Citation:

PANGAEA.946567

Name: Seawater carbonate chemistry and whole community and functional gene changes of bioflms on marine plastic debris
Published: 2022-07-25
License: https://creativecommons.org/licenses/by/4.0/
Keywords: CO2 vent; Coast and continental shelf; Community composition and diversity; Entire community; Field observation; Gene expression (incl. proteomics); North Pacific; Pelagos; Temperate

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Abstract:

Plastics are accumulating in the world's oceans, while ocean waters are becoming acidified by increased CO2. We compared metagenome of biofilms on tethered plastic bottles in subtidal waters off Japan naturally enriched in CO2, compared to normal ambient CO2 levels. Extending from an earlier amplicon study of bacteria, we used metagenomics to provide direct insights into changes in the full range of functional genes and the entire taxonomic tree of life in the context of the changing plastisphere. We found changes in the taxonomic community composition of all branches of life. This included a large increase in diatom relative abundance across the treatments but a decrease in diatom diversity. Network complexity among families decreased with acidification, showing overall simplification of biofilm integration. With acidification, there was decreased prevalence of genes associated with cell–cell interactions and antibiotic resistance, decreased detoxification genes, and increased stress tolerance genes. There were few nutrient cycling gene changes, suggesting that the role of plastisphere biofilms in nutrient processes within an acidified ocean may not change greatly. Our results suggest that as ocean CO2 increases, the plastisphere will undergo broad-ranging changes in both functional and taxonomic composition, especially the ecologically important diatom group, with possible wider implications for ocean ecology.

Keyword(s):

CO2 vent; Coast and continental shelf; Community composition and diversity; Entire community; Field observation; Gene expression (incl. proteomics); North Pacific; Pelagos; Temperate

Supplement to:

Kerfahi, Dorsaf; Harvey, Ben P; Kim, Hyoki; Yang, Ying; Adams, Jonathan M; Hall-Spencer, Jason M (2022): Whole community and functional gene changes of biofilms on marine plastic debris in response to ocean acidification. Microbial Ecology, https://doi.org/10.1007/s00248-022-01987-w

Further details:

Raw data of functional genes and taxonomy

Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James (2021): seacarb: seawater carbonate chemistry with R. R package version 3.2.16. https://cran.r-project.org/web/packages/seacarb/index.html

Project(s):

Ocean Acidification International Coordination Centre (OA-ICC)

Coverage:

Latitude: 34.533300 * Longitude: 139.333300

Event(s):

Shikine_Island * Latitude: 34.533300 * Longitude: 139.333300 * Method/Device: Experiment (EXP)

Comment:

In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2022-07-22.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type	Type		Adams, Jonathan M		Study
2	Figure	Fig		Adams, Jonathan M
3	Treatment	Treat		Adams, Jonathan M
4	Taxa	Taxa		Adams, Jonathan M
5	Abundance	Abund	%	Adams, Jonathan M
6	Species	Species		Adams, Jonathan M
7	Phylum	Phylum		Adams, Jonathan M
8	Family	Family		Adams, Jonathan M
9	Function	Function		Adams, Jonathan M		Stress_Response
10	Function	Function		Adams, Jonathan M		Phages_Prophages_Transposable_elements_Plasmids
11	Function	Function		Adams, Jonathan M		Membrane_Transport
12	Function	Function		Adams, Jonathan M		Miscellaneous
13	Function	Function		Adams, Jonathan M		Virulence_Disease_and_Defense
14	Function	Function		Adams, Jonathan M		Secondary_Metabolism
15	Function	Function		Adams, Jonathan M		Cell_Wall_and_Capsule
16	Function	Function		Adams, Jonathan M		Regulation_and_Cell_sig0ling
17	Function	Function		Adams, Jonathan M		Metabolism_of_Aromatic_Compounds
18	Function	Function		Adams, Jonathan M		Nucleosides_and_Nucleotides
19	Function	Function		Adams, Jonathan M		Carbohydrates
20	Function	Function		Adams, Jonathan M		Dormancy_and_Sporulation
21	Function	Function		Adams, Jonathan M		Iron_acquisition_and_metabolism
22	Function	Function		Adams, Jonathan M		Clustering_based_subsystems
23	Function	Function		Adams, Jonathan M		Cofactors_Vitamins_Prosthetic_Groups_Pigments
24	Function	Function		Adams, Jonathan M		DNA_Metabolism
25	Sample ID	Sample ID		Adams, Jonathan M
26	Shannon Diversity Index	H'		Adams, Jonathan M
27	Functional diversity	wFDc		Adams, Jonathan M
28	pH	pH		Adams, Jonathan M		total scale
29	pH, standard deviation	pH std dev	±	Adams, Jonathan M		total scale
30	Temperature, water	Temp	°C	Adams, Jonathan M
31	Temperature, water, standard deviation	Temp std dev	±	Adams, Jonathan M
32	Salinity	Sal		Adams, Jonathan M
33	Salinity, standard deviation	Sal std dev	±	Adams, Jonathan M
34	Alkalinity, total	AT	µmol/kg	Adams, Jonathan M
35	Alkalinity, total, standard deviation	AT std dev	±	Adams, Jonathan M
36	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Adams, Jonathan M	Calculated using CO2SYS
37	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Adams, Jonathan M	Calculated using CO2SYS
38	Carbon, inorganic, dissolved	DIC	µmol/kg	Adams, Jonathan M	Calculated using CO2SYS
39	Carbon, inorganic, dissolved, standard deviation	DIC std dev	±	Adams, Jonathan M	Calculated using CO2SYS
40	Bicarbonate ion	[HCO3]-	µmol/kg	Adams, Jonathan M	Calculated using CO2SYS
41	Bicarbonate ion, standard deviation	[HCO3]- std dev	±	Adams, Jonathan M	Calculated using CO2SYS
42	Carbonate ion	[CO3]2-	µmol/kg	Adams, Jonathan M	Calculated using CO2SYS
43	Carbonate ion, standard deviation	[CO3]2- std dev	±	Adams, Jonathan M	Calculated using CO2SYS
44	Calcite saturation state	Omega Cal		Adams, Jonathan M	Calculated using CO2SYS
45	Calcite saturation state, standard deviation	Omega Cal std dev	±	Adams, Jonathan M	Calculated using CO2SYS
46	Aragonite saturation state	Omega Arg		Adams, Jonathan M	Calculated using CO2SYS
47	Aragonite saturation state, standard deviation	Omega Arg std dev	±	Adams, Jonathan M	Calculated using CO2SYS
48	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
49	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
50	Carbon dioxide, standard deviation	CO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
51	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
52	Fugacity of carbon dioxide in seawater, standard deviation	fCO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
53	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
54	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
55	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
56	Bicarbonate ion, standard deviation	[HCO3]- std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
57	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
58	Carbonate ion, standard deviation	[CO3]2- std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
59	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
60	Carbon, inorganic, dissolved, standard deviation	DIC std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
61	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
62	Aragonite saturation state, standard deviation	Omega Arg std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
63	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
64	Calcite saturation state, standard deviation	Omega Cal std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)

License:

Creative Commons Attribution 4.0 International (CC-BY-4.0)

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

22824 data points

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