Complete genome sequence of Citroniella saccharovorans DSM 29873, isolated from human fecal sample

A complete genome was recovered from Citroniella saccharovorans, strain DSM 29873, using Oxford Nanopore Technologies. The genome assembly contains 1,413,868 bp with 30.23% G+C content. The species belongs to the family Peptoniphilaceae and, as of yet, is the only cultivated representative of the genus Citroniella.

A low-methane rice with high-yield potential realized via optimized carbon partitioning

Global rice cultivation significantly contributes to anthropogenic methane emissions. The methane emissions are caused by methane-producing microorganisms (methanogenic archaea) that are favoured by the anoxic conditions of paddy soils and small carbon molecules released from rice roots. However, different rice cultivars are associated with differences in methane emission rates suggesting that there is a considerable natural variation in this trait. Starting from the hypothesis that sugar allocation within a plant is an important factor influencing both yields and methane emissions, the aim of this study was to produce high-yielding rice lines associated with low methane emissions. In this study, the offspring (here termed progeny lines) of crosses between a newly characterized low-methane rice variety, Heijing 5, and three high-yielding elite varieties, Xiushui, Huayu and Jiahua, were selected for combined low-methane and high-yield properties. Analyses of total organic carbon and carbohydrates showed that the progeny lines stored more carbon in above-ground tissues than the maternal elite varieties. Also, metabolomic analysis of rhizospheric soil surrounding the progeny lines showed reduced levels of glucose and other carbohydrates. The carbon allocation, from roots to shoots, was further supported by a transcriptome analysis using massively parallel sequencing of mRNAs that demonstrated elevated expression of the sugar transporters SUT-C and SWEET in the progeny lines as compared to the parental varieties. Furthermore, measurement of methane emissions from plants, grown in greenhouse as well as outdoor rice paddies, showed a reduction in methane emissions by approximately 70 % in the progeny lines compared to the maternal elite varieties. Taken together, we report here on three independent low-methane-emission rice lines with high yield potential. We also provide a first molecular characterisation of the progeny lines that can serve as a foundation for further studies of candidate genes involved in sugar allocation and reduced methane emissions from rice cultivation.

Characterisation of meropenem-resistant Bacillus sp. FW 1 isolated from biogas digestate

Recently a Bacillus sp. strain FW 1 was isolated from biogas digestate and shown to have novel resistance to meropenem (MEM), of critical importance in human medicine. MEM-resistance has so far only been described for one species within the genus Bacillus, that is, Bacillus cereus. Bacillus is an abundant representative of the microbial community in biogas digesters and consequently, the finding indicates a risk of spreading such resistance when using the digestate as fertiliser. In this study, the Bacillus strain was characterised and classified as Heyndrickxia oleronia (previous Bacillus oleronius), previously not described to harbour MEM-resistance. The mechanism of resistance was explored by metallo-β-lactamase (MBL) production, mapping of carbapenemase genes and genome analysis. The transferability of MEM-resistance in strain FW 1 was investigated by plasmid transformation/conjugation, combined with genome analysis. The results confirmed MBL production for both strain FW 1 and the type strain H. oleronia DSM 9356T . However, elevated MEM resistance was found for strain FW 1, which was suggested to be caused by the production of unclassified carbapenemase, or overexpression of MBL. Moreover, the results suggest that the MEM-resistance of strain FW 1 is not transferable, thus representing a limited risk of MEM-resistance spread to the environment when using digestate on arable land.

Sulfide in engineered methanogenic systems - Friend or foe?

Sulfide ions are regarded to be toxic to microorganisms in engineered methanogenic systems (EMS), where organic substances are anaerobically converted to products such as methane, hydrogen, alcohols, and carboxylic acids. A vast body of research has addressed solutions to mitigate process disturbances associated with high sulfide levels, yet the established paradigm has drawn the attention away from the multifaceted sulfide interactions with minerals, organics, microbial interfaces and their implications for performance of EMS. This brief review brings forward sulfide-derived pathways other than toxicity and with potential significance for anaerobic organic matter degradation. Available evidence on sulfide reactions with organic matter, interventions with key microbial metabolisms, and interspecies electron transfer are critically synthesized as a guidance for comprehending the sulfide effects on EMS apart from the microbial toxicity. The outcomes identify existing knowledge gaps and specify future research needs as a step forward towards realizing the potential of sulfide-derived mechanisms in diversifying and optimizing EMS applications.

Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions

Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.

Characterisation of a low methane emission rice cultivar suitable for cultivation in high latitude light and temperature conditions

Rice cultivation on paddy soil is commonly associated with emissions of methane, a greenhouse gas, but rice varieties may differ in their actual level of emissions. This study analysed methane emissions associated with 22 distinct rice genotypes, using gas chromatography, and identified the cultivar Heijing 5 from northern China as a potential low-methane rice variety. To confirm this and to examine whether Heijing 5 can perform similarly at higher latitudes, Heijing 5 was cultivated in field trials in China (lat. 32° N) and Sweden (lat. 59° N) where (i) methane emissions were measured, (ii) methanogen abundance in the rhizosphere was determined using quantitative PCR, and (iii) the concentrations of nutrients in water and of heavy metals in rice grain and paddy soil were analysed. The results demonstrated that the low-methane rice cultivar Heijing 5 can successfully complete an entire growth period at high-latitude locations such as central Sweden. Massively parallel sequencing of mRNAs identified candidate genes involved in day length and cold acclimatisation. Cultivation of Heijing 5 in central Sweden was also associated with relatively low heavy metal accumulation in rice grains and lowered nutrient losses to neighbouring water bodies.

Improved bioenergy value of residual rice straw by increased lipid levels from upregulation of fatty acid biosynthesis

BACKGROUND

Rice (Oryza sativa) straw is a common waste product that represents a considerable amount of bound energy. This energy can be used for biogas production, but the rate and level of methane produced from rice straw is still low. To investigate the potential for an increased biogas production from rice straw, we have here utilized WRINKLED1 (WRI1), a plant AP2/ERF transcription factor, to increase triacylglycerol (TAG) biosynthesis in rice plants. Two forms of Arabidopsis thaliana WRI1 were evaluated by transient expression and stable transformation of rice plants, and transgenic plants were analyzed both for TAG levels and biogas production from straw.

