Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an acidic West-Siberian peat bog

Microbial communities and functions are structured by vertical geochemical zones in a northern peatland

Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L-1. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm-3·d-1, while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.

Ectoine production from a novel bacterial strain and high-purity purification with a cost-effective and single-step method

This study marks the exploration into the production of ectoine, a valuable compound with significant potential as an antioxidant, osmoprotectant, anti-inflammatory agent, and stabilizer of cell membranes, proteins, and DNA integrity. Our focus centred on investigating the presence of ectoine and optimizing its production by the novel ectoine producer bacterial strain, Piscibacillus halophilus. For the optimization of ectoine production the effects of carbon and nitrogen sources, salt, pH, agitation and incubation period were optimized by one-factor-at-a-time. We started with an initial ectoine content of 46.92 mg/L, and through a series of optimization processes, we achieved a remarkable increase, resulting in an ectoine content of 1498.2 mg/L. The bacterial species P. halophilus achieved its highest ectoine production after 48 h of incubation, with conditions set at 10 % (w/v) salinity, pH of 7.50, and an agitation speed of 160 rpm. These precise conditions were found to be the most favourable for maximizing ectoine production by this strain. Besides, we have achieved successful purification of ectoine from the crude extract through a streamlined single-step process. This purification method has delivered an exceptional level of purity, surpassing 99.15 %, and an impressive yield of over 99 %. Importantly, we accomplished this using readily available and cost-effective strong acids (HCl) and strong bases (NaOH) to arrange pH gradients. The use of acid and base in the purification process of ectoine reflects an innovative and sustainable methodology.

Anaerobic methane oxidation is quantitatively important in deeper peat layers of boreal peatlands: Evidence from anaerobic incubations, in situ stable isotopes depth profiles, and microbial communities

Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is important for future climate predictions. Herein, we aimed to understand whether anaerobic methane oxidation (AMO) could explain the high CO2/CH4 anaerobic production ratios that are widely observed for the deeper peat layers of boreal peatlands. Furthermore, we quantified the metabolic pathways of methanogenesis to examine whether hydrogenotrophic methanogenesis is a dominant methane production pathway for the presumably recalcitrant deeper peat. To assess the CH4 cycling in deeper peat, we combined laboratory anaerobic incubations with a pathway-specific inhibitor, in situ depth patterns of stable isotopes in CH4, and 16S rRNA gene amplicon sequencing for three representative boreal peatlands in Western Siberia. We found up to a 69 % reduction in CH4 production due to AMO, which largely explained the high CO2/CH4 anaerobic production ratios and the in situ depth-related patterns of δ13C and δD in methane. The absence of acetate accumulation after inhibiting acetotrophic methanogenesis and the presence of sulfate- and nitrate-reducing anaerobic acetate oxidizers in the deeper peat indicated that these microorganisms use SO42- and NO3- as electron acceptors. Acetotrophic methanogenesis dominated net CH4 production in the deeper peat, accounting for 81 ± 13 %. Overall, anaerobic oxidation is quantitatively important for the methane cycle in the deeper layers of boreal peatlands, affecting both methane and its main precursor concentrations.

Responses of methane production and methanogenic pathways to polystyrene nanoplastics exposure in paddy soil

Nanoplastics (NPs) have attracted increasing attention within terrestrial ecosystems. However, our understanding of their impacts on the intricate anaerobic methanogenesis processes occurring in paddy soils microbial communities remains limited with respect to nanoplastics shape, function, and metabolic effects. Herein, we explored the effects of polystyrene nanoplastics (PS-NPs) and microplastics (PS-MPs) on anaerobic methanogenesis in a typical paddy soil. The results show that PS-NPs delayed methane production and the time to reach peak acetate content in incubation process of paddy soils, and the methanogenic rate increased rapidly after 13 days, with a maximum increase of 87.97%. However, PS-MPs had no marked effect on CH4, CO2 and acetate production. In addition, PS-NPs affected soil physicochemical properties by reducing pH and increasing electrical conductivity. Acetoclastic methanogens were enriched and the relative abundance of the genes ackA, pta, ACSS, cdhC, cdhD and cdhE in the acetoclastic pathways were significantly increased under PS-NPs exposure. In addition, PS-MPs had significant effect on the microbial community structure but no effect on methanogenic pathways of the paddy soils. This study provides important insights into the response of key microorganisms, functional genes and methanogenesis pathways to NPs during anaerobic methanogenesis in paddy soils.

Biological Activity of Poly(1,3-propanediol citrate) Films and Nonwovens: Mechanical, Thermal, Antimicrobial, and Cytotoxicity Studies

Polymers are of great interest for medical and cosmeceutical applications. The current trend is to combine materials of natural and synthetic origin in order to obtain products with appropriate mechanical strength and good biocompatibility, additionally biodegradable and bioresorbable. Citric acid, being an important metabolite, is an interesting substance for the synthesis of materials for biomedical applications. Due to the high functionality of the molecule, it is commonly used in biomaterials chemistry as a crosslinking agent. Among citric acid-based biopolyesters, poly(1,8-octanediol citrate) is the best known. It shows application potential in soft tissue engineering. This work focuses on a much less studied polyester, poly(1,3-propanediol citrate). Porous and non-porous materials based on the synthesized polyesters are prepared and characterized, including mechanical, thermal, and surface properties, morphology, and degradation. The main focus is on assessing the biocompatibility and antimicrobial properties of the materials.

Metatranscriptome revealed how carbon brush addition affected the fermentation of food wastewater in the low-temperature environment

Improving the anaerobic digestion (AD) performance in low-temperature environments has become a key factor in the development of waste treatment and resource recovery in cold regions. The utilization of external carriers to form a biofilm is the simplest and most practical way to enhance the psychrophilic AD performance in cold regions. In this study, the effect of carrier addition on the fermentation performance of low-temperature (15 ± 2 °C) food wastewater was investigated by forming biofilms with carbon brushes. The results showed that although the biofilm formation enhanced methane yields (15.24%), it also caused more accumulation of propionic acid (306.99-626.89 mg/L), and the concentration of acetic acid (86.78-254.71 mg/L) was relatively low. The microbial community revealed the highest abundance of the fermentative bacterium Firmicutes and the carbon brush carrier significantly increased its relative abundance (23.74%). Metatranscriptomic sequencing revealed that the abundance level of Clostridium, Bacteroides, Sedimentibacter and Pelotomaculum was the highest, reaching 80% in all groups. In addition, the abundance level of electroactive microorganisms in biofilms was higher, while the fermentation bacteria and methanogens were lower. This showed that biofilm can enrich more electroactive microorganisms, and granular sludge needs to enrich more fermentation bacteria and methanogens to ensure metabolic activity. Further studies have found that carbon metabolism had the highest activity (27.86%-30.39%) and H+-transporting ATPase (atp) was the most dominant functional enzyme (85.50%-86.65%) involved in electron transport in low-temperature fermentation of food wastewater. Interestingly, these expression levels of active granular sludge were higher than the biofilm formed by carbon brushes. Meanwhile, analysis of the methanogenic pathway found that active granular sludge tends to be directly metabolized to realize acetate to acetyl-CoA by acetyl-CoA synthetase (ACSS), while biofilms were not significantly different in the two metabolic pathways of acetate. These results deepen the understanding of treating low-temperature food wastewater.

