Dominant Methanogens Research Articles

16s rRNA gene sequencing and radioisotopic analysis reveal the composition of ammonia acclimatized methanogenic consortia

Different mesophilic and thermophilic methanogenic consortia were acclimatised and enriched to extreme total ammonia (9.0 and 5.0 g NH4+-N L−1, respectively) and free ammonia (1.0 and 1.4 g NH3-N L−1, respectively) levels in this study. [2-14C] acetate radioisotopic analyses showed the dominance of aceticlastic methanogenesis in all enriched consortia. According to 16S rRNA gene sequencing result, in mesophilic consortia, methylotrophic Methanomassiliicoccus luminyensis was predominant, followed by aceticlastic Methanosarcina soligelidi. A possible scenario explaining the dominance of M. luminyensis includes the use of methylamine produced by Tissierella spp. and biomass build-up by metabolizing acetate. Nevertheless, further studies are needed to pinpoint the exact metabolic pathway of M. luminyensis. In thermophilic consortia, aceticlastic Methanosarcina thermophila was the sole dominant methanogen. Overall, results derived from this study demonstrated the efficient biomethanation ability of these ammonia-tolerant methanogenic consortia, indicating a potential application of these consortia to solve ammonia toxicity problems in future full-scale reactors.

Granular Carbon-Based Electrodes as Cathodes in Methane-Producing Bioelectrochemical Systems.

Methane-producing bioelectrochemical systems generate methane by using microorganisms to reduce carbon dioxide at the cathode with external electricity supply. This technology provides an innovative approach for renewable electricity conversion and storage. Two key factors that need further attention are production of methane at high rate, and stable performance under intermittent electricity supply. To study these key factors, we have used two electrode materials: granular activated carbon (GAC) and graphite granules (GG). Under galvanostatic control, the biocathodes achieved methane production rates of around 65 L CH4/m2catproj/d at 35 A/m2catproj, which is 3.8 times higher than reported so far. We also operated all biocathodes with intermittent current supply (time-ON/time-OFF: 4–2′, 3–3′, 2–4′). Current-to-methane efficiencies of all biocathodes were stable around 60% at 10 A/m2catproj and slightly decreased with increasing OFF time at 35 A/m2catproj, but original performance of all biocathodes was recovered soon after intermittent operation. Interestingly, the GAC biocathodes had a lower overpotential than the GG biocathodes, with methane generation occurring at −0.52 V vs. Ag/AgCl for GAC and at −0.92 V for GG at a current density of 10 A/m2catproj. 16S rRNA gene analysis showed that Methanobacterium was the dominant methanogen and that the GAC biocathodes experienced a higher abundance of proteobacteria than the GG biocathodes. Both cathode materials show promise for the practical application of methane-producing BESs.

Methanogenic degradation of tetramethylammonium hydroxide by Methanomethylovorans and Methanosarcina

This study evaluated the methanogens responsible for methanogenic degradation of tetramethylammonium hydroxide (TMAH) in a continuous flow bioreactor. The enriched methanogens attained an estimated maximum specific TMAH degradation rate and half-saturation constant of 39.5 mg TMAH/gVSS/h and 820 mg/L, following the Monod-type kinetic expression for methanogenic TMAH degradation. Presence of sulfide more than 20 mg/L significantly extended lag period and slowed down specific TMAH degradation rates. The results of terminal restriction fragment length polymorphism (T-RFLP), cloning/sequencing, and quantitative real-time PCR analyses targeting on the methyl coenzyme M reductase alpha subunit (mcrA) genes retrieved from the bioreactor and batch experiments indicated that Methanomethylovorans species were the dominant methanogens responsible for methanogenic degradation of TMAH. The isolated TMAH-degrading methanogen from the bioreactor, however, was identified closely related to Methanosarcina mazei. It is likely that a very low TMAH environment in the bioreactor favored the growth of Methanomethylovorans hollandica, while the much higher TMAH in the isolation growth medium proliferated Methanosarcina mazei.