RESULTS

Both full-length AtWRI1, and a truncated form lacking the initial 141 amino acids (including the N-terminal AP2 domain), increased fatty acid and TAG levels in vegetative and reproductive tissues of Indica rice. The stimulatory effect of the truncated AtWRI1 was significantly lower than that of the full-length protein, suggesting a role for the deleted AP2 domain in WRI1 activity. Full-length AtWRI1 increased TAG levels also in Japonica rice, indicating a conserved effect of WRI1 in rice lipid biosynthesis. The bio-methane production from rice straw was 20% higher in transformants than in the wild type. Moreover, a higher producing rate and final yield of methane was obtained for rice straw compared with rice husks, suggesting positive links between methane production and a high amount of fatty acids.

CONCLUSIONS

Our results suggest that heterologous WRI1 expression in transgenic plants can be used to improve the metabolic potential for bioenergy purposes, in particular methane production.

Effects on rumen microbiome and milk quality of dairy cows fed a grass silage-based diet supplemented with the macroalga Asparagopsis taxiformis

The objective was to determine the effects on rumen microbiome and milk quality of reducing the methane (CH4) produced from enteric fermentation by the addition of Asparagopsis taxiformis (AT) to the diets of dairy cows. Six Nordic Red cows at 122 ± 13.7 (mean ± SD) days in milk, of parity 2.7 ± 0.52 and producing 36 kg ± 2.5 kg milk per day at the start of the trial were divided into three blocks by milk yield and assigned to an extra-period Latin-square change-over design comprising two dietary treatments. An extra period of observation was added to the Latin-square change-over design to control for carry-over effects. The dietary treatments were a diet consisting of grass silage and a commercial concentrate mixture (60:40) either not supplemented or supplemented with 0.5% AT on an organic matter intake basis. On average, daily CH4 production, CH4 yield, and CH4 intensity decreased by 60%, 54%, and 58%, respectively, in cows fed the diet supplemented with AT. Furthermore, hydrogen gas emitted by cows fed diets supplemented with AT increased by more than five times compared with cows fed a non-AT-supplemented diet. Feed intake was decreased and milk production altered, reflecting a decreased yield of milk fat in cows fed an AT-supplemented diet, but feed efficiency increased. Rumen fermentation parameters were changed to promote propionate rather than acetate and butyrate fermentation. The most prominent change in milk quality was an increase in bromine and iodine when the diet was supplemented with AT. The reduction in CH4 was associated with a shift from Methanobrevibacter to Methanomethylophilaceae in the archaeal population and a lower relative abundance of Prevotella in the bacterial population. Changes in milk fat odd-numbered and branched-chain fatty acids in the current study of AT supplementation support observed differences in ruminal archaeal and bacterial populations.

Current trends in waste valorization

This paper presents the scientific breakthroughs made in bioprocess engineering and microbial biotechnology for the conversion of wastes into products with added value and/or biofuels. The significant results obtained in the emerging fields of hybrid electrosynthesis, the role of enzymes in the degradation of plastics, polyhydroxyalkanoate and 5-aminolevulinic acid production, fermentation technology and the application of molecular engineering tools to bioprocess technology are highlighted.

Co-substrate composition is critical for enrichment of functional key species and for process efficiency during biogas production from cattle manure

Cattle manure has a low energy content and high fibre and water content, limiting its value for biogas production. Co-digestion with a more energy-dense material can improve the output, but the co-substrate composition that gives the best results in terms of degree of degradation, gas production and digestate quality has not yet been identified. This study examined the effects of carbohydrate, protein and fat as co-substrates for biogas production from cattle manure. Laboratory-scale semi-continuous mesophilic reactors were operated with manure in mono-digestion or in co-digestion with egg albumin, rapeseed oil, potato starch or a mixture of these, and chemical and microbiological parameters were analysed. The results showed increased gas yield for all co-digestion reactors, but only the reactor supplemented with rapeseed oil showed synergistic effects on methane yield. The reactor receiving potato starch indicated improved fibre degradation, suggesting a priming effect by the easily accessible carbon. Both these reactors showed increased species richness and enrichment of key microbial species, such as fat-degrading Syntrophomonadaceae and families known to include cellulolytic bacteria. The addition of albumin promoted enrichment of known ammonia-tolerant syntrophic acetate- and potential propionate-degrading bacteria, but still caused slight process inhibition and less efficient overall degradation of organic matter in general, and of cellulose in particular.

Uncovering antimicrobial resistance in three agricultural biogas plants using plant-based substrates

Antimicrobial resistance (AMR) is becoming an increasing global concern and the anaerobic digestion (AD) process represents a potential transmission route when digestates are used as fertilizing agents. AMR contaminants, e.g. antibiotic-resistant bacteria (ARB) and plasmid-mediated antibiotic resistance genes (ARGs) have been found in different substrates and AD systems, but not yet been investigated in plant-based substrates. AMR transfer from soils to vegetable microbiomes has been observed, and thus crop material potentially represents a so far neglected AMR load in agricultural AD processes, contributing to AMR spread. In order to test this hypothesis, this study examined the AMR situation throughout the process of three biogas plants using plant-based substrates only, or a mixture of plant-based and manure substrates. The evaluation included a combination of culture-independent and -dependent methods, i.e., identification of ARGs, plasmids, and pathogenic bacteria by DNA arrays, and phylogenetic classification of bacterial isolates and their phenotypic resistance pattern. To our knowledge, this is the first study on AMR in plant-based substrates and the corresponding biogas plant. The results showed that the bacterial community isolated from the investigated substrates and the AD processing facilities were mainly Gram-positive Bacillus spp. Apart from Pantoea agglomerans, no other Gram-negative species were found, either by bacteria culturing or by DNA typing array. In contrast, the presence of ARGs and plasmids clearly indicated the existence of Gram-negative pathogenic bacteria, in both substrate and AD process. Compared with substrates, digestates had lower levels of ARGs, plasmids, and culturable ARB. Thus, digestate could pose a lower risk of spreading AMR than substrates per se. In conclusion, plant-based substrates are associated with AMR, including culturable Gram-positive ARB and Gram-negative pathogenic bacteria-associated ARGs and plasmids. Thus, the AMR load from plant-based substrates should be taken into consideration in agricultural biogas processing.

AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters

AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood–Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences.

