Today in Scientific Data, two compendia of geochemical and multi-omic sequence information (DNA, RNA, protein) generated over almost a decade of time series monitoring in a seasonally anoxic coastal marine setting are presented to the scientific community. These data descriptors introduce a model ecosystem for the study of microbial responses to ocean deoxygenation, a phenotype that is currently expanding due to climate change. Public access to this time series information is intended to promote scientific collaborations and the generation of new hypotheses relevant to microbial ecology, biogeochemistry and global change issues.
The ocean is changing. In addition to becoming warmer and more acidic, dissolved
O2 concentrations within coastal and interior regions are decreasing,
resulting in oxygen minimum zone (OMZ) expansion1,
As water column oxygen levels decline, less energy is available to higher trophic levels,
increasing the role of microbial metabolism in nutrient and energy cycling through the
use of alternative terminal electron acceptors (TEAs)4. This results in fixed nitrogen loss and the production of
greenhouse gases like nitrous oxide (N2O) and methane (CH4) that
influence global warming8,9. Both of these gases contribute to
warming by increasing the amount of solar energy that is absorbed by the planet measured
as radiative forcing in Watts per square meter. However, the global warming potential
(GWP) of N2O and CH4 varies substantially from the most common
greenhouse gas, carbon dioxide (CO2) by 300- and 30-fold respectively (based
on one-hundred year atmospheric residence times). Current research efforts are defining
the interaction networks underlying microbial metabolism in OMZs and generating new
insights into coupled biogeochemical processes in the ocean driving climate active trace
Model organismal systems such as Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster have provided unifying frameworks for community-driven research that have revealed fundamental organizing principles of life and the dynamics of cellular networks. The development of similar frameworks in which to evaluate ecological interactions and response to perturbation at ecosystem scales is becoming increasingly tractable with the advent of high-throughput sequencing and mass spectrometry platforms that reveal the hidden metabolic powers of uncultivated microbial communities. In 2014, the Scientific Committee on Oceanic Research (SCOR) initiated Working Group 144