Effect of Temperature on the Performance and Microbial Community Structure in an Integrated Anaerobic Fluidized-bed Membrane Bioreactor Treating Benzothiazole Wastewater

An integrated anaerobic fluidized-bed membrane bioreactor (IAFMBR) was applied to treat synthetic high-strength benzothiazole wastewater. This study investigated the effect of temperature on the performance, membrane fouling and microbial community structure of IAFMBR. The results showed that decreasing temperature had an adverse effect on the performance and the cycle of membrane fouling. When temperature declined from 35℃ to 15℃, the COD efficiency dropped 7.4%, benzothiazole removal efficiency dropped 49.2%, the accumulation of total VFAs increased 225.66 mg·L-1, and methane yield (in CH4/CODremoved) dropped 0.118 m3·kg-1. The membrane fouling cycle shortened from 5.2 d to 2.5 d. For cake layer, the concentration of soluble microbial product (SMP) increased from 42.47 mg·L-1 to 70.62 mg·L-1, and the extracellular polymeric substance (EPS) content (in VSS) increased from 46.30 mg·g-1 to 82.22 mg·g-1 when the TMP was 15 kPa. For mixed liquor, the concentration of SMP increased from 36.46 mg·L-1 to 69.35 mg·L-1 and the EPS content increased from 47.47 mg·g-1 to 81.63 mg·g-1. Protein was the main component of EPS and SMP, and occurred in proportion of 80%.The microbial community structure showed that the dominant phyla were Firmicutes and Chloroflexi, which accounted for 42.6%-61.0% of the total relative abundance. The genera Clostridium (13.7%), Levilinea (15.2%), and Lactococus (17.9%) dominated with decreasing temperatures. The dominant methanogen was Methanosaeta.

Effect of Mild-Temperature Thermo-Alkaline Pretreatment on the Solubilization and Anaerobic Digestion of Spent Coffee Grounds

Mild-temperature thermo-alkaline pretreatment of spent coffee grounds (SCG) was studied to improve its solubilization and methanation. The simultaneous effects of NaOH concentration (0–0.2 M) and temperature (60–90 °C) were investigated. Significant solubilization of SCG was achieved by the pretreatment, particularly under high-NaOH-concentration and high-temperature conditions. However, adding NaOH above a certain concentration adversely affected the methane production. Therefore, the degree of solubilization (SD) correlated poorly with methane yield (Ym). Response surface models of SD and Ym were successfully generated. The maximum response of SD (36.4%) was obtained at 0.18 M NaOH and 90.0 °C, while that of Ym (263.31 mL CH4/g COD added) was obtained at 0.13 M NaOH and 70.5 °C. Hydrogenotrophic Methanospirillum species were the dominant methanogens in all the SCG digestion tests. It is likely that NaOH concentration had a more significant influence on the development of microbial community structure, particularly of methanogens than temperature.

Methanosarcina plays a main role during methanogenesis of high-solids food waste and cardboard

Anaerobic digestion of food waste is a complex process often hindered by high concentrations of volatile fatty acids and ammonia. Methanogenic archaea are more sensitive to these inhibitors than bacteria and thus the structure of their community is critical to avoid reactor acidification. In this study, the performances of three different inocula were compared using batch digestion tests of food waste and cardboard mixtures. Particular attention was paid to the archaeal communities in the inocula and after digestion. While the tests started with inocula rich in Methanosarcina led to efficient methane production, VFAs accumulated in the reactors where inocula initially were poor in this archaea and no methane was produced. In addition, higher substrate loads were tolerated when greater proportions of Methanosarcina were initially present in the inoculum. Independently of the inoculum origin, Methanosarcina were the dominant methanogens in the digestates from the experiments that efficiently produced methane. These results suggest that the initial archaeal composition of the inoculum is crucial during reactor start-up to achieve stable anaerobic digestion at high concentrations of ammonia and organic acids.

