methanogenic archaea

Aminoacyl-tRNA synthetases (aaRSs) play an integral role in protein synthesis, functioning to attach the correct amino acid with its cognate tRNA molecule. AaRSs are known to associate into higher-order multi-aminoacyl-tRNA synthetase complexes (MSC) involved in archaeal and eukaryotic translation, although the precise biological role remains largely unknown. To gain further insights into archaeal MSCs, possible proteinprotein interactions with the atypical Methanothermobacter thermautotrophicus seryl-tRNA synthetase (MtSerRS) were investigated. Yeast two-hybrid analysis revealed arginyl-tRNA synthetase (MtArgRS) as an interacting partner of MtSerRS. Surface plasmon resonance confirmed stable complex formation, with a dissociation constant (K D ) of 250 nM. Formation of the MtSerRS⅐MtArgRS complex was further supported by the ability of GST-MtArgRS to co-purify MtSerRS and by coelution of the two enzymes during gel filtration chromatography. The MtSerRS⅐MtArgRS complex also contained tRNA Arg , consistent with the existence of a stable ribonucleoprotein complex active in aminoacylation. Steady-state kinetic analyses revealed that addition of MtArgRS to MtSerRS led to an almost 4-fold increase in the catalytic efficiency of serine attachment to tRNA, but had no effect on the activity of MtArgRS. Further, the most pronounced improvements in the aminoacylation activity of MtSerRS induced by MtArgRS were observed under conditions of elevated temperature and osmolarity. These data indicate that formation of a complex between Mt-SerRS and MtArgRS provides a means by which methanogenic archaea can optimize an early step in translation under a wide range of extreme environmental conditions.

The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community c...

Biochar has been proposed as an effective material for mitigating greenhouse gas emissions from farmlands, but comparable information for earthen aquaculture ponds is limited. A field study was conducted to investigate the effects of adding biochar (200–1600 kg ha􀀀 1) derived from the invasive plant Spartina alterniflora on sediment physico-chemical properties, CH4 production potential (PCH4), and the relevant functional gene abundances in earthen aquaculture ponds during the non-farming period. The results indicated that biochar treatments increased sediment porosity and salinity, while decreasing dissolved organic carbon and microbial biomass carbon. Biochar-treated sediments also exhibited a significantly lower abundance of mcrA gene especially in the early drainage stage, and a higher abundance of pmoA gene especially in the intermediate and final drainage stages. Consequently, the mean PCH4 in biochar-treated sediments (1.28–21.12 ng g􀀀 1 d􀀀 1) was 57–73% lower
than in the control group (5.41–39.45 ng g􀀀 1 d􀀀 1). The reduction in PCH4 did not differ between biochar produced at 300 ◦C vs. 500 ◦C and was not dependent on the amount of biochar added. The findings suggest that
using biochar derived from S. alterniflora can be a cost-effective method to control the spread of this invasive plant and reduce CH4 production in aquaculture pond sediment during the non-farming period.

Plant invasion and land reclamation have drastically transformed the landscape of coastal wetlands globally, but their resulting effects on soil organic nitrogen (SON) mineralization and nitrous oxide (N 2 O) production remain unclear. In this study, we examined 21 coastal wetlands across southern China that have undergone habitat transformation from native mudflats (MFs) to Spartina alterniflora marshes (SAs), and subsequently to earthen aquaculture ponds (APs). We determined the SON net mineralization rate and the presence of pertinent enzyme-encoding genes, namely chiA, pepA, and pepN. The SON net mineralization rate increased by 46.7% following the conversion of MFs to SAs but decreased by 33.1% in response to the transformation of SAs to APs. Nevertheless, there was no significant difference in the estimated mineralization efficiency of soil microbes among the habitat types. The results of structural equation modeling showed that Nmineralization gene abundance played a major role in regulating SON mineralization. Although less than 20% of the SON was estimated to be labile/semi-labile, SON mineralization was important in sustaining soil N 2 O production, with 5.8% of the mineralized N being fed into N 2 O production. Overall, our findings showed that the presence of S. alterniflora increased both SON content and mineralization rate, which would in turn promote further proliferation of this exotic plant along the coast. The conversion of S. alterniflora marshes to APs partially mitigated the positive effects of exotic plant invasion on SON turnover.

This study investigated the operation of ex-situ biological methanation at two thermophilic temperatures (55°C and 65°C). Methane composition of 85 to 88% was obtained and volumetric productivities of 0.45 and 0.4 L CH 4 /L reactor were observed at 55°C and 65°C after 24h respectively. It is postulated that at 55°C the process operated as a mixed culture as the residual organic substrates in the starting inoculum were still available. These were consumed prior to the assessment at 65°C; thus the methanogens were now dependent on gaseous substrates CO 2 and H 2. The experiment was repeated at 65°C with fresh inoculum (a mixed culture); methane composition and volumetric productivity of 92% and 0.46 L CH 4 /L reactor were achieved in 24 hours. Methanothermobacter species represent likely and resilient candidates for thermophilic biogas upgrading.

