Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

Reducing methane emissions by developing low-fumarate high-ethanol eco-friendly rice

Methane in rice paddies is mainly produced by methanogenic communities feeding on carbon from root exudates and debris. However, the dominant root secretion governing methane emissions is not yet identified after decades of studies, even though secreted carbohydrates and organic acids have been shown to contribute to methane emissions. In this study, we discovered that fumarate and ethanol are two major rice-orchestrated secretions and play a key role in regulating methane emissions. Fumarate released in the rhizosphere is metabolized by microorganisms, supporting the growth of methanogenic archaea that produce methane as an end carbon product, while ethanol mitigates methane emissions through inhibition of methanogenic activity and growth as well as reducing fumarate synthesis in the rice root. Furthermore, we elucidated the route of fumarate metabolism in the anoxic rhizospheric zone. We found that fumarate in the rice root is produced from acetate via propionate and succinate, and when released into soil directly is oxidized to propionate before conversion via acetate into methane as the end product. The knowledge on fumarate and ethanol metabolism in rice was then used for hybrid breeding of new rice varieties with the property of low methane emission. Cultivation of these novel rice lines or employing our findings for rice cultivation managements showed up to 70% reductions in methane production from seven paddy field sites during 3 years of cultivation trials. Taken together, these findings offer great possibilities for effective mitigation of the global climatic impact of rice cultivation.

Fumarate reductase drives methane emissions in the genus Oryza through differential regulation of the rhizospheric ecosystem

The emergence of waterlogged Oryza species ∼15Mya (million years ago) supplied an anoxic warm bed for methane-producing microorganisms, and methane emissions have hence accompanied the entire evolutionary history of the genus Oryza. However, to date no study has addressed how methane emission has been altered during Oryza evolution. In this paper we used a diverse collection of wild and cultivated Oryza species to study the relation between Oryza evolution and methane emissions. Phylogenetic analyses and methane detection identified a co-evolutionary pattern between Oryza and methane emissions, mediated by the diversity of the rhizospheric ecosystems arising from different oxygen levels. Fumarate was identified as an oxygen substitute used to retain the electron transport/energy production in the anoxic rice root, and the contribution of fumarate reductase to Oryza evolution and methane emissions has also been assessed. We confirmed the between-species patterns using genetic dissection of the traits in a cross between a low and high methane-emitting species. Our findings provide novel insights on the evolutionary processes of rice paddy methane emissions: the evolution of wild rice produces different Oryza species with divergent rhizospheric ecosystem attributing to the different oxygen levels and fumarate reductase activities, methane emissions are comprehensively assessed by the rhizospheric environment of diversity Oryza species and result in a co-evolution pattern.

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

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

Microbial activity contributes to spatial heterogeneity of wetland methane fluxes

The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these emissions, it remains unclear what drives large, within-site variations. While geophysical factors (e.g., soil temperature) are known to correlate with methane (CH4) flux, measurable variance in these parameters often declines as spatial and temporal scales become finer. As methane emitted from wetlands is the direct, net product of microbial metabolisms which both produce and degrade CH4, it stands to reason that characterizing the spatial variability of microbial communities within a wetland-both horizontally and vertically-may help explain observed variances in flux. To that end, we surveyed microbial communities to a depth of 1 m across an ombrotrophic peat bog in Maine, USA using amplicon sequencing and gene expression techniques. Surface methane fluxes and geophysical factors were concurrently measured. Across the first meter of peat at the site, we observed significant changes in the abundance and composition of methanogenic taxa at every depth sampled, with variance in methanogen abundance explaining 70% of flux heterogeneity at a subset of plots. Among measured environmental factors, only peat depth emerged as correlated with flux, and had significant impact on the abundance and composition of methane-cycling communities. These conclusions suggest that a heightened awareness of how microbial communities are structured and spatially distributed within wetlands could offer improved insights into predicting CH4 flux dynamics. IMPORTANCE Globally, wetlands are one of the largest sources of methane (CH4), a greenhouse gas with a warming impact significantly greater than CO2. Methane produced in wetlands is the byproduct of a group of microorganisms which convert organic carbon into CH4. Despite our knowledge of how this process works, it is still unclear what drives dramatic, localized (<10 m) variance in emission rates from the surface of wetlands. While environmental conditions, like soil temperature or water table depth, correlate with methane flux when variance in these factors is large (e.g., spring vs fall), the explanatory power of these variables decline when spatial and temporal scales become smaller. As methane fluxes are the direct product of microbial activity, we profiled how the microbial community varied, both horizontally and vertically, across a peat bog in Maine, USA, finding that variance in microbial communities was likely contributing to much of the observed variance in flux.

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

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

Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples

Methanogenic archaea are an important component of the human and animal intestinal microbiota, and yet their presence is rarely reported in publications describing the subject. One of the methods of quantifying the prevalence of methanogens is quantitative real-time PCR (qPCR) of the methanogen-specific mcrA gene, and one of the possible reasons for detection failure is usually a methodology bias. Here, we refined the existing protocol by changing one of the primers and improving the conditions of the qPCR reaction. As a result, at the expense of a slightly lower yet acceptable PCR efficiency, the new assay was characterized by increased specificity and sensitivity and a wider linear detection range of 7 orders of magnitude. The lowest copy number of mcrA quantified at a frequency of 100% was 21 copies per reaction. The other validation parameters tested, such as reproducibility and linearity, also gave satisfactory results. Overall, we were able to minimize the negative impacts of primer dimerization and other cross-reactions on qPCR and increase the number of not only detectable but also quantifiable stool samples—or in this case, chicken droppings.