Effects of CO on hydrogenotrophic methanogenesis under thermophilic and extreme-thermophilic conditions: Microbial community and biomethanation pathways

Coke oven gas is considered as a potential hydrogen source for biogas bio-upgrading. In this study, the effects of CO on biomethanation performance and microbial community structure of hydrogenotrophic mixed cultures were investigated under thermophilic (55 °C) and extreme-thermophilic (70 °C) conditions. 5% (v/v) CO did not inhibit hydrogenotrophic methanogenesis during semi-continuous operation, and 83–97% CO conversion to CH4 was achieved. Methanothermobacter thermoautotrophicus was the dominant methanogen at both temperatures and was the main functional archaea associated with CO biomethanation. Specific methanogenic activity test results showed that long-term 5% CO acclimation shortened the lag phase from 5 h to 1 h at 55 °C and 15 h to 3 h at 70 °C. CO2 was the preferred carbon source over CO for hydrogenotrophic methanogens and CO consumption only started when CO2 was completely depleted. M. thermoautotrophicus dominated mixed cultures showed a great potential in simultaneous hydrogenotrophic methanogenesis and CO biomethanation.

Comprehensive analysis of microbial communities in full-scale mesophilic and thermophilic anaerobic digesters treating food waste-recycling wastewater

Microbes were sampled for a year in a full-scale mesophilic anaerobic digester (MD) and a thermophilic anaerobic digester (TD) treating food waste-recycling wastewater (FRW), then microbial community structure, dynamics and diversity were quantified. In the MD, Fastidiosipila, Petrimonas, vadinBC27, Syntrophomonas, and Proteiniphilum were dominant bacterial genera; they may contribute to hydrolysis and fermentation. In the TD, Defluviitoga, Gelria and Tepidimicrobium were dominant bacteria; they may be responsible for hydrolysis and acid production. In the MD, dominant methanogens changed from Methanobacterium (17.1 ± 16.9%) to Methanoculleus (67.7 ± 17.8%) due to the increase in ammonium concentration. In the TD, dominant methanogens changed from Methanoculleus (42.8 ± 13.6%) to Methanothermobacter (49.6 ± 11.0%) due to the increase of pH. Bacteria and archaea were more diverse in the MD than in the TD. These results will guide development of microbial management methods to improve the process stability of MD and TD treating FRW.

Hydrogenotrophic methanogenesis is the dominant methanogenic pathway in neotropical tank bromeliad wetlands.

Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that emits substantial amounts of CH4 . Tank bromeliads growing in the forest canopy (functional type-II tank bromeliads) were found to emit more CH4 than tank bromeliads growing on the forest floor (functional type-I tank bromeliads) but the reasons for this difference and the underlying microbial CH4 -cycling processes have not been studied. Therefore, we characterized archaeal communities in bromeliad tanks of the two different functional types in a neotropical montane forest of southern Ecuador using terminal-restriction fragment length polymorphism (T-RFLP) and performed tank-slurry incubations to measure CH4 production potential, stable carbon isotope fractionation and pathway of CH4 formation. The archaeal community composition was dominated by methanogens and differed between bromeliad functional types. Hydrogenotrophic Methanomicrobiales were the dominant methanogens and hydrogenotrophic methanogenesis was the dominant methanogenic pathway among all bromeliads. The relative abundance of aceticlastic Methanosaetaceae and the relative contribution of aceticlastic methanogenesis increased in type-I tank bromeliads probably due to more oxic conditions in type-I than in type-II bromeliads leading to the previously observed lower in situ CH4 emissions from type-I tank bromeliads but to higher CH4 production potentials in type-I tank bromeliad slurries.

Anaerobic digestion using ultrasound as pretreatment approach: Changes in waste activated sludge, anaerobic digestion performances and digestive microbial populations

To solve the problem of slow hydrolysis rate during anaerobic digestion, 20 kHz of ultrasound and energy density of 0.5 W/mL were applied as pretreatments for mesophilic anaerobic digestion of waste activated sludge. The sludge was digested at hydraulic retention time (HRT) of 20 d after sonication of 0–100 min. Results showed that ultrasonic pretreatment was beneficial to the dissolution of soluble chemical oxygen demand (SCOD) from the waste activated sludge, coupled with the rapid degradation in the dewatering performance of the sludge. In the succeeding anaerobic digestion, when sonication of the treated sludge was more than 80 min, the removal rate of total chemical oxygen demand (TCOD) and the sludge reduction rate also decreased significantly. Gas and methane productions were highest at the reactor fed with sludge sonicated at 80 min. At this condition, the content of CH4 was more than 53.8%, and the average yield of methane was about 36.2 mL/gVS. Through the analysis of microbial diversity, we observed that hydrolytic and acidification bacteria were abundant in the reactors. Methanocorpusculum and Methanosaeta were the alternating dominant methanogens in the anaerobic reactors, with adding sludge suffered different ultrasonic time. In the sludge pretreated with ultrasonication after 80 min, the relative abundance of Methanocorpusculum decreased rapidly, and the dominant substrate for anaerobic methanogenesis changed from hydrogen to acetic acid.

