Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions--II: Microbial population dynamics

Microbial population dynamics were evaluated in anaerobic codigesters treating municipal solid waste and sewage sludge. Ribosomal RNA based oligonucleotide probes were used to characterize changes in population abundance of syntrophic volatile fatty acid degrading bacteria and methanogens. Changes in community structure were linked to traditional performance parameters during the recovery of previously unstable codigesters induced by a reduction in mixing levels. Methanosarcina spp. were the most abundant aceticlastic methanogens in unstable codigesters with high acetate concentrations, while Methanosaeta concilii was dominant in stable systems with low levels of acetate. Growth of Syntrophobacter wolinii was enhanced during stabilization of a codigester with a well-developed population of Methanobacteriaceae, possibly because the presence of adequate numbers of these hydrogenotrophic methanogens encouraged the syntrophic oxidation of propionate. Mesophilic saturated fatty acid beta-oxidizing syntrophs were most abundant in previously unstable codigesters. One minimally mixed reactor became unstable after switching to continuously mixed conditions. After the switch, total archaeal abundance decreased sharply, though Methanobacteriaceae and Methanosarcina spp. levels increased as the fermentation became unbalanced. Based on the results presented here, mixing appears to inhibit the syntrophic oxidation of volatile fatty acids, possibly by disrupting the spatial juxtaposition of syntrophic bacteria and their methanogenic partners.

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom

Archaea are common constituents of the gut microbiome of humans, ruminants, and termites but little is known about their diversity and abundance in other animals. Here, we analyse sequencing and quantification data of archaeal and bacterial 16S rRNA genes from 250 species of animals covering a large taxonomic spectrum. We detect the presence of archaea in 175 animal species belonging to invertebrates, fish, amphibians, birds, reptiles and mammals. We identify five dominant gut lineages, corresponding to Methanobrevibacter, Methanosphaera, Methanocorpusculum, Methanimicrococcus and "Ca. Methanomethylophilaceae". Some archaeal clades, notably within Methanobrevibacter, are associated to certain hosts, suggesting specific adaptations. The non-methanogenic lineage Nitrososphaeraceae (Thaumarchaeota) is frequently present in animal samples, although at low abundance, but may have also adapted to the gut environment. Host phylogeny, diet type, fibre content, and intestinal tract physiology are major drivers of the diversity and abundance of the archaeome in mammals. The overall abundance of archaea is more influenced by these factors than that of bacteria. Methanogens reducing methyl-compounds with H2 can represent an important fraction of the overall methanogens in many animals. Together with CO2-reducing methanogens, they are influenced by diet and composition of gut bacteria. Our results provide key elements toward our understanding of the ecology of archaea in the gut, an emerging and important field of investigation.

Improved methane production from sugarcane vinasse with filter cake in thermophilic UASB reactors, with predominance of Methanothermobacter and Methanosarcina archaea and Thermotogae bacteria

Biogas production from sugarcane vinasse has enormous economic, energy, and environmental management potential. However, methane production stability and biodigested vinasse quality remain key issues, requiring better nutrient and alkalinity availability, operational strategies, and knowledge of reactor microbiota. This study demonstrates increased methane production from vinasse through the use of sugarcane filter cake and improved effluent recirculation, with elevated organic loading rates (OLR) and good reactor stability. We used UASB reactors in a two-stage configuration, with OLRs up to 45gCODL^-1d^-1, and obtained methane production as high as 3LL^-1d^-1. Quantitative PCR indicated balanced amounts of bacteria and archaea in the sludge (10⁹-10¹⁰copiesg^-1VS), and of the predominant archaea orders, Methanobacteriales and Methanosarcinales (10⁶-10⁸copiesg^-1VS). 16S rDNA sequencing also indicated the thermophilic Thermotogae as the most abundant class of bacteria in the sludge.

