Klotz, Franziska; Pester, Michael (2021): Abundance of freshwater Nitrososphaeria in Lake Constance, Germany [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.934520, In: Klotz, F; Pester, M (2021): Archaeal nitrification in Lake Constance, Germany [dataset bundled publication]. PANGAEA, https://doi.org/10.1594/PANGAEA.934577
Always quote citation above when using data! You can download the citation in several formats below.
Abstract:
The aim of this work was to study freshwater Nitrososphaeria and their impact on the nitrogen cycling in lakes. We followed their absolute abundance in oligotrophic Lake Constance (Germany) with quantitative polymerase chain reaction (qPCR) over a time frame of two consecutive years from November 2017 until November 2019. During this time we took water samples monthly (2017/2018) or as required (2019) at a depth of 85 m. Water was taken with a Niskin bottle and filtered on board directly using 5 μm and 0.2 μm polycarbonate filters. The indicated time represents the sampling time.
We extracted DNA with a phenol-chloroform protocol (Klotz et al., 2021). We used the primer pair CamoA420F (50-CGT ACT GGT AGG AAT GTC-30; Herber et al., 2020) and CamoA616R (50-GCC ATC CAB CKR TAN GTC CA-30; Tourna et al., 2008), which are specific for the archaeal ammonia monooxygenase (amoA). The universal primer pair 1389F (50-TGY ACA CAC CGC CCG T-30) and 1492R (50-GGY TAC CTT GTT ACG ACT T-30; Hausmann et al., 2016) was applied to target the 16S rRNA gene of total Archaea and Bacteria. With this, we were able to gain absolute abundances of ammonia oxidizing archaea based on their functional marker gene amoA and relative abundances by comparing it to total Archaea and Bacteria abundances over a cycle of two years.
Supplement to:
Klotz, Franziska; Kitzinger, Katharina; Ngugi, David Kamanda; Büsing, Petra; Littmann, Sten; Kuypers, Marcel MM; Schink, Bernhard; Pester, Michael (2021): Quantification of archaea-driven freshwater nitrification: from single cell to ecosystem level. bioRxiv, https://doi.org/10.1101/2021.07.22.453385
Related to:
Hausmann, Bela; Knorr, Klaus-Holger; Schreck, Katharina; Tringe, Susannah G; Glavina del Rio, Tijana; Loy, Alexander; Pester, Michael (2016): Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. The ISME Journal, 10, 2365-2375, https://doi.org/10.1038/ismej.2016.42
Herber, Janina; Klotz, Franziska; Frommeyer, Benjamin; Weis, Severin; Straile, Dietmar; Kolar, Allison; Sikorski, Johannes; Egert, Markus; Dannenmann, Michael; Pester, Michael (2020): A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance. Environmental Microbiology, 22(1), 212-228, https://doi.org/10.1111/1462-2920.14840
Tourna, Maria; Freitag, Thomas E; Nicol, Graeme W; Prosser, James I (2008): Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environmental Microbiology, 10(5), 1357-1364, https://doi.org/10.1111/j.1462-2920.2007.01563.x
Coverage:
Latitude: 47.757880 * Longitude: 9.126170
Date/Time Start: 2017-11-21T12:00:00 * Date/Time End: 2019-11-05T12:00:00
Minimum DEPTH, water: 85 m * Maximum DEPTH, water: 85 m
Event(s):
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | DATE/TIME | Date/Time | Klotz, Franziska | Geocode | ||
| 2 | 16S rRNA gene, copy number | 16S rRNA copies | #/ml | Klotz, Franziska | Fluorescence-based quantitative real-time PCR (qPCR) | copies/ml |
| 3 | amoA gene, copy number | amoA copies | #/ml | Klotz, Franziska | Fluorescence-based quantitative real-time PCR (qPCR) | copies/ml |
| 4 | amoA/16S rRNA gene ratio, relative abundance | amoA/16S rRNA | Klotz, Franziska | Calculated | ||
| 5 | Sample volume | Samp vol | l | Klotz, Franziska | filtered | |
| 6 | Method comment | Method comm | Klotz, Franziska | |||
| 7 | DEPTH, water | Depth water | m | Klotz, Franziska | Geocode – Lake | |
| 8 | Location | Location | Klotz, Franziska | |||
| 9 | LATITUDE | Latitude | Klotz, Franziska | Geocode | ||
| 10 | LONGITUDE | Longitude | Klotz, Franziska | Geocode |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
444 data points