Nitrification and urease inhibitors mitigate global warming potential and ammonia volatilization from urea in rice-wheat system in India: A field to lab experiment

The efficacy of alternative nitrogenous fertilizers for mitigating greenhouse gas and ammonia emissions from a rice-wheat cropping system in northern India was addressed in a laboratory incubation experiment using soil from a 10-year residue management field experiment (crop residue removal, CRR, vs. incorporation, CRI). Neem coated urea (NCU), standard urea (U), urea ammonium sulfate (UAS), and two alternative fertilizers, urea + urease inhibitor NBPT (UUI) and urea + urease inhibitor NBPT + nitrification inhibitor DMPSA (UUINI) were compared to non-fertilized controls for four weeks in incubation under anaerobic condition. Effects of fertilizers on global warming potential (GWP) and ammonia volatilization were dependent on residue treatment. Relative to standard urea, NCU reduced GWP by 11 % in CRI but not significantly in CRR; conversely, UAS reduced GWP by 12 % in CRR but not significantly in CRI. UUI and UUINI reduced GWP in both residue treatments and were more effective in CRI (21 % and 26 %) than CRR (15 % and 14 %). Relative to standard urea, NCU increased ammonia volatilization by 8 % in CRI but not significantly in CRR. Ammonia volatilization was reduced most strongly by UUI (40 % in CRI and 37 % in CRR); it was reduced 28-29 % by UUINI and 12-15 % by UAS. Overall, the urease inhibitor, alone and in combination with the nitrification inhibitor, was more effective in mitigating greenhouse gas and ammonia emissions than NCU. However, these products need to be tested in field settings to validate findings from the controlled laboratory experiment.

Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea

BACKGROUND

Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination.

RESULTS

We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.

Complexity of temperature dependence in methanogenic microbial environments

There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH₄, an important greenhouse gas. Microbial CH₄ production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO₂ and CH₄. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH₄ production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H₂/CO₂ as immediate CH₄ precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH₄ production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (E_a). Interestingly, CH₄ release from defined microbial cultures, from environmental samples and from wetland field sites all show similar E_a values around 100 kJ mol^-1 indicating that CH₄ production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.

Effect of extreme pH conditions on methanogenesis: Methanogen metabolism and community structure

The control of pH is effective for inhibiting methanogenesis in the chain elongation fermentation (CEF) system. However, obscure conclusions exist especially with regard to the underlying mechanism. This study comprehensively explored the responses of methanogenesis in granular sludge at various pH levels, ranging from 4.0 to 10.0, from multiple aspects including methane production, methanogenesis pathway, microbial community structure, energy metabolism and electron transport. Results demonstrated that compared with that at pH 7.0, pH at 4.0, 5.5, 8.5 and 10.0 triggered a 100%, 71.7%, 23.8% and 92.1% suppression on methanogenesis by the end of 3 cycles lasting 21 days. This might be explained by the remarkably inhibited metabolic pathways and intracellular regulations. To be more specific, extreme pH conditions decreased the abundance of the acetoclastic methanogens. However, obligate hydrogenotrophic and facultative acetolactic/hydrogenotrophic methanogens were significantly enriched by 16.9%-19.5 fold. pH stress reduced the gene abundance and/or activity of most enzymes involved in methanogenesis such as acetate kinase (by 81.1%-93.1%), formylmethanofuran dehydrogenase (by 10.9%-54.0%) and tetrahydromethanopterin S-methyltransferase (by 9.3%-41.5%). Additionally, pH stress suppressed electron transport via improper electron carriers and decreased electron amount as evidenced by 46.3%-70.4% reduced coenzyme F₄₂₀ content and diminished abundance of CO dehydrogenase (by 15.5%-70.5%) and NADH:ubiquinone reductase (by 20.2%-94.5%). pH stress also regulated energy metabolism with inhibited ATP synthesis (e.g., ATP citrate synthase level reduced by 20.1%-95.3%). Interestingly, the protein and carbohydrate content secreted in EPS failed to show consistent responses to acidic and alkaline conditions. Specifically, when compared with pH 7.0, the acidic condition remarkably reduced the levels of total EPS and EPS protein while both levels were enhanced in the alkaline condition. However, the EPS carbohydrate content at pH 4.0 and 10.0 both decreased. This study is expected to promote the understanding of the pH control-induced methanogenesis inhibition in the CEF system.

Optimization of ectoine production from Nesterenkonia xinjiangensis and one-step ectoine purification

In the current study, the optimization of ectoine production byNesterenkonia xinjiangensisand purification of ectoine from the bacterial cell extract were performed for the first time. Various carbon sources (glucose, sucrose, maltose, lactose, mannitol, and xylose) and nitrogen sources (ammonium nitrate, ammonium phosphate, ammonium chloride, ammonium oxalate, ammonium sulphate, and ammonium acetate), were used to optimize ectoine production. Subsequently, the effects of salt, pH and, concentrations of carbon and nitrogen source on ectoine production were optimized by response surface methodology (RSM). Ultimately, high pure (over 99%) and yield (98%) of ectoine from bacterial cells extracted was obtained by a single-step process using cation exchange chromatography. This study provides information that higher ectoine production can be achieved from this bacterial isolate by optimizing the factors influencing ectoine production and thus can be used as a new and alternative ectoine producer.

Influence of applied voltage on bioelectrochemical enhancement of biomethanation for low-rank coal and microbial community distribution

The performance of peat biomethanation was investigated in bioelectrochemical anaerobic digestion at different applied voltages, and compared to conventional anaerobic digestion. The methane yield was stabilized at 16 mL/g peat in the conventional anaerobic digestion. However, in the bioelectrochemical anaerobic digestion, the methane yield was significantly increased to 264 mL/g peat at the applied voltage of 4 V, followed by 1 V, 2 V, 0.5 V and 0 V. The bioelectrochemical system could enrich more electroactive microorganisms on the electrode, as well as in the bulk solution, and further improve the direct interspecies electron transfer for methane production. The 16S rRNA analysis showed a significant increase in the abundance of specific microorganisms in the bulk solution, including Firmicutes phylum and Proteobacteria phylum, in addition to a gradual increase in acetoclastic methanogenesis with an increase in applied voltage. These results provide a solution to turn low-rank coal into a new alternative energy.

Influence of inoculum-to-substrate ratio on biogas enhancement during biochar-assisted co-digestion of food waste and sludge

High accumulation of volatile fatty acids (VFAs) is one of the major concerns during mesophilic anaerobic co-digestion of food waste (FW) and sewage sludge (SS). Therefore, improving the stability of the anaerobic digestion process could surpass quick acidification while accelerating methanogenesis. In this study, the suitability of biochar-assisted co-digestion was evaluated at different inoculum and substrate ratios (I/S ratios: 0.1, 0.3, 0.6, and 0.9). The maximum methane yield of 256.85 mL/gVSadd was observed at an I/S ratio of 0.6. The results indicated fast volatile solid removal (∼ 47.17% to 73%) and a critical role of biochar addition in alleviating the underlying inhibitions. Substantial changes in the microbial community composition including Methanosata, Methanobrevibacter, and Methanosarcina were also observed which predominated and stabilised the methanogenesis process at higher I/S ratios. These results emphasised that the anaerobic co-digestion of FW/sludge is a promising approach, wherein the biochar amendment at different I/S ratios should be well maintained to avoid inhibitions from excess microbial VFA acidification of organic waste feedstocks.