The physiology of trace elements in biological methane production

Trace element (TE) requirements of Methanothermobacter okinawensis and Methanothermobacter marburgensis were examined in silico, and using closed batch and fed-batch cultivation experiments. In silico analysis revealed genomic differences among the transport systems and enzymes related to the archaeal Wood-Ljungdahl pathway of these two methanogens. M. okinawensis responded to rising concentrations of TE by increasing specific growth rate (µ) and volumetric productivity (MER) during closed batch cultivation, and can grow and produce methane (CH₄) during fed-batch cultivation. M. marburgensis showed higher µ and MER during fed-batch cultivation and was therefore prioritized for subsequent optimization of CO₂-based biological CH₄ production. Multiple-parameter cultivation dependency on growth and productivity of M. marburgensis was finally examined using exponential fed-batch cultivation at different medium-, TE- and sulphide dilution rates, and different gas inflow rates. MER of 476mmolL^-1h^-1 and µ of 0.69h^-1 were eventually obtained during exponential fed-batch cultivations employing M. marburgensis.

Anaerobic co-digestion of three commercial bio-plastic bags with food waste: Effects on methane production and microbial community structure

The emergence of bioplastic bags as a replacement for traditional petroleum-based plastic bags is promising for their simultaneous anaerobic digestion with food waste. In this study, the degradation of three bioplastic bags is evaluated during anaerobic co-digestion with food waste under mesophilic/thermophilic conditions, and the results indicated PBAT/PLA/starch > PLA > PBAT for methane production rate. The PBAT/PLA/starch mixture produced 23.4 ml/g of methane at 55 °C, and the cumulative methane production increased by 28.4 % compared to the control. In addition, the lag time before methane production was reduced by one to four days when anaerobic co-digestion was performed under thermophilic conditions, and the conversion of the bioplastics improved by 9.11-11.2 %. Microscopy further showed obvious physical degradation of the PBAT/PLA/starch material. The FTIR analysis showed that the characteristic peaks of the material at 3320, 2957, and 934 cm^-1 decreased significantly after anaerobic fermentation. The biodegradability of the polymer decreased with an increase in the content of the crystalline area in the structure. The addition of a comonomer reduced the crystallinity of the polymer. In addition, the biodegradability was increased by adjusting the hydrolysis reaction and microbial activity of the polymer surface. An analysis of the structural features of the microbial communities revealed that Archaea exhibited different biodiversity at distinct temperatures. In particular, under thermophilic conditions, the relative abundance of Methanothermobacter was 56.0 %, and it plays an important role in the anaerobic degradation of PBAT/PLA/starch materials, while bacterial communities showed smaller differences. Overall, the bioplastic was able to be co-digested anaerobically with food waste to produce renewable energy. This study provides a plan for the practical application of biodegradable plastic bag collection for the combined treatment of food waste in anaerobic digesters. It provides a theoretical basis for modifications of bioplastic and domestication of anaerobic microorganisms.

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.

Characteristics of in-situ hydrogen biomethanation at mesophilic and thermophilic temperatures

In-situ hydrogen biomethanation is a promising technology to upgrade biogas. The efficiency of biomethanation relies on various parameters, e.g. gas supplement, temperature and hydrogenotrophic methanogens. Therefore, it is important to investigate the characteristics of in-situ hydrogen biomethanation under different conditions. In this study, two experiments (lasted for 91 days and 105 days) were carried out to investigate the impacts of feeding gas and operating conditions on performances of reactors and microorganisms. During the whole experiment, no obvious fluctuation of pH and limitation of gas-liquid mass transfer were found. Results showed that the hydrogenotrophic methanogenesis performed better at thermophilic condition, while the dominant archaea genera at mesophilic and thermophilic temperature was determined to be Methanobacterium and Methanothermobacter, respectively. The highest CH₄ content (greater than 90%) was obtained when H₂ and CO₂ was feeding at ratio of 4:1 and Methanothermobacter was dominant. These findings can provide useful information for promoting hydrogen biomethanation.