Database URL: https://acetobase.molbio.slu.se

Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane

This study aims to elucidate the role of sulfide and its precursors in anaerobic digestion (i.e., cysteine, representing sulfur-containing amino acids, and sulfate) on microbial oleate conversion to methane. Serine, with a similar structure to cysteine but with a hydroxyl group instead of a thiol, was included as a control to assess potential effects on methane formation that were not related to sulfur functionalities. The results showed that copresence of sulfide and oleate in anaerobic batch assays accelerated the methane formation compared to assays with only oleate and mitigated negative effect on methane formation caused by increased sulfide level. Nuclear magnetic resonance spectroscopy of sulfide-exposed oleate suggested that sulfide reaction with oleate double bonds likely contributed to negation of the negative effect on the methanogenic activity. Methane formation from oleate was also accelerated in the presence of cysteine or serine, while sulfate decreased the cumulative methane formation from oleate. Neither cysteine nor serine was converted to methane, and their accelerating effects was associated to different mechanisms due to establishment of microbial communities with different structures, as evidenced by high-throughput sequencing of 16S rRNA gene. These outcomes contribute with new knowledge to develop strategies for optimum use of sulfur- and lipid-rich wastes in anaerobic digestion processes.

Miniphocaeibacter halophilus sp. nov., an ammonium-tolerant acetate-producing bacterium isolated from a biogas system

An anaerobic bacterial strain, designated AMB_01T, recovered from mesophilic propionate enrichment of a high-ammonia biogas digester, was characterised using phenotypic and molecular taxonomic methods. Cells of AMB_01T are coccus-shaped and often occur arranged as diplococci or sarcina. Growth occurred at 20–45 °C, initial pH 5.5–8.5 and with up to 0.7 M NH4Cl, with optimum growth at 37–42 °C and pH 8.0. AMB_01T achieved high cell density and highest acetate production when grown on carbohydrates, including monomers, disaccharides and polysaccharides, such as glucose, maltose, cellobiose and starch. The strain was also able to use amino acids and some organic acids and alcoholic compounds for growth. Acetate was formed as the main product and yeast was not required for growth. The major cellular fatty acids were summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B), C18 : 1ω7, C14 : 0, C16 : 0 and summed feature 3 (C16 : 1ω7 and/or iso-C15 : 0 2OH). The highest 16S rRNA gene sequence similarity found was with Miniphocaeibacter massiliensis (96.6 %), within the family Peptoniphilaceae , phylum Bacillota (Firmicutes). The genomic DNA G+C content was 29.0 mol%. An almost complete set of genes for the acetyl-CoA pathway was found. Genome comparisons between AMB_01T and close relatives showed highest digital DNA–DNA hybridisation to Finegoldia magna (23 %), highest average nucleotide identity with genome nucleotide and amino acid sequences to M. massiliensis (72 and 73 %, respectively) and highest average nucleotide identity (87 %) with Schnuerera ultunensis , indicating that AMB_01T represents a novel species. Analysis of genomic, chemotaxonomic, biochemical and physiological data confirmed that strain AMB_01T represents a novel species, for which the name Miniphocaeibacter halophilus sp. nov. is proposed. The type strain is AMB_01T (=DSM 110247T=JCM 39107 T).

Identifying targets for increased biogas production through chemical and organic matter characterization of digestate from full-scale biogas plants: what remains and why?

Background

This study examines the destiny of macromolecules in different full-scale biogas processes. From previous studies it is clear that the residual organic matter in outgoing digestates can have significant biogas potential, but the factors dictating the size and composition of this residual fraction and how they correlate with the residual methane potential (RMP) are not fully understood. The aim of this study was to generate additional knowledge of the composition of residual digestate fractions and to understand how they correlate with various operational and chemical parameters. The organic composition of both the substrates and digestates from nine biogas plants operating on food waste, sewage sludge, or agricultural waste was characterized and the residual organic fractions were linked to substrate type, trace metal content, ammonia concentration, operational parameters, RMP, and enzyme activity.

Results

Carbohydrates represented the largest fraction of the total VS (32–68%) in most substrates. However, in the digestates protein was instead the most abundant residual macromolecule in almost all plants (3–21 g/kg). The degradation efficiency of proteins generally lower (28–79%) compared to carbohydrates (67–94%) and fats (86–91%). High residual protein content was coupled to recalcitrant protein fractions and microbial biomass, either from the substrate or formed in the degradation process. Co-digesting sewage sludge with fat increased the protein degradation efficiency with 18%, possibly through a priming mechanism where addition of easily degradable substrates also triggers the degradation of more complex fractions. In this study, high residual methane production (> 140 L CH₄/kg VS) was firstly coupled to operation at unstable process conditions caused mainly by ammonia inhibition (0.74 mg NH₃-N/kg) and/or trace element deficiency and, secondly, to short hydraulic retention time (HRT) (55 days) relative to the slow digestion of agricultural waste and manure.

Conclusions

Operation at unstable conditions was one reason for the high residual macromolecule content and high RMP. The outgoing protein content was relatively high in all digesters and improving the degradation of proteins represents one important way to increase the VS reduction and methane production in biogas plants. Post-treatment or post-digestion of digestates, targeting microbial biomass or recalcitrant protein fractions, is a potential way to achieve increased protein degradation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02103-3.

Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community

Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.

Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP

Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.

Effluent solids recirculation to municipal sludge digesters enhances long-chain fatty acids degradation capacity

BACKGROUND

Slow degradation kinetics of long-chain fatty acids (LCFA) and their accumulation in anaerobic digesters disrupt methanogenic activity and biogas production at high loads of waste lipids. In this study, we evaluated the effect of effluent solids recirculation on microbial LCFA (oleate) degradation capacity in continuous stirred-tank sludge digesters, with the overall aim of providing operating conditions for efficient co-digestion of waste lipids. Furthermore, the impacts of LCFA feeding frequency and sulfide on process performance and microbial community dynamics were investigated, as parameters that were previously shown to be influential on LCFA conversion to biogas.

RESULTS

Effluent solids recirculation to municipal sludge digesters enabled biogas production of up to 78% of the theoretical potential from 1.0 g oleate l-1 day-1. In digesters without effluent recirculation, comparable conversion efficiency could only be reached at oleate loading rates up to 0.5 g l-1 day-1. Pulse feeding of oleate (supplementation of 2.0 g oleate l-1 every second day instead of 1.0 g oleate l-1 every day) did not have a substantial impact on the degree of oleate conversion to biogas in the digesters that operated with effluent recirculation, while it marginally enhanced oleate conversion to biogas in the digesters without effluent recirculation. Next-generation sequencing of 16S rRNA gene amplicons of bacteria and archaea revealed that pulse feeding resulted in prevalence of fatty acid-degrading Smithella when effluent recirculation was applied, whereas Candidatus Cloacimonas prevailed after pulse feeding of oleate in the digesters without effluent recirculation. Combined oleate pulse feeding and elevated sulfide level contributed to increased relative abundance of LCFA-degrading Syntrophomonas and enhanced conversion efficiency of oleate, but only in the digesters without effluent recirculation.

