Data for: Dissolved organic matter (DOM) offsets the detrimental effects of climate change in the nitrogen fixing cyanobacterium Crocosphaera
Data files
Feb 12, 2024 version files 358.92 KB
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active_cell_nanosims.xlsx
10.09 KB
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Carbonate_System.xlsx
17.93 KB
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DE_genes_bw_Day4_Day2.xlsx
56.24 KB
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DE_genes_bw_DOM_and_unamended.xlsx
105.12 KB
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DE_genes_bw_treatments_unamended.xlsx
102.16 KB
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Nutrients_Croco_Abundance.xlsx
16.13 KB
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Per_cell_rates_Nanosims.xlsx
34.83 KB
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README.md
5.38 KB
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Temp_Sal_pH.xlsx
11.04 KB
Abstract
Diazotrophs provide a significant reactive nitrogen source in the ocean. Increased warming and stratification may decrease nutrient availability in the future, forcing microbial communities to use dissolved organic matter (DOM). Not depending on reactive nitrogen availability, diazotrophs may be "winners" in a nutrient depleted ocean. However, their ability to exploit DOM may influence this success. We exposed cultures of the widespread Crocosphaera to low (26°C, pH 8.1), moderate (28°C, pH 8.0), and extreme (30°C, pH 7.9) climate change scenarios, under control or DOM-amended conditions. Growth was suboptimal in the low and extreme treatments, and favoured in the moderate treatment. DOM was preferred as a carbon source regardless of the treatment, and promoted N2 fixation in extreme conditions. This was reflected in the increased expression of photosynthesis genes to obtain energy. DOM provides Crocosphaera with a key ecological advantage, possibly dictating diazotroph-derived nitrogen inputs in the future ocean.
README: DOM offsets the detrimental effects of climate change in the nitrogen fixing cyanobacterium Crocosphaera
https://doi.org/10.5061/dryad.70rxwdc5j
In this study, we examine the response of Crocosphaera to DOM additions under three climate change scenarios ('low', 'intermediate' an 'extreme'; simulating representative concentration pathways (RCP) 2.6, 4.5 and 6.0; see below). Our findings show that the availability of dissolved organic matter helps diazotrophs facing energetic stress under high temperature and low pH, allowing a more balanced metabolism and a winning strategy to survive in the future warm and acidified ocean.
This dataset contains the core parameters including pH, temperature, nutrients as well as cell abundance. In addition, differential gene expression results of the main metabolic pathways of the diazotroph Crocosphaera between treatments, experimental time points, and different conditions (e.g. DOM versus unamended samples) are included in this dataset.
Figures (and data) presenting some of the ancillary data as well as illustrating the experimental setup are available in a Figshare repository (www.doi.org/10.6084/m9.figshare.22773503.
Description of the data and file structure
The experiment was run for eight days (here days -2 to 5). Negative day values (days -2 to 0) correspond to the post-acclimation period, when Crocosphaera cells are transferred from concentrated cultures to the larger tanks, while positive day values (days 0 to 5) correspond to the experimental period. In the data files, the experimental time is given in numerical values corresponding to the different days (-2 to 5) or written as Day or 'd' followed by the number of the day, e.g. for day 0, it would be 'd0'.
Low (26ºC, pH 8.1), Intermediate (28ºC, pH 8.0), and Extreme (30ºC, pH 7.9) treatments or 'treat' are often depicted by 1 or T1, 2 or T2, and 3 or T3, respectively.
A mix of 13C-labelled organic compounds representative of marine DOM including the amino acids alanine, leucine, and arginine, and the carbohydrates glucose and N-acetylglucosamine was used to measure DOM uptake rates, and its influence in N2 fixation and RNA expression. Unamended (no DOM additions) incubations were kept as controls. In the data files under the heading condition, might be written 'DOM' or 'unamended' for incubations with or without DOM.
Temp_Sal_pH.xlsx
Temperature, salinity and pH values (corrected for in situ treatment temperature using Liu et al. 2011 formula) for each treatment and sampling point are provided in the file 'Temp_Sal_pH.xlsx'.
