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opencc-by-4.0Apr 2022View details →

Data archive for Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics

Data collected during annual sampling campaigns to the coastal oxygen minimum zone of Golfo Dulce, carried out in January-February 2018, 2019 and 2020. Methods and results are presented and discussed in Steinsdóttir et al. 2022. Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics. Environmental Microbiology, in press, doi: 10.1111/1462-2920.16003 The content of files is as follows: nutrient_and_methane_concentrations.csv - Concentrations of methane, nitrite, nitrate, and ammonium. methane_oxidation_rates.csv - Rates of anaerobic methane oxidation. kinetics_of_anaerobic_methane_oxidation.csv - Kinetics of anaerobic methane oxidation, carried out in 2019. methylococcales.fa - Methylococcales 16S rRNA amplicon sequences methanofastidiosa.fa - Methanofastidiosa 16S rRNA amplicon sequences

opencc-by-4.0Sep 2022View details →

Data Set for_Integrating torrefaction of pulp industry sludge with anaerobic digestion to produce biomethane and volatile fatty acids: An example of industrial symbiosis for circular bioeconomy

Industrial symbiosis, which allows the sharing of resources between different industries, could help to improve the overall feasibility of bio-based chemicals production. In that regard, this study focused on integrating the torrefaction of pulp industry sludge with anaerobic digestion. More specifically, anaerobic digestion (AD) of pulp sludge-derived torrefaction condensate (TC) was studied to evaluate the biomethane and volatile fatty acid (VFA) potential. The torrefaction condensate produced at 275 and 300 °C was used in AD. The volatile solid content (VS) was 6.69 and 9.01% for the condensate produced at 275 and 300 °C, respectively. The organic fraction of TC mainly contained acetic acid, 2-furanmethanol, and syringol. The methane yield was in the range of 481–772 mL/g VS for the mesophilic and 401–746 mL/g VS for the thermophilic process, respectively. The VFA yield was in the range of 1.1 to 3.4 g/g VS for mesophilic and from 1.5 to 4.7 g/g VS in thermophilic conditions, when methanogenesis was inhibited. Finally, pulp sludge TC is a feasible feedstock to produce platform chemicals like VFA. However, at higher substrate loading, signs of process inhibition were observed because of the relatively increasing concentration of microbial inhibitors

Data part of the manuscript Anaerobic methanotrophy is stimulated by graphene oxide in a brackish urban canal sediment

We surveyed three canals in the city of Amsterdam (Netherlands) for it methane emissions and potential to filter methane through anaerobic oxidation of methane in the canal sediment. To unravel the mechanisms involved we characterised the sediment geochemically. All data present in the manuscript is available in the Excel file.

opencc-by-4.0Aug 2023View details →

Dataset of scientific article "Variability in Arsenic Methylation Efficiency across Aerobic and Anaerobic Microorganisms"