This study investigated the operation of ex-situ biological methanation at two thermophilic temperatures (55°C and 65°C). Methane composition of 85 to 88% was obtained and volumetric productivities of 0.45 and 0.4 L CH 4 /L reactor were observed at 55°C and 65°C after 24h respectively. It is postulated that at 55°C the process operated as a mixed culture as the residual organic substrates in the starting inoculum were still available. These were consumed prior to the assessment at 65°C; thus the methanogens were now dependent on gaseous substrates CO 2 and H 2. The experiment was repeated at 65°C with fresh inoculum (a mixed culture); methane composition and volumetric productivity of 92% and 0.46 L CH 4 /L reactor were achieved in 24 hours. Methanothermobacter species represent likely and resilient candidates for thermophilic biogas upgrading.

The formation of mineral-bound organic carbon (OC) complexes is important for the long-term preservation of soil organic carbon (SOC) in wetlands. Many coastal wetlands globally have been threatened by plant invasion and land development, but information on the effects on mineral-bound OC is limited. We measured the soil contents of Ca-OC, Fe(Al)-OC and residual OC across 21 coastal wetlands in southern China that have gone through the same sequence of land cover change, from native mudflats (MFs) to Spartina alterniflora marshes (SAs) then to earthen aquaculture ponds (APs). Residual-OC was the main component of SOC (74.1-78.2 %), followed by Fe(Al)-OC (18.4-22.8 %) and Ca-OC (<3.5 %). All three components in the soil increased when MFs were converted to SAs, but decreased in subsequent conversion of SAs to APs. Land cover change affected Fe(Al)-OC the most, but SOC storage increased more strongly with increasing Ca-OC. Nitrogen supply in the form of NH 4 +-N and clay content both positively affected the changes in mineral-bound OC. Our results suggest that different land cover change scenarios had different effects on the amounts of mineral-bound OC and their liability to microbial turnover, resulting in different degrees of SOC preservation and carbon emissions.

Aquaculture ponds are potential hotspots for carbon cycling and emission of greenhouse gases (GHGs) like CO 2 and CH 4 , but they are often poorly assessed in the global GHG budget. This study determined the temporal variations of CO 2 and CH 4 concentrations and diffusive fluxes and their environmental drivers in coastal aquaculture ponds in southeastern China over a five-year period (2017-2021). The findings indicated that CH 4 flux from aquaculture ponds fluctuated markedly year-to-year, and CO 2 flux varied between positive and negative between years. The coefficient of inter-annual variation of CO 2 and CH 4 diffusive fluxes was 168% and 127%, respectively, highlighting the importance of long-term observations to improve GHG assessment from aquaculture ponds. In addition to chlorophyll-a and dissolved oxygen as the common environmental drivers, CO 2 was further regulated by total dissolved phosphorus and CH 4 by dissolved organic carbon. Feed conversion ratio correlated positively with both CO 2 and CH 4 concentrations and fluxes, showing that unconsumed feeds fueled microbial GHG production. A linear regression based on binned (averaged) monthly CO 2 diffusive flux data, calculated from CO 2 concentrations, can be used to estimate CH 4 diffusive flux with a fair degree of confidence (r 2 = 0.66; p < 0.001). This algorithm provides a simple and practical way to assess the total carbon diffusive flux from aquaculture ponds. Overall, this study provides new insights into mitigating the carbon footprint of aquaculture production and assessing the impact of aquaculture ponds on the regional and global scales.

Our goal was to examine the composition of methanogenic archaea (MA) and sulfate-reducing (SRP) and sulfur-oxidizing (SOP) prokaryotes in the extreme athalassohaline and particularly sulfate-rich sediment of Tirez Lagoon (Spain). Thus, adenosine-5′-phosphosulfate (APS) reductase α (aprA) and methyl coenzyme M reductase α (mcrA) gene markers were amplified given that both enzymes are specific for SRP, SOP, and MA, respectively. Anaerobic populations sampled at different depths in flooded and dry seasons from the anoxic sediment were compared qualitatively via denaturing gradient gel electrophoresis (DGGE) fingerprint analysis. Phylogenetic analyses allowed the detection of SRP belonging to Desulfobacteraceae, Desulfohalobiaceae, and Peptococcaceae in ∂-proteobacteria and Firmicutes and SOP belonging to Chromatiales/Thiotrichales clade and Ectothiorhodospiraceae in γ-proteobacteria as well as MA belonging to methylotrophic species in Methanosarcinaceae and one hydrogenotrophic species...

