfat thickness (BFT), and intramuscular fatness (IMF) of 91 Enshi pigs at 260 days of age, then genotyped each one individually using a 50K single nucleotide polymorphism array and performed 16S ribosomal RNA gene sequencing on 455 microbial samples from the jejunum, ileum, cecum, colon, and rectum. The microbial diversity showed notable spatial variation across the entire intestinal tract, with the cecum and colon having the highest α-diversity. The cecal and colonic microbiotas made greater contributions to BW and ADG and accounted for 22-37% of the phenotypic variance. The jejunal and cecal microbiotas contributed more (13-31%) to the BFT and IMF than the other segments. Finally, from cecum, colon, and jejunum, we identified eight microbial taxa that were significantly correlated with the target traits. The genera Alloprevotella and Ruminococcaceae UCG-005 were highly positively correlated with BW and ADG. The genera Prevotellaceae UCG-001 and Alistipes in the cecum and Clostridium sensu stricto 1 in the jejunum were highly positively correlated with BFT and IMF. The genera Stenotrophomonas, Sphaerochaeta, and Desulfovibrio were negatively associated with the mentioned traits. These findings could aid in developing strategies for manipulating the gut microbiota to alter production performance in pigs.

Microbial Communities and Sulfate-Reducing Microorganisms Abundance and Diversity in Municipal Anaerobic Sewage Sludge Digesters from a Wastewater Treatment Plant (Marrakech, Morocco)

Both molecular analyses and culture-dependent isolation were combined to investigate the diversity of sulfate-reducing prokaryotes and explore their role in sulfides production in full-scale anaerobic digesters (Marrakech, Morocco). At global scale, using 16S rRNA gene sequencing, Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Synergistetes, and Euryarchaeota were the most dominant phyla. The abundance of Archaea (3.1–5.7%) was linked with temperature. The mcrA gene ranged from 2.18 × 105 to 1.47 × 107 gene copies.g−1 of sludge. The sulfate-reducing prokaryotes, representing 5% of total sequences, involved in sulfides production were Peptococcaceae, Syntrophaceae, Desulfobulbaceae, Desulfovibrionaceae, Syntrophobacteraceae, Desulfurellaceae, and Desulfobacteraceae. Furthermore, dsrB gene ranged from 2.18 × 105 to 1.92 × 107 gene copies.g−1 of sludge. The results revealed that exploration of diversity and function of sulfate-reducing bacteria may play a key role in decreasing sulfide production, an undesirable by-product, during anaerobic digestion.

Effect of sulfate addition on carbon flow and microbial community composition during thermophilic digestion of cellulose

Substrates with high sulfate levels pose problems for biogas production as they allow sulfate reducing bacteria to compete with syntrophic and methanogenic members of the community. In addition, the end product of sulfate reduction, hydrogen sulfide, is toxic and corrosive. Here we show how sulfate addition affects physiological processes in a thermophilic methanogenic system by analyzing the carbon flow and the microbial community with quantitative PCR and amplicon sequencing of the 16s rRNA gene. A sulfate addition of 0.5 to 3 g/L caused a decline in methane production by 73-92%, while higher sulfate concentrations had no additional inhibitory effect. Generally, sulfate addition induced a shift in the composition of the microbial community towards a higher dominance of Firmicutes and decreasing abundances of Bacteroidetes and Euryarchaeota. The abundance of methanogens (e.g., Methanoculleus and Methanosarcina) was reduced, while sulfate reducing bacteria (especially Candidatus Desulforudis and Desulfotomaculum) increased significantly in presence of sulfate. The sulfate addition had a significant impact on the carbon flow within the system, shifting the end product from methane and carbon dioxide to acetate and carbon dioxide. Interestingly, methane production quickly resumed, when sulfate was no longer present in the system. Despite the strong impact of sulfate addition on the carbon flow and the microbial community structure during thermophilic biogas production, short-term process disturbances caused by unexpected introduction of sulfate may be overcome due to the high resilience of the engaged microorganisms.

Integrating stereo-elastic packing into ecological floating bed for enhanced denitrification in landscape water

The effects of stereo-elastic packing, as additional bio-carriers, on nitrogen removal in enhanced ecological floating beds (EFBs) are evaluated. Enhanced EFBs with additional stereo-elastic packing was demonstrated to enhance maximum TN removal efficiency (65.8%) over that of EFBs with plant and ceramisite only (54.9%). Performance enhancement was attributable to a 40.6% increase in sediment N accretion and intensification of denitrification by biomass on other carriers in the presence of stereo-elastic packing. Nonetheless, nitrogen uptake by plants was inhibited slightly. Stereo-elastic packing intensified denitrification rates on plant roots and ceramisite by increasing the attached biomass and enhancing the biomass activity, albeit to different extents. The increase in denitrification rate on plant root by 25.7% was significantly higher than that of 4.6% on ceramisite via increased NO₂-N removal. Moreover, bacterial diversity on the carriers was significantly altered, and the enrichment of genera such as Aridibacter, Hyphomicrobium and Gemmobacter promoted denitrification processes.

Effects of moisture and carbon/nitrogen ratio on gaseous emissions and maturity during direct composting of cornstalks used for filtration of anaerobically digested manure centrate

This study investigated the maturity and gaseous emission during direct composting of cornstalks used as organic media for filtration of anaerobically digested manure centrate. Effects of moisture and carbon/nitrogen (C/N) ratio on composting performance were evaluated. Results show that cornstalks could effectively retain suspended solids and organic matter in digested manure centrate to lower their C/N ratio and attain microbial inoculation. Filtered cornstalks became more compostable when their moisture decreased from 76% to 60% or C/N ratio increased from 12 to 24. Nevertheless, such adjustment aggravated the emission of greenhouse and odours gases during composting. Regardless of composting conditions, the phylum Firmicutes was the most dominant with reduced abundance during composting. Similar reduction also occurred to several abundant phyla, including Atribacteria, Synergistetes and Euryarchaeota. By contrast, the phylum Bacteroidetes, Chloroflexi, Proteobacteria and Actinobacteria enriched as composting progressed. In addition, compost maturity was insignificantly affected by matrix moisture and C/N ratio.