Characteristic archaebacterial 16S rRNA oligonucleotides

A method of analyzing 16S rRNA catalog data has been developed in which groupings at various taxonomic levels can be characterized in terms of specific "signature" oligonucleotides. This approach provides an alternative means for evaluating higher order branching possibilities and can be used to assess the phylogenetic position of isolates that are poorly placed by the usual clustering procedures. This signature approach has been applied to forty archaebacterial catalogs and every oligonucleotide with significant signature value has been identified. Sets of specific oligonucleotides were identified for every major group on a dendrogram produced by cluster analysis procedures. Signatures that would establish between group relationships were also sought and found. In the case of the Methanobacteriaceae the clustering methods suggest a specific relationship to the Methanococcaceae. This inclusion is in fact supported by six strong signature oligonucleotides. However there are also significant numbers of signature oligonucleotides supporting a specific relationship of the Methanobacteriaceae to either the Halobacteriaceae or the Methanomicrobiaceae. Thus the placement of the Methanobacteriaceae is less certain than the usual dendrograms imply. The signature approach also was used to assess the phylogenetic position of Thermoplasma acidophilum which is found to be more closely related to the methanogen/halophile Division than to the sulfur dependent Division of the archaebacteria. This does not imply however that Thermoplasma acidophilum is properly regarded as being in the methanogen/halophile Division.

Microbial ecology overview during anaerobic codigestion of dairy wastewater and cattle manure and use in agriculture of obtained bio-fertilisers

The anaerobic co-digestion of dairy wastewater (DW) and cattle manure (CM) was examined and associated with microbial community's structures using Denaturing Gradient Gel Electrophoresis (DGGE). The highest volatile solids (VS) reduction yield of 88.6% and biogas production of 0.87 L/g VS removed were obtained for the C/N ratio of 24.7 at hydraulic retention time (HRT) of 20 days. The bacterial DGGE profile showed significant abundance of Uncultured Bacteroidetes, Firmicutes and Synergistetes bacterium. The Syntrophomonas strains were discovered in dependent association to H2-using bacteria such as Methanospirillum sp., Methanosphaera sp. and Methanobacterium formicicum. These syntrophic associations are essential in anaerobic digesters allow them to keep low hydrogen partial pressure. However, high concentrations of VFA produced from dairy wastes acidification allow the growth of Methanosarcina species. The application of the stabilised anaerobic effluent on the agriculture soil showed significant beneficial effects on the forage corn and tomato plants growth and crops.

Long-term in situ bioelectrochemical monitoring of biohythane process: Metabolic interactions and microbial evolution

Microbial stability and evolution are a critical aspect for biosensors, especially in detecting dynamic and emerging anaerobic biohythane production. In this study, two upflow air-cathode chamber microbial fuel cells (UMFCs) were developed for in situ monitoring of the biohydrogen and biomethane reactors under a COD range of 1000-6000 mg/L and 150-1000 mg/L, respectively. Illumina MiSeq sequencing evidenced the dramatic shift of dominant microbial communities in UMFCs from hydrolytic and acidification bacteria (Clostridiaceae_1, Ruminococcaceae, Peptostreptococcaceae) to acetate-oxidizing bacteria (Synergistaceae, Dysgonomonadaceae, Spirochaetaceae). In addition, exoelectroactive bacteria evaluated from Enterobacteriaceae and Burkholderiaceae to Desulfovibrionaceae and Propionibacteriaceae. Especially, Hydrogenotrophic methanogens (Methanobacteriaceae) were abundant at 93.41% in UMFC (for monitoring hydrogen reactor), which was speculated to be a major metabolic pathway for methane production. Principal component analysis revealed a similarity in microbial structure between UMFCs and methane bioreactors. Microbial network analysis suggested a more stable community structure of UMFCs with 205 days' operation.

Syngas biomethanation: effect of biomass-gas ratio, syngas composition and pH buffer

The concept of syngas biomethanation is attractive, however, it still needs improvement in optimizing the operational conditions. In the present study, syngas fermentations under different carbon monoxide (CO), carbon dioxide (CO₂) and hydrogen (H₂) compositions were conducted under two different biomass-gas ratio (BGR) systems. The results showed that high BGR enhanced the CO consumption rate, achieving a 60% enhancement with CO as the sole substrate. Stoichiometric H₂ addition could successfully convert all the CO and CO₂ to pure methane, however, higher H₂ partial pressure might decline the CO consumption due to pH inhibition from consumption of bicarbonate. Microbial analysis showed different syngas composition could affect the bacteria community, while, archaea community was only slightly affected with Methanothermobacter as the dominant methanogen. This study provided strategy for efficient syngas biomethanation and deeper insight into effect of H₂ addition on CO conversion under different BGR systems.