Direct measurement of methane emissions is cost-prohibitive for greenhouse gas offset projects, necessitating the development of alternative accounting methods such as proxies. Salinity is a useful proxy for tidal marsh CH4 emissions when comparing across a wide range of salinity regimes but does not adequately explain variation in brackish and freshwater regimes, where variation in emissions is large. We sought to improve upon the salinity proxy in a marsh complex on Deal Island Peninsula, Maryland, USA by comparing emissions from four strata differing in hydrology and plant community composition. Mean CH4 chamber-collected emissions measured as mg CH4 m−2 h−1 ranked as S. alterniflora (1.2 ± 0.3) ≫ High-elevation J. roemerianus (0.4 ± 0.06) &gt; Low-elevation J. roemerianus (0.3 ± 0.07) = S. patens (0.1 ± 0.01). Sulfate depletion generally reflected the same pattern with significantly greater depletion in the S. alterniflora stratum (61 ± 4%) than in the S. patens stratum (1 ± 9%)...

Additional file 1. Additional information is available at Biotechnology for Biofuels journal&#39;s website as pdf document, Maus_et_al_v2016-08-03_additional_file_1.pdf. This file contains Additional information on methods as well as additional figures and tables as follows: (i) Additional information on methods for extraction of total microbial RNA. (ii) Additional information on methods for identification of isolates. (iii) Table S1. Statistics of quality-controlled metagenomes sequences data for the microbial community of the thermophilic production-scale biogas plant. (iv) Table S2. Statistics of taxonomically classified sequences obtained from the metagenome and metatranscriptome datasets. (v) Table S3. Number of 16S rRNA sequences and corresponding percentages of bacterial and archaeal genera within the analyzed metagenome and metatranscriptome datasets. The number of metatranscriptome-derived 16S rRNA sequences, i.e. 532,381, was normalized to the number of metagenome-derived...

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, an Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport.

Aquaculture ponds are potential hotspots for carbon cycling and emission of greenhouse gases (GHGs) like CO2 and CH4, but they are often poorly assessed in the global GHG budget. This study determined the temporal
variations of CO2 and CH4 concentrations and diffusive fluxes and their environmental drivers in coastal aquaculture ponds in southeastern China over a five-year period (2017–2021). The findings indicated that CH4 flux from aquaculture ponds fluctuated markedly year-to-year, and CO2 flux varied between positive and negative between years. The coefficient of inter-annual variation of CO2 and CH4 diffusive fluxes was 168% and 127%, respectively, highlighting the importance of long-term observations to improve GHG assessment from aquaculture ponds. In addition to chlorophyll-a and dissolved oxygen as the common environmental drivers, CO2 was further regulated by total dissolved phosphorus and CH4 by dissolved organic carbon. Feed conversion ratio correlated positively with both CO2 and CH4 concentrations and fluxes, showing that unconsumed feeds fueled microbial GHG production. A linear regression based on binned (averaged) monthly CO2 diffusive flux data, calculated from CO2 concentrations, can be used to estimate CH4 diffusive flux with a fair degree of confidence (r2 = 0.66; p < 0.001). This algorithm provides a simple and practical way to assess the total carbon diffusive flux from aquaculture ponds. Overall, this study provides new insights into mitigating the carbon footprint of aquaculture production and assessing the impact of aquaculture ponds on the regional and global scales.

Aquaculture ponds serve as focal points for carbon cycling and act as anthropogenic contributors to the emission of carbon dioxide (CO 2). To understand the seasonal CO 2 dynamics within the ponds, we measured the CO 2 concentrations in sediment porewater and the water column in aquaculture ponds in the Shanyutan Wetland in China. Subsequently, the sediment-to-water and water-to-air CO 2 fluxes were calculated based on the gas transfer coefficient model. Our results showed that that CO 2 flux ranged 0.01-4.58 mmol m −2 h −1 across the sediment-towater interface and −0.08 to 0.45 mmol m −2 h −1 across the water-to-air interface throughout the farming period. Photosynthetic activity was the key driver of the temporal variations in water column CO 2 concentration and water-to-air CO 2 flux, while the change in porewater CO 2 concentration and sediment-to-water CO 2 flux were governed by sediment temperature which drive the microbial decomposition of organic matter. Based on a simple mass balance approach, the apparent CO 2 consumption (ACC) in the water column across all seasons ranged from 0.24 to 2.32 mmol m −2 h −1 , indicating that the pond water body had a high capacity to "consume" the excess CO 2. Our results highlight that the contrasting roles between the sediment compartment and water column compartment in CO 2 dynamics, and the possibility to manipulate ACC to reduce the aquaculture carbon footprint.