Anaerobic digestion of chicken manure: Mitigating process inhibition at high ammonia concentrations by selenium supplementation

In this study, the anaerobic digestion of nitrogen-rich chicken manure from egg-laying hens was investigated via long-term continuous experiments with and without the addition of different trace elements. With trace element supplementation, a CH4 yield of 0.26 ± 0.03 m3 kg−1 of volatile solids (VS) added was achieved at an organic loading rate (OLR) of 3.62 kg m−3 day−1 based on VS and total ammonia nitrogen (TAN) content greater than 7200 g m−3. Selenium (Se) was identified as the critical trace element for the stable anaerobic digestion of chicken manure. The dominant methanogen in the reactors was the hydrogenotrophic methanogen Methanoculleus bourgensis. Therefore, we concluded that at elevated TAN concentrations, the CH4 production stimulated by Se supplementation likely occurred through syntrophic acetate oxidation. Without trace element supplementation, severe acetic and propionic acid accumulation occurred, causing the CH4 yield to decrease below 0.12 m3 kg−1 of VS added.

Comparative study of rumen fermentation and microbial community differences between water buffalo and Jersey cows under similar feeding conditions

ABSTRACTDifferences in rumen volatile fatty acids (VFAs), microbial population and community composition between water buffalo and Jersey cows were compared to explore the effects of animal species on ruminal microbiota. Ruminally fistulated buffalo (n = 4) and Jersey cows (n = 4) with similar body weights were selected and provided with similar diets. After feeding for 30 days, rumen fluid was collected to quantify the ruminal VFA, and determine microbial population and community composition. Results revealed that concentrations of total VFA, acetate and propionate in buffalo were higher (P > .05), while butyrate concentration and acetate/propionate ratio were lower than those in Jersey cows (P < .05). Populations of ruminal bacteria, protozoa, fungi and F. succinogenes were higher in buffalo (P < .05). The abundance of Firmicutes was higher (P < .05), while the abundance of Bacteroidetes was lower in buffalo (P < .05). The abundances of dominant bacterial genus Prevotella and dominant methanogen genus Methanobrevibacter were higher in Jersey cows (P < .05). Protozoal genus Metadinium was dominant in buffalo, while Entodinium was dominant in Jersey cows. Concluded that not only rumen microbial population, but also microbial community composition were different between two species. The higher bacterial, protozoal and fungal populations, and different microbial community can explain why buffalo are more efficient to digest fibre.

Fast anaerobic sludge granulation at elevated salinity

It is commonly accepted that high salt concentrations negatively affect microbial activity in biological wastewater treatment reactors such as upflow anaerobic sludge blanket (UASB) reactors. Microbial aggregation in such reactors is equally important. It is well documented that anaerobic granules, when exposed to high salinity become weak and disintegrate, causing wash-out, operational problems and decreasing process performance. In this research, the possibility of microbial granule formation from dispersed biomass was investigated at salinity levels of 5 and 20 g Na+/L. High removal efficiencies of soluble influent organics were achieved at both salinity levels and this was accompanied by fast and robust formation of microbial granules. The process was found to be stable for the entire operational period of 217 days. As far as we know this is the first time it has been demonstrated that stable granule formation is possible at a salinity level as high as 20 g Na+/L. Methanosaeta was identified as the dominant methanogen at both salinity levels. Streptococcus spp. and bacteria belonging to the family Lachnospiraceae were identified as the dominant microbial population at 5 and 20 and g Na+/L, respectively.

Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments.

Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica's Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ13C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ13C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.

Recovery of methane turnover and the associated microbial communities in restored cutover peatlands is strongly linked with increasing Sphagnum abundance

Vegetation succession is known to affect carbon-cycling patterns of recovering cutover peatlands, displayed as shifts in emissions of the greenhouse gases CO2 and CH4. However, the related plant-microbe interactions are still poorly understood. We aimed to link the recovery of the organisms responsible for CH4 turnover, the methanogens and the methanotrophs, to the re-vegetation related compositional changes of three functional plant types (Sphagna, sedges and shrubs). In peat layers, the Sphagnum coverage was the most influential factor for the activity, abundance and community structures of both these microbial groups, demonstrating a succession pattern towards a pristine stage. Analysis of mcrA and pmoA genes revealed Methanoregulaceae and Methylocystis as the most dominant methanogens and methanotrophs, respectively. The relatively fast recovery of both CH4 production and oxidation in the peat layers supports earlier flux based results from these same fen-type peatland sites. In contrast to peat, CH4 oxidation in living Sphagnum mosses appeared to be independent of vegetation succession as CH4 oxidation potential was similar throughout the succession stages. This indicated that Sphagnum may be a valuable CH4 biofilter especially in the early re-vegetation stages when the oxidation in the peat has not yet recovered. Therefore, we recommend Sphagnum transplantation as a tool for climate friendly peatland restoration with faster recovery of the carbon sink function and altered CH4 emissions.

Clarifying electron transfer and metagenomic analysis of microbial community in the methane production process with the addition of ferroferric oxide

Direct interspecies electron transfer (DIET) is a new mechanism responsible for syntrophic methane production. Supplementation of conductive material in syntrophic communities can facilitate electron transfer and enhance methane production. Ferroferric oxide (Fe3O4) was dosed in an anaerobic sequencing batch reactor (ASBR) fed with tryptone-based synthetic wastewater to examine its effect on the anaerobic treatment process. Long-term dosage of Fe3O4 not only enhanced the maximum methane production rate by 78.3% in a reaction cycle but also improved methane production when hydrogen/carbon dioxide or acetate was used as the substrate. The conductivity of anaerobic sludge, activity of the electron transport chain, and extracellular electron transfer ability were enhanced with the addition of Fe3O4, inducing enhanced system performance for methane production. Proteiniclasticum and Prolixibacter were the enriched acidogens responsible for hydrolysis and acidification. With the addition of Fe3O4, Methanosarcina was the dominant methanogen, and metagenomic analysis further revealed the genes involved in the hydrogenotrophic pathway of methanogenesis. Methanosarcina might be involved in DIET, and Fe3O4 was responsible for its stimulation.

Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: Key process parameters and microbial indicators of process instability

In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1–2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M. thermophilus, and Methanobacterium beijingense were revealed as dominant methanogens. Bacterial community structures were clearly differentiated by digesters; archaeal community structures of each digester were dominated by one or two methanogen species. Temperature, ammonia, propionate, Na+, and acetate in the digester were significant factors shaping microbial community structures. The total microbial populations, microbial diversity, and specific bacteria genera showed potential as indicators of process instability in the anaerobic digestion of FWW.

Methanogenic Community Was Stable in Two Contrasting Freshwater Marshes Exposed to Elevated Atmospheric CO2.

