Dataset: Modeled thermal traits

Name: Estimated thermal traits for phytoplankton
Published: 2021-02-04
Keywords: oceans

DOI:10.26008/1912/bco-dmo.839689.1

Spatial Extent: N:74.65 E:174.81 S:-65 W:-155

Project:

Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients (Phytoplankton Community Responses)

Program:

Dimensions of Biodiversity (Dimensions of Biodiversity)

Narragansett Bay Long-Term Plankton Time Series (NBPTS)

Principal Investigator:

Tatiana A. Rynearson (University of Rhode Island, URI-GSO)

Contact:

Stephanie I. Anderson (University of Rhode Island, URI-GSO)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-02-04

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Data URL:

https://www.bco-dmo.org/dataset/839689/data

Estimated thermal traits for phytoplankton

Abstract:

Estimated thermal traits for phytoplankton assessed in Anderson et al., Marine Phytoplankton Functional Types Exhibit Diverse Responses to Thermal Change (in review).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2021-02-04	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.839689.1	2021-02-09

Description

Phytoplankton thermal traits were estimated for diatoms (n=135), dinoflagellates (n=46), coccolithophores (n=30), and cyanobacteria (n=32). This dataset contains estimated traits and parameters presented in Thomas et al (2012) as well as those for 59 additional strains (Anderson et al, in review). Study selection followed the criteria outlined in Thomas et al (2012) and Anderson et al (in review).

Acquisition Description

Thermal reaction norms were used to describe phytoplankton thermal responses following the equation presented in Thomas et al. (2012). For strains compiled previously, parameters for thermal reaction norms were provided (Thomas et al 2012 & 2016). For added strains, parameters were estimated using the thermal growth rates found in the related dataset, https://www.bco-dmo.org/dataset/839696, and the maximum likelihood approach described in Thomas et al. (2012) and the bbmle package in R 3.6.1 (2019).

Traits were then estimated for each strain using their respective thermal reaction norms, as outlined previously (Thomas et al. 2012 & 2016; Anderson and Rynearson, 2020). This included the thermal optima (Topt), thermal maxima (Tmax) and thermal niche width. The thermal maxima were quality controlled according to Thomas et al. (2016) to ensure validity.

Processing Description

BCO-DMO Processing:
- replaced "NA" with "nd" as missing data value;
- renamed fields (replaced periods with underscores);
- removed commas from "study" and "source" columns;
- replaced commas with semi-colons in the "name", "strain", and "clone" columns;
- replaced comments with codes due to length and generated file "derived_traits_comment_codes.csv";
- replaced/removed un-renderable characters from the "source" column.

Definitions/descriptions for "comment_code" columns:
Note 1 = Latitude approximate. Based on information from Jacques (1983), Fiala & Oriol (1984), & Fiala & Oriol (1990), there are 5 possible isolation locations, all along the same longitude: 48S, 54S, 58S, 60S, and 65S. In the absence of further information from the authors, I have used the median location.

Note 2= Growth rates estimated from nonlinear fitting. One value presented was measured in previous study.

Note 3 = location approximate

Supplemental Files

File
data_sources.pdf (Portable Document Format (.pdf), 144.02 KB) MD5:c6fb59a3eca1a2654a9e1a49c12b8ecf Complete citations for the papers referenced in the "study" column of dataset 839689.
derived_traits_comment_codes.csv (Comma Separated Values (.csv), 467 bytes) MD5:4bfd2ca2b91639cbf70effcf56d49ff1 Complete comments/notes for the codes in the "comment_code" column of dataset 839689.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1638834

Deployments

None available yet

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
isolate_code	Unique isolate ID adpated from Thomas et al. (2012).	unitless	taxon_code
study	source publication; refer to supplemental file "data_sources.pdf" for complete citations	unitless	reference_paper
source	geographical location of isolation	unitless	site
isolation_latitude	latitude of isolation location	degrees North	lat
isolation_longitude	longitude of isolation location	degrees East (-180 to 180)	lon
habitat	isolation location habitat type: marine or estuarine	unitless	site_descrip
name	Full current name of species with strain or clone name if available	unitless	species
speciesname	Full current name of species, omitting strain and clone names	unitless	species
strain	strain name, if given	unitless	species
clone	clone name, if given	unitless	taxon
species	taxonomic classification, species name	unitless	species
genus	taxonomic classification, genus name	unitless	genus
family	taxonomic classification, family name	unitless	family
order	taxonomic classification, order name	unitless	order
class	taxonomic classification, class name	unitless	class
phylum	taxonomic classification, phylum name	unitless	phylum
kingdom	taxonomic classification, kingdom name	unitless	kingdom
domain	taxonomic classification, domain name	unitless	animal_group
group	phytoplankton functional type that the species belongs to	unitless	animal_group
mu_wlist	estimated thermal niche width (parameter 'omega' in the thermal reaction norm model)	unitless	unknown
mu_alist	estimate of parameter ‘a’ in the thermal reaction norm model	unitless	unknown
mu_blist	estimate of parameter ‘b’ in the thermal reaction norm model	unitless	unknown
mu_c_opt_list	estimate of parameter ‘z’ in the thermal reaction norm model	unitless	unknown
mu_c_opt_val_list	estimated specific growth rate (per day) when temperature is at ‘z’ (i.e. mu.c.opt.list)	per day	growth
mu_g_opt_list	estimated optimum temperature for growth	degrees Celsius	temp
mu_g_opt_val_list	estimated maximum specific growth rate (per day) based on the thermal reaction norm model fit	per day	growth
mu_n	number of points (i.e. number of growth rate measurements) in the curve	unitless	unknown
tmin	Tmin, or minimum persistence temperature, estimated from the thermal reaction norm model fit	degrees Celsius	temp
tmax	Tmax, or maximum persistence temperature, estimated from the thermal reaction norm model fit	degrees Celsius	temp
minqual	quality of Tmin estimate (quality control criteria found in supplementary info)	unitless	unknown
maxqual	quality of Tmax estimate (quality control criteria found in supplementary info)	unitless	unknown
comment_code	notes about isolation location, taxonomy, and other sources of uncertainty; refer to metadata 'Processing Description' for definitions or to the supplemental file "derived_traits_comment_codes.csv"	unitless	unknown

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Dataset: Modeled thermal traits