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Husmann, Eva; Klaas, Christine (2023): Diatom specific growth rates based on cell concentrations and PDMPO staining [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.954982, In: Husmann, E; Klaas, C (2023): Using the silica deposition fluorescent probe PDMPO to determine growth rates of diatoms in the laboratory [dataset bundled publication]. PANGAEA, https://doi.org/10.1594/PANGAEA.954985

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Abstract:
While in culture, specific growth rate (μ) can be easily determined through cell counts (N0 and Nt). This is not the case for incubations with natural assemblages, where grazers and other processes lead to cell loss and consequently an underestimation of Nt. Incubations with [2-(4-pyridyl)-5{[4-dimethylaminoethyl-aminocarbamoyl)-methoxy]phenyl}oxazole] (PDMPO) overcomes this issue by allowing the determination of N0 (Nt=N0×e^(μt) (Eq. 1)) based on the relative proportion of PDMPO stained cells (newly divided) and unstained cell at the end of an incubation as follows: Given Nt, the total cell number of a species from a subsample at a time t after PDMPO addition. Nt=nt+nt', with nt the total number of non-(PDMPO) stained cells of the species in the same subsample (cells that did not divide yet), and nt' the total number of cells with one PDMPO stained valve (cells issued from the first division after PDMPO addition to the culture media). All things being equal, the population (N0) at the time when PDMPO was added that gave rise to Nt should be N0=nt+((nt')/2)=Nt-((nt')/2) (Eq. 2). Growth rates from cells counts were estimated using (Eq. 1), while growth rates using PDMPO were calculated from the number of non-stained (nt), half-stained (nt') and fully stained (nt'') cells using μ[d-1]=ln((nt+nt')/(nt+(nt')/2))×(1/t) (Eq. 3) or μ[d-1]=ln((nt'+nt'')/((nt')/2))×(1/t) (Eq. 4). Cells attached to each other (potentially in the final phase of division) were also considered as non-stained, half-stained and fully-stained individuals, respectively, based on the presence/absence of a PDMPO signal on the valves.
Keyword(s):
biological oceanography; diatoms; in situ growth rates; Laboratory experiment; method; Phytoplankton
Supplement to:
Husmann, Eva; Klaas, Christine (2022): Testing the use of the silica deposition fluorescent probe PDMPO to estimate in situ growth rates of diatoms. Limnology and Oceanography-Methods, 20(9), 568-580, https://doi.org/10.1002/lom3.10505
References:
Utermöhl, H (1958): Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitteilungen der Internationalen Vereinigung für Theoretische und Angewandte Limnologie, 9, 1-38
Coverage:
Median Latitude: -27.053402 * Median Longitude: 21.788440 * South-bound Latitude: -69.000000 * West-bound Longitude: 0.099790 * North-bound Latitude: 78.953000 * East-bound Longitude: 75.000000
Date/Time Start: 2018-05-10T00:00:00 * Date/Time End: 2018-12-31T12:12:00
Minimum Elevation: -4679.0 m * Maximum Elevation: -4500.0 m
Event(s):
Kongsfjorden_CC_Sed  * Latitude: 78.953000 * Longitude: 11.953830 * Date/Time: 2018-05-10T00:00:00 * Location: Kongsfjorden, Spitsbergen, Arctic * Method/Device: Hand net (HN) * Comment: Collection site of Thalassiosira sp. strain CC_Sed, cultured at Alfred Wegener Institute, Helmholtz Centre for Polare and Marine Research, Bremerhaven
Prydz_Bay_CS-624  * Latitude: -69.000000 * Longitude: 75.000000 * Location: Prydz Bay * Method/Device: Hand net (HN) * Comment: Collection site of Chaetoceros simplex strain CS-624, sampled before 2008, formerly cultured by ANACC
PS117_22-6  * Latitude Start: -59.083220 * Longitude Start: 0.099790 * Latitude End: -59.083390 * Longitude End: 0.100140 * Date/Time Start: 2018-12-31T12:10:00 * Date/Time End: 2018-12-31T12:12:00 * Elevation Start: -4500.0 m * Elevation End: -4679.0 m * Location: South Atlantic Ocean * Campaign: PS117 * Basis: Polarstern * Method/Device: Hand net (HN)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1 Event labelEventHusmann, Eva
2 Type of studyStudy typeHusmann, Eva
3 Date/time start, experimentDate/time start expHusmann, Eva
4 SpeciesSpeciesHusmann, Eva
5 Taxon/taxa, unique identificationTaxa UIDHusmann, Eva
6 Taxon/taxa, unique identification (URI)Taxa UID (URI)Husmann, Eva
7 Taxon/taxa, unique identification (Semantic URI)Taxa UID (Semantic URI)Husmann, Eva
8 StrainStrainHusmann, Eva
9 Experimental treatmentExp treatHusmann, Eva
10 Treatment: light intensityT:Ioµmol/m2/sHusmann, Eva
11 Temperature, waterTemp°CHusmann, Eva
12 Incubation durationInc durhHusmann, Eva
13 Phytoplankton growth rate, specificPhytopl µ spec1/dayHusmann, EvaLight microscopy (Utermöhl 1958)
14 Specific growth rate, standard deviationSGR std dev±Husmann, EvaCalculated
15 Phytoplankton growth rate, specificPhytopl µ spec1/dayHusmann, EvaEpifluorescence microscopy
16 Specific growth rate, standard deviationSGR std dev±Husmann, EvaCalculated
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
194 data points