Regulation of nitrite-dependent anaerobic methane oxidation bacteria by available phosphorus and microbial communities in lake sediments of cold and arid regions

As global anthropogenic nitrogen inputs continue to rise, nitrite-dependent anaerobic methane oxidation (N-DAMO) plays an increasingly significant role in CH4 consumption in lake sediments. However, there is a dearth of knowledge regarding the effects of anthropogenic activities on N-DAMO bacteria in lakes in the cold and arid regions. Sediment samples were collected from five sampling areas in Lake Ulansuhai at varying depth ranges (0-20, 20-40, and 40-60 cm). The ecological characterization and niche differentiation of N-DAMO bacteria were investigated using bioinformatics and molecular biology techniques. Quantitative PCR confirmed the presence of N-DAMO bacteria in Lake Ulansuhai sediments, with 16S rRNA gene abundances ranging from 1.72 × 104 to 5.75 × 105 copies·g-1 dry sediment. The highest abundance was observed at the farmland drainage outlet with high available phosphorus (AP). Anthropogenic disturbances led to a significant increase in the abundance of N-DAMO bacteria, though their diversity remained unaffected. The heterogeneous community of N-DAMO bacteria was affected by interactions among various environmental characteristics, with AP and oxidation-reduction potential identified as the key drivers in this study. The Mantel test indicated that the N-DAMO bacterial abundance was more readily influenced by the presence of the denitrification genes (nirS and nirK). Network analysis revealed that the community structure of N-DAMO bacteria generated numerous links (especially positive links) with microbial taxa involved in carbon and nitrogen cycles, such as methanogens and nitrifying bacteria. In summary, N-DAMO bacteria exhibited sensitivity to both environmental and microbial factors under various human disturbances. This study provides valuable insights into the distribution patterns of N-DAMO bacteria and their roles in nitrogen and carbon cycling within lake ecosystems.

Combining a robust thermophilic methanogen and packing material with high liquid hold-up to optimize biological methanation in trickle-bed reactors

The hydrogen gas-to-liquid mass transfer is the limiting factor in biological methanation. In trickle-bed reactors, mass transfer can be increased by high flow velocities in the liquid phase, by adding a packing material with high liquid hold-up or by using methanogenic archaea with a high methane productivity. This study developed a polyphasic approach to address all methods at once. Various methanogenic strains and packings were investigated from a microbial and hydrodynamic perspective. Analyzing the ability to produce high-quality methane and to form biofilms, pure cultures of Methanothermobacter performed better than those of the genus Methanothermococcus. Liquid and static hold-up of a packing material and its capability to facilitate attachment was not attributable to a single property. Consequently, it is recommended to carefully match organism and packing for optimized performance of trickle-bed reactors. The ideal combination for the ORBIT-system was identified as Methanothermobacter thermoautotrophicus IM5 and DuraTop®.

Methane flux at the water-gas interface is influenced by complex interactions among phytoplankton, phosphorus inputs and methane-functional bacteria: A microcosm systems study