Understanding the mechanism of polybrominated diphenyl ethers reducing the anaerobic co-digestion efficiency of excess sludge and kitchen waste

Polybrominated diphenyl ethers (PBDEs) widely existing in the environment can pose a serious threat to the ecological safety. However, the influence of PBDEs on methane production by excess sludge (ES) and kitchen waste (KW) anaerobic co-digestion and its mechanism is not clear. To fill this gap, in this work, the co-digestion characteristics of ES and KW exposed to different levels of PBDEs at medium temperature were investigated in sequencing batch reactor, and the related mechanisms were also revealed. The results showed that PBDEs reduced methane production and the proportion of methane in the biogas. Methane yield decreased from 215.3 mL/g· volatile suspended solids (VSS) to 161.5 mL/(g·VSS), accompanied by the increase of PBDE content from 0 to 8.0 mg/Kg. Volatile fatty acid (VFA) yield was also inhibited by PBDEs; especially when PBDEs were 8.0 mg/Kg, VFA production was only 215.6 mg/g VSS, accounting for 75.7% of that in the control. Mechanism investigation revealed PBDEs significantly inhibited the processes of hydrolysis, acidogenesis, acetogenesis, and methanogenesis. Further study showed that PBDEs could inhibit the degradation and bioavailability of ES and KW, but it had a greater inhibition on the utilization of KW. Enzyme activity investigation revealed that all the key enzyme activities related to methane production were suppressed by PBDEs.

Anaerobic methane oxidation linked to Fe(III) reduction in a Candidatus Methanoperedens-enriched consortium from the cold Zoige wetland at Tibetan Plateau

Anaerobic oxidation of methane (AOM) is a microbial process degrading ample methane in anoxic environments, and Ca. Methanoperedens mediated nitrate- or metal-reduction linked AOM is believed important in freshwater systems. This work, via 16S rRNA gene diversity survey and 16S rRNA quantification, found abundant Ca. Methanoperedens along with iron in the cold Zoige wetland at Tibetan Plateau. The wetland soil microcosm performed Fe(III) reduction, rather than nitrate- nor sulphate-reduction, coupled methane oxidation (3.87 μmol d^-1 ) with 32.33 μmol Fe(II) accumulation per day at 18°C, but not at 30°C. A metagenome-assembled genome (MAG) recovered from the microcosm exhibits ~74% average nucleotide identity with the reported Ca. Methanoperedens spp. that perform Fe(III) reduction linked AOM, thus a novel species Ca. Methanoperedens psychrophilus was proposed. Ca. M. psychrophilus contains the whole suite of CO₂ reductive methanogenic genes presumably involving in AOM via a reverse direction, and comparative genome analysis revealed its unique gene categories: the multi-heme clusters (MHCs) cytochromes, the S-layer proteins highly homologous to those recovered from lower temperature environments and type IV pili, those could confer Ca. M. psychrophilus of cold adaptability. Therefore, this work reports the first methanotroph implementing AOM in an alpine wetland.

Comprehensive analysis of SUSIBA2 rice: The low-methane trait and associated changes in soil carbon and microbial communities

Rice cultivation is the primary source of anthropogenic methane (CH₄), which dramatically impacts global climate change. A growing body of evidence shows that optimizing photosynthate distribution is important for increasing rice yields and mitigating CH₄ emissions. Therefore, the molecular rice breeding with a barley HvSUSIBA2 gene that confers elevated photosynthate flux to grains, is predicted to enhance rice yield and mitigate CH₄ emissions in paddies. Here, in a series of field experiments with differences in growing season and rice variety, we show that SUSIBA2 rice reduced CH₄ emissions from paddies. SUSIBA2 rice grown in the early rice season and late rice season showed similar mitigation effects, with reduction rates of 50.98% for early rice and 50.97% for late rice. The reduction rate of SUSIBA2 rice during the winter rice season was significantly lower (22.26%) than those of other rice seasons. The reduction rates also varied between rice varieties, and SUSIBA2 japonica rice showed a more significant CH₄ mitigation effect than SUSIBA2 indica rice. Further yield-scaled CH₄ emission analyses indicated that the SUSIBA2 effect did not mitigate CH₄ emissions at the expense of yield. Compared with the wild type, SUSIBA2 rice significantly reduced soil organic carbon properties and the abundance of CH₄-related microbes, and altered methanogenic and methanotrophic communities, indicating that SUSIBA2 rice released less carbon to the soil, which reduced CH₄ production. Furthermore, a comparison of microbial communities between SUSIBA2 japonica and indica rice revealed different responses of methanogenic and methanotrophic communities, which may partly explain their differences in growth performance and CH₄ mitigation effect. Thus, our results show that SUSIBA2 rice substantially reduces CH₄ emissions and that SUSIBA2 can potentially mitigate the CH₄ emissions of japonica and indica rice under distinct cultivation conditions.