Recent orbital and landed missions have provided substantial evidence for ancient liquid water on the Martian surface as well as evidence of more recent sedimentary deposits formed by water and/or ice. These observations raise serious questions regarding an independent origin and evolution of life on Mars. Future missions seek to identify signs of extinct Martian biota in the form of biomarkers or morphological characteristics, but the inherent danger of space craft-borne terrestrial life makes the possibility of forward contamination a serious threat not only to the life detection experiments, but also to any extant Martian ecosystem. A variety of cold and desiccation-tolerant organisms were exposed to 40 days of simulated Martian surface conditions while embedded within several centimeters of regolith simulant in order to ascertain the plausibility of such organisms' survival as a function of environmental parameters and burial depth. Relevant amino acid biomarkers associated with terrestrial life were also analyzed in order to understand the feasibility of detecting biomarker evidence for previous biological activity. Results indicate that stresses due to desiccation, oxidation, and UV-associated damage were the primary deterrent to organism survival, and that the effect of diurnal temperature variations and reactive atmospheric species were minimal. Organisms with resistance to desiccation and radiation environments showed increased levels of survival after the experiment compared to organisms characterized as psychrotolerant. Amino 2 acid biomarker analyses indicated the presence of an oxidation mechanism that migrated downward through the samples during the course of the experiment and likely represents the formation of various oxidizing species at mineral surfaces as water vapor diffused through the regolith. Current sterilization protocols may specifically select for organisms best adapted to survival at the Martian surface, namely species that show tolerance to radical-induced oxidative damage and low water activity environments. Additionally, any hypothetical Martian ecosystems may have evolved similar physiological traits that allow sporadic metabolism during periods of increased water activity.

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, an Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport.

Objectives: Methanogenic archaea are constant members of the human oral and digestive microbiota retrieved, in particular, from periodontitis lesions. The objective of the study was to determine their susceptibility to antimicrobials. Methods: Using the macrodilution method in Hungate tubes with optical microscope observation combined with monitoring methane production, we determined the antibiotic resistance characteristics of eight methanogenic archaea. Results: Methanobrevibacter smithii strains were resistant to ampicillin, streptomycin, gentamicin, rifampicin, ofloxacin, tetracycline and amphotericin B, with MICs ≥100 mg/L; these strains were also highly resistant to vancomycin (MIC ≥50 mg/L). They were moderately resistant to chloramphenicol (MIC ≤25 mg/L), and were susceptible to bacitracin (MIC ≤4 mg/L), metronidazole, ornidazole and squalamine (MIC ≤1 mg/L). The susceptibility of Methanosphaera stadtmanae was the same as M. smithii, except for chloramphenicol (MIC ≤4 mg/L), and Methanobrevibacter oralis yielded the same data as M. smithii, except for bacitracin (MIC ≤25 mg/L). The antibiotic susceptibility pattern of 'Methanomassiliicoccus luminyensis', which was recently isolated from human faeces, was identical to that of M. smithii. Conclusions: Human methanogenic archaea are highly resistant to antibiotics, being susceptible only to molecules that are also effective against both bacteria and eukarya. Methanogenic archaea are good candidates to test for antimicrobial activity against members of this unique domain of life. Further studies to develop new molecules specifically targeting archaea as potential causes of infection are warranted.

Our goal was to examine the composition of methanogenic archaea (MA) and sulfate-reducing (SRP) and sulfur-oxidizing (SOP) prokaryotes in the extreme athalassohaline and particularly sulfate-rich sediment of Tirez Lagoon (Spain). Thus, adenosine-5′-phosphosulfate (APS) reductase α (aprA) and methyl coenzyme M reductase α (mcrA) gene markers were amplified given that both enzymes are specific for SRP, SOP, and MA, respectively. Anaerobic populations sampled at different depths in flooded and dry seasons from the anoxic sediment were compared qualitatively via denaturing gradient gel electrophoresis (DGGE) fingerprint analysis. Phylogenetic analyses allowed the detection of SRP belonging to Desulfobacteraceae, Desulfohalobiaceae, and Peptococcaceae in ∂-proteobacteria and Firmicutes and SOP belonging to Chromatiales/Thiotrichales clade and Ectothiorhodospiraceae in γ-proteobacteria as well as MA belonging to methylotrophic species in Methanosarcinaceae and one hydrogenotrophic species...