Phytoplankton affect carbon cycling and emissions in eutrophic reservoirs dramatically, but our knowledge about carbon emissions response to phytoplankton bloom and phosphorus enrichment is rather limited. Here we performed a microcosm experiment with five treatments to investigate how phytoplankton blooms and phosphorus addition will impact the carbon emissions and the methane-functional bacterial community. During the 43-day incubation, the CH4 and CO2 flux at the water-air interface in the five water columns fluctuated between 7.536 and 16.689 μmol and between 2788.501 and 4142.726 μmol, respectively. The flux of CH4 and CO2 during phytoplankton decay was 1.542 to 10.397 times and 4.203 to 8.622 times higher, respectively, compared to that during phytoplankton growth. Furthermore, exogenous phosphorus increases bloom biomass of phytoplankton and subsequent CH4 production, even with low nitrogen concentrations. The addition of 1 mg KH2PO4 resulted in a conservative increase of 0.0715 μmol in CH4 emission and 11.911 μmol in CO2 emission in the water column, respectively, compared to the in-situ water column. High throughput sequencing determined that hydrogenotrophic Methanoregula dominated methanogens (MPB) and Methylocystaceae dominated methanotrophs (MOB) in the sediment. Phosphorus inhibited the relative abundance of Methanoregula after incubation, resulting in a significant decrease. Real-time quantitative polymerase chain reaction indicated that the absolute abundance of MPB and MOB (i.e., the mcrA gene and the pmoA gene) in the sediments ranged from 5.1354E+06 to 6.3176E+07 copies·g-1 and 1.1656E+06 to 9.5056E+06 copies·g-1, respectively. The mcrA gene showed a preference for sediments with high organic carbon content. The effect of eutrophication on CH4 emissions is closely related to nutrient load and distinct niche of methane-functional bacteria.

Investigation of variations in microbial diversity in anaerobic reactors treating landfill leachate

A young landfill leachate containing elevated total ammonia concentrations frequently as high as 2,700 mg/l was anaerobically treated for 1,015 days in two different laboratory-scale anaerobic reactors configured as sludge blanket and hybrid bed. In this paper, the last 265 days of this long-term anaerobic treatability study are presented. Effects of high ammonia concentrations on reactor performances were correlated to the variations in microbial diversity by identifying the dominant microorganisms with FISH (fluorescent in-situ hybridization), cloning, DGGE (denaturing gradient gel electrophoresis) and morphological analysis. The results have indicated that the high ammonia landfill leachate can be treated successfully by using either an UASB or a hybrid bed reactor if temporary pH adjustments in the reactor influents are made when high ammonia concentrations are experienced. Consequently, COD removal efficiency is independent of microbial diversity and reactor configuration and it depends on the biodegradable portion of the leachate. Under this circumstance, stability of the reactors with low levels of acetate was supported by the abundance of Methanosaeta population. In both of the reactors, some populations of Methanobacteriaceae were also detected while other methanogenic species were virtually absent. However, after the termination of pH adjustment at Day 860, reactors immediately became unstable due to the sudden increase in free ammonia concentration up to 400 mg/l. COD removal efficiency decreased to 42% in the hybrid bed and to 48% in the UASB reactor. The durations of inhibitions were not long enough to severely deteriorate the massive Methanosaeta cells; therefore, many of them were again identified after two free ammonia inhibitions. However, subsequently, long filamentous morphologies of Methanosaeta cells shifted to shorter filaments and they lost their aggregating property.

Class III hybrid cluster protein homodimeric architecture shows evolutionary relationship with Ni, Fe-carbon monoxide dehydrogenases

Hybrid cluster proteins (HCPs) are Fe-S-O cluster-containing metalloenzymes in three distinct classes (class I and II: monomer, III: homodimer), all of which structurally related to homodimeric Ni, Fe-carbon monoxide dehydrogenases (CODHs). Here we show X-ray crystal structure of class III HCP from Methanothermobacter marburgensis (Mm HCP), demonstrating its homodimeric architecture structurally resembles those of CODHs. Also, despite the different architectures of class III and I/II HCPs, [4Fe-4S] and hybrid clusters are found in equivalent positions in all HCPs. Structural comparison of Mm HCP and CODHs unveils some distinct features such as the environments of their homodimeric interfaces and the active site metalloclusters. Furthermore, structural analysis of Mm HCP C67Y and characterization of several Mm HCP variants with a Cys67 mutation reveal the significance of Cys67 in protein structure, metallocluster binding and hydroxylamine reductase activity. Structure-based bioinformatics analysis of HCPs and CODHs provides insights into the structural evolution of the HCP/CODH superfamily.