Dataset for journal paper entitled "Variability in Arsenic Methylation Efficiency across Aerobic and Anaerobic Microorganisms" (DOI: 10.1021/acs.est.0c03908). Partial publication's abstract: "Microbially-mediated methylation of arsenic (As) plays an important role in the As biogeochemical cycle, particularly in rice paddy soils where methylated As, generated microbially, is translocated into rice grains. The presence of the arsenite (As(III)) methyltransferase gene (arsM) in soil microbes has been used as an indication of their capacity for As methylation. Here, we evaluate the ability of seven microorganisms encoding active ArsM enzymes to methylate As. Amongst those, only the aerobic species were efficient methylators. The anaerobic microorganisms presented high resistance to As exposure, presumably through their efficient As(III) efflux, but methylated As poorly. The only exception were methanogens, for which efficient As methylation was seemingly an artifact of membrane disruption." The files deposited include: the flow cytometry data and fluorescence microscopy pictures used to assess membrane disruption of the methanogen Methanosarcina mazei, for experimental details please refer to publication, and the supporting information of the publication. Files: <ol> <li>Figure 3_flowcytometry files.zip: flow cytometry measurements reported in Figure 3 of publication. Measurements were performed with a 5-laser LSRII SORP flow cytometer. SYBR Green I (SG) (Invitrogen) was excited by the Blue laser (488 nm) and detected using a 530/30 band pass filter. propidium iodide (PI) (Sigma) was excited by the YG laser (561 nm) and detected using a 610/20 band pass filter. 30’000 events per sample were analyzed into four populations (no fluorescence, SG, SG/PI, or PI). Cells could be assigned to the membrane-compromised population, based on the gating of double-stained and single-stained controls of glutaraldehyde- fixed and ethanol-permeabilized cells. Cytometric data were acquired and analyzed using BD TM FACSDiva software v. 8.0.1 (BD Biosciences, CA, USA). The files consist of the reports generated by BD TM FACSDiva software in .jpg format.</li> <li>Figure S14_fluorescence microscopy files.zip: Fluorescence microscopy pictures in .lsm format of single-stained SG control (SG), single-stained PI control (PI), double-stained control (SG/PI), 16-days sample (16 days) and 20-day sample (20 days) of a Methanosarcina mazei culture grown with 10 μM As(III) as initial concentration. The pictures are published as Figure S14 of the publication. The pictures were taken using Zeiss LSM 700 in the upright configuration equipped with a Plan-Apochromat 63x/1.40 oil immersion objective. For more details please refer to supplementary information in publicaiton. Recommended software for .lsm format included in .zip file.</li> <li>SI_tables_Viacava_et_al_for_publication: file in .xlsx format including the tables: Accession numbers for As(III)-efflux and ArsM proteins and genes; primers used in preparing mutants of C. pasteurianum; growth curves and growth rates values for all sampled cultures; relative abundance of flow-cytometry populations; ICP-MS settings for As analysis; primers for arsM gene amplifications; primers for RT-qPCR of C. pasteurianum; HPLC-ICP-MS spectrum values ; values of arsM and acr3 expression in C. pasteurianum WT and Δacr3; and concentration of total soluble arsenic and soluble arsenic species in filtered medium from all sampled cultures.</li> <li>SI_Viacava_et_al_for_publication: file in .pdf format including: <ol> <li>Materials and methods: total arsenic and arsenic speciation analysis; cloning the arsM genes and gene expression in E. coli AW3110 (DE3); growth conditions of C. pasteurianum H0D0R4, strain used for genetic modification; isolation of the Δacr3 and ΔpyrE::Δacr3 mutants; arsenic methylation by C. pasteurianum Δacr3; transcription of arsM in C. pasteurianum WT and Δacr3; and membrane-integrity assessment of M. mazei cells using flow cytometry.</li> <li>Figures: growth rate of each individual species; abiotic control growth curves; total soluble anaerobic bacterium culture; soluble arsenic species in filtered medium from anaerobic bacterial cultures grown with 50 μM As(III); soluble arsenic species in filtered medium and volatile arsenic species from an A. rosenii culture; soluble arsenic in filtered medium from S. vietnamensis, M. mazei and M. acetivorans cultures; soluble arsenic species in abiotic controls; spiked HPLC-ICP-MS spectra; growth and concentration of soluble arsenic species in ArsM-expressing E. coli AW3110 (DE3); fluorescence microscopy pictures of flow cytometry controls from the membrane-integrity assessment from a M. mazei culture grown with 50 μM As(III); expression of arsM and acr3 in C. pasteurianum WT and Δacr3 mutant; and alignment of ArsM proteins.</li> </ol> </li> <li>README.txt: .txt file with this description text.</li> </ol>

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Hydroxycinnamic acid extraction from prairie biomass for enhancing performance in anaerobic digestion, Iowa, 2021-2022.

This dataset contains a series of batch and continuous anaerobic digestion (AD) experiments that document the effects of hydroxycinnamic acid (HCA) extraction as a pretreatment strategy for prairie biomass to enhance methane production and digestion performance. It includes data on chemical composition of raw inputs (prairie biomass, manure, inoculum), including elemental and solids content; methane and biogas yields under various conditions: untreated vs. HCA-treated biomass, co-digestion with manure at different ratios, and operational enhancements such as biochar supplementation and liquid digestate recirculation; digestate characteristics, including pH, ammonia concentration, and total phenolic content, under different treatment and operational scenarios; optimization data for HCA extraction, detailing the influence of temperature and time on HCA yield and lignin removal; and HCA composition data, including cumulative and species-specific yields (ferulic and p-coumaric acids), and acetyl bromide soluble lignin content.

openCC (other)Sep 2025View details →

opencc-by-4.0Dec 2023View details →

The vOTUs collected in the anaerobic digestion system

The contigs >5.0 kb were collected, de-replicated and then piped through VirSorter2 (based on sequence similarity and other viral-like features such as GC skew) and VirFinder (based on k-mer signatures) for the identification of viral sequences. The identified viral contigs from VirSorter2 and VirFinder were merged and de-replicated with CD-HIT v4.7 at local identity of 100%. The valid 21,518 viral contigs were subjected to species-level clustering to create viral operational taxonomic units (vOTUs) using the ClusterGenomes scripts, following the MIUViG recommended criteria of 95% average nucleotide identity (ANI) and 85% alignment fraction (AF), resulting in the identification of 13,895 vOTUs.

opencc-by-4.0Apr 2024View details →

Data for : Effects of electrokinetic and ultrasonication pre-treatment and two-step anaerobic digestion of biowastes on the nitrogen fertiliser value by injection or surface banding to cereal crops