Tidal salt marsh soils can be a dynamic source of greenhouse gases such as carbon dioxide (CO 2), methane (CH 4), and nitrous oxide (N 2 O), as well as sulfur-based trace gases such as carbon disulfide (CS 2) and dimethylsulfide (DMS) which play roles in global climate and carbon-sulfur biogeochemistry. Due to the difficulty in measuring trace gases in coastal ecosystems (e.g., flooding, salinity), our current understanding is based on snapshot instantaneous measurements (e.g., performed during daytime low tide) which complicates our ability to assess the role of these ecosystems for natural climate solutions. We performed continuous, automated measurements of soil trace gas fluxes throughout the growing season to obtain high-temporal frequency data and to provide insights into magnitudes and temporal variability across rapidly changing conditions such as tidal cycles. We found that soil CO 2 fluxes did not show a consistent diel pattern, CH 4 , N 2 O, and CS 2 fluxes were highly variable with frequent pulse emissions (> 2500 %, > 10 000 %, and > 4500 % change, respectively), and DMS fluxes only occurred midday with changes > 185 000 %. When we compared continuous measurements with discrete temporal measurements (during daytime, at low tide), discrete measurements of soil CO 2 fluxes were comparable with those from continuous measurements but misrepresent the temporal variability and magnitudes of CH 4 , N 2 O, DMS, and CS 2. Discrepancies between the continuous and discrete measurement data result in differences for calculating the sustained global warming potential (SGWP), mainly by an overestimation of CH 4 fluxes when using discrete measurements. The high temporal variability of trace gas fluxes complicates the accurate calculation of budgets for use in blue carbon accounting and earth system models.

Additional file 1. Additional information is available at Biotechnology for Biofuels journal&#39;s website as pdf document, Maus_et_al_v2016-08-03_additional_file_1.pdf. This file contains Additional information on methods as well as additional figures and tables as follows: (i) Additional information on methods for extraction of total microbial RNA. (ii) Additional information on methods for identification of isolates. (iii) Table S1. Statistics of quality-controlled metagenomes sequences data for the microbial community of the thermophilic production-scale biogas plant. (iv) Table S2. Statistics of taxonomically classified sequences obtained from the metagenome and metatranscriptome datasets. (v) Table S3. Number of 16S rRNA sequences and corresponding percentages of bacterial and archaeal genera within the analyzed metagenome and metatranscriptome datasets. The number of metatranscriptome-derived 16S rRNA sequences, i.e. 532,381, was normalized to the number of metagenome-derived...

The extensive conversion of carbon-rich coastal wetland to aquaculture ponds in the Asian Pacific region has caused significant changes to the sediment properties and carbon cycling. Using field sampling and incubation experiments, the sediment anaerobic CO 2 production and CO 2 emission flux were compared between a brackish marsh and the nearby constructed aquaculture ponds in the Min River Estuary in southeastern China over a three-year period. Marsh sediment had a higher total carbon and lower C:N ratio than aquaculture pond sediment, suggesting the importance of marsh vegetation in supplying labile organic carbon to the sediment. Conversion to aquaculture ponds significantly decreased sediment anaerobic CO 2 production rates by 69.2% compared to the brackish marsh, but increased CO 2 emission, turning the CO 2 sink (−490.8 ± 42.0 mg m −2 h −1 in brackish marsh) into a source (6.2 ± 3.9 mg m −2 h −1 in aquaculture pond). Clipping the marsh vegetation resulted in the highest CO 2 emission flux (382.6 ± 46.7 mg m −2 h −1), highlighting the critical role of marsh vegetation in capturing and sequestering carbon. Sediment anaerobic CO 2 production and CO 2 uptake (in brackish marsh) and emission (in aquaculture ponds) were highest in the summer, followed by autumn, spring and winter. Redundancy analysis and structural equation modeling showed that the changes of sediment temperature, salinity and total carbon content accounted for more than 50% of the variance in CO 2 production and emission. Overall, the results indicate that vegetation clearing was the main cause of change in CO 2 production and emission in the land conversion, and marsh replantation should be a primary strategy to mitigate the climate impact of the aquaculture sector.

Wetlands are considered to be among the most productive but vulnerable ecosystems (Kirwan & Megonigal, 2013; Su et al., 2021; Wen et al., 2019). Despite covering just 4%-6% of the total land area, wetlands hold approximately 450 Pg of the global soil carbon, representing 25%-30% of the terrestrial biosphere carbon pool (Kayranli et al., 2010). Coastal wetlands are a crucial sink in the global carbon cycle due to high sedimentation rate and burial of organic matter (Drake et al., 2015; Packalen et al., 2014; Zhang, Bai, et al., 2021), and it is estimated that coastal wetlands globally store at least 53.7 Tg C yr −1 (Wang et al., 2021). However, wetland habitats have been impacted around the world, and despite international initiative to protect these habitats (e.g., Ramsar Convention on Wetlands), wetland degradation and loss rate remain high in Asia (Davidson, 2014), potentially altering the land's carbon source-sink dynamics over different time and spatial scales (Mitsch et al., 2013).

