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Laurent, Mélissa; Fuchs, Matthias; Treat, Claire C; Liebner, Susanne; Runge, Alexandra (2023): Microbe quantification during short term anaerobic incubation measurements (CH4+CO2) from samples of Lena Delta collected in 2018. PANGAEA, https://doi.org/10.1594/PANGAEA.945680, In: Laurent, M et al. (2023): One year anaerobic incubation measurements (CH4+CO2) and microbe quantification from samples of Lena Delta collected in 2018. PANGAEA, https://doi.org/10.1594/PANGAEA.945685

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Abstract:
The data sets were made during the summer 2021, with samples collected from three cores, at two depths (active and permafrost layers). In total, six samples (3 replicates by samples) were incubated for 67 days at two temperatures (4°C and 20°C). Core sampling were performed during the joint Russian-German LENA 2018 expedition.
This data set compiles microbial quantification (DNA extraction + qPCR) for methanotrophs and methanogenic archaea. Key genes coding for the enzyme methyl coenzyme-M reductase (mcrA) (Thauer 1998) and for the enzyme particulate methane monooxygenase (pmoA) (Theisen et Murrell 2005) were examined to identify methanogens and methanotrophs, respectively. Microbial quantification was monitored at 3 different times during the incubation. Samples were collected before the incubation, after 60 days of incubation and after glucose addition. Due to the pandemic, it has not been possible to perform microbial quantification for all the samples after the glucose treatment. DNA extractions were performed with a GeneMATRIX Soil DNA purification kit according to the manufacturer's protocol. Quantification of gene copy numbers was done with a SYBRGreen quantitative PCR (qPCR) assay using the KAPA SYBRFAST qPCR Master Mix (Sigma-Aldrich, Germany) on a CFX96 real-time thermal cycler (Bio-Rad Laboratories Inc., United States). The data was collected at Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research and GeoForschungsZentrum Helmholtz-Zentrum, Potsdam, Germany.
Keyword(s):
Anaerobic incubation; CH4; CO2; Laboratory experiment; Lena Delta; methanogens; methanotrophs; Permafrost; qPCR
Related to:
Thauer, Rudolf K (1998): Biochemistry of methanogenesis: a tribute to Marjory Stephenson:1998 Marjory Stephenson Prize Lecture. Microbiology, 144(9), 2377-2406, https://doi.org/10.1099/00221287-144-9-2377
Theisen, Andreas R; Murrell, Michael T (2005): Facultative Methanotrophs Revisited. Journal of Bacteriology, 187(13), 4303-4305, https://doi.org/10.1128/JB.187.13.4303-4305.2005
Funding:
European Research Council (ERC), grant/award no. 851181: The role of non-growing season processes in the methane and nitrous oxide budgets in pristine northern ecosystems
Coverage:
Median Latitude: 72.356000 * Median Longitude: 126.314647 * South-bound Latitude: 72.355450 * West-bound Longitude: 126.312370 * North-bound Latitude: 72.356580 * East-bound Longitude: 126.316960
Date/Time Start: 2018-08-13T00:00:00 * Date/Time End: 2018-08-13T00:00:00
Minimum DEPTH, sediment/rock: 0.105 m * Maximum DEPTH, sediment/rock: 1.025 m
Event(s):
KUR18-P15-YED-4 (P15-A) * Latitude: 72.355450 * Longitude: 126.312370 * Date/Time: 2018-08-13T00:00:00 * Elevation Start: 13.0 m * Elevation End: 15.0 m * Location: central Lena Delta * Campaign: RU-Land_2018_Lena (Lena 2018) * Basis: AWI Arctic Land Expedition * Method/Device: Fixed volume cylinder (250 cm3)
KUR18-P15-YED-7 (P15-F) * Latitude: 72.355450 * Longitude: 126.312370 * Date/Time: 2018-08-13T00:00:00 * Elevation Start: 13.0 m * Elevation End: 15.0 m * Location: central Lena Delta * Campaign: RU-Land_2018_Lena (Lena 2018) * Basis: AWI Arctic Land Expedition * Method/Device: SIPRE Auger (SA)
KUR18-P16-SLO-3 (P16-A) * Latitude: 72.355970 * Longitude: 126.314610 * Date/Time: 2018-08-13T00:00:00 * Elevation Start: 8.0 m * Elevation End: 10.0 m * Location: central Lena Delta * Campaign: RU-Land_2018_Lena (Lena 2018) * Basis: AWI Arctic Land Expedition * Method/Device: Fixed volume cylinder (250 cm3)
Comment:
#999: below detection limit
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Event labelEventLaurent, Mélissa
2Sample code/labelSample labelLaurent, Mélissa
3Latitude of eventLatitudeLaurent, Mélissa
4Longitude of eventLongitudeLaurent, Mélissa
5Date/Time of eventDate/TimeLaurent, Mélissa
6Location of eventLocationLaurent, Mélissa
7CountryCountryLaurent, Mélissa
8SiteSiteLaurent, Mélissa
9Vegetation typeVegetation typeLaurent, Mélissa
10EcosystemEcosystemLaurent, Mélissa
11SiteSiteLaurent, MélissaType
12Sample positionSamp posLaurent, MélissaLandscape position
13SiteSiteLaurent, MélissaNumber
14Soil typeSoil typeLaurent, Mélissa
15Sample typeSamp typeLaurent, Mélissasample collected from AL (active layer) or permafrost (PF)
16State of permafrostStateLaurent, Mélissais permafrost present
17State of permafrostStateLaurent, Mélissadiscontinuous, continuous, isolated, sporadic
18Incubation durationInc durdaysLaurent, Mélissatotal
19Time, incubationT incubationdayLaurent, Mélissa
20Incubation temperatureInc Temp°CLaurent, Mélissa
21ReplicatesRepl#Laurent, Mélissanumber of laboratory replications for each site/ sample
22Depth, top/minDepth topmLaurent, Mélissa
23Depth, bottom/maxDepth botmLaurent, Mélissa
24DEPTH, sediment/rockDepth sedmLaurent, MélissaGeocode
25Experimental treatmentExp treatLaurent, Mélissa
26DNA concentrationDNA concng/µlLaurent, MélissaSYBRGreen quantitative PCR (qPCR) assay using the KAPA SYBRFAST qPCR Master Mix (Sigma-Aldrich, Germany) on CFX96 real-time thermal cycler (Bio-Rad Laboratories Inc., United States)
27VolumeVµlLaurent, MélissaElution volue
28Dilution factorDilutionLaurent, Mélissa
29Methane oxygenase, pmoA gene, abundancepmoALaurent, MélissaSYBRGreen quantitative PCR (qPCR) assay using the KAPA SYBRFAST qPCR Master Mix (Sigma-Aldrich, Germany) on CFX96 real-time thermal cycler (Bio-Rad Laboratories Inc., United States)copies per gram wet soil of pmoA protein
30Methyl coenzyme M reductase, mcrA gene, abundancemcrALaurent, MélissaSYBRGreen quantitative PCR (qPCR) assay using the KAPA SYBRFAST qPCR Master Mix (Sigma-Aldrich, Germany) on CFX96 real-time thermal cycler (Bio-Rad Laboratories Inc., United States)copies per gram wet soil of mrcA protein
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
617 data points

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