Response of methanogenic community and their activity to temperature rise in alpine swamp meadow at different water level of the permafrost wetland on Qinghai-Tibet Plateau

Wetlands are an important source of atmospheric methane (CH₄) and are sensitive to global climate change. Alpine swamp meadows, accounting for ~50% of the natural wetlands on the Qinghai-Tibet Plateau, were considered one of the most important ecosystems. Methanogens are important functional microbes that perform the methane producing process. However, the response of methanogenic community and the main pathways of CH₄ production to temperature rise remains unknown in alpine swamp meadow at different water level in permafrost wetlands. In this study, we investigated the response of soil CH₄ production and the shift of methanogenic community to temperature rise in the alpine swamp meadow soil samples with different water levels collected from the Qinghai-Tibet Plateau through anaerobic incubation at 5°C, 15°C and 25°C. The results showed that the CH₄ contents increased with increasing incubation temperature, and were 5-10 times higher at the high water level sites (GHM1 and GHM2) than that at the low water level site (GHM3). For the high water level sites (GHM1 and GHM2), the change of incubation temperatures had little effect on the methanogenic community structure. Methanotrichaceae (32.44-65.46%), Methanobacteriaceae (19.30-58.86%) and Methanosarcinaceae (3.22-21.24%) were the dominant methanogen groups, with the abundance of Methanotrichaceae and Methanosarcinaceae having a significant positive correlation with CH₄ production (p < 0.01). For the low water level site (GHM3), the methanogenic community structure changed greatly at 25°C. The Methanobacteriaceae (59.65-77.33%) was the dominant methanogen group at 5°C and 15°C; In contrast, the Methanosarcinaceae (69.29%) dominated at 25°C, and its abundance showed a significant positive correlation with CH₄ production (p < 0.05). Collectively, these findings enhance the understanding of methanogenic community structures and CH₄ production in permafrost wetlands with different water levels during the warming process.

Metagenomic evidence of suppressed methanogenic pathways along soil profile after wetland conversion to cropland

Wetland conversion to cropland substantially suppresses methane (CH4) emissions due to the strong suppression of methanogenesis, which consists of various pathways. In this study, we evaluated the cultivation impacts on four predominant CH4 production pathways, including acetate, carbon dioxide (CO2), methylamines, and methanol, in a wetland and cultivated cropland in northeastern China. The results showed significant suppression of CH4 production potential and the abundance of genes for all four methanogenic pathways in cropland. The consistency between CH4 production and methanogenesis genes indicates the robustness of genomic genes in analyzing methanogenesis. The suppression effects varied across seasons and along soil profiles, most evident in spring and 0 to 30 cm layers. The acetate pathway accounted for 55% in wetland vs. 70% in the cropland of all functional genes for CH4 production; while the other three pathways were stronger in response to cultivation, which presented as stronger suppressions in both abundance of functional genes (declines are 52% of CO2 pathway, 68% of methanol pathway, and 62% of methylamines pathway, vs. 19% of acetate pathway) and their percentages in four pathways (from 20 to 15% for CO2, 15 to 9% for methylamines, and 10 to 6% for methanol pathway vs. 55 to 70% for acetate pathway). The structural equation models showed that substrate availability was most correlated with CH4 production potential in the wetland, while the positive correlations of acetate, CO2, and methylamine pathways with CH4 production potential were significant in the cropland. The quantitative responses of four CH4 production pathways to land conversion reported in this study provide benchmark information for validating the CH4 model in simulating CH4 cycling under land use and land cover change.

Physiological suitability of sulfate reducing granules for the development of bioconcrete

Regular monitoring and timely repair of concrete cracks are required to minimise further deterioration. Self-healing of cracks has been proposed as an alternative to the crack maintenance procedures. One of the proposed techniques is to use axenic cultures to exploit microbial induced calcite precipitation (MICP). However, such healing agents are not cost-effective for in situ use. As the market for bio-based self-healing concrete necessitates a low-cost bio-agent, non-axenic sulfate reducing bacterial (SRB) granules were investigated in this study through cultivation in an upflow anaerobic sludge blanket (UASB) reactor. The compact granules can protect the bacteria from adverse conditions without encapsulation. This study investigated the microbial activities of SRB granules at different temperatures, pH, and COD concentrations which the microbes would experience during the concrete casting and curing process. The attenuation and recovery of microbial activities were measured before and after the exposure. Moreover, the MICP yield was also tested for a possible use in self-healing bioconcrete. The results consistently showed that SRB granules were able to survive starvation, high temperature (50-60 ^o C), and high pH (12), together with SEM/EDS/XRD evidence. Microbial staining analysis demonstrated the formation of spores in the granules during their exposure to the harsh conditions. SRB granule was thus demonstrated to be a viable self-healing non-axenic agent for low-cost bioconcrete. This article is protected by copyright. All rights reserved.

Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane

Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.

A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes

The full plethora of environmental bacteria is often poorly represented in vitro as the majority remain difficult, if not impossible, to culture under standard laboratory settings. These bacteria often require native conditions for the formation of cell masses that collectively have higher chances of survival. With that, a 3D-printed version of the isolation chip (iChip) was used to cultivate bacteria from a tropical peat swamp in situ prior to growth and maintenance in vitro. Briefly, plates made from either acrylonitrile butadiene styrene (ABS), polylactic acid (PLA), or epoxy resin were tested in terms of their usability and durability under acidic conditions similar to those of peat matter. The epoxy resin plates were then found to be most optimal for the sampling conditions. Peat soil samples were collected from the base of a Koompassia malaccensis tree and reconstituted in molten 10% (wt/vol) tryptone soy agar (TSA) prior to inoculation. The iChips were subsequently assembled and buried in the site of origin. As a comparison, bacteria from the same soil sample were cultivated directly on TSA and incubated at 28 °C for two weeks. Thereafter, agar plugs from the iChip were transferred to TSA plates to allow microcolonies within each plug to grow. Each pure isolate from both cultivation approaches that grew was then pooled and extracted for total DNA prior to 16S rRNA gene amplification and sequencing via Illumina MiSeq. Taxonomic abundance comparison revealed that the bacterial taxa at the level of order were significantly different between the two approaches, particularly in the orders, Burkholderiales, Xanthomonodales, Enterobacteriales, and Actinomycetales (differences of 12.0, 7.1, 8.0, and 4.2%, respectively). This indicated that the 3D-printed iChips present a possible low-cost tool for the isolation of bacterial genera that may not be able to grow on media directly in vitro.

Green Hydrogen-Compressed natural gas (bio-H-CNG) production from food waste: Organic load influence on hydrogen and methane fusion

Biogenic hydrogen (bioH₂) enriched compressed natural gas (bio-H-CNG or biohythane) is emerging interest due to its feasibility to use in the existing transportation infrastructure with induced environmental benefits. This study evaluated the production of bioH₂and biomethane (bioCH₄) towards bio-H-CNG formation at a varying organic load (OL: 30,40,50 g COD/L) of food waste (FW). Acidogenic reactor operated with FW at 40 g COD/L showed the highest cumulative bioH₂production while elevated OL (50 g COD/L)showedhigher cumulative bioCH₄production (C_MP: 11.92 L) from the methanogenic reactor. BioH₂ and bioCH₄ produced at different time intervals were combined to assess bio-H-CNG. The nature of biocatalyst and OLsignificantly regulated the composition of bio-H-CNG varying between 0.1 and 0.3 of H₂/(H₂+CH₄) ratio accounting for5-12.6 kJ/g COD. Chain elongation, converting short (C2-C4) to medium-chain fatty acids(Caproic acid,1.16 g/L) was specifically observed during the acidogenic process.