Carbonate_system.xlsx
Seawater carbonate chemistry parameters from the three experimental treatments were calculated with the seacarb R package at the corresponding incubation temperature using pH values (see 'Temp_Sal_pH.xlsx' file) measured by spectrophotometry and a constant value for total alkalinity from the source water (2650 µmol kg-1). All seawater carbonate chemistry data from this experiment can be found in the file 'Carbonate_system.xlsx'. See package for variable definitions: https://CRAN.R-project.org/package=seacarb
Nutrients_Croco_Abundance.xlsx
Crocosphaera cell abundance (Croco; cell / mL) and nutrient concentrations (µM) including nitrate (NO3) and phosphate (DIP), and dissolved organic nitrogen (DON) and phosphorus (DOP) are included in the file 'Nutrients_Croco_Abundance.xlsx'.
Per_cell_rates_Nanosims.xlsx
Carbon (DIC) and N2 fixation and dissolved organic matter (DOM) uptake rates are expressed in fmol C cell-1 day-1, as they correspond to substrate (DIC, N2 or DOM) incorporation rates per cell. These data are from individual Crocosphaera cells analysed with nanoSIMS after the necessary incubations with the stable isotopes of nitrogen (15N2) and carbon (H13CO3 and 13C-labeled DOM). The data of these measurements can be found in the file 'Per_cell_rates_Nanosims.xlsx'.
active_cell_nanosims.xlsx
The file 'active_cell_nanosims.xlsx' show the amount of active cells (%) incorporating either N2, DIC or DOM. The percentage (value) indicates how many Crocosphaera cells showed active isotopic enrichment over time as compared with total number of cells analysed, for each treatment and time point.
DE_genes_[xx].xlsx
Differential expression of Crocosphaera genes between treatments, experimental time points and different conditions (e.g. DOM versus unamended samples) are provided in files 'DE_genes_bw_treatments_unamended.xlsx', 'DE_genes_bw_Day4_Day2.xlsx' and 'DE_genes_bw_DOM_and_unamended.xlsx', respectively. The parameters shown in the table (e.g., baseMean, Log2FoldChange, lfcSE, etc.) were calculated using the DESeq2 v1.28.0 package in R (Love et al. 2014) and are frequently used metrics to compare level of expression between two samples of specific genes. For each query number (id), the gene name (id) as well as the main associated metabolism are provided. The RNAseq data are deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE229037 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE229037).
Methods
To provide a comprehensive assessment of the behaviour of Crocosphaera under future ocean conditions, we combined temperature and pH levels simulating representative concentration pathways (RCP) 2.6 (26 °C and pH 8.1), 4.5 (28 °C and pH 8.0) and 6.0 (30 °C and pH 7.9) (IPCC 2014), here called "low", "intermediate" and "extreme" treatments (10.6084/m9.figshare.22773503). Cultures of Crocosphaera were acclimated to the different treatments for one month in 500 mL bottles before the start of the experiment in larger volumes (40 L; duplicate low and triplicate intermediate and extreme treatments) with a starting concentration of ~1.5 x 104 cells mL-1 (Fig. 1A). The experiment was run for eight days (here days -2 to 5) under a 12h light:dark cycle with a light intensity of ~250 µmol photons s-1. The temperature and pH levels of each treatment were maintained constant throughout the experiment using an IKS aquastar system. Temperature and salinity were measured daily with a YSI Pro30 probe, while pH was measured spectrophotometrically. Cell abundance and nutrient concentrations were measured daily using standard microscopy and colorimetry methods. On alternate days (day 0, 2, and 4) subvolumes were sampled from each treatment and incubated to measure single-cell N2 and dissolved inorganic carbon (DIC) fixation using dissolved 15N2 and 13C-HCO3, respectively. Similarly, a mix of 13C-labelled organic compounds representative of marine DOM including the amino acids alanine, leucine, and arginine, and the carbohydrates glucose and N-acetylglucosamine was used to measure DOM uptake rates and RNA expression responses. RNA was sequenced using an Illumina NovaSeq 6000 platform generating more than 30 million paired end reads per sample (2 x 50 bp). RNA reads were annotated using Diamond and the databases Kofam UniProt’s Swissprot, trEMBL, and NCBI's RefSeq.