| Contributors | Affiliation | Role |
|---|---|---|
| Johnson, Zackary I. | Duke University | Principal Investigator |
| Konstantinidis, Kostas | Georgia Institute of Technology (GA Tech) | Co-Principal Investigator |
| Biddle, Mathew | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
This dataset contains Biosample and GenBank Short Read Archive (SRA) sequence accession numbers for metatranscriptomic samples obtained from acidified, warmed and control mesocosms from ocean and coastal waters.
Ocean acidification (OA) is one of the major issues caused by the rising of atmospheric CO2 with immediate effects in the oceans carbonate chemistry. The oceanic microbial communities are key players in the biochemical cycles of the marine ecosystem and are expected to respond to the ocean’s changing chemistry in a feedback loop of intertwined microbial mediated processes. While the microbial response and effect to OA is challenging to predict due to the complexity of the system, experimental manipulations under controlled conditions can help us understand the major mechanisms of microbial adaptation to a changing oceanic chemistry. In this work we established replicated mesocosms in order to evaluate the effect of decreasing ph in the microbial community composition and gene expression using metatranscriptomics. We examined the effect of both decreasing ph and increasing temperature, one of the major parameters that is expected to have synergistic effects on the microbial response to OA. We examined the effect of both decreasing ph and increasing temperature, one of the major parameters that is expected to have synergistic effects on the microbial response to OA. Additionally, we established mesocosms with either coastal or ocean waters, with the expectation to observe less gene expression responses from the coastal communities which are adapted to a constantly changing water chemistry in comparison to the more sensitive to change ocean communities. In order to account for the variation in gene expression profiles from environmental samples we established two replicates for each of the following incubations (a) control (b) acidified (-0.3 from the in situ ph) (c) warmed (+3oC from the in situ temperature) (d) warmed and acidified. Each mesocosm was maintained under stable conditions for 5 days, after which we isolated samples for 16S rRNA amplicon sequencing and metatranscriptomic sequencing. Additionally, we sequenced the metatranscriptome of the original coastal and ocean samples in order to obtain a baseline gene expression profile of the in situ communities.
In situ or mesocosms water samples were collected within less than 6min using a peristaltic pump. All samples were pre filtered through 3um porosity in line filters, and the bacterial biomass was collected on 0.22 um strive filters. The filters were immediately frozen in liquid nitrogen and store at -80oC until further processing.
Total RNA was extracted from the material collected on the filter using an organic extraction method described previously (Tsementzi et al, 2014; https://doi.org/10.1111/1758-2229.12180). Briefly Lysis buffer (50 mM Tris-HCl, 40 mM EDTA, 0.75 M sucrose) was added to the filters with 1 mg/ml lysozyme and subsequently incubated for 30 min at 37°C. A second 2-h incubation at 55°C was performed after the addition of 1% SDS and 10 mg/ml proteinase K. Acid phenol and chloroform extractions were performed twice on the lysates, and RNA was isolated using filter columns from the mirVANA RNA isolation kit (Ambion), washed twice by following the manufacturer’s instructions, and eluted in Tris-EDTA buffer. DNase treatment was performed using the TURBO DNA-free kit (Ambion, Austin, TX). Libraries were prepared from total RNA using the Ribo-Zero rRNA Removal Kit (Bacteria) following the manufacturer;s instructions and without including the rRNA depletion step. The resulting cDNA libraries were sequenced (250-bp single-end reads) using the Illumina HiSeq 2500 sequencer at the Georgia Institute of Technology Genomics Facility.
| Parameter | Description | Units |
| biosample_accession | biosample_accession | unitless |
| sample_name | sample_name | unitless |
| sample_title | sample_title | unitless |
| bioproject_accession | bioproject_accession | unitless |
| organism | organism | unitless |
| host | host | unitless |
| isolation_source | isolation_source | unitless |
| collection_date | collection_date | unitless |
| geo_loc_name | geo_loc_name | unitless |
| lat_lon | lat_lon | unitless |
| samp_mat_process | samp_mat_process | unitless |
| samp_size | samp_size | unitless |
| source_material_id | source_material_id | unitless |
| description | description | unitless |
| library_ID | library_ID | unitless |
| title | title | unitless |
| library_strategy | library_strategy | unitless |
| library_source | library_source | unitless |
| library_selection | library_selection | unitless |
| library_layout | library_layout | unitless |
| platform | platform | unitless |
| instrument_model | instrument_model | unitless |
| design_description | design_description | unitless |
| filetype | filetype | unitless |
| filename | filename | unitless |
| filename2 | filename2 | unitless |
| filename3 | filename3 | unitless |
| filename4 | filename4 | unitless |
| assembly | assembly | unitless |
| ISO_datetime_UTC | ISO_datetime_UTC | yyyy-MM-dd'T'HH:mm:ss'Z' |
| lat | latitude with north positive | degrees |
| lon | longitude with east positive | degrees |
| Dataset-specific Instrument Name | Illumina HiSeq 2500 sequencer |
| Generic Instrument Name | Automated DNA Sequencer |
| Dataset-specific Description | The resulting cDNA libraries were sequenced (250-bp single-end reads) using the Illumina HiSeq 2500 sequencer at the Georgia Institute of Technology Genomics Facility. |
| Generic Instrument Description | General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. |
Extracted from the NSF award abstract:
This collaborative project by Duke University and Georgia Institute of Technology researchers will combine oceanographic and advanced molecular techniques to characterize the adaptive responses of microbial communities to multiple stressors associated with OA. In particular, microbial communities from estuarine and coastal ecosystems as well as open ocean waters will be incubated under conditions of increased acidity or temperature or both, and their activities will be measured and quantified.
Preliminary data from time-series observations of a coastal temperate estuary shows that pH, temperature and other stressors vary over multiple space and time scales, and this variability is relatively higher than that observed in open ocean waters. Based on this evidence, the guiding hypothesis of this work is that microbes in coastal ecosystems are better adapted to ocean acidification as well as multiple stressors compared to similar microbes from the open ocean. To quantify the adaptive genetic, physiological and biogeochemical responses of microbes to OA, the team's specific goals are to: (1) characterize complex natural microbial community responses to multiple stressors using factorial mesocosm manipulations, (2) assemble a detailed view of genomic and physiological (including transcriptional) adaptations to OA at the single species level using cultured model marine microbes (e.g. Prochlorococcus, Synechococcus, Vibrio) identified as responsive to stressors in whole community mesocosm experiments, and (3) assess the power of model microbial strains and mesocosm experiments to predict microbial community responses to natural OA variability in a temporally dynamic, temperate estuary and along a trophic/pH gradient from the Neuse-Pamlico Sound to the Sargasso Sea. By comparing an estuarine ecosystem to its open ocean counterpart, this study will assess the sensitivity of microbial structure and function in response to ocean acidification.
This project is associated with Pivers Island Coastal Observatory.
NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).
In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.
Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.
PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)
NSF media releases for the Ocean Acidification Program:
Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification
Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?
Press Release 13-102 World Oceans Month Brings Mixed News for Oysters
| Funding Source | Award |
|---|---|
| NSF Division of Ocean Sciences (NSF OCE) |