Prediction of Genes That Function in Methanogenesis and CO2 Pathways in Extremophiles

Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO₂ into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO₂ emissions.

Temperature differently affected methanogenic pathways and microbial communities in sub-Antarctic freshwater ecosystems

Freshwater ecosystems are responsible for an important part of the methane (CH₄) emissions which are likely to change with global warming. This study aims to evaluate temperature-induced (from 5 to 20 °C) changes on microbial community structure and methanogenic pathways in five sub-Antarctic lake sediments from Magallanes strait to Cape Horn, Chile. We combined in situ CH₄ flux measurements, CH₄ production rates (MPRs), gene abundance quantification and microbial community structure analysis (metabarcoding of the 16S rRNA gene). Under unamended conditions, a temperature increase of 5 °C doubled MPR while microbial community structure was not affected. Stimulation of methanogenesis by methanogenic precursors as acetate and H₂/CO₂, resulted in an increase of MPRs up to 127-fold and 19-fold, respectively, as well as an enrichment of mcrA-carriers strikingly stronger under acetate amendment. At low temperatures, H₂/CO₂-derived MPRs were considerably lower (down to 160-fold lower) than the acetate-derived MPRs, but the contribution of hydrogenotrophic methanogenesis increased with temperature. Temperature dependence of MPRs was significantly higher in incubations spiked with H₂/CO₂ (c. 1.9 eV) compared to incubations spiked with acetate or unamended (c. 0.8 eV). Temperature was not found to shape the total microbial community structure, that rather exhibited a site-specific variability among the studied lakes. However, the methanogenic archaeal community structure was driven by amended methanogenic precursors with a dominance of Methanobacterium in H₂/CO₂-based incubations and Methanosarcina in acetate-based incubations. We also suggested the importance of acetogenic H₂-production outcompeting hydrogenotrohic methanogenesis especially at low temperatures, further supported by homoacetogen proportion in the microcosm communities. The combination of in situ-, and laboratory-based measurements and molecular approaches indicates that the hydrogenotrophic pathway may become more important with increasing temperatures than the acetoclastic pathway. In a continuously warming environment driven by climate change, such issues are crucial and may receive more attention.

Impact of river channel lateral migration on microbial communities across a discontinuous permafrost floodplain

Permafrost soils store approximately twice the amount of carbon currently present in Earth's atmosphere and are acutely impacted by climate change due to the polar amplification of increasing global temperature. Many organic-rich permafrost sediments are located on large river floodplains, where river channel migration periodically erodes and re-deposits the upper tens of meters of sediment. Channel migration exerts a first-order control on the geographic distribution of permafrost and floodplain stratigraphy and thus may affect microbial habitats. To examine how river channel migration in discontinuous permafrost environments affects microbial community composition, we used amplicon sequencing of the 16S rRNA gene on sediment samples from floodplain cores and exposed riverbanks along the Koyukuk River, a large tributary of the Yukon River in west-central Alaska. Microbial communities are sensitive to permafrost thaw: communities found in deep samples thawed by the river closely resembled near-surface active layer communities in non-metric multidimensional scaling analyses but did not resemble floodplain permafrost communities at the same depth. Microbial communities also displayed lower diversity and evenness in permafrost than in both the active layer and permafrost-free point bars recently deposited by river channel migration. Taxonomic assignments based on 16S and quantitative PCR for the methyl-coenzyme M reductase functional gene demonstrated that methanogens and methanotrophs are abundant in older permafrost-bearing deposits, but not in younger, non-permafrost point bar deposits. The results suggested that river migration, which regulates the distribution of permafrost, also modulates the distribution of microbes potentially capable of producing and consuming methane on the Koyukuk River floodplain. Importance Arctic lowlands contain large quantities of soil organic carbon that is currently sequestered in permafrost. With rising temperatures, permafrost thaw may allow this carbon to be consumed by microbial communities and released to the atmosphere as carbon dioxide or methane. We used gene sequencing to determine the microbial communities present in the floodplain of a river running through discontinuous permafrost. We found the river's lateral movement across its floodplain influences the occurrence of certain microbial communities-in particular, methane-cycling microbes were present on the older, permafrost-bearing eroding riverbank but absent on the newly deposited river bars. Riverbank sediment had microbial communities more similar to the floodplain active layer than permafrost samples from the same depth. Therefore, spatial patterns of river migration influence the distribution of microbial taxa relevant to the warming Arctic climate.

Influence of metabolic cosubstrates on methanogenic potential and degradation of triclosan and propranolol in sanitary sewage

Triclosan (TCS) and propranolol (PRO) are emerging micropollutants that are difficult to remove in wastewater treatment plants. In this study, methanogenic potential (P) of anaerobic sludge submitted to TCS (3.6 ± 0.1 to 15.5 ± 0.1 mg L^-1) and PRO (6.1 ± 0.1 to 55.9 ± 1.2 mg L^-1) in sanitary sewage, was investigated in batch reactors. The use of cosubstrates (200 mg L^-1 of organic matter) ethanol, methanol:ethanol and fumarate was evaluated for micropollutant degradation. Without cosubstrates, P values for 5.0 ± 0.1 mgTCS L^-1, 15.5 ± 0.1 mgTCS L^-1 and 55.0 ± 1.3 mgPRO L^-1 were 50.53%, 98.24% and 17.66% lower in relation to Control assay (855 ± 5 μmolCH4) with sanitary sewage, without micropollutants and cosubstrates, respectively. The use of fumarate, ethanol and methanol:ethanol favored greater methane production, with P values of 2144 ± 45 μmolCH₄, 2960 ± 185 μmolCH₄ and 2239 ± 171 μmolCH₄ for 5.1 ± 0.1 mgTCS L^-1, respectively; and of 10,827 ± 185 μmolCH₄, 10,946 ± 108 μmolCH₄ and 10,809 ± 210 μmolCH₄ for 55.0 ± 1.3 mgPRO L^-1, respectively. Greater degradation of TCS (77.1 ± 0.1% for 5.1 ± 0.1 mg L^-1) and PRO (24.1 ± 0.1% for 55.9 ± 1.2 mg L^-1) was obtained with ethanol. However, with 28.5 ± 0.5 mg PRO L^-1, greater degradation (88.4 ± 0.9%) was obtained without cosubstrates. With TCS, via sequencing of rRNA 16S gene, for Bacteria Domain, greater abundance of phylum Chloroflexi and of the genera Longilinea, Arcobacter, Mesotoga and Sulfuricurvum were identified. With PRO, the genus VadinBC27 was the most abundant. Methanosaeta was dominant in TCS with ethanol, while in PRO without cosubstrates, Methanobacterium and Methanosaeta were the most abundant. The use of metabolic cosubstrates is a favorable strategy to obtain greater methanogenic potential and degradation of TCS and PRO.