The effects of elevated atmospheric CO2 concentration on soil microbial communities have been previously recorded. However, limited information is available regarding the response of methanogenic communities to elevated CO2 in freshwater marshes. Using high-throughput sequencing and real-time quantitative PCR, we compared the abundance and community structure of methanogens in different compartments (bulk soil, rhizosphere soil, and roots) of Calamagrostis angustifolia and Carex lasiocarpa growing marshes under ambient (380 ppm) and elevated CO2 (700 ppm) atmospheres. C. lasiocarpa rhizosphere was a hotspot for potential methane production, based on the 10-fold higher abundance of the mcrA genes per dry weight. The two marshes and their compartments were occupied by different methanogenic communities. In the C. lasiocarpa marsh, archaeal family Methanobacteriaceae, Rice Cluster II, and Methanosaetaceae co-dominated in the bulk soil, while Methanobacteriaceae was the exclusively dominant methanogen in the rhizosphere soil and roots. Families Methanosarcinaceae and Methanocellaceae dominated in the bulk soil of C. angustifolia marsh. Conversely, Methanosarcinaceae and Methanocellaceae together with Methanobacteriaceae dominated in the rhizosphere soil and roots, respectively, in the C. angustifolia marsh. Elevated atmospheric CO2 increased plant photosynthesis and belowground biomass of C. lasiocarpa and C. angustifolia marshes. However, it did not significantly change the abundance (based on mcrA qPCR), diversity, or community structure (based on high-throughput sequencing) of methanogens in any of the compartments, irrespective of plant type. Our findings suggest that the population and species of the dominant methanogens had weak responses to elevated atmospheric CO2. However, minor changes in specific methanogenic taxa occurred under elevated atmospheric CO2. Despite minor changes, methanogenic communities in different compartments of two contrasting freshwater marshes were rather stable under elevated atmospheric CO2.

Non-autotrophic methanogens dominate in anaerobic digesters

Anaerobic digesters are man-made habitats for fermentative and methanogenic microbes, and are characterized by extremely high concentrations of organics. However, little is known about how microbes adapt to such habitats. In the present study, we report phylogenetic, metagenomic, and metatranscriptomic analyses of microbiomes in thermophilic packed-bed digesters fed acetate as the major substrate, and we have shown that acetoclastic and hydrogenotrophic methanogens that utilize acetate as a carbon source dominate there. Deep sequencing and precise binning of the metagenomes reconstructed complete genomes for two dominant methanogens affiliated with the genera Methanosarcina and Methanothermobacter, along with 37 draft genomes. The reconstructed Methanosarcina genome was almost identical to that of a thermophilic acetoclastic methanogen Methanosarcina thermophila TM-1, indicating its cosmopolitan distribution in thermophilic digesters. The reconstructed Methanothermobacter (designated as Met2) was closely related to Methanothermobacter tenebrarum, a non-autotrophic hydrogenotrophic methanogen that grows in the presence of acetate. Met2 lacks the Cdh complex required for CO2 fixation, suggesting that it requires organic molecules, such as acetate, as carbon sources. Although the metagenomic analysis also detected autotrophic methanogens, they were less than 1% in abundance of Met2. These results suggested that non-autotrophic methanogens preferentially grow in anaerobic digesters containing high concentrations of organics.

Vertical profiles of sediment methanogenic potential and communities in two plateau freshwater lakes

Abstract. Microbial methanogenesis in sediment plays a crucial role in CH4 emission from freshwater lake ecosystems. However, knowledge of the layer-depth-related changes of methanogen community structure and activities in freshwater lake sediment is still limited. The present study was conducted to characterize the methanogenesis potential in different sediment-layer depths and the vertical distribution of microbial communities in two freshwater lakes of different trophic status on the Yunnan Plateau (China). Incubation experiments and inhibitor studies were carried out to determine the methanogenesis potential and pathways. 16S rRNA and mcrA genes were used to investigate the abundance and structure of methanogen and archaeal communities, respectively. Hydrogenotrophic methanogenesis was mainly responsible for methane production in sediments of both freshwater lakes. The layer-depth-related changes of methanogenesis potential and the abundance and community structure of methanogens were observed in both Dianchi Lake and Erhai Lake. Archaeal 16S rRNA and mcrA genes displayed a similar abundance change pattern in both lakes, and the relative abundance of methanogens decreased with increasing sediment-layer depth. Archaeal communities differed considerably in Dianchi Lake and Erhai Lake, but methanogen communities showed a slight difference between these two lakes. However, methanogen communities illustrated a remarkable layer-depth-related change. Order Methanomicrobiales was the dominant methanogen group in all sediments, while Methanobacteriales showed a high proportion only in upper layer sediments. The trophic status of the lake might have a notable influence on the depth-related change pattern of methanogenesis activity, while the methanogen community structure was mainly influenced by sediment depth.