Data file for article:  Effects of electrokinetic and ultrasonication pre-treatment and two-step anaerobic digestion of biowastes on the nitrogen fertiliser value by injection or surface banding to cereal crops (https://doi.org/10.1016/j.jenvman.2022.116699).

opencc-by-4.0Nov 2024View details →

Assessment of whole-site methane emissions from anaerobic digestion plants: towards establishing emission factors for various plant configurations

This dataset supplements the publication "Assessment of whole-site methane emissions from anaerobic digestion plants: towards establishing emission factors for various plant configurations" by Wechselberger et al. (2025). The dataset contains primary and secondary data underlying the statistical analysis and reported methane emission factors. Emission factors were calculated as described in section 2.3 of the paper.  Available files (UTF-8 encoded): <ul> <li>Data.csv (dataset)</li> <li>Glossary.csv (column/variable descriptions of dataset)</li> </ul> The dataset includes plant characteristics and whole-site methane losses of 135 anaerobic digestion plants, covering normal and various other-than-normal operating conditions (155 rows). For statistical analysis, only periods during normal operation and plants with information on the analyzed emission factors and plant characteristics were considered (cf. supplementary information C of the paper). Consequently, the final dataset contained 109 anaerobic digestion plants for statistical analysis on the methane emission factor (% of methane produced) and 28 plants when analyzing the wastewater-specific emission factor (kg methane per population equivalent and year). All but one facility continuously processed feedstock without any post-rotting stages. Plant DE-MH_WP5_1 of the secondary data implemented garage digesters. Data from three plants were collected only after completion of statistical analyses. These data were used to compare methane losses during normal and other-than-normal operating conditions. The respective rows are marked accordingly in the dataset (column “data_collected_after_statistical_analyses”). Version v2 contains the final reference to the publication Wechselberger et al. (2025). The data are the same as in version v1.

opencc-by-4.0Mar 2022View details →

Meta-omics-aided isolation of elusive anaerobic arsenic-methylating soil bacteria

Data pertaining to the manuscript "Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium" by Karen Viacava, Jiangtao, Qiao, Andrew Janowczyk, Suresh Poudel, Nicolas Jacquemin, Karin Lederballe Meibom, Him K. Shrestha, Matthew C. Reid, Robert L. Hettich and Rizlan Bernier-Latmani published in ISME journal.

opencc-by-4.0Jul 2022View details →

DATASET: What is the best scale for implementing anaerobic digestion according to environmental and economic indicators?

DATASET: What is the best scale for implementing anaerobic digestion according to environmental and economic indicators? Journal of Water Process Engineering, Volume 35, June 2020, 101235 https://doi.org/10.1016/j.jwpe.2020.101235

opencc-by-4.0Jul 2024View details →

On the relationship between methane production in anaerobic incubations of peat material and in-situ methane emissions

These files are meant to accompany the publication: On the relationship between methane production in anaerobic incubations of peat material and in-situ methane emissions  Alexandra B. Cory1, Rachel M. Wilson1*, Olivia C. Ogles1, Patrick M. Crill2, Zhen Li3, Kuang-Yu Chang3, Samantha Bosman1, EMERGE Project Coordinators4, Isogenie Field Team5, Virginia I. Rich3, and Jeffrey P. Chanton1 <a name="_Hlk72229759"></a>1Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, <a name="_Hlk72229408"></a>USA 2Dept of Geological Sciences and Bolin Centre for Climate Research, Stockholm University; Stockholm, 106 91 Stockholm, Sweden <a name="_Hlk72229459"></a>3Department of Microbiology, The Ohio State University, Columbus, OH, USA 4Lawrence Berkeley National Laboratory; Berkeley, CA, USA. 5EMERGE Project Coordinators list of authors and affiliations appears in Acknowledgements.   Corresponding author: Rachel M. Wilson (rmwilson@fsu.edu) Key Points: ·         Laboratory incubations predict field methane emissions from a peatland ·         Interannual variation is best represented by the modeled results ·         Daily-scale variation is driven by processes other than temperature and water table depth   This paper is being submitted for consideration for publication and includes the following archived files: The file:   (1)    UPLOAD_chamber_CO2_and_CH4_with_T.xlsx contains 3 tabs of data measured from the field: (1) CH4 daily, (2) CO2 daily, (3) temp.   The first tab, CH4 daily contains the measured methane fluxes from the field auto chambers spanning 2012-2018. Column headers are             Date:  date of year measurement taken             DOY:  day of year measurement taken             seqday: sequential day of measurement since 01/01/2002 year: year of measurement site: indicates the autochamber site from which the data are measured cH4_flx (mg CH4/m2/d): measured methane emission in milligrams CH4 per m2 per day gC/m2/d: fluxes in grams of C per m2 per day gC/m2/y: fluxes in grams of C per m2 per year   The second tab, CO2 daily contains the measured CO2 fluxes from the field auto chambers spanning 2012-2018. Column headers are similar to the CH4 daily tab revised for CO2 when appropriate.   The third tab, temp provides the temperature in the peat below the surface at 50cm, 20cm and 10cm for 2012-2018.   (2)    UPLOAD_Incubation_All_Temp_Timesaeries_Data.xlsx contains the CO2 and CH4 production for the incubation vials at the various temperature treatments. The headers are: Habitat: indicates the habitat type from which the incubated peat was taken Depth: indicates shallow (9-19cm) peat vs. deep (25-35cm) peat Temp_C: indicates the temperature at which the incubation was conducted in °C Sample: gives a laboratory unique sample identification code Day: indicates day of incubation CH4_umoles_gDry: is the accumulated CH4 production in micromoles per g dry weight of peat CO2_umoles_gDry: is the accumulated CO2 production in micromoles per g dry weight of peat.   (3)    Fen Python Code and Bog Python Code contain all the files required to recreate the modeling results for the Fen and bog respectively.