Critical insights into psychrophilic anaerobic digestion: Novel strategies for improving biogas production

Anaerobic digestion (AD) under psychrophilic temperature has only recently garnered deserved attention. In major parts of Europe, USA, Canada and Australia, climatic conditions are more suited for psychrophilic (<20 ℃) rather than mesophilic (35 - 37 ℃) and thermophilic (55 - 60 ℃) AD. Low temperature has adverse effects on important cellular processes which may render the cell biology inactive. Moreover, cold climate can also alter the physical and chemical properties of wastewater, thereby reducing the availability of substrate to microbes. Hence, the use of low temperature acclimated microbial biomass could overcome thermodynamic constraints and carry out flexible structural and conformational changes to proteins, membrane lipid composition, expression of cold-adapted enzymes through genotypic and phenotypic variations. Reduction in organic loading rate is beneficial to methane production under low temperatures. Moreover, modification in the design of existing reactors and the use of hybrid reactors have already demonstrated improved methane generation in the lab-scale. This review also discusses some novel strategies such as direct interspecies electron transfer (DIET), co-digestion of substrate, bioaugmentation, and bioelectrochemical system assisted AD which present promising prospects. While DIET can facilitate syntrophic electron exchange in diverse microbes, the addition of organic-rich co-substrate can help in maintaining suitable C/N ratio in the anaerobic digester which subsequently can enhance methane generation. Bioaugmentation with psychrophilic strains could reduce start-up time and ensure daily stable performance for wastewater treatment facilities at low temperatures. In addition to the technical discussion, the economic assessment and future outlook on psychrophilic AD are also highlighted.

Microbial diversity dynamics during the self-acidification of dairy slurry

Slurry acidification has been shown to be effective in reducing environmentally damaging gases. However, this involved the use of concentrated acids on farms. Therefore, due to the health and safety concerns, there is an interest in self-acidification of slurry technique. This study was designed to determine the microbial dynamics leading to self-acidification of slurry. A fresh cattle slurry was amended 10% brewing sugar and stored over 30 days. This fermentable carbon source promoted self-acidification of the slurry from pH 7.0 to 4.7 within four days, and was associated with the accumulation of lactic acid and a reduction in methane and relative ammonia emissions. A metagenomics approach through next generation sequencing (NGS) using an Illumina MiSeq platform was used to determine the microbial diversity and dynamics (bacteria and archaea) in the stored amended slurry. 16S ribosomal ribonucleic acid (rRNA) sequence data revealed the presence of the Order of Lactobacillales was associated with the lactic acid production. The operational taxonomic units (OTUs) abundance indicates that the methanogenic community was dominated by hydrogenotrophic methanogens from the member Order of Methanobacteriales, Methanomicrobiales, and Methanosarcinales. The decrease in tolerance by the methanogens in the self-acidified slurry was probably the main reason for the reduced methane emission. These results confirm, at the microbial level, the mechanism of inhibiting methane production via self-acidification during storage period.

Responses of Soil Fungal Communities to Lime Application in Wheat Fields in the Pacific Northwest

Liming is an effective agricultural practice and is broadly used to ameliorate soil acidification in agricultural ecosystems. Our understanding of the impacts of lime application on the soil fungal community is scarce. In this study, we explored the responses of fungal communities to liming at two locations with decreasing soil pH in Oregon in the Pacific Northwest using high-throughput sequencing (Illumina MiSeq). Our results revealed that the location and liming did not significantly affect soil fungal diversity and richness, and the impact of soil depth on fungal diversity varied among locations. In contrast, location and soil depth had a strong effect on the structure and composition of soil fungal communities, whereas the impact of liming was much smaller, and location- and depth-dependent. Interestingly, families Lasiosphaeriaceae, Piskurozymaceae, and Sordariaceae predominated in the surface soil (0–7.5 cm) and were positively correlated with soil OM and aluminum, and negatively correlated with pH. The family Kickxellaceae which predominated in deeper soil (15–22.5 cm), had an opposite response to soil OM. Furthermore, some taxa in Ascomycota, such as Hypocreales, Peziza and Penicillium, were increased by liming at one of the locations (Moro). In conclusion, these findings suggest that fungal community structure and composition rather than fungal diversity responded to location, soil depth and liming. Compared to liming, location and depth had a stronger effect on the soil fungal community, but some specific fungal taxa shifted with lime application.

Sulphate-Reducing Bacteria’s Response to Extreme pH Environments and the Effect of Their Activities on Microbial Corrosion

Sulphate-reducing bacteria (SRB) are dominant species causing corrosion of various types of materials. However, they also play a beneficial role in bioremediation due to their tolerance of extreme pH conditions. The application of sulphate-reducing bacteria (SRB) in bioremediation and control methods for microbiologically influenced corrosion (MIC) in extreme pH environments requires an understanding of the microbial activities in these conditions. Recent studies have found that in order to survive and grow in high alkaline/acidic condition, SRB have developed several strategies to combat the environmental challenges. The strategies mainly include maintaining pH homeostasis in the cytoplasm and adjusting metabolic activities leading to changes in environmental pH. The change in pH of the environment and microbial activities in such conditions can have a significant impact on the microbial corrosion of materials. These bacteria strategies to combat extreme pH environments and their effect on microbial corrosion are presented and discussed.

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation

Mechanisms controlling CO₂ and CH₄ production in wetlands are central to understanding carbon cycling and greenhouse gas exchange. However, the volatility of these respiration products complicates quantifying their rates of production in the field. Attempts to circumvent the challenges through closed system incubations, from which gases cannot escape, have been used to investigate bulk in situ geochemistry. Efforts towards mapping mechanistic linkages between geochemistry and microbiology have raised concern regarding sampling and incubation-induced perturbations. Microorganisms are impacted by oxygen exposure, increased temperatures and accumulation of metabolic products during handling, storage, and incubation. We probed the extent of these perturbations, and their influence on incubation results, using high-resolution geochemical and microbial gene-based community profiling of anaerobically incubated material from three wetland habitats across a permafrost peatland. We compared the original field samples to the material anaerobically incubated over 50 days. Bulk geochemistry and phylum-level microbiota in incubations largely reflected field observations, but divergence between field and incubations occurred in both geochemistry and lineage-level microbial composition when examined at closer resolution. Despite the changes in representative lineages over time, inferred metabolic function with regards to carbon cycling largely reproduced field results suggesting functional consistency. Habitat differences among the source materials remained the largest driver of variation in geochemical and microbial differences among the samples in both incubations and field results. While incubations may have limited usefulness for identifying specific mechanisms, they remain a viable tool for probing bulk-scale questions related to anaerobic C cycling, including CO₂ and CH₄ dynamics.

Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology

The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identification techniques, such as selective enrichment and pure-culture isolation, have been used for a long time to study diversity of methanogens and methanotrophs. However, these techniques are characterized by significant limitations, since only a relatively small fraction of the microbial community could be cultured. Modern molecular methods for quantitative analysis of the microbial community such as real-time PCR (Polymerase chain reaction), DNA fingerprints and methods based on high-throughput sequencing together with different “omics” techniques overcome the limitations imposed by culture-dependent approaches and provide new insights into the diversity and ecology of microbial communities in the methane cycle. Here, we review available knowledge concerning the abundances, composition, and activity of methanogenic and methanotrophic communities in a wide range of natural and anthropogenic environments. We suggest that incorporation of microbial data could fill the existing microbiological gaps in methane flux modeling, and significantly increase the predictive power of models for different environments.