Waste to Energy: A Focus on the Impact of Substrate Type in Biogas Production

Anaerobic digestion is an efficient technology for a sustainable conversion of various organic wastes such as animal manure, municipal solid waste, agricultural residues and industrial waste into biogas. This technology offers a unique set of benefits, some of which include a good waste management technique, enhancement in the ecology of rural areas, improvement in health through a decrease of pathogens and optimization of the energy consumption of communities. The biogas produced through anaerobic digestion varies in composition, but it consists mainly of carbon dioxide methane together with a low quantity of trace gases. The variation in biogas composition are dependent on some factors namely the substrate type being digested, pH, operating temperature, organic loading rate, hydraulic retention time and digester design. However, the type of substrate used is of greater interest due to the direct dependency of microorganism activities on the nutritional composition of the substrate. Therefore, the aim of this review study is to provide a detailed analysis of the various types of organic wastes that have been used as a substrate for the sustainable production of biogas. Biogas formation from various substrates reported in the literature were investigated, an analysis and characterization of these substrates provided the pro and cons associated with each substrate. The findings obtained showed that the methane yield for all animal manure varied from 157 to 500 mL/gVS with goat and pig manure superseding the other animal manure whereas lignocellulose biomass varied from 160 to 212 mL/gVS. In addition, organic municipal solid waste and industrial waste showed methane yield in the ranges of 143–516 mL/gVS and 25–429 mL/gVS respectively. These variations in methane yield are primarily attributed to the nutritional composition of the various substrates.

Methylotrophic methanogens everywhere - physiology and ecology of novel players in global methane cycling

Research on methanogenic Archaea has experienced a revival, with many novel lineages of methanogens recently being found through cultivation and suggested via metagenomics approaches, respectively. Most of these lineages comprise Archaea (potentially) capable of methanogenesis from methylated compounds, a pathway that had previously received comparably little attention. In this review, we provide an overview of these new lineages with a focus on the Methanomassiliicoccales. These lack the Wood-Ljungdahl pathway and employ a hydrogen-dependent methylotrophic methanogenesis pathway fundamentally different from traditional methylotrophic methanogens. Several archaeal candidate lineages identified through metagenomics, such as the Ca. Verstraetearchaeota and Ca. Methanofastidiosa, encode genes for a methylotrophic methanogenesis pathway similar to the Methanomassiliicoccales. Thus, the latter are emerging as a model system for physiological, biochemical and ecological studies of hydrogen-dependent methylotrophic methanogens. Methanomassiliicoccales occur in a large variety of anoxic habitats including wetlands and animal intestinal tracts, i.e. in the major natural and anthropogenic sources of methane emissions, respectively. Especially in ruminant animals, they likely are among the major methane producers. Taken together, (hydrogen-dependent) methylotrophic methanogens are much more diverse and widespread than previously thought. Considering the role of methane as potent greenhouse gas, resolving the methanogenic nature of a broad range of putative novel methylotrophic methanogens and assessing their role in methane emitting environments are pressing issues for future research on methanogens.

Dietary supplemental plant oils reduce methanogenesis from anaerobic microbial fermentation in the rumen

Ruminants contribute to the emissions of greenhouse gases, in particular methane, due to the microbial anaerobic fermentation of feed in the rumen. The rumen simulation technique was used to investigate the effects of the addition of different supplemental plant oils to a high concentrate diet on ruminal fermentation and microbial community composition. The control (CTR) diet was a high-concentrate total mixed ration with no supplemental oil. The other experimental diets were supplemented with olive (OLV), sunflower (SFL) or linseed (LNS) oils at 6%. Rumen digesta was used to inoculate the fermenters, and four fermentation units were used per treatment. Fermentation end-products, extent of feed degradation and composition of the microbial community (qPCR) in digesta were determined. Compared with the CTR diet, the addition of plant oils had no significant (P > 0.05) effect on ruminal pH, substrate degradation, total volatile fatty acids or microbial protein synthesis. Gas production from the fermentation of starch or cellulose were decreased by oil supplementation. Methane production was reduced by 21-28% (P < 0.001), propionate production was increased (P < 0.01), and butyrate and ammonia outputs and the acetate to propionate ratio were decreased (P < 0.001) with oil-supplemented diets. Addition of 6% OLV and LNS reduced (P < 0.05) copy numbers of total bacteria relative to the control. In conclusion, the supplementation of ruminant diets with plant oils, in particular from sunflower or linseed, causes some favorable effects on the fermentation processes. The addition of vegetable oils to ruminant mixed rations will reduce methane production increasing the formation of propionic acid without affecting the digestion of feed in the rumen. Adding vegetable fats to ruminant diets seems to be a suitable approach to decrease methane emissions, a relevant cleaner effect that may contribute to alleviate the environmental impact of ruminant production.

Understanding gaseous reduction in swine manure resulting from nanoparticle treatments under anaerobic storage conditions

Manure is an impending source of carbon (C), sulfur (S) and water (H₂O). Consequently, microbial populations utilize these constituents to produce methane (CH₄), carbon dioxide (CO₂), greenhouse gases (GHGs), and hydrogen sulfide (H₂S). Application of nanoparticles (NPs) to stored manure is an emerging GHG mitigation technique. In this study, two NPs: nano zinc oxide (nZnO) and nano silver (nAg) were tested in swine manure stored under anaerobic conditions to determine their effectiveness in mitigating gaseous emissions and total gas production. The biological sources of gas production, i.e., microbial populations were characterized via Quantitative Polymerase Chain Reaction (qPCR) analysis. Additionally, pH, redox, and VFAs were determined using standard methods. Each treatment of the experiment was replicated three times and NPs were applied at a dose of 3 g/L of manure. Also, headspace gas from all treatment replicates were analyzed for CH₄ and CO₂ gas concentrations using an SRI-8610 Gas Chromatograph and H₂S concentrations were measured using a Jerome 631X meter. Nanoparticles tested in this study reduced the cumulative gas volume by 16%-79% compared to the control. Among the NPs tested, only nZnO consistently reduced GHG concentrations by 37%-97%. Reductions in H₂S concentrations ranged from 87% to 97%. Gaseous reductions were likely due to decreases in the activity and numbers of specific gas producing methanogenic archaea and sulfate reducing bacterial (SRB) species.