Data

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

1 
Event		2 
Study type		3 
Date/time start exp		4 
Species		5 
Taxa UID		6 
Taxa UID (URI)		7 
Taxa UID (Semantic URI)		8 
Strain		9 
Exp treat		10 
T:Io [µmol/m2/s]		11 
Temp [°C]		12 
Inc dur [h]		13 
Phytopl µ spec [1/day]
(Light microscopy (Utermöhl 1958))		14 
SGR std dev [±]
(Calculated)		15 
Phytopl µ spec [1/day]
(Epifluorescence microscopy)		16 
SGR std dev [±]
(Calculated)
PS117_22-6 laboratory experiment2019-12-04T21:45Pseudo-nitzschia subcurvataPseudo-nitzschia subcurvatamarinespecies.orgurn:lsid:marinespecies.org:taxname:41176722_35Control204240.5810.136
PS117_22-6laboratory experiment2019-12-04T21:45Pseudo-nitzschia subcurvataPseudo-nitzschia subcurvatamarinespecies.orgurn:lsid:marinespecies.org:taxname:41176722_350.125µM PDMPO204240.6450.1110.6780.008
PS117_22-6laboratory experiment2019-12-04T21:45Pseudo-nitzschia subcurvataPseudo-nitzschia subcurvatamarinespecies.orgurn:lsid:marinespecies.org:taxname:41176722_350.125µM PDMPO20480.6540.3630.9960.086
PS117_22-6laboratory experiment2019-12-04T21:45Pseudo-nitzschia subcurvataPseudo-nitzschia subcurvatamarinespecies.orgurn:lsid:marinespecies.org:taxname:41176722_350.6µM PDMPO204240.6780.008
Prydz_Bay_CS-624 laboratory experiment2019-12-18T21:45Chaetoceros simplexChaetoceros simplexmarinespecies.orgurn:lsid:marinespecies.org:taxname:149294CS 624, ANACCControl204240.5060.234
Prydz_Bay_CS-624laboratory experiment2019-12-18T21:45Chaetoceros simplexChaetoceros simplexmarinespecies.orgurn:lsid:marinespecies.org:taxname:149294CS 624, ANACCControl20480.6790.391
Prydz_Bay_CS-624laboratory experiment2019-12-18T21:45Chaetoceros simplexChaetoceros simplexmarinespecies.orgurn:lsid:marinespecies.org:taxname:149294CS 624, ANACC0.125µM PDMPO204240.3070.2280.4560.005
Prydz_Bay_CS-624laboratory experiment2019-12-18T21:45Chaetoceros simplexChaetoceros simplexmarinespecies.orgurn:lsid:marinespecies.org:taxname:149294CS 624, ANACC0.125µM PDMPO20480.3361.0960.9220.107
Prydz_Bay_CS-624laboratory experiment2019-12-18T21:45Chaetoceros simplexChaetoceros simplexmarinespecies.orgurn:lsid:marinespecies.org:taxname:149294CS 624, ANACC0.6µM PDMPO204240.4660.1040.4990.042
Kongsfjorden_CC_Sed laboratory experiment2019-12-17T21:45Thalassiosira sp.Thalassiosiramarinespecies.orgurn:lsid:marinespecies.org:taxname:148912CC_SedControl204240.5190.120
Kongsfjorden_CC_Sedlaboratory experiment2019-12-17T21:45Thalassiosira sp.Thalassiosiramarinespecies.orgurn:lsid:marinespecies.org:taxname:148912CC_SedControl2048-0.0140.394
Kongsfjorden_CC_Sedlaboratory experiment2019-12-17T21:45Thalassiosira sp.Thalassiosiramarinespecies.orgurn:lsid:marinespecies.org:taxname:148912CC_Sed0.125µM PDMPO204240.4820.1190.6760.029
Kongsfjorden_CC_Sedlaboratory experiment2019-12-17T21:45Thalassiosira sp.Thalassiosiramarinespecies.orgurn:lsid:marinespecies.org:taxname:148912CC_Sed0.125µM PDMPO20480.1590.4750.8290.056
Kongsfjorden_CC_Sedlaboratory experiment2019-11-07T09:45Thalassiosira sp.Thalassiosiramarinespecies.orgurn:lsid:marinespecies.org:taxname:148912CC_SedControl1104240.8030.075
Kongsfjorden_CC_Sedlaboratory experiment2019-11-07T09:45Thalassiosira sp.Thalassiosiramarinespecies.orgurn:lsid:marinespecies.org:taxname:148912CC_Sed0.125µM PDMPO1104240.6070.1890.7440.043
Kongsfjorden_CC_Sedlaboratory experiment2019-11-07T09:45Thalassiosira sp.Thalassiosiramarinespecies.orgurn:lsid:marinespecies.org:taxname:148912CC_Sed0.6µM PDMPO1104240.6840.1810.5610.184