Emissions of the potent greenhouse gas nitrous oxide (N 2 O) from aquaculture remain a large knowledge gap in the global N 2 O budget. The water column and the sediment of aquaculture ponds present very different environmental conditions, but their relative contributions to N 2 O production and emission are poorly resolved. We sampled three aquaculture ponds in the Min River Estuary in southeastern China monthly throughout the farming season. Based on the dissolved N 2 O concentrations within the water column and in sediment porewater, we calculated the diffusive N 2 O fluxes across the water-atmosphere interface (WAI) and sediment-water interface (SWI). The diffusive N 2 O flux averaged 216.9 nmol m − 2 h − 1 across WAI and 16.0 nmol m − 2 h − 1 across SWI. The estimated N 2 O production rate under steady-state condition was 0.13 nmol L − 1 h − 1 in the water column and 1.07 nmol L − 1 h − 1 in sediment porewater. Hence, the water column compartment and the sediment compartment of the aquaculture ponds played different roles in N 2 O dynamics. Based on our data, it is calculated that China's coastal aquacultural ponds would emit 0.2 Gg N 2 O yr − 1 , or less than 1% of all aquaculture N 2 O emission in China. Therefore, coastal shrimp aquaculture has a relative minor climate impact compared to other aquaculture operations. Future studies should examine the role of N-cycling functional genes on N 2 O production and the mechanisms regulating N 2 O emission from aquaculture ecosystems.

Methane emissions from aquatic ecosystems play an important role in global carbon cycle and climate change. Reclamation of coastal wetlands for aquaculture use has been shown to have opposite effects on sediment CH 4 production potential and CH 4 emission flux, but the underlying mechanism remained unclear. In this study, we compared sediment properties, CH 4 production potential, emission flux, and CH 4 transport pathways between a brackish marsh and the nearby reclaimed aquaculture ponds in the Min River Estuary in southeastern China. Despite that the sediment CH 4 production potential in the ponds was significantly lower than the marsh, CH 4 emission flux in the ponds (17.4 ± 2.7 mg m − 2 h − 1) was 11.9 times higher than the marsh (1.3 ± 0.2 mg m − 2 h − 1). Plant-mediated transport accounted for 75% of the total CH 4 emission in the marsh, whereas ebullition accounted for 95% of the total CH 4 emission in the ponds. CH 4 emission fluxes in both habitat types were highest in the summer. These results suggest that the increase in CH 4 emission following the conversion of brackish marsh to aquaculture ponds was not caused by increased sediment CH 4 production, but rather by eliminating rhizospheric oxidation and shifting the major transport pathway to ebullition, allowing sediment CH 4 to bypass oxidative loss. This study improves our understanding of the impacts of modification of coastal wetlands on greenhouse gas dynamics.

Small-scale aquaculture operation is being increasing practised around the world, particularly in the developing countries, but the greenhouse gas (GHG) dynamics and fluxes from small aquaculture ponds are still poorly assessed. In this study, the dissolved concentrations and fluxes of CO 2 and CH 4 were determined in three coastal earthen shrimp ponds over one whole year, covering both the farming and non-farming periods, in the Min River Estuary, southeastern China. Both ebullitive and diffusive CH 4 fluxes were measured, which were rarely done in previous studies. The average concentrations of dissolved CO 2 and CH 4 in water column in the farming period varied between 18.1 ± 0.1 and 79.6 ± 1.1 μmol L −1 , and 1.3 ± 0.1 and 55.9 ± 3.2 μmol L −1 , respectively. When averaged across the whole year, the mean CO 2 and CH 4 fluxes from the ponds were − 18.4 ± 7.4 and 22.6 ± 6.9 mg m −2 h −1 , respectively, suggesting that the shrimp ponds acted as a CO 2 sink and a CH 4 source. Based on the sustained-flux global warming potential (SGWP) and sustained-flux global cooling potential (SGCP) models, the annual warming potential was estimated to be 7.1 × 10 3 g CO 2-eq m −2 yr −1 , with approximately 90% of this arising from the farming period. Ebullition was the dominant emission pathway for CH 4 , accounting for over 90% of the total CH 4 emission during the farming period. This full-year study improves our understanding of carbon cycling in coastal aquaculture ponds and provides a scientific basis for updating the GHG inventories.

Recent orbital and landed missions have provided substantial evidence for ancient liquid water on the Martian surface as well as evidence of more recent sedimentary deposits formed by water and/or ice. These observations raise serious questions regarding an independent origin and evolution of life on Mars. Future missions seek to identify signs of extinct Martian biota in the form of biomarkers or morphological characteristics, but the inherent danger of space craft-borne terrestrial life makes the possibility of forward contamination a serious threat not only to the life detection experiments, but also to any extant Martian ecosystem. A variety of cold and desiccation-tolerant organisms were exposed to 40 days of simulated Martian surface conditions while embedded within several centimeters of regolith simulant in order to ascertain the plausibility of such organisms' survival as a function of environmental parameters and burial depth. Relevant amino acid biomarkers associated with terrestrial life were also analyzed in order to understand the feasibility of detecting biomarker evidence for previous biological activity. Results indicate that stresses due to desiccation, oxidation, and UV-associated damage were the primary deterrent to organism survival, and that the effect of diurnal temperature variations and reactive atmospheric species were minimal. Organisms with resistance to desiccation and radiation environments showed increased levels of survival after the experiment compared to organisms characterized as psychrotolerant. Amino 2 acid biomarker analyses indicated the presence of an oxidation mechanism that migrated downward through the samples during the course of the experiment and likely represents the formation of various oxidizing species at mineral surfaces as water vapor diffused through the regolith. Current sterilization protocols may specifically select for organisms best adapted to survival at the Martian surface, namely species that show tolerance to radical-induced oxidative damage and low water activity environments. Additionally, any hypothetical Martian ecosystems may have evolved similar physiological traits that allow sporadic metabolism during periods of increased water activity.