Electro-conversion of carbon dioxide (CO2) to low-carbon methane by bioelectromethanogenesis process in microbial electrolysis cells: The current status and future perspective

Given the aggravated greenhouse effect caused by CO₂ and the current energy shortage, CO₂ capture and reuse has been gaining ever-increasing concerns. Microbial Electrolysis Cells (MECs) has been considered to be a promising alternative to recycle CO₂ bioelectrochemically to low-carbon electrofuels such as CH₄ by combining electroactive microorganisms with electrochemical stimulation, enabling both CO₂ fixation and energy recovery. In spite of the numerous efforts dedicated in this field in recent years, there are still many problems that hinder CO₂ bioelectroconversion technique from the scaling-up and potential industrialization. This review comprehensively summarized the working principles, extracellular electron transfers behaviors, and the critical factors limiting the wide-spread utilization of CO₂ electromethanogenesis. Various characterization and electrochemical testing methods for helping to uncover the underlying mechanisms in CO₂ electromethanogenesis have been introduced. In addition, future research needs for pushing forward the development of MECs technology in real-world CO₂ fixation and recycling were elaborated.

Enhancing the anaerobic digestion process through carbon dioxide enrichment: initial insights into mechanisms of utilization

Carbon dioxide (CO₂) enrichment of anaerobic digesters (ADs) without hydrogen addition has been demonstrated to provide a potential solution to manage CO₂ streams generated in the water and organic waste sectors, with concomitant increases in methane (CH₄) production. This study investigates the CO₂ utilization mechanisms, by considering chemical and biological pathways in food waste and sewage sludge ADs. Methanosaetaceae was observed to be the dominant methanogen in sewage sludge ADs (Abundance of 83.8-98.8%) but scarce in food waste units (3.5-5.8%). Methanosarcinaceae was dominant in food waste (14.3-32.4%), likely due to a higher tolerance to the free ammonia nitrogen concentration recorded (885 mg L^-1). R_{Methanosaetaceae} (ratio of Methanosaetaceae fluorescence signal between test and control) of 1.45 and 1.79 were observed for sludge ADs enriched once and periodically with CO₂, respectively (p-value  < .05), suggesting a higher Methanosaetaceae activity associated with CO₂ enrichment. Reduction of CO₂ by homoacetogenesis followed by acetoclastic methanogenesis was proposed as a CO₂ utilization mechanism, which requires validation by radiolabelling or carbon isotope analysis.

Nanoparticles in mitigating gaseous emissions from liquid dairy manure stored under anaerobic condition

A number of mitigation techniques exist to reduce the emissions of pollutant gases and greenhouse gases (GHGs) from anaerobic storage of livestock manure. Nanoparticle (NP) application is a promising mitigating treatment option for pollutant gases, but limited research is available on the mode of NP application and their effectiveness in gaseous emission reduction. In this study, zinc silica nanogel (ZnSNL), copper silica nanogel (CuSNL), and N-acetyl cysteine (NACL) coated zinc oxide quantum dot (Qdot) NPs were compared to a control lacking NPs. All three NPs tested significantly reduced gas production and concentrations compared to non-treated manure. Overall, cumulative gas volumes were reduced by 92.73%-95.83%, and concentrations reduced by 48.98%-99.75% for H₂S, and 20.24%-99.82% for GHGs. Thus, application of NPs is a potential treatment option for mitigating pollutant and GHG emissions from anaerobically stored manure.

Machine learning analysis of microbial flow cytometry data from nanoparticles, antibiotics and carbon sources perturbed anaerobic microbiomes

BACKGROUND

Flow cytometry, with its high throughput nature, combined with the ability to measure an increasing number of cell parameters at once can surpass the throughput of prevalent genomic and metagenomic approaches in the study of microbiomes. Novel computational approaches to analyze flow cytometry data will result in greater insights and actionability as compared to traditional tools used in the analysis of microbiomes. This paper is a demonstration of the fruitfulness of machine learning in analyzing microbial flow cytometry data generated in anaerobic microbiome perturbation experiments.

RESULTS

Autoencoders were found to be powerful in detecting anomalies in flow cytometry data from nanoparticles and carbon sources perturbed anaerobic microbiomes but was marginal in predicting perturbations due to antibiotics. A comparison between different algorithms based on predictive capabilities suggested that gradient boosting (GB) and deep learning, i.e. feed forward artificial neural network with three hidden layers (DL) were marginally better under tested conditions at predicting overall community structure while distributed random forests (DRF) worked better for predicting the most important putative microbial group(s) in the anaerobic digesters viz. methanogens, and it can be optimized with better parameter tuning. Predictive classification patterns with DL (feed forward artificial neural network with three hidden layers) were found to be comparable to previously demonstrated multivariate analysis. The potential applications of this approach have been demonstrated for monitoring the syntrophic resilience of the anaerobic microbiomes perturbed by synthetic nanoparticles as well as antibiotics.

CONCLUSION

Machine learning can benefit the microbial flow cytometry research community by providing rapid screening and characterization tools to discover patterns in the dynamic response of microbiomes to several stimuli.

FISH analysis of microbial communities in a full-scale technology for biogas production

The anaerobic digestion is a biological process that consists of four stages. At the final step of the biodegradation of the organics the most sensitive to the ambient factors group of microorganisms - the methanogens, produces biogas with main component methane. Common problems of these technologies are low biogas yield, production of biogas with low quality or situations in which the plant gets out of exploitation. These problems are related to the lack of biological indicators of the process used in the practice and lack of understanding of the structure and functioning of the methanogenic consortium. Different fluorescent techniques have the potential to fulfill this gap and to contribute to the deep understanding of the structure of the microbial communities. In this study it was applied fluorescence in situ hybridization analysis for identifying and localization of microorganisms by the Archaea domain in digesters of wastewater treatment plant "Kubratovo". High negative correlation between the quantity of Archaea and the biogas and methane production has been registered. This method has the potential to be used as a tool for analyzing the structure of the microbial communities in the digesters and thus to allow the adaptation of the consortium and the optimization of the whole process.