CONCLUSIONS

Effluent solids recirculation improves microbial LCFA degradation capacity, providing possibilities for co-digestion of larger amounts of waste lipids with municipal sludge.

Enrichment and description of novel bacteria performing syntrophic propionate oxidation at high ammonia level

Inefficient syntrophic propionate degradation causes severe operating disturbances and reduces biogas productivity in many high-ammonia anaerobic digesters, but propionate-degrading microorganisms in these systems remain unknown. Here, we identified candidate ammonia-tolerant syntrophic propionate-oxidising bacteria using propionate enrichment at high ammonia levels (0.7-0.8 g NH₃ L^-1 ) in continuously-fed reactors. We reconstructed 30 high-quality metagenome-assembled genomes (MAGs) from the propionate-fed reactors, which revealed two novel species from the families Peptococcaceae and Desulfobulbaceae as syntrophic propionate-oxidising candidates. Both MAGs possess genomic potential for the propionate oxidation and electron transfer required for syntrophic energy conservation and, similar to ammonia-tolerant acetate degrading syntrophs, both MAGs contain genes predicted to link to ammonia and pH tolerance. Based on relative abundance, a Peptococcaceae sp. appeared to be the main propionate degrader and has been given the provisional name "Candidatus Syntrophopropionicum ammoniitolerans". This bacterium was also found in high-ammonia biogas digesters, using quantitative PCR. Acetate was degraded by syntrophic acetate-oxidising bacteria and the hydrogenotrophic methanogenic community consisted of Methanoculleus bourgensis and a yet to be characterised Methanoculleus sp. This work provides knowledge of cooperating syntrophic species in high-ammonia systems and reveals that ammonia-tolerant syntrophic propionate-degrading populations share common features, but diverge genomically and taxonomically from known species.

Post-treatment of dewatered digested sewage sludge by thermophilic high-solid digestion for pasteurization with positive energy output

This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Linköping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH₄/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19-29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS.

Isolation of antibiotic-resistant bacteria in biogas digestate and their susceptibility to antibiotics

Antibiotics are widely used to prevent and treat diseases and promote animal growth in the livestock industry, and therefore antibiotic residues can end up in biogas digestate from processes treating animal manure (AM) and food waste (FW). These digestates represent a potential source of spread of antimicrobial resistance (AMR) when used as fertilisers. This study evaluated AMR risks associated with biogas digestates from two processes, using AM and FW as substrate, by isolation and identification of antibiotic-resistant bacteria (ARB) and testing their susceptibility to different antibiotics. ARB from the digestates were isolated by selective plating. The antibiotic susceptibility profile of isolates was determined using ampicillin, ceftazidime, meropenem, vancomycin, ciprofloxacin, rifampicin, chloramphenicol, clindamycin, erythromycin, tetracycline, gentamicin or sulfamethoxazole/trimethoprim, representing different antibiotic classes with differing mechanisms of action. In total, 30 different bacterial species belonging to seven genera were isolated and classified. Bacillus and closely related genera, including Paenibacillus, Lysinibacillus and Brevibacillus, were the dominant ARB in both digestates. Most of the ARB strains isolated were non-pathogenic and some were even known to be beneficial to plant growth. However, some were potentially pathogenic, such as an isolate identified as Bacillus cereus. Many of the isolated species showed multi resistance and the AM digestate and FW digestate both contain bacterial species resistant to all antibiotics tested here, except gentamicin. A higher level of resistance was displayed by the FW isolates, which may indicate higher antibiotic pressure in FW compared with AM digestate. Overall, the results indicate a risk of AMR spread when these digestates are used as fertiliser. However, most of the ARB identified are species commonly found in soil, where AMR in many cases is abundant already, so the contribution of digestate-based fertiliser to the spread of AMR may still be very limited.

Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne

The use of straw for biofuel production is encouraged by the European Union. A previous study showed the feasibility of producing biomethane in upflow anaerobic sludge blanket (UASB) reactors using hydrolyzed, steam-pretreated wheat straw, before and after dark fermentation with Caldicellulosiruptor saccharolyticus, and lucerne. This study provides information on overall microbial community development in those UASB processes and changes related to acidification. The bacterial and archaeal community in granular samples was analyzed using high-throughput amplicon sequencing. Anaerobic digestion model no. 1 (ADM1) was used to predict the abundance of microbial functional groups. The sequencing results showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification. Canonical correspondence analysis showed significant negative correlations between the concentration of organic acids and three phyla, and positive correlations with seven phyla. Organic loading rate and total COD fed also showed significant correlations with microbial community structure, which changed over time. ADM1 predicted a decrease in acetate degraders after a decrease to pH ≤ 6.5. Acidification had a sustained effect on the microbial community and process performance.

High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline “AcetoScan” presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.

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

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

Inoculum Source Determines Acetate and Lactate Production during Anaerobic Digestion of Sewage Sludge and Food Waste

Acetate production from food waste or sewage sludge was evaluated in four semi-continuous anaerobic digestion processes. To examine the importance of inoculum and substrate for acid production, two different inoculum sources (a wastewater treatment plant (WWTP) and a co-digestion plant treating food and industry waste) and two common substrates (sewage sludge and food waste) were used in process operations. The processes were evaluated with regard to the efficiency of hydrolysis, acidogenesis, acetogenesis, and methanogenesis and the microbial community structure was determined. Feeding sewage sludge led to mixed acid fermentation and low total acid yield, whereas feeding food waste resulted in the production of high acetate and lactate yields. Inoculum from WWTP with sewage sludge substrate resulted in maintained methane production, despite a low hydraulic retention time. For food waste, the process using inoculum from WWTP produced high levels of lactate (30 g/L) and acetate (10 g/L), while the process initiated with inoculum from the co-digestion plant had higher acetate (25 g/L) and lower lactate (15 g/L) levels. The microbial communities developed during acid production consisted of the major genera Lactobacillus (92–100%) with food waste substrate, and Roseburia (44–45%) and Fastidiosipila (16–36%) with sewage sludge substrate. Use of the outgoing material (hydrolysates) in a biogas production system resulted in a non-significant increase in bio-methane production (+5–20%) compared with direct biogas production from food waste and sewage sludge.