Ammonium Utilization in Microalgae: A Sustainable Method for Wastewater Treatment

In plant cells, ammonium is considered the most convenient nitrogen source for cell metabolism. However, despite ammonium being the preferred N form for microalgae, at higher concentrations, it can be toxic, and can cause growth inhibition. Microalgae’s tolerance to ammonium depends on the species, with various taxa showing different thresholds of tolerability and symptoms of toxicity. In the environment, ammonium at high concentrations represents a dangerous pollutant. It can affect water quality, causing numerous environmental problems, including eutrophication of downstream waters. For this reason, it is important to treat wastewater and remove nutrients before discharging it into rivers, lakes, or seas. A valid and sustainable alternative to conventional treatments could be provided by microalgae, coupling the nutrient removal from wastewater with the production of valuable biomass. This review is focused on ammonium and its importance in algal nutrition, but also on its problematic presence in aquatic systems such as wastewaters. The aim of this work is to provide recent information on the exploitation of microalgae in ammonium removal and the role of ammonium in microalgae metabolism.

Much stronger tundra methane emissions during autumn freeze than spring thaw

Warming in the Arctic has been more apparent in the non-growing season than in the typical growing season. In this context, methane (CH₄ ) emissions in the non-growing season, particularly in the shoulder seasons, account for a substantial proportion of the annual budget. However, CH₄ emissions in spring and autumn shoulders are often underestimated by land models and measurements due to limited data availability and unknown mechanisms. This study investigates CH₄ emissions during spring thaw and autumn freeze using eddy covariance CH₄ measurements from three Arctic sites with multi-year observations. We find that the shoulder seasons contribute to about a quarter (25.6 ± 2.3%, mean ± SD) of annual total CH₄ emissions. Our study highlights the three to four times higher contribution of autumn freeze CH₄ emission to total annual emission than that of spring thaw. Autumn freeze exhibits significantly higher CH₄ flux (0.88 ± 0.03 mg m^-2  hr^-1 ) than spring thaw (0.48 ± 0.04 mg m^-2  hr^-1 ). The mean duration of autumn freeze (58.94 ± 26.39 days) is significantly longer than that of spring thaw (20.94 ± 7.79 days), which predominates the much higher cumulative CH₄ emission during autumn freeze (1,212.31 ± 280.39 mg m^-2  year^-1 ) than that during spring thaw (307.39 ± 46.11 mg m^-2  year^-1 ). Near-surface soil temperatures cannot completely reflect the freeze-thaw processes in deeper soil layers and appears to have a hysteresis effect on CH₄ emissions from early spring thaw to late autumn freeze. Therefore, it is necessary to consider commonalities and differences in CH₄ emissions during spring thaw versus autumn freeze to accurately estimate CH₄ source from tundra ecosystems for evaluating carbon-climate feedback in Arctic.

Methanogenic archaea in peatlands

Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.

Towards the practical application of bioelectrochemical anaerobic digestion (BEAD): Insights into electrode materials, reactor configurations, and process designs

Anaerobic digestion (AD) is one of the most widely adopted bioenergy recovery technologies globally. Despite the wide adoption, AD has been challenged by the unstable performances caused by imbalanced substrate and/or electron availability among different reaction steps. Bioelectrochemical anaerobic digestion (BEAD) is a promising concept that has demonstrated potential for balancing the electron transfer rates and enhancing the methane yield in AD during shocks. While great progress has been made, a wide range of, and sometimes inconsistent engineering and technical strategies were attempted to improve BEAD. To consolidate past efforts and guide future development, a comprehensive review of the fundamental bioprocesses in BEAD is provided herein, followed by a critical evaluation of the engineering and technical optimizations attempted thus far. Further, a few novel directions and strategies that can enhance the performance and practicality of BEAD are proposed for future research to consider. This review and outlook aim to provide a fundamental understanding of BEAD and inspire new research ideas in AD and BEAD in a mechanism-informed fashion.

Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study

Ombrotrophic bogs accumulate large stores of soil carbon that eventually decompose to carbon dioxide and methane. Carbon accumulates because Sphagnum mosses slow microbial carbon decomposition processes, leading to the production of labile intermediate compounds. Acetate is a major product of Sphagnum degradation, yet rates of hydrogenotrophic methanogenesis far exceed rates of aceticlastic methanogenesis, suggesting that alternative acetate mineralization processes exist. Two possible explanations are aerobic respiration and anaerobic respiration via humic acids as electron acceptors. While these processes have been widely observed, microbial community interactions linking Sphagnum degradation and acetate mineralization remain cryptic. In this work, we use ordination and network analysis of functional genes from 110 globally distributed peatland metagenomes to identify conserved metabolic pathways in Sphagnum bogs. We then use metagenome-assembled genomes (MAGs) from McLean Bog, a Sphagnum bog in New York State, as a local case study to reconstruct pathways of Sphagnum degradation and acetate mineralization. We describe metabolically flexible Acidobacteriota MAGs that contain all genes to completely degrade Sphagnum cell wall sugars under both aerobic and anaerobic conditions. Finally, we propose a hypothetical model of acetate oxidation driven by changes in peat redox potential that explain how bogs may circumvent aceticlastic methanogenesis through aerobic and humics-driven respiration.

Methodological Aspects of Multiplex Terminal Restriction Fragment Length Polymorphism-Technique to Describe the Genetic Diversity of Soil Bacteria, Archaea and Fungi

The molecular fingerprinting methods used to evaluate soil microbial diversity could also be used as effective biosensors for the purposes of monitoring ecological soil status. The biodiversity of microorganisms is a relevant index of soil activity and there is a necessity to develop tools to generate reliable results for an emerging approach in the field of environmental control using microbial diversity biosensors. This work reports a method under development for determining soil microbial diversity using high efficiency Multiplex PCR-Terminal Restriction Fragment Length Polymorphism (M-T-RFLP) for the simultaneous detection of bacteria, archaea and fungi. Three different primer sets were used in the reaction and the analytical conditions were optimized. Optimal analytical conditions were achieved using 0.5 µM of primer for bacteria and 1 µM for archaea and fungi, 4 ng of soil DNA template, and HaeIII restriction enzyme. Comparative tests using the proposed analytical approach and a single analysis of each microorganism group were carried out to indicate that both genetic profiles were similar. The Jaccard similarity coefficient between single and multiplexing approach ranged from 0.773 to 0.850 for bacteria and fungi, and 0.208 to 0.905 for archaea. In conclusion, the multiplexing and pooling approaches significantly reduced the costs and time required to perform the analyses, while maintaining a proper effectiveness.

Diversity and Distribution of Methanogenic Community Between Two Typical Alpine Ecosystems on the Qinghai-Tibetan Plateau

Alpine permafrost regions are important sources of biogenic CH₄ and methanogens play an important role in the methane-producing process. The alpine permafrost on the Qinghai-Tibetan plateau comprises about one-sixth of China's land area, and there are various types of alpine ecosystems. However, the methanogenic communities in the typical alpine ecosystems are poorly understood. In this study, the active layers and permafrost layers of the natural ecosystem of alpine grassland (DZ2-1) and alpine swamp meadow (DZ2-5) were selected to investigate the diversity and abundance of methanogenic communities. Methanobacterium (63.65%) are overwhelmingly dominant in the active layer of the alpine grassland (DZ2-1A). ZC-I cluster (26.13%), RC-I cluster (19.56%), and Methanobacterium (15.02%) are the dominant groups in the permafrost layer of the alpine grassland (DZ2-1P). Methanosaeta (32.92%), Fen cluster (29.59%), Methanosarcina (16.33%), and Methanobacterium (13.95%) are the dominant groups in the active layer of the alpine swamp meadow (DZ2-5A), whereas the Fen cluster (50.85%), ZC-I cluster (27.63%), and RC-I cluster (14.15%) are relatively abundant in the permafrost layer of the alpine swamp meadow (DZ2-5P). qPCR data showed that the abundance of methanogens was higher in the natural ecosystem of alpine swamp meadow than in alpine grassland. We found that the community characteristics of methanogens were related to environmental factors. Pearson correlation analyses indicated that the relative abundance of Methanobacterium had a significantly positive correlation with hydrogen concentration (P < 0.01), while the relative abundances of Methanosaeta and Methanosarcina were positively correlated with acetate concentration (P < 0.05). This study will help us to understand the methanogenic communities and their surrounding environments in alpine ecosystems.