Response of morphology and microbial community structure of granules to influent COD/SO42 - ratios in an upflow anaerobic sludge blanket (UASB) reactor treating starch wastewater

Biochemical properties of granules are of vital importance to UASB performance. This study characterized the granules cultivated at different COD/SO₄^2- ratios to elucidate the influence of sulfidogenesis on starch wastewater (1000 mg-COD L^-1) biodegradation kinetics and process stability. Suitable sulfate addition enriched granular microecosystems and stimulated the secretion of extracellular substances, facilitating cells cohersion and sludge aggregation. The percentage of granules larger than 2.8 mm increased from <10.0% to 58.8-69.4% with decreasing COD/SO₄^2- ratio from 10 to 2. Starch-fed granules tended to grow flagella-like filaments on the surface. The filaments overwhelmed by hydrophilic biopolymers had high affinity for biogas-bubbles and water-molecules aggravating granule floatation and washout. 16 s rRNA gene analysis revealed that decreasing COD/SO₄^2- ratio shifted Syntrophobacterales to Desulfovibrio, which co-worked with Methanosaeta while suppressing Methanobacterium thereby altering starch bioconversion routes. Decrease in Syntrophobacterales caused propionate accumulation and slight process upset.

Genome-Enhanced Detection and Identification (GEDI) of plant pathogens

Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.

A role for methanogens and methane in the regulation of GLP-1

INTRODUCTION

The gastrointestinal (GI) microbiome has emerged as a potential regulator of metabolism. However, the precise mechanisms of how microorganisms may influence physiology remain largely unknown. Interestingly, GI microorganisms, including methanogens, are localized within the same regions as the glucagon-like peptide-1 (GLP-1) secreting L cells. GLP-1 plays key roles appetite and glucose regulation. Furthermore, both methane and GLP-1 levels are altered in obese humans with metabolic disease. We predict that high-fat diet-induced obesity alters the abundance of GI methanogens and that methane may play a role in the GLP-1 secretory response from the L cell.

METHODS

To demonstrate this, GLP-1 secretion response and faecal methanogens were examined in mice given a high-fat diet for 14 weeks. In addition, the direct effect of methane on GLP-1 secretion was assessed in two L-cell models (NCI-H716 and GLUTag).

RESULTS

High-fat diet caused a significant increase in both GLP-1 secretion and faecal methanogen content. There was a direct correlation between GLP-1 secretion response and faecal methanogen levels. In L cells, methane stimulated GLP-1 secretion and enhanced intracellular cAMP content.

CONCLUSION

These results indicate that alterations in the methanogen communities occurring in obesity may play a vital role in directly enhancing GLP-1 secretion, and that methane can directly stimulate the secretion of GLP-1.

Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment

The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for "fraction of read abundance times cells"), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio, Desulfobacter, and Desulfobacterium, increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community.IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes.

Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence

Background

The widely established production of CH₄ from renewable biomass in industrial scale anaerobic reactors may play a major role in the future energy supply. It relies on methanogenic archaea as key organisms which represent the bottleneck in the process. The quantitative analysis of these organisms can help to maximize process performance, uncover disturbances before failure, and may ultimately lead to community-based process control schemes. Existing qPCR and fluorescence microscopy-based methods are very attractive but can be cost-intensive and laborious.

Results

In this study we present an autofluorescence-based, flow cytometric method for the fast low-cost quantification of methanogenic archaea in complex microbial communities and crude substrates. The method was applied to a methanogenic enrichment culture (MEC) and digester samples (DS). The methanogenic archaea were quantified using the distinct fluorescence of their cofactor F₄₂₀ in a range from 3.7 × 10⁸ (± 3.3 × 10⁶) cells mL⁻¹ and 1.8 x 10⁹ (± 1.1 × 10⁸) cells mL⁻¹. We evaluated different fixation methods and tested the sample stability. Stable abundance and fluorescence intensity were recorded up to 26 days during aerobic storage in PBS at 6 °C. The discrimination of the whole microbial community from the ubiquitous particle noise was facilitated by SYBR Green I staining and enabled calculation of relative abundances of methanogenic archaea of up to 9.64 ± 0.23% in the MEC and up to 4.43 ± 0.74% in the DS. The metaprofiling of the mcrA gene reinforced the results.

Conclusions

The presented method allows for fast and reliable quantification of methanogenic archaea in microbial communities under authentic digester conditions and can thus be useful for process monitoring and control in biogas digesters.

Electronic supplementary material

The online version of this article (10.1186/s12934-017-0793-7) contains supplementary material, which is available to authorized users.

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.

