Citation:

PANGAEA.945685

Name: Microbe quantification during short term anaerobic incubation measurements (CH4+CO2) from samples of Lena Delta collected in 2018
Published: 2023-05-24
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Anaerobic incubation; CH4; CO2; Laboratory experiment; Lena Delta; methanogens; methanotrophs; Permafrost; qPCR

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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

Project(s):

The role of non-growing season processes in the methane and nitrous oxide budgets in pristine northern ecosystems (FluxWIN)

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: (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: (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: (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

Data

Download dataset as tab-delimited text — use the following character encoding:

1 Event	2 Sample label	3 Latitude	4 Longitude	5 Date/Time	6 Location	7 Country	8 Site	9 Vegetation type	10 Ecosystem	11 Site (Type)	12 Samp pos (Landscape position)	13 Site (Number)	14 Soil type	15 Samp type (sample collected from AL (act...)	16 State (is permafrost present)	17 State (discontinuous, continuous, is...)	18 Inc dur [days] (total)	19 T incubation [day]	20 Inc Temp [°C]	21 Repl [#] (number of laboratory replicat...)	22 Depth top [m]	23 Depth bot [m]	24 Depth sed [m]	25 Exp treat	26 DNA conc [ng/µl]	27 V [µl] (Elution volue)	28 Dilution	29 pmoA (copies per gram wet soil of p...)	30 mcrA (copies per gram wet soil of m...)
KUR18-P15-YED-4	A-P15-A	72.3555	126.3124	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Upland	P15	Mineral	AL	Yes	Continuous	67	0		3	0.38	0.45	0.415	Frozen	0.090	50	10	#999.000000	#999.000000
KUR18-P15-YED-7	A-P15-F	72.3555	126.3124	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Upland	P15	Mineral	PF	Yes	Continuous	67	0		3	0.79	0.84	0.815	Frozen	#999.000	50	10	#999.000000	#999.000000
KUR18-P15-YED-4	C-P15-A.1.20	72.3555	126.3124	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Upland	P15	Mineral	AL	Yes	Continuous	67	60	20	3	0.38	0.45	0.415	No	0.186	50	10	#999.000000	781.513879
KUR18-P15-YED-7	C-P15-F.1.20	72.3555	126.3124	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Upland	P15	Mineral	PF	Yes	Continuous	67	60	20	3	0.79	0.84	0.815	No	0.057	50	10	#999.000000	1017.001053
KUR18-P15-YED-4	C-P15-A.1.4	72.3555	126.3124	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Upland	P15	Mineral	AL	Yes	Continuous	67	60	4	3	0.38	0.45	0.415	No	0.710	50	10	455.913756	828.632516
KUR18-P15-YED-7	C-P15-F.1.4	72.3555	126.3124	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Upland	P15	Mineral	PF	Yes	Continuous	67	60	4	3	0.79	0.84	0.815	No		50	10	#999.000000	762.092475
KUR18-P16-SLO-3	A-P16-A	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	AL	Yes	Continuous	67	0		3	0.07	0.14	0.105	Frozen	0.189	50	10	#999.000000	#999.000000
KUR18-P16-SLO-7	A-P16-F	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	PF	Yes	Continuous	67	0		3	1.00	1.05	1.025	Frozen	0.221	50	10	#999.000000	3834.735105
KUR18-P16-SLO-3	C-P16-A.1.20	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	AL	Yes	Continuous	67	60	20	3	0.07	0.14	0.105	No	0.217	50	10	1083.761384	#999.000000
KUR18-P16-SLO-7	C-P16-F.1.20	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	PF	Yes	Continuous	67	60	20	3	1.00	1.05	1.025	No	0.233	50	10	429.696634	47744.263350
KUR18-P16-SLO-3	C-P16-A.1.4	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	AL	Yes	Continuous	67	60	4	3	0.07	0.14	0.105	No	0.228	50	10	1226.155360	#999.000000
KUR18-P16-SLO-7	C-P16-F.1.4	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	PF	Yes	Continuous	67	60	4	3	1.00	1.05	1.025	No	0.244	50	10	#999.000000	5351.272987
KUR18-P16-SLO-3	D-P16-A.1.20	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	AL	Yes	Continuous	67	67	20	3	0.07	0.14	0.105	No	0.223	50	10	896.907107	#999.000000
KUR18-P16-SLO-3	D-P16-A.1.4	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	AL	Yes	Continuous	67	67	4	3	0.07	0.14	0.105	No	0.260	50	10	1981.171926	#999.000000
KUR18-P16-SLO-3	G-P16-A.2.20	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	AL	Yes	Continuous	67	67	20	3	0.07	0.14	0.105	Glucose	0.250	50	10	#999.000000	2802.612947
KUR18-P16-SLO-3	G-P16-A.2.4	72.3560	126.3146	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Tundra	Slope	P16	Mineral	AL	Yes	Continuous	67	67	4	3	0.07	0.14	0.105	Glucose	0.249	50	10	572.063006	#999.000000
KUR18-P17-FLO-2	A-P17-A	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	AL	Yes	Continuous	67	0		3	0.28	0.35	0.315	Frozen	0.232	50	10	381.270332	5771.069064
KUR18-P17-FLO-7	A-P17-F	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	PF	Yes	Continuous	67	0		3	0.76	0.81	0.785	Frozen	0.260	50	10	138.741316	#999.000000
KUR18-P17-FLO-2	C-P17-A.1.20	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	AL	Yes	Continuous	67	60	20	3	0.28	0.35	0.315	No	0.248	50	10	3425.130714	534341.154900
KUR18-P17-FLO-7	C-P17-F.1.20	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	PF	Yes	Continuous	67	60	20	3	0.76	0.81	0.785	No	0.246	50	10	#999.000000	#999.000000
KUR18-P17-FLO-2	C-P17-A.1.4	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	AL	Yes	Continuous	67	60	4	3	0.28	0.35	0.315	No	0.220	50	10	4526.594470	14907.229260
KUR18-P17-FLO-7	C-P17-F.1.4	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	PF	Yes	Continuous	67	60	4	3	0.76	0.81	0.785	No	0.220	50	10	330.164082	#999.000000
KUR18-P17-FLO-2	D-P17-A.1.20	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	AL	Yes	Continuous	67	67	20	3	0.28	0.35	0.315	No	0.271	50	10	867.152442	1019407.242000
KUR18-P17-FLO-2	D-P17-A.1.4	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	AL	Yes	Continuous	67	67	4	3	0.28	0.35	0.315	No	0.249	50	10	3916.772100	16354.813450
KUR18-P17-FLO-2	G-P17-A.2.20	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	AL	Yes	Continuous	67	67	20	3	0.28	0.35	0.315	Glucose	0.261	50	10	1078.507124	1075248.321000
KUR18-P17-FLO-2	G-P17-A.2.4	72.3566	126.3170	2018-08-13	central Lena Delta	Russia	Kurungnakh Island	Tundra	Tundra	Floodplain	Floodplain	P17	Mineral	AL	Yes	Continuous	67	67	4	3	0.28	0.35	0.315	Glucose	0.264	50	10	1764.973764	8088.739615