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, an Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport.

Additional file 1. Additional information is available at Biotechnology for Biofuels journal&#39;s website as pdf document, Maus_et_al_v2016-08-03_additional_file_1.pdf. This file contains Additional information on methods as well as additional figures and tables as follows: (i) Additional information on methods for extraction of total microbial RNA. (ii) Additional information on methods for identification of isolates. (iii) Table S1. Statistics of quality-controlled metagenomes sequences data for the microbial community of the thermophilic production-scale biogas plant. (iv) Table S2. Statistics of taxonomically classified sequences obtained from the metagenome and metatranscriptome datasets. (v) Table S3. Number of 16S rRNA sequences and corresponding percentages of bacterial and archaeal genera within the analyzed metagenome and metatranscriptome datasets. The number of metatranscriptome-derived 16S rRNA sequences, i.e. 532,381, was normalized to the number of metagenome-derived...

Environmental variables as well as methanogenic abundance and activity were analysed in selected human impacted regions of Ashtamudi estuary. Sediment samples were collected during summer and monsoon of 2013. Each was analysed for environmental variables such as temperature, pH, electrical conductivity, sulphate, total kjeldahl nitrogen, organic carbon, organic matter and redox potential. Abundance and methanogenic potential of two distinct groups of methanogenic archaea (i.e. aceticlastic and methylotrophic methanogens) were quantified by incubating the sediment samples in basal media, added with acetate or methanol as substrate. Most of the environmental variables showed significant differences spatially and temporally. Among the environmental variables, temperature, pH, electrical conductivity and salinity were higher during summer, while total kjeldahl nitrogen, sulphate and organic carbon were higher during monsoon. Abundance of both aceticlastic and methylotrophic methanogens showed significant variations both spatially and temporally. Aceticlastic methanogens were abundant during monsoon, with a maximum value of 810 ± 13 CFU g À1 , and methylotrophic methanogens were abundant during summer, with a maximum value of 1770 ± 30 CFU g À1. Results of methanogenic potential of sediment samples showed a range of 0.01 ± 0.00 to 12.03 ± 0.35 mol m À3. Among the two substrates, methanol favoured the abundance of methylotrophic methanogens, while acetate induced the methanogenic activity. Methanogenic activity was higher during monsoon than summer that can be attributed to the favourable sedimentary conditions (like reduced redox potential and increased substrate availability). Aceticlastic methanogens were abundant at bottom layers and methylotrophic methanogens in top layers of the sediments. The results of canonical correspondence analysis revealed the existence of linear relationship between methanogenic archaea and environmental variables among the sampling stations. Higher values of salinity, electrical conductivity and total kjeldahl nitrogen favoured the distribution and abundance of aceticlastic methanogens. However, the abundance of methylotrophic methanogens was favoured by highly reduced conditions and high pH values.

Methanogenic archaea resident in the mammalian gastrointestinal tract have long been recognised for their capacity to participate in interspecies hydrogen transfer, with commensurate positive effects on plant biomass conversion. However, there is also still much to learn about these methanogenic archaea in regards to their metabolic versatility, host adaptation, and immunogenic properties that is of relevance to host health and nutrition.

Methane (CH 4) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH 4 cycle. Recent studies have focused on quantifying tree stems as sources of CH 4 and understanding abiotic CH 4 emissions in plant canopies, with the role of microbial in situ CH 4 formation receiving less attention. Moreover, despite initial reports revealing CH 4 consumption, studies have not adequately evaluated the potential of microbial CH 4 oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH 4 exchange of plants, and particularly in boreal trees. We detected CH 4-producing methanogens and novel monooxygenases, potentially involved in CH 4 consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH 4 emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH 4 exchange. Our findings, together with the emerging diversity of novel CH 4-producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH 4 exchange.