Characterization of zinc oxide nanoparticle (nZnO) alginate beads in reducing gaseous emission from swine manure

Hydrogen sulfide (H₂S) and greenhouse gases' emission from livestock production facilities are of concern to human welfare and the environment. Application of nanoparticles (NPs) has emerged as a potential option for minimizing these gaseous emissions. Application of bare NPs, however, could have an adverse effect on plants, soil, human health, and the environment. To minimize NPs' exposure to the environment by recovering them, NPs were entrapped in polymeric beads for treating livestock manure. The objectives of the research were to understand the mechanism of gaseous reduction in swine manure treated for 33 days with zinc oxide nanoparticles (nZnO) or nZnO-entrapped alginate (alginate-nZnO) beads by different characterization techniques. Headspace gases from treated manure flasks were collected in 2-6-day intervals during the experimental period and were analyzed for methane (CH₄), carbon dioxide (CO₂), and H₂S concentrations. The microbial analysis of manure was carried out using bacterial plate counts and Real-Time Polymerase Chain Reaction methods. Morphology and chemical composition of alginate-nZnO beads were analyzed by Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS), and X-ray Photoelectron Spectroscopy (XPS). Alginate-nZnO beads or bare nZnO proved to be an effective NP in reducing H₂S (up to 99%), CH₄ (49-72%), and CO₂ (46-62%) from manure stored under anaerobic conditions and these reductions are likely due to the microbial inhibitory effect from nZnO, as well as chemical conversion. Both SEM-EDS and XPS analysis confirmed the presence of zinc sulfide (ZnS) in the beads, which is likely formed by reacting nZnO with H₂S.

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

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

Biogas Production: Microbiology and Technology

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

Comparison of bacterial and archaeal communities in depth-resolved zones in an LNAPL body

Advances in our understanding of the microbial ecology at sites impacted by light non-aqueous phase liquids (LNAPLs) are needed to drive development of optimized bioremediation technologies, support longevity models, and develop culture-independent molecular tools. In this study, depth-resolved characterization of geochemical parameters and microbial communities was conducted for a shallow hydrocarbon-impacted aquifer. Four distinct zones were identified based on microbial community structure and geochemical data: (i) an aerobic, low-contaminant mass zone at the top of the vadose zone; (ii) a moderate to high-contaminant mass, low-oxygen to anaerobic transition zone in the middle of the vadose zone; (iii) an anaerobic, high-contaminant mass zone spanning the bottom of the vadose zone and saturated zone; and (iv) an anaerobic, low-contaminant mass zone below the LNAPL body. Evidence suggested that hydrocarbon degradation is mediated by syntrophic fermenters and methanogens in zone III. Upward flux of methane likely contributes to promoting anaerobic conditions in zone II by limiting downward flux of oxygen as methane and oxygen fronts converge at the top of this zone. Observed sulfate gradients and microbial communities suggested that sulfate reduction and methanogenesis both contribute to hydrocarbon degradation in zone IV. Pyrosequencing revealed that Syntrophus- and Methanosaeta-related species dominate bacterial and archaeal communities, respectively, in the LNAPL body below the water table. Observed phylotypes were linked with in situ anaerobic hydrocarbon degradation in LNAPL-impacted soils.

Distinctive non-methanogen archaeal populations in anaerobic digestion

Methanogens define the archaeal communities involved in anaerobic digestion. Recently, non-methanogen archaeal populations have been unexpectedly identified in anaerobic digestion processes. To gain insight into the ecophysiology of these uncharacterized archaeal populations, for the first time, a phylogenetic analysis was performed on a collection of non-methanogen archaeal 16S rRNA gene sequences from anaerobic digesters of broad geographic distribution, revealing a distinct clade formed by these sequences in subgroup 6 of the Miscellaneous Crenarchaeotal Group in the newly proposed archaeal phylum Bathyarchaeota. This exclusive phylogenetic assemblage enabled the development of a real-time quantitative PCR (qPCR) assay specifically targeting these non-methanogen archaeal populations in anaerobic digestion. Application of the qPCR assay in continuous anaerobic digesters indicated that these archaeal populations were minor constituents of the archaeal communities, and the abundance of these populations remained relatively constant irrespective of process perturbations. Analysis of the archaeal populations in methanogenic communities further revealed the co-occurrence of these non-methanogen archaea with acetoclastic methanogens. Nevertheless, the low abundance of non-methanogen archaea as compared with acetoclastic methanogens suggests that the non-methanogen archaeal populations were not major players in animal waste-fed methanogenic processes investigated in this study and the functions of these archaeal populations remain to be identified.

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

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

Microbial community composition and ultrastructure of granules from a full-scale anammox reactor

Granules in anammox reactors contain besides anammox bacteria other microbial communities whose identity and relationship with the anammox bacteria are not well understood. High calcium concentrations are often supplied to anammox reactors to obtain sufficient bacterial aggregation and biomass retention. The aim of this study was to provide the first characterization of bacterial and archaeal communities in anammox granules from a full-scale anammox reactor and to explore on the possible role of calcium in such aggregates. High magnification imaging using backscattered electrons revealed that anammox bacteria may be embedded in calcium phosphate precipitates. Pyrosequencing of 16S rRNA gene fragments showed, besides anammox bacteria (Brocadiacea, 32%), substantial numbers of heterotrophic bacteria Ignavibacteriacea (18%) and Anaerolinea (7%) along with heterotrophic denitrifiers Rhodocyclacea (9%), Comamonadacea (3%), and Shewanellacea (3%) in the granules. It is hypothesized that these bacteria may form a network in which heterotrophic denitrifiers cooperate to achieve a well-functioning denitrification system as they can utilize the nitrate intrinsically produced by the anammox reaction. This network may provide a niche for the proliferation of archaea. Hydrogenotrophic methananogens, which scavenge the key fermentation product H2, were the most abundant archaea detected. Cells resembling the polygon-shaped denitrifying methanotroph Candidatus Methylomirabilis oxyfera were observed by electron microscopy. It is hypothesized that the anammox process in a full-scale reactor triggers various reactions overall leading to efficient denitrification and a sink of carbon as biomass in anammox granules.