opencc-by-4.0Dec 2020View details →

Fig. 2 in A report of 37 unrecorded anaerobic bacterial species isolated from the Geum River in South Korea

Fig. 2. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationship between the strains isolated in this study. Bootstrap values (expressed as percentages of 1000 replications) of above 70% are shown at branch points. Filled circles and empty circles indicate nodes recovered by all three or two algorithms (neighbor-joining, maximum likelihood, and maximum parsimony), respectively. Halolamina sediminis halo-7T (CVUA01000001) was used as an outgroup. Bar, 0.05 substitutions per nucleotide position.

opencc-by-4.0Dec 2020View details →

Fig. 1 in A report of 37 unrecorded anaerobic bacterial species isolated from the Geum River in South Korea

Fig. 1. Transmission electron micrographs of cells. Strains: 1, CBA7501; 2, CBA7502; 3, CBA7503; 4, CBA7505; 5, CBA7506; 6, CBA7507; 7, CBA7508; 8, CBA7510; 9, CBA7511; 10, CBA7512; 11, CBA7513; 12, CBA7514; 13, CBA7516; 14, CBA7517; 15, CBA7518; 16, CBA7519; 17, CBA7520; 18, CBA7521; 19, CBA7522; 20, CBA7523; 21, CBA7524; 22, CBA7526; 23, CBA7527; 24, CBA7528; 25, CBA7529; 26, CBA7530; 27, CBA7531; 28, CBA7532; 29, CBA7533; 30, CBA7534; 31, CBA7535; 32, CBA7536; 33, CBA7537; 34, CBA7538; 35, CBA7539; 36, CBA7540; 37, CBA7541.

Fig. 1 in New record of five anaerobic ciliate species from South Korea

Fig. 1. Brachonella contorta in life (A) and after protargol impregnation (B, C). A. Ventral view showing the body shape, the adoral zone of polykinetids, which extends to posterior body end and spirals 360° around long body axis, and the long preoral dome. B, C. Ventral and dorsal view showing the somatic and oral ciliature, the perizonal ciliary stripe, and the nuclear apparatus. AZP, adoral zone of polykinetids; MA, macronucleus; MI, micronucleus; PS. Perizonal ciliary stripe. Scale bars 20 μm.

Fig. 3 in New record of five anaerobic ciliate species from South Korea

Fig. 3. Metopus setosus in life (A-C), in the scanning electron microscope (D-F), and after protargol impregnation (G, H). A-C. Ventral (A) and ventrolateral (B, C) views showing the torsion of the body, the adoral zone of membranelles, the very long caudal cilia, and the large, terminal contractile vacuole. D-F. Dorsal (D, E) and ventrolateral (F) view, showing the body shape, the somatic ciliature, and the very long caudal cilia. G, H. Ventral and dorsal view showing the somatic and oral ciliature, the perizonal ciliary stripe, and the nuclear apparatus. AZP, adoral zone of polykinetids; CC, caudal cilia; CV, contractile vacuole; MA, macronucleus; PM, paroral membrane; PS, perizonal ciliary stripe. Scale bars 30 μm (A-D) and 20 μm (E-H).

Fig. 2 in New record of five anaerobic ciliate species from South Korea

Fig. 2. Brachonella pulchra in life (A-C) and after protargol impregnation (D-F). A-C. Ventral (A, B) and dorsal (C) view showing the body shape, the adoral zone of polykinetids, the cortical granules, and the large preoral dome. D-F. Ventral (D, E) and dorsal (F) view showing the somatic and oral ciliature, the perizonal ciliary stripe, and the nuclear apparatus. AZP, adoral zone of polykinetids; CG, cortical granules; MA, macronucleus; MI, micronucleus; PM, paroral membrane; PS, perizonal ciliary stripe. Scale bars 20 μm.