DOI: 10.5061/dryad.70rxwdc5j
title: Data for: Dissolved organic matter (DOM) offsets the detrimental effects of climate change in the nitrogen fixing cyanobacterium Crocosphaera

description: 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.
description: To provide a comprehensive assessment of the behaviour of
 <em>Crocosphaera</em> 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 <em>Crocosphaera</em> 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 10<sup>4</sup> cells mL<sup>-1 </sup>(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<sup>-1</sup>. 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
 N<sub>2</sub> and dissolved inorganic carbon (DIC) fixation
 using dissolved <sup>15</sup>N<sub>2</sub> and
 <sup>13</sup>C-HCO<sub>3</sub>, respectively.
 Similarly, a mix of <sup>13</sup>C-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.
description: # DOM offsets the detrimental effects of climate change in the nitrogen
 fixing cyanobacterium *Crocosphaera*
 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](http://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<sup>-1</sup>). All seawater carbonate chemistry data from this experiment can be found in the file *'Carbonate_system.xlsx'*. See package for variable definitions: #### Nutrients\_Croco\_Abundance.xlsx *Crocosphaera* cell abundance (Croco; cell / mL) and nutrient concentrations (µM) including nitrate (NO<sub>3</sub>) 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 N<sub>2</sub> fixation and dissolved organic matter (DOM) uptake rates are expressed in fmol C cell<sup>-1</sup> day<sup>-1</sup>, as they correspond to substrate (DIC, N<sub>2</sub> 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 (<sup>15</sup>N<sub>2</sub>) and carbon (H<sup>13</sup>CO<sub>3</sub> and <sup>13</sup>C-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 N<sub>2</sub>, 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 ().