Understanding methane bioelectrosynthesis from carbon dioxide in a two-chamber microbial electrolysis cells (MECs) containing a carbon biocathode

To better understand the underlying mechanisms for methane bioelectrosynthesis, a two-chamber MECs containing a carbon biocathode was developed and studied. Methane production substantially increased with increasing cathode potential. Considerable methane yield was achieved at a poised potential of -0.9 V (vs. Ag/AgCl), reaching 2.30±0.34 mL after 5 h of operation with a faradaic efficiency of 24.2±4.7%. Confirmatory tests done at 0.9 V by switching the type of flushed substrates (CO2/N2) or the electrical exposure modes (ON/OFF) demonstrated that cathode serving as an electron donor was the vital driving force for methanogenesis occurring at microbe-electrode surface. Fluorescence in situ hybridization reveled Methanobacteriaceae (particularly Methanobacterium) was the predominant methanogens, supporting the mechanisms of direct electron transfer between cell-electrode. Additionally, the analysis of scanning electron microscope confirmed that the multiple pathways of electron transfer, including direct cathode-to-cell, interspecies exchange and semi-conductive conduits all together ensured the successful electromethanogenesis process.

Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration

Sequestration of CO₂ in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO₂ building up and also for the in situ potential bioconversion of stored CO₂ to methane. However, the information on these functional microbial communities and the impact of CO₂ storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO₂-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO₂. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO₂ injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO₂ injection and, if so, demonstrated the potential for microbial fixation and conversion of CO₂ into methane in subsurface oil reservoirs.

Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes

Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 10⁶ copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 10⁶ copies per gram dry weight) was observed, but higher abundance (6.9 × 10⁶ to 1.02 × 10⁸ copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 10⁵ copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 10⁵ copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 10⁸ copies per gram dry weight) and pmoA gene (1.56 × 10⁷ copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.

Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters

Anaerobic digestion (AD) is a biological process where different trophic groups of microorganisms break down biodegradable organic materials in the absence of oxygen. A wide range of AD technologies is being used to convert livestock manure, municipal and industrial wastewaters, and solid organic wastes into biogas. AD gains importance not only because of its relevance in waste treatment but also because of the recovery of carbon in the form of methane, which is a renewable energy and is used to generate electricity and heat. Despite the advances on the engineering and design of new bioreactors for AD, the microbiology component always poses challenges. Microbiology of AD processes is complicated as the efficiency of the process depends on the interactions of various trophic groups involved. Due to the complex interdependence of microbial activities for the functionality of the anaerobic bioreactors, the genetic expression of mcrA, which encodes a key enzyme in methane formation, is proposed as a parameter to monitor the process performance in real time. This review evaluates the current knowledge on microbial groups, their interactions, and their relationship to the performance of anaerobic biodigesters with a focus on using mcrA gene expression as a tool to monitor the process.

New PCR primers based on mcrA gene for retrieving more anaerobic methanotrophic archaea from coastal reedbed sediments

Two pairs of PCR primes ANMEallF/R and ANME23F/R were designed by Codehop method based on sequences available to retrieve more anaerobic methanotrophic (ANME) archaea mcrA gene sequences and ANME 2 and 3 subtypes from reedbed in two seasons. Overall, the PCR primers showed slightly favor for ANME group mcrA gene sequences. Due to the predominance of methanogens mainly affiliated to Methanomicrobiales in the samples, a large portion of mcrA gene sequences amplified in the clone libraries belonged to methanogens. Differences in PCR primers and performance affected the mcrA gene-PCR-amplified community composition to a minor extent. PCR primers targeting ANME mcrA group g-h were designed to apply real-time PCR for quantifying more groups of mcrA gene-affiliated ANME archaea and tested with these same samples, and the most abundant group in the whole ANME mcrA community was ANME group g-h. In addition, a stable mcrA gene-harboring archaeal community pattern was detected in the reedbed sediment samples collected from two distinctively different seasons. The PCR and qPCR primers designed in this study can expand our knowledge on the distribution of ANME mcrA genes and community composition in the ecosystem to better understand the carbon cycle.

Mechanism for stabilizing mRNAs involved in methanol-dependent methanogenesis of cold-adaptive Methanosarcina mazei zm-15

Methylotrophic methanogenesis predominates at low temperatures in the cold Zoige wetland in Tibet. To elucidate the basis of cold-adapted methanogenesis in these habitats, Methanosarcina mazei zm-15 was isolated, and the molecular basis of its cold activity was studied. For this strain, aceticlastic methanogenesis was reduced 7.7-fold during growth at 15°C versus 30°C. Methanol-derived methanogenesis decreased only 3-fold under the same conditions, suggesting that it is more cold adaptive. Reverse transcription-quantitative PCR (RT-qPCR) detected <2-fold difference in the transcript abundances of mtaA1, mtaB1, and mtaC1, the methanol methyltransferase (Mta) genes, in 30°C versus 15°C culture, while ackA and pta mRNAs, encoding acetate kinase (Ack) and phosphotransacetylase (Pta) in aceticlastic methanogenesis, were 4.5- and 6.8-fold higher in 30°C culture than in 15°C culture. The in vivo half-lives of mtaA1 and mtaC1B1 mRNAs were similar in 30°C and 15°C cultures. However, the pta-ackA mRNA half-life was significantly reduced in 15°C culture compared to 30°C culture. Using circularized RNA RT-PCR, large 5' untranslated regions (UTRs) (270 nucleotides [nt] and 238 nt) were identified for mtaA1 and mtaC1B1 mRNAs, while only a 27-nt 5' UTR was present in the pta-ackA transcript. Removal of the 5' UTRs significantly reduced the in vitro half-lives of mtaA1 and mtaC1B1 mRNAs. Remarkably, fusion of the mtaA1 or mtaC1B1 5' UTRs to pta-ackA mRNA increased its in vitro half-life at both 30°C and 15°C. These results demonstrate that the large 5' UTRs significantly enhance the stability of the mRNAs involved in methanol-derived methanogenesis in the cold-adaptive M. mazei zm-15.