Constraints on microbial communities, decomposition and methane production in deep peat deposits

Peatlands play outsized roles in the global carbon cycle. Despite occupying a rather small fraction of the terrestrial biosphere (~3%), these ecosystems account for roughly one third of the global soil carbon pool. This carbon is largely comprised of undecomposed deposits of plant material (peat) that may be meters thick. The fate of this deep carbon stockpile with ongoing and future climate change is thus of great interest and has large potential to induce positive feedback to climate warming. Recent in situ warming of an ombrotrophic peatland indicated that the deep peat microbial communities and decomposition rates were resistant to elevated temperatures. In this experiment, we sought to understand how nutrient and pH limitations may interact with temperature to limit microbial activity and community composition. Anaerobic microcosms of peat collected from 1.5 to 2 meters in depth were incubated at 6°C and 15°C with elevated pH, nitrogen (NH4Cl), and/or phosphorus (KH2PO4) in a full factorial design. The production of CO2 and CH4 was significantly greater in microcosms incubated at 15°C, although the structure of the microbial community did not differ between the two temperatures. Increasing the pH from ~3.5 to ~5.5 altered microbial community structure, however increases in CH4 production were non-significant. Contrary to expectations, N and P additions did not increase CO2 and CH4 production, indicating that nutrient availability was not a primary constraint in microbial decomposition of deep peat. Our findings indicate that temperature is a key factor limiting the decomposition of deep peat, however other factors such as the availability of O2 or alternative electron donors and high concentrations of phenolic compounds, may also exert constraints. Continued experimental peat warming studies will be necessary to assess if the deep peat carbon bank is susceptible to increased temperatures over the longer time scales.

Bacterial and archeal dynamics of a labscale HYBRID gas fermentation bioreactor fed with CO2 and H2

16s rDNA-based methods were used in order to identify the dynamics of microbial profiles in a HYBRID gas fermentation bio-methanization reactor. The effects of various H₂ and CO₂ ratios on microbial community were investigated. The HYBRID gas fermentation reactor was composed of granular anaerobic seed and the system fed with only H₂ and CO₂ gases. No additional organic material and trace element was fed during the throughout the experiments; thus, the microbial diversity was directly related to production of methane. The dynamics of the microbial communities were investigated with DGGE and real-time PCR analysis. The results showed that Methanobacteriales members were more dominated than Methanosarcinales and Methanomicrobiales members in the system. DGGE results indicated that Methanosaeta concilii, Methanoculleus sp., Methanosphaerula palustris, Methanofollis formosanus, Methanolinea sp., and Methanobacterium palustre were the most prominent methanogens depending on different H₂/CO₂ ratios. DGGE profiles suggested that hydrogenotrophic and acetoclastic species were responsible for the production of methane. The survival of syntrophic bacteria and acetoclastic methanogens was attributed to their utilization of organic materials provided by lysis. To the best of our knowledge, this is the first microbial profile detection study in a hybrid bioreactor system operated with only pure hydrogen and carbon dioxide.

Anaerobic Digestion of Food Waste with Unconventional Co-Substrates for Stable Biogas Production at High Organic Loading Rates

Anaerobic digestion (AD) is widely considered a more sustainable food waste management method than conventional technologies, such as landfilling and incineration. To improve economic performance while maintaining AD system stability at commercial scale, food waste is often co-digested with animal manure, but there is increasing interest in food waste-only digestion. We investigated the stability of anaerobic digestion with mixed cafeteria food waste (CFW) as the main substrate, combined in a semi-continuous mode with acid whey, waste bread, waste energy drinks, and soiled paper napkins as co-substrates. During digestion of CFW without any co-substrates, the maximum specific methane yield (SMY) was 363 mL gVS−1d−1 at organic loading rate (OLR) of 2.8 gVSL−1d−1, and reactor failure occurred at OLR of 3.5 gVSL−1d−1. Co-substrates of acid whey, waste energy drinks, and waste bread resulted in maximum SMY of 455, 453, and 479 mL gVS−1d−1, respectively, and it was possible to achieve stable digestion at OLR as high as 4.4 gVSL−1d−1. These results offer a potential approach to high organic loading rate digestion of food waste without using animal manure. Process optimization for the use of unconventional co-substrates may help enable deployment of anaerobic digesters for food waste management in urban and institutional applications and enable increased diversion of food waste from landfills in heavily populated regions.

Microbial Degradation of Cellulosic Material and Gas Generation: Implications for the Management of Low- and Intermediate-Level Radioactive Waste

Deep geologic repositories (DGR) in Canada are designed to contain and isolate low- and intermediate-level radioactive waste. Microbial degradation of the waste potentially produces methane, carbon dioxide and hydrogen gas. The generation of these gases increase rock cavity pressure and limit water ingress which delays the mobility of water soluble radionuclides. The objective of this study was to measure gas pressure and composition over 7 years in experiments containing cellulosic material with various starting conditions relevant to a DGR and to identify micro-organisms generating gas. For this purpose, we conducted experiments in glass bottles containing (1) wet cellulosic material, (2) wet cellulosic material with compost Maker, and (3) wet cellulosic material with compost Accelerator. Results demonstrated that compost accelerated the pressure build-up in the containers and that methane gas was produced in one experiment with compost and one experiment without compost because the pH remained neutral for the duration of the 464 days experiment. Methane was not formed in the other experiment because the pH became acidic. Once the pressure became similar in all containers after 464 days, we then monitored gas pressure and composition in glass bottle containing wet cellulosic material in (1) acidic conditions, (2) neutral conditions, and (3) with an enzyme that accelerated degradation of cellulose over 1965 days. In these experiments, acetogenic bacteria degraded cellulose and produced acetic acid, which acidity suppressed methane production. Microbial community analyses suggested a diverse community of archaea, bacteria and fungi actively degrading cellulose. DNA analyses also confirmed the presence of methanogens and acetogens in our experiments. This study suggests that methane gas will be generated in DGRs if pH remains neutral. However, our results showed that microbial degradation of cellulose not only generated gas, but also generated acidity. This finding is important as acids can limit bentonite swelling and potentially degrade cement and rock barriers, thus this requires consideration in the safety case as appropriate.