The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei

Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a > 5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical phosphate starvation control.

Volatile fatty acids production via mixed culture fermentation: Revealing the link between pH, inoculum type and bacterial composition

The aim of the study was to investigate the effects of operational parameters, inoculum type and bacterial community on mixed culture fermentation to produce one dominant acid type in the mixture of volatile fatty acids (VFA). The study was performed using three different inocula (large&small granular and slurry) with glucose under various initial pH. The VFA production efficiency reached to 0,97 (gCOD/gSCOD) by granular sludge. VFA composition was changed by initial pH: in neutral conditions, acetic acid; in acidic conditions, acetic and butyric acids, in alkali conditions butyric acid were dominated, respectively. The VFA production was positively affected by the high relative abundance of Firmicutes. On the contrary, a negative correlation was seen between VFA production and the relative abundance of Chloroflexi. The results revealed the physical sludge structure of inoculum was the key factor for production efficiency, whereas, pH was the most important parameter to affect VFA composition.

Effects of thermal hydrolytic pre-treatment on biogas process efficiency and microbial community structure in industrial- and laboratory-scale digesters

This study examined the impact of thermal hydrolysis process (THP) pre-treatment on anaerobic co-digestion of wastewater sludge and household waste and assessed whether THP was vital to achieve higher process capacity. Performance data were collected for both industrial- and laboratory-scale digesters and response in microbial community structure was evaluated by Illumina sequencing. Implementation of THP at the industrial-scale plant increased methane yield by 15% and enhanced substrate degradability. Possibility to extend the sludge retention time due to a higher solid content of the substrate, sanitisation of the digestate and improved fertiliser quality of the digestate were other industrial-scale benefits of THP installation. Continuously-fed laboratory-scale digesters were fed THP-treated or untreated substrate at an organic loading rate (OLR) of 5 g volatile solid (VS)/L/day, a feeding rate necessary at the corresponding industrial-scale plant to meet the estimated population increase within the municipality. The results indicated that the plant could have increased the capacity with unimpaired stability independently of THP installation, even though the retention time was significantly shortened during operation with untreated substrate. Microbial community analyses revealed increased contribution of the Clostridia class after THP installation in industrial-scale digesters and positive correlation between Firmicutes:Bacteriodetes and methane yield in all digesters. Differentiated profiles in laboratory-scale digesters indicated that a temperature increase from 37 to 42 °C in association with THP installation and altered substrate composition were strong determining factors shaping the microbial community. Overall, these findings can assist industrial-scale plants in choosing management strategies aimed at improving the efficiency of anaerobic digestion processes.

Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers

Syntrophic acetate oxidation (SAO) plays a pivotal role in biogas production processes when aceticlastic methanogens are inhibited. Despite the importance of SAO, the metabolic interactions and syntrophic growth of the organisms involved are still poorly understood. Therefore, we studied growth parameters and interactions within constructed defined cocultures comprising the methanogen Methanoculleus bourgensis and one, or several, of the syntrophic acetate oxidizers Syntrophaceticus schinkii, [ Clostridium] ultunense, and Tepidanaerobacter acetatoxydans and a novel, uncharacterized bacterium. Cultivation experiments in a design-of-experiment approach revealed positive effects on methane production rate of increased ammonium levels (up to 0.2 M), temperature (up to 45 °C), and acetate concentrations (0.15-0.30 M). Molecular analyses and thermodynamic calculations demonstrated close interlinkages between the microorganisms, with available energies of -10 kJ/mol for acetate oxidation and -20 kJ/mol for hydrogenotrophic methanogenesis. The estimated generation time varied between 3 and 20 days for all syntrophic microorganisms involved, and the acetate minimum threshold level was 0.40-0.45 mM. The rate of methanogenesis depended on the SAO bacteria present in the culture. These data are beneficial for interpretation of SAO prevalence and competiveness against aceticlastic methanogens in anaerobic environments.

Sulfide level in municipal sludge digesters affects microbial community response to long-chain fatty acid loads

BACKGROUND

Waste lipids are attractive substrates for co-digestion with primary and activated sewage sludge (PASS) to improve biogas production at wastewater treatment plants. However, slow conversion rates of long-chain fatty acids (LCFA), produced during anaerobic digestion (AD), limit the applicability of waste lipids as co-substrates for PASS. Previous observations indicate that the sulfide level in PASS digesters affects the capacity of microbial communities to convert LCFA to biogas. This study assessed the microbial community response to LCFA loads in relation to sulfide level during AD of PASS by investigating process performance and microbial community dynamics upon addition of oleate (C_18:1) and stearate (C_18:0) to PASS digesters at ambient and elevated sulfide levels.

RESULTS

Conversion of LCFA to biogas was limited (30% of theoretical biogas potential) during continuous co-digestion with PASS, which resulted in further LCFA accumulation. However, the accumulated LCFA were converted to biogas (up to 66% of theoretical biogas potential) during subsequent batch-mode digestion, performed without additional substrate load. Elevated sulfide level stimulated oleate (but not stearate) conversion to acetate, but oleate and sulfide imposed a synergistic limiting effect on acetoclastic methanogenesis and biogas formation. Next-generation sequencing of 16S rRNA gene amplicons of bacteria and archaea showed that differences in sulfide level and LCFA type resulted in microbial community alterations with distinctly different patterns. Taxonomic profiling of the sequencing data revealed that the phylum Cloacimonetes is likely a key group during LCFA degradation in PASS digesters, where different members take part in degradation of saturated and unsaturated LCFA; genus W5 (family Cloacimonadaceae) and family W27 (order Cloacimonadales), respectively. In addition, LCFA-degrading Syntrophomonas, which is commonly present in lipid-fed digesters, increased in relative abundance after addition of oleate at elevated sulfide level, but not without sulfide or after stearate addition. Stearate conversion to biogas was instead associated with increasing abundance of hydrogen-producing Smithella and hydrogenotrophic Methanobacterium.

CONCLUSIONS

Long-chain fatty acid chain saturation and sulfide level are selective drivers for establishment of LCFA-degrading microbial communities in municipal sludge digesters.

AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood-Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.

Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD.

Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria

Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) that are found in engineered biogas processes operating with high ammonia concentrations. It has been proven to oxidise acetate in cooperation with hydrogenotrophic methanogens. There is evidence that the Wood-Ljungdahl (WL) pathway plays an important role in acetate oxidation. In this study, we analysed the physiological and metabolic capacities of C. ultunense strain Esp and strain BS^T on genome scale and conducted a comparative study of all the known characterised SAOB, namely Syntrophaceticus schinkii, Thermacetogenium phaeum, Tepidanaerobacter acetatoxydans, and Pseudothermotoga lettingae. The results clearly indicated physiological robustness to be beneficial for anaerobic digestion environments and revealed unexpected metabolic diversity with respect to acetate oxidation and energy conservation systems. Unlike S. schinkii and Th. phaeum, C. ultunense clearly does not employ the oxidative WL pathway for acetate oxidation, as its genome (and that of P. lettingae) lack important key genes. In both of those species, a proton motive force is likely formed by chemical protons involving putative electron-bifurcating [Fe-Fe] hydrogenases rather than proton pumps. No genes encoding a respiratory Ech (energy-converting hydrogenase), as involved in energy conservation in Th. phaeum and S. schinkii, were identified in C. ultunense and P. lettingae. Moreover, two respiratory complexes sharing similarities to the proton-translocating ferredoxin:NAD⁺ oxidoreductase (Rnf) and the Na⁺ pumping NADH:quinone hydrogenase (NQR) were predicted. These might form a respiratory chain that is involved in the reduction of electron acceptors rather than protons. However, involvement of these complexes in acetate oxidation in C. ultunense and P. lettingae needs further study. This genome-based comparison provides a solid platform for future meta-proteomics and meta-transcriptomics studies and for metabolic engineering, control, and monitoring of SAOB.

Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches

To enrich syntrophic acetate‐oxidizing bacteria (SAOB), duplicate chemostats were inoculated with sludge from syntrophic acetate oxidation (SAO)‐dominated systems and continuously supplied with acetate (0.4 or 7.5 g l⁻¹) at high‐ammonia levels. The chemostats were operated under mesophilic (37°C) or thermophilic (52°C) temperature for about six hydraulic retention times (HRT 28 days) and were sampled over time. Irrespective of temperature, a methane content of 64–69% and effluent acetate level of 0.4–1.0 g l⁻¹ were recorded in chemostats fed high acetate. Low methane production in the low‐acetate chemostats indicated that the substrate supply was below the threshold for methanization of acetate via SAO. Novel representatives within the family Clostridiales and genus Syntrophaceticus (class Clostridia) were identified to represent putative SAOB candidates in mesophilic and thermophilic conditions respectively. Known SAOB persisted at low relative abundance in all chemostats. The hydrogenotrophic methanogens Methanoculleus bourgensis (mesophilic) and Methanothermobacter thermautotrophicus (thermophilic) dominated archaeal communities in the high‐acetate chemostats. In line with the restricted methane production in the low‐acetate chemostats, methanogens persisted at considerably lower abundance in these chemostats. These findings strongly indicate involvement in SAO and tolerance to high ammonia levels of the species identified here, and have implications for understanding community function in stressed anaerobic processes.

Importance of inoculum source and initial community structure for biogas production from agricultural substrates

This study evaluated the importance of inoculum source for start-up and operation of biogas processes. Three different inocula with different community structure were used to initiate six laboratory continuous stirred tank reactor (CSTR) processes operated with a grass manure mixture as substrate. The processes were evaluated by chemical and microbiological analysis, by targeting the overall bacterial community and potential cellulose-degrading bacteria. As expected, the results showed a large difference in community structure in the inocula and in process performance during the first hydraulic retention time (HRT). However, the performance and overall microbial community structure became similar in the reactors over time. An inoculum from a high-ammonia process, characterized by low diversity and low degradation efficiency, took the longest time to reach stability and final methane yield. The overall bacterial community was mainly shaped by the operating conditions but, interestingly, potential cellulose-degrading bacteria seemed mainly to originate from the substrate.

Comparative characterization of digestate versus pig slurry and cow manure - Chemical composition and effects on soil microbial activity

The growing number of biogas plants in Europe has resulted in increased production of nutrient-rich digestate with great potential as fertilizer for arable land. The nutrient composition of digestate varies with the substrate treated in the biogas plant and may contain compounds that stimulate or inhibit soil microbial activity. This study compared 20 digestates (D) with 10 pig slurries (PS) and 10 cow manures (CM) regarding their chemical content and their effect on soil microbial activities, i.e. potential ammonia oxidation rate (PAO) and soil respiration. The results showed no significant differences within the D group when divided based on substrate type. i.e. manure dominated vs. other organic waste materials in any of the tests. In general D contained significantly higher concentrations of ammonium while the concentrations of total carbon and volatile fatty acids were higher in PS and CM than in D. The D showed both stimulating and inhibiting effects on PAO, while all CM and all PS except one showed inhibiting effects on PAO. However, PAO activity was negatively correlated with the content of volatile fatty acids in the residues indicating that these compounds may be the cause of the inhibition. The maximum respiration activity (h_peakmax) was lower and the time point for the maximum respiration activity (t_peakmax) occurred earlier for D compared with CM and PS. This earlier peak time could be indicative of a high proportion of easily degradable carbon in D compared with PS and CM. However, the utilization rate of carbon, i.e. the proportion of added organic C converted to CO₂-C during 12days, did not differ significantly between D, PS and CM, indicating that overall carbon quality in the different fertilizers was still roughly comparable. In short, our results suggest that digestates were different compared with PS and CM but without posing a higher risk with respect to their impact on soil microbial activity.

Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure

Methane (CH₄) is produced as an end product from feed fermentation in the rumen. Yield of CH₄ varies between individuals despite identical feeding conditions. To get a better understanding of factors behind the individual variation, 73 dairy cows given the same feed but differing in CH₄ emissions were investigated with focus on fiber digestion, fermentation end products and bacterial and archaeal composition. In total 21 cows (12 Holstein, 9 Swedish Red) identified as persistent low, medium or high CH₄ emitters over a 3 month period were furthermore chosen for analysis of microbial community structure in rumen fluid. This was assessed by sequencing the V4 region of 16S rRNA gene and by quantitative qPCR of targeted Methanobrevibacter groups. The results showed a positive correlation between low CH₄ emitters and higher abundance of Methanobrevibacter ruminantium clade. Principal coordinate analysis (PCoA) on operational taxonomic unit (OTU) level of bacteria showed two distinct clusters (P < 0.01) that were related to CH₄ production. One cluster was associated with low CH₄ production (referred to as cluster L) whereas the other cluster was associated with high CH₄ production (cluster H) and the medium emitters occurred in both clusters. The differences between clusters were primarily linked to differential abundances of certain OTUs belonging to Prevotella. Moreover, several OTUs belonging to the family Succinivibrionaceae were dominant in samples belonging to cluster L. Fermentation pattern of volatile fatty acids showed that proportion of propionate was higher in cluster L, while proportion of butyrate was higher in cluster H. No difference was found in milk production or organic matter digestibility between cows. Cows in cluster L had lower CH₄/kg energy corrected milk (ECM) compared to cows in cluster H, 8.3 compared to 9.7 g CH₄/kg ECM, showing that low CH₄ cows utilized the feed more efficient for milk production which might indicate a more efficient microbial population or host genetic differences that is reflected in bacterial and archaeal (or methanogens) populations.

Effect of Nickel Levels on Hydrogen Partial Pressure and Methane Production in Methanogens

Hydrogen (H₂) consumption and methane (CH₄) production in pure cultures of three different methanogens were investigated during cultivation with 0, 0.2 and 4.21 μM added nickel (Ni). The results showed that the level of dissolved Ni in the anaerobic growth medium did not notably affect CH₄ production in the cytochrome-free methanogenic species Methanobacterium bryantii and Methanoculleus bourgensis MAB1, but affected CH₄ formation rate in the cytochrome-containing Methanosarcina barkeri grown on H₂and CO₂. Methanosarcina barkeri also had the highest amounts of Ni in its cells, indicating that more Ni is needed by cytochrome-containing than by cytochrome-free methanogenic species. The concentration of Ni affected threshold values of H₂ partial pressure (pH₂) for all three methanogen species studied, with M. bourgensis MAB1 reaching pH₂ values as low as 0.1 Pa when Ni was available in amounts used in normal anaerobic growth medium. To our knowledge, this is the lowest pH₂ threshold recorded to date in pure methanogen culture, which suggests that M.bourgensis MAB1 have a competitive advantage over other species through its ability to grow at low H₂ concentrations. Our study has implications for research on the H₂-driven deep subsurface biosphere and biogas reactor performance.

Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii

Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F1F0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome limiting bioenergetic barriers, and drive efficient energy conservation from reactions operating close to the thermodynamic equilibrium, which might enable S. schinkii to occupy the same niche as the aceticlastic methanogens. The knowledge gained here will help specify process conditions supporting efficient and robust biogas production and will help identify mechanisms important for the syntrophic lifestyle.

Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB)

Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of mesophilic acetate-oxidising bacteria, a syntrophic relationship operating close to the thermodynamic equilibrium and of considerable importance in ammonia-rich engineered biogas processes. Methanoculleus bourgensis strain MAB1 belongs to the order Methanomicrobiales, family Methanomicrobiaceae, within the phylum Euryarchaeota. The genome shows a total size of 2,859,299 bp encoding 3450 predicted protein-encoding genes, of which only 1472 (43 %) have been assigned tentative functions. The genome encodes further 44 tRNA genes and three rRNA genes (5S, 16S and 23S rRNA). This study presents assembling and annotation features as well as genomic traits related to ammonia tolerance and methanogenesis.

Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust

The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens. The symbiotic cooperation between anaerobic fungi and methanogens in the rumen enhance the metabolic rate and growth of both. Methanogens and other hydrogen-consuming anaerobic archaea are known from subseafloor basalt; however, the abiotic production of hydrogen is questioned to be sufficient to support such communities. Alternatively, biologically produced hydrogen could serve as a continuous source. Here, we propose anaerobic fungi as a source of bioavailable hydrogen in the oceanic crust, and a close interplay between anaerobic fungi and hydrogen-driven prokaryotes.

Ammonia threshold for inhibition of anaerobic digestion of thin stillage and the importance of organic loading rate

Biogas production from nitrogen-rich feedstock results in release of ammonia (NH3), causing inhibition of the microbial process. The reported threshold ammonia value for stable biogas production varies greatly between studies, probably because of differences in operating conditions. Moreover, it is often difficult to separate the effect of ammonia inhibition from that of organic loading rate (OLR), as these two factors are often interrelated. This study attempted to distinguish the effects of ammonia and OLR by analysis of two laboratory-scale biogas reactors operating with thin stillage and subjected to an increase in free ammonia (from 0.30 to 1.1 g L(-1)) either by addition of an external nitrogen source (urea) or by increasing the OLR (3.2-6.0 g volatile solids L(-1) d(-1)). The results showed that ammonia concentration was detrimental for process performance, with the threshold for stability in both processes identified as being about 1 g NH3-N L(-1), irrespective of OLR. Analysis of the methanogenic community showed limited differences between the two reactors on order level and a clear increase in the abundance of Methanomicrobiales, particularly Methanoculleus sp., in response to increasing ammonia concentration. Further comprehensive molecular analysis revealed that diverse Methanoculleus species dominated in the reactors at a given ammonia level at different OLR. The acetogenic community was clearly affected by both ammonia concentration and OLR, suggesting that the volatile fatty acid load in relation to the higher OLR was important for the dynamics of this community.

Biogas Production: Microbiology and Technology

Biogas, containing energy-rich methane, is produced by microbial decomposition of organic material under anaerobic conditions. Under controlled conditions, this process can be used for the production of energy and a nutrient-rich residue suitable for use as a fertilising agent. The biogas can be used for production of heat, electricity or vehicle fuel. Different substrates can be used in the process and, depending on substrate character, various reactor technologies are available. The microbiological process leading to methane production is complex and involves many different types of microorganisms, often operating in close relationships because of the limited amount of energy available for growth. The microbial community structure is shaped by the incoming material, but also by operating parameters such as process temperature. Factors leading to an imbalance in the microbial community can result in process instability or even complete process failure. To ensure stable operation, different key parameters, such as levels of degradation intermediates and gas quality, are often monitored. Despite the fact that the anaerobic digestion process has long been used for industrial production of biogas, many questions need still to be resolved to achieve optimal management and gas yields and to exploit the great energy and nutrient potential available in waste material. This chapter discusses the different aspects that need to be taken into consideration to achieve optimal degradation and gas production, with particular focus on operation management and microbiology.