Technical note: Comparison of biomarker and molecular biological methods for estimating methanogen abundance

Quantitative real-time PCR (qPCR) has become a popular method for estimation of methanogen abundance in the ruminant digestive tract. However, there is no established method in terms of primer choice and quantification, which means that results are variable and not directly comparable between studies. Archaeol has been proposed as an alternative marker for methanogen abundance, as it is ubiquitous in methanogenic Archaea, and can be quantified by gas chromatography-mass spectrometry (GC-MS). The aim of this experiment was to compare total methanogen populations estimated using the new archaeol approach with estimates based on qPCR. Specific primer sets and probes were used to detect dominant ruminal methanogen species Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanosphaera stadtmanae, and total methanogen populations. There was variation in the relationships among total methanogen abundance estimates based on archaeol and qPCR. In addition, the universal methanogen primers appeared to preferentially amplify genes from M. smithii. Archaeol had the strongest relationship with the dominant rumen methanogen M. ruminantium, whereas the total methanogen primers had a comparatively weak relationship with archaeol. Archaeol analysis was a useful adjunct to molecular biology methods, but it seems that a valid specific primer for M. ruminantium would be more useful than a biased primer for total methanogens.

Use of a hierarchical oligonucleotide primer extension approach for multiplexed relative abundance analysis of methanogens in anaerobic digestion systems

In this study, we established a rapid multiplex method to detect the relative abundances of amplified 16S rRNA genes from known cultivatable methanogens at hierarchical specificities in anaerobic digestion systems treating industrial wastewater and sewage sludge. The method was based on the hierarchical oligonucleotide primer extension (HOPE) technique and combined with a set of 27 primers designed to target the total archaeal populations and methanogens from 22 genera within 4 taxonomic orders. After optimization for their specificities and detection sensitivity under the conditions of multiple single-nucleotide primer extension reactions, the HOPE approach was applied to analyze the methanogens in 19 consortium samples from 7 anaerobic treatment systems (i.e., 513 reactions). Among the samples, the methanogen populations detected with order-level primers accounted for >77.2% of the PCR-amplified 16S rRNA genes detected using an Archaea-specific primer. The archaeal communities typically consisted of 2 to 7 known methanogen genera within the Methanobacteriales, Methanomicrobiales, and Methanosarcinales and displayed population dynamic and spatial distributions in anaerobic reactor operations. Principal component analysis of the HOPE data further showed that the methanogen communities could be clustered into 3 distinctive groups, in accordance with the distribution of the Methanosaeta, Methanolinea, and Methanomethylovorans, respectively. This finding suggested that in addition to acetotrophic and hydrogenotrophic methanogens, the methylotrophic methanogens might play a key role in the anaerobic treatment of industrial wastewater. Overall, the results demonstrated that the HOPE approach is a specific, rapid, and multiplexing platform to determine the relative abundances of targeted methanogens in PCR-amplified 16S rRNA gene products.

Archaeal diversity in biofilm technologies applied to treat urban and industrial wastewater: recent advances and future prospects

Biological wastewater treatment (WWT) frequently relies on biofilms for the removal of anthropogenic contaminants. The use of inert carrier materials to support biofilm development is often required, although under certain operating conditions microorganisms yield structures called granules, dense aggregates of self-immobilized cells with the characteristics of biofilms maintained in suspension. Molecular techniques have been successfully applied in recent years to identify the prokaryotic communities inhabiting biofilms in WWT plants. Although methanogenic Archaea are widely acknowledged as key players for the degradation of organic matter in anaerobic bioreactors, other biotechnological functions fulfilled by Archaea are less explored, and research on their significance and potential for WWT is largely needed. In addition, the occurrence of biofilms in WWT plants can sometimes be a source of operational problems. This is the case for membrane bioreactors (MBR), an advanced technology that combines conventional biological treatment with membrane filtration, which is strongly limited by biofouling, defined as the undesirable accumulation of microbial biofilms and other materials on membrane surfaces. The prevalence and spatial distribution of archaeal communities in biofilm-based WWT as well as their role in biofouling are reviewed here, in order to illustrate the significance of this prokaryotic cellular lineage in engineered environments devoted to WWT.

Characterization of the methanogen community in a household anaerobic digester fed with swine manure in China

Household anaerobic digesters have been installed across rural China for biogas production, but information on methanogen community structure in these small biogas units is sparsely available. By creating clone libraries for 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes, we investigated the methanogenic consortia in a household biogas digester treating swine manure. Operational taxonomic units (OTUs) were defined by comparative sequence analysis, seven OTUs were identified in the 16S rRNA gene library, and ten OTUs were identified in the mcrA gene library. Both libraries were dominated by clones highly related to the type strain Methanocorpusculum labreanum Z, 64.0 % for 16S rRNA gene clones and 64.3 % for mcrA gene clones. Additionally, gas chromatography assays showed that formic acid was 84.54 % of the total volatile fatty acids and methane was 57.20 % of the biogas composition. Our results may help further isolation and characterization of methanogenic starter strains for industrial biogas production.

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

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