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
Always quote citation above when using data! You can download the citation in several formats below.
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):
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
Project(s):
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):
# | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
---|---|---|---|---|---|---|
1 | Event label | Event | Laurent, Mélissa | |||
2 | Sample code/label | Sample label | Laurent, Mélissa | |||
3 | Latitude of event | Latitude | Laurent, Mélissa | |||
4 | Longitude of event | Longitude | Laurent, Mélissa | |||
5 | Date/Time of event | Date/Time | Laurent, Mélissa | |||
6 | Location of event | Location | Laurent, Mélissa | |||
7 | Country | Country | Laurent, Mélissa | |||
8 | Site | Site | Laurent, Mélissa | |||
9 | Vegetation type | Vegetation type | Laurent, Mélissa | |||
10 | Ecosystem | Ecosystem | Laurent, Mélissa | |||
11 | Site | Site | Laurent, Mélissa | Type | ||
12 | Sample position | Samp pos | Laurent, Mélissa | Landscape position | ||
13 | Site | Site | Laurent, Mélissa | Number | ||
14 | Soil type | Soil type | Laurent, Mélissa | |||
15 | Sample type | Samp type | Laurent, Mélissa | sample collected from AL (active layer) or permafrost (PF) | ||
16 | State of permafrost | State | Laurent, Mélissa | is permafrost present | ||
17 | State of permafrost | State | Laurent, Mélissa | discontinuous, continuous, isolated, sporadic | ||
18 | Incubation duration | Inc dur | days | Laurent, Mélissa | total | |
19 | Time, incubation | T incubation | day | Laurent, Mélissa | ||
20 | Incubation temperature | Inc Temp | °C | Laurent, Mélissa | ||
21 | Replicates | Repl | # | Laurent, Mélissa | number of laboratory replications for each site/ sample | |
22 | Depth, top/min | Depth top | m | Laurent, Mélissa | ||
23 | Depth, bottom/max | Depth bot | m | Laurent, Mélissa | ||
24 | DEPTH, sediment/rock | Depth sed | m | Laurent, Mélissa | Geocode | |
25 | Experimental treatment | Exp treat | Laurent, Mélissa | |||
26 | DNA concentration | DNA conc | ng/µl | Laurent, Mélissa | SYBRGreen 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) | |
27 | Volume | V | µl | Laurent, Mélissa | Elution volue | |
28 | Dilution factor | Dilution | Laurent, Mélissa | |||
29 | Methane oxygenase, pmoA gene, abundance | pmoA | Laurent, Mélissa | SYBRGreen 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 | |
30 | Methyl coenzyme M reductase, mcrA gene, abundance | mcrA | Laurent, Mélissa | SYBRGreen 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 |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
617 data points