Widespread conversion of coastal wetlands into aquaculture ponds in coastal region often results in degradation of the wetland ecosystems, but its effects on sediment's potential to produce greenhouse gases remain unclear. Using field sampling, incubation experiments and molecular analysis, we studied the sediment CH 4 production potential and the relevant microbial communities in a brackish marsh and the nearby aquaculture ponds in the Min River Estuary in southeastern China. Sediment CH 4 production potential was higher in the summer and autumn months than in spring and winter months, and it was significantly correlated with sediment carbon content among all environmental variables. The mean sediment CH 4 production potential in the aquaculture ponds (20.1 ng g −1 d −1) was significantly lower than that in the marsh (45.2 ng g −1 d −1). While Methanobacterium dominated in both habitats (41-59%), the overall composition of sediment methanogenic archaea communities differed significantly between the two habitats (p < 0.05) and methanogenic archaea alpha diversity was lower in the aquaculture ponds (p < 0.01). Network analysis revealed that interactions between sediment methanogenic archaea were much weaker in the ponds than in the marsh. Overall, these findings suggest that conversion of marsh land to aquaculture ponds significantly altered the sediment methanogenic archaea community structure and diversity and lowered the sediment's capacity to produce CH 4. ☆ This paper has been recommended for acceptance by Jörg Rinklebe.

Caffeic acid in waste comes from a variety of industries, and its disposal is likely to increase due to emerging processes such as graphene production and use in healthcare products. The current sustainable option to treat waste caffeic acid and prevent its natural transformation in soil to greenhouse gases, is anaerobic digestion. However, little is known about the toxic and inhibitory effects of caffeic acid on biogas production as well as its ultimate anaerobic biodegradability; or about the reactive-adsorptive processes taking place with caffeic acid in sludge, metabolic intermediates, thermodynamic limitations and the effects on extracellular polymeric substances (EPS). Standard methods revealed that 80% of biogas production (EC 80) from a readily digestible biomass was inhibited at 389 mg caffeic acid·g-1 VSS. Up to 52% of caffeic acid was biodegraded. β-oxidation and reductive dehydroxylation were the initial activation reactions transforming caffeic acid into typical polyphenol structural units (protocatechuic acid and 4HBA). Adsorption of caffeic acid (53.3% and 28.6%) to the sludge occurred even at inhibitory concentrations. The EPS structure remained unchanged regardless of the increase in concentration of caffeic acid. Reasonable concentrations of caffeic acid could be co-digested with a similar readily digestible biomass with an expected reduction in biogas production. It is feasible to treat waste caffeic acid by anaerobic digestion and adsorption of its derivates, in order to reduce the contribution to global warming and to protect the environment.

Sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) share common niches in coastal sediments during the terminal phases of the anaerobic mineralization of organic matter. The purpose of this study was to analyze the spatial-temporal variation of SRB and MA in the sediments of a tropical coastal lagoon with ephemeral inlet (La Mancha, Veracruz, Gulf of Mexico) and its relationship with environmental changes. A total of 24 sediment samples were collected during the dry (April, May), rainy (July, September) and Northern (November, February) seasons in the period 2013-2014. Microbiological analyses included the quantification of the viable SRB and MA with different substrates, as well as mineralization experiments to determine the effect of sulfate on acetate oxidation. The analyzed environmental variables in the sediments included: temperature, pH, Eh, salinity, sulfates, H 2 S, volatile solids, carbohydrates, and granulometric characteristics. Major changes occurred between the dry and rainy seasons. During the dry season, sulfate-reducing abundance was significantly greater with lactate (8.3x10 5-1.2x10 7 cells / g) and propionate (1.8x10 5-6.6x10 6 cells / g) as substrates, while the MA that use methanol were dominant (4.2x10 5-9.1x10 6 cells / g). In contrast, during the rainy season, hydrogenophylic (2.6x10 5-8.3x10 6 cells/g) and acetoclastic (5.4x10 5-6.4x10 6 cells / g) MA increased significantly and SRB decreased in the analyzed substrates. An apparent competition for acetate was observed, with a greater oxidation in the media with sulfates in the dry season (0.06 mM acetate / g sediment / day), and a greater oxidation in the media without sulfates in the rainy season (0.02 mM acetate / g sediment / day). SRB and MA were present throughout the sediment column, however SRB dominated in the first centimeters of the sediment while MA were abundant in deeper layers. In conclusion, SRB and MA together played a role in the mineralization of organic matter in the sediments of La Mancha lagoon, with sulfate-reduction dominating in the dry season (closed inlet) and methanogenesis during the rainy season (open inlet). Changes in rainfall and river input in this lagoon significantly affect salinity and sulfate content, the main factors that regulate the dynamics of SRB and MA in the sediments. Rev. Biol. Trop. 64 (4): 1759-1770. Epub 2016 December 01.

Dinámica de las bacterias anaeróbicas en las fases terminales de la mineralización de la materia orgánica en el sedimento de los ecosistemas Carretas-Pereyra y Chantuto-Panzacola Vives. 2006. Dinámica de las bacterias anaeróbicas en las fases terminales de la mineralización de la materia orgánica en el sedimento de los ecosistemas Carretas-Pereyra y Chantuto-Panzacola. Hidrobiológica 16 (1): 183-196.