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.

Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria

BACKGROUND

Syntrophic acetate oxidation (SAO) is the predominant pathway for methane production in high ammonia anaerobic digestion processes. The bacteria (SAOB) occupying this niche and the metabolic pathway are poorly understood. Phylogenetic diversity and strict cultivation requirements hinder comprehensive research and discovery of novel SAOB. Most SAOB characterised to date are affiliated to the physiological group of acetogens. Formyltetrahydrofolate synthetase is a key enzyme of both acetogenic and SAO metabolism. The encoding fhs gene has therefore been identified as a suitable functional marker, using a newly designed primer pair. In this comparative study, we used a combination of terminal restriction fragment length polymorphism profiling, clone-based comparison, qPCR and Illumina amplicon sequencing to assess the bacterial community and acetogenic sub-community prevailing in high- and low-ammonia laboratory-scale digesters in order to delineate potential SAOB communities. Potential candidates identified were further tracked in a number of low-ammonia and high-ammonia laboratory-scale and large-scale digesters in order to reveal a potential function in SAO.

RESULTS

All methodical approaches revealed significant changes in the bacterial community composition concurrently with increasing ammonia and predominance of SAO. The acetogenic community under high ammonia conditions was revealed to be generally heterogeneous, but formed distinct phylogenetic clusters. The clusters differed clearly from those found under low-ammonia conditions and represented an acetogenic assemblage unique for biogas processes and recurring in a number of high-ammonia processes, indicating potential involvement in SAO.

CONCLUSIONS

The phylogenetic affiliation and population dynamics observed point to a key community, belonging mainly to the Clostridia class, in particular to the orders Clostridiales and Thermoanaerobacterales, which appear to specialise in SAO rather than being metabolically versatile. Overall, the results reported here provide evidence of functional importance of the bacterial families identified in high-ammonia systems and extend existing knowledge of bacterial and acetogenic assemblages at low and high ammonia levels. This information will be of help in monitoring and assessing the impacts on the SAOB community in order to identify characteristics of robust and productive high ammonia biogas processes.

Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3

Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belonging to the Clostridia class within the phylum Firmicutes, originally isolated from a mesophilic methanogenic digester. It has been shown to oxidize acetate in co-cultivation with hydrogenotrophic methanogens forming methane. The draft genome shows a total size of 3,196,921 bp, encoding 3,688 open reading frames, which includes 3,445 predicted protein-encoding genes and 55 RNA genes. Here, we are presenting assembly and annotation features as well as basic genomic properties of the type strain Sp3.

Trace element and temperature effects on microbial communities and links to biogas digester performance at high ammonia levels

BACKGROUND

High levels of ammonia and the presence of sulphide have major impacts on microbial communities and are known to cause operating problems in anaerobic degradation of protein-rich material. Operating strategies that can improve process performance in such conditions have been reported. The microbiological impacts of these are not fully understood, but their determination could help identify important factors for balanced, efficient operation. This study investigated the correlations between microbial community structure, operating parameters and digester performance in high-ammonia conditions.

METHOD

Continuous anaerobic co-digestion of household waste and albumin was carried out in laboratory-scale digesters at high ammonia concentrations (0.5-0.9 g NH3/L). The digesters operated for 320 days at 37 or 42 °C, with or without addition of a trace element mixture including iron (TE). Abundance and composition of syntrophic acetate-oxidising bacteria (SAOB) and of methanogenic and acetogenic communities were investigated throughout the study using 16S rRNA and functional gene-based molecular methods.

RESULTS

Syntrophic acetate oxidation dominated methane formation in all digesters, where a substantial enhancement in digester performance and influence on microbial community by addition of TE was shown dependent on temperature. At 37 °C, TE addition supported dominance and strain richness of Methanoculleus bourgensis and altered the acetogenic community, whereas the same supplementation at 42 °C had a low impact on microbial community structure. Both with and without TE addition operation at 42 °C instead of 37 °C had low impact on digester performance, but considerably restricted acetogenic and methanogenic community structure, evenness and richness. The abundance of known SAOB was higher in digesters without TE addition and in digesters operating at 42 °C. No synergistic effect on digester performance or microbial community structure was observed on combining increased temperature with TE addition.

CONCLUSIONS

Our identification of prominent populations related to enhanced performance within methanogenic (high dominance and richness of M. bourgensis) and acetogenic communities are valuable for continued research and engineering to improve methane production in high-ammonia conditions. We also show that a temperature increase of only 5 °C within the mesophilic range results in an extreme dominance of one or a few species within these communities, independent of TE addition. Furthermore, functional stable operation was possible despite low microbial temporal dynamics, evenness and richness at the higher temperature.

Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice

Atmospheric methane is the second most important greenhouse gas after carbon dioxide, and is responsible for about 20% of the global warming effect since pre-industrial times. Rice paddies are the largest anthropogenic methane source and produce 7-17% of atmospheric methane. Warm waterlogged soil and exuded nutrients from rice roots provide ideal conditions for methanogenesis in paddies with annual methane emissions of 25-100-million tonnes. This scenario will be exacerbated by an expansion in rice cultivation needed to meet the escalating demand for food in the coming decades. There is an urgent need to establish sustainable technologies for increasing rice production while reducing methane fluxes from rice paddies. However, ongoing efforts for methane mitigation in rice paddies are mainly based on farming practices and measures that are difficult to implement. Despite proposed strategies to increase rice productivity and reduce methane emissions, no high-starch low-methane-emission rice has been developed. Here we show that the addition of a single transcription factor gene, barley SUSIBA2 (refs 7, 8), conferred a shift of carbon flux to SUSIBA2 rice, favouring the allocation of photosynthates to aboveground biomass over allocation to roots. The altered allocation resulted in an increased biomass and starch content in the seeds and stems, and suppressed methanogenesis, possibly through a reduction in root exudates. Three-year field trials in China demonstrated that the cultivation of SUSIBA2 rice was associated with a significant reduction in methane emissions and a decrease in rhizospheric methanogen levels. SUSIBA2 rice offers a sustainable means of providing increased starch content for food production while reducing greenhouse gas emissions from rice cultivation. Approaches to increase rice productivity and reduce methane emissions as seen in SUSIBA2 rice may be particularly beneficial in a future climate with rising temperatures resulting in increased methane emissions from paddies.