Reduction in Methane Emissions From Acidified Dairy Slurry Is Related to Inhibition of Methanosarcina Species

Liquid dairy manure treated with sulfuric acid was stored in duplicate pilot-scale storage tanks for 120 days with continuous monitoring of CH₄ emissions and concurrent examination of changes in the structure of bacterial and methanogenic communities. Methane emissions were monitored at the site using laser-based Trace Gas Analyzer whereas quantitative real-time polymerase chain reaction and massively parallel sequencing were employed to study bacterial and methanogenic communities using 16S rRNA and methyl-coenzyme M Reductase A (mcrA) genes/transcripts, respectively. When compared with untreated slurries, acidification resulted in 69–84% reductions of cumulative CH₄ emissions. The abundance, activity, and proportion of bacterial communities did not vary with manure acidification. However, the abundance and activity of methanogens (as estimated from mcrA gene and transcript copies, respectively) in acidified slurries were reduced by 6 and 20%, respectively. Up to 21% reduction in mcrA transcript/gene ratios were also detected in acidified slurries. Regardless of treatment, Methanocorpusculum predominated archaeal 16S rRNA and mcrA gene and transcript libraries. The proportion of Methanosarcina, which is the most metabolically-diverse methanogen, was the significant discriminant feature between acidified and untreated slurries. In acidified slurries, the relative proportions of Methanosarcina were ≤ 10%, whereas in untreated slurries, it represented up to 24 and 53% of the mcrA gene and transcript libraries, respectively. The low proportions of Methanosarcina in acidified slurries coincided with the reductions in CH₄ emissions. The results suggest that reduction of CH₄ missions achieved by acidification was due to an inhibition of the growth and activity of Methanosarcina species.

Modelling the specific pathway of CH4 and CO2 formation using carbon isotope fractionation: an example for a boreal mesotrophic fen

We described mathematically the process of peat methanization in a boreal mesotrophic fen. Gaseous and dissolved CH₄ and CO₂ as well as their δ¹³C signatures were considered in the dynamic equations for incubation bottles. In accordance with the model, acetate, H₂, and CO₂ were produced during cellulose hydrolysis and acidogenesis. ¹³C/¹²C in CO₂ was a key variable reflecting dynamic changes in the rates of cellulose hydrolysis and acidogenesis, acetoclastic and hydrogenotrophic methanogenesis. As CO₂ is the substrate in hydrogenotrophic methanogenesis, δ¹³C-CO₂ increased from the start till the dissolved hydrogen concentration became very low. Thereafter, the rate of acetoclastic methanogenesis with the significant current acetate concentration dominated over the rate of hydrogenotrophic methanogenesis leading to the decreasing δ¹³C-CO₂ and the increasing δ¹³C-CH₄. The model was validated by describing the system's dynamics under strong and weak inhibition of acetoclastic and hydrogenotrophic methanogenesis by methyl fluoride, respectively. During peat methanization at the lowered temperature of 10 °C, the processes of hydrogenotrophic methanogenesis and homoacetogenesis competing for H₂ may occur. However, based on dynamics of the carbon isotope signatures, especially on dynamics of δ¹³C-CO₂, the model showed no significant contribution of homoacetogens in peat methanization.

Acclimatization of a mixed-animal manure inoculum to the anaerobic digestion of Axonopus compressus reveals the putative importance of Mesotoga infera and Methanosaeta concilii as elucidated by DGGE and Illumina MiSeq

In this study, a multifarious microbial mix from different sources is acclimatized over a period of three months to digesting cowgrass, and the changes in the community structure are examined with both a traditional denaturing gradient gel electrophoresis method as well as a next generation sequencing MiSeq method. It is shown that the much more in depth analysis by Illumina gives more information about the relative abundance and thus putative importance of the role of various microbes, in particular the bacterium Mesotoga infera and the archaeon Methanosaeta concilii.

Aquatic export of young dissolved and gaseous carbon from a pristine boreal fen: Implications for peat carbon stock stability

The stability of northern peatland's carbon (C) store under changing climate is of major concern for the global C cycle. The aquatic export of C from boreal peatlands is recognized as both a critical pathway for the remobilization of peat C stocks as well as a major component of the net ecosystem C balance (NECB). Here, we present a full year characterization of radiocarbon content (¹⁴ C) of dissolved organic carbon (DOC), carbon dioxide (CO₂ ), and methane (CH₄ ) exported from a boreal peatland catchment coupled with ¹⁴ C characterization of the catchment's peat profile of the same C species. The age of aquatic C in runoff varied little throughout the year and appeared to be sustained by recently fixed C from the atmosphere (<60 years), despite stream DOC, CO₂ , and CH₄ primarily being sourced from deep peat horizons (2-4 m) near the mire's outlet. In fact, the ¹⁴ C content of DOC, CO₂ , and CH₄ across the entire peat profile was considerably enriched with postbomb C compared with the solid peat material. Overall, our results demonstrate little to no mobilization of ancient C stocks from this boreal peatland and a relatively large resilience of the source of aquatic C export to forecasted hydroclimatic changes.

Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm

Biogas production from animal waste is an economically viable way to reduce environmental pollution and produce valuable products, i.e<i>.</i>, methane and a nutrient-rich organic waste product. An anaerobic digestion reactor for biogas production from pig waste was sampled at the entrance, middle (digestion chamber), and exit of a digester, while the bacterial and archaeal community structure was studied by 16S rRNA gene metagenomics. The number of bacterial operational taxonomic units (OTU)-97% was 3-7 times larger than that of archaeal ones. Bacteria and Archaea found in feces of animals (e.g., Clostridiaceae, Lachnospiraceae, Ruminococcaceae, <i>Methanosarcina</i>, <i>Methanolobus</i>, <i>Methanosaeta</i>, and <i>Methanospirillum</i>) dominated the entrance of the digester. The digestion chamber was dominated by anaerobic sugar-fermenting OP9 bacteria and the syntrophic bacteria <i>Candidatus</i> Cloacamonas (Waste Water of Evry 1; WWE1). The methanogens dominant in the digestion chamber were the acetoclastic <i>Methanosaeta</i> and the hydrogenothrophic <i>Methanoculleus</i> and <i>Methanospirillum</i>. Similar bacterial and archaeal groups that dominated in the middle of the digestion chamber were found in the waste that left the digester. Predicted functions associated with degradation of xenobiotic compounds were significantly different between the sampling locations. The microbial community found in an anaerobic digestion reactor loaded with pig manure contained microorganisms with biochemical capacities related to the 4 phases of methane production.

Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems

About half of the global methane (CH₄ ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH₄ emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.

Metagenomic assessment of methane production-oxidation and nitrogen metabolism of long term manured systems in lowland rice paddy

Biochemical pathways of methanogenesis and methanotrophy coupled with carbon (C)-nitrogen (N) metabolism were studied in long term (13years) manured systems in lowland rice paddy through metagenomics approach. Manured systems included in this study were, control (exclusion of application of any manure), farm yard manure (FYM, @5Mgha^-1yr^-1) and green manuring (GM with Sesbania aculeata). Metagenomic sequence data revealed the dominance of C decomposing bacterial communities' like Proteobacteria, Planctomycetes, Actinobacteria, Firmicutes, Acidobacteria, in manure amended soils as compared to control. Diversities for assimilatory and dissimilatory N-fixing microorganisms at phylum level were found higher under GM as compared to rest. Two genera responsible for methanogenesis, viz. Methanolobus and Methanotorris were absent in manured systems as compared to control. The acetoclastic and serine pathway was found as the predominant pathway for methanogenesis and methanotrophy, respectively, in tropical lowland rice paddy. Abundance reads of enzymes were in the range of 254-445 in the acetoclastic methanogenesis pathway. On the other hand, these were varied from 165 to 216 in serine pathway of methanotrophy. Lowland paddy soil exhibited higher functional and structural diversities in manured systems as compared to unamended control in respect to labile C pools and CH₄ production. Methane (CH₄) emission was 31% higher in FYM system than GM. However, nitrous oxide (N₂O) emission was found 25% higher in GM as compared to FYM. As a whole, bacterial diversities were higher under FYM system in tropical lowland rice paddy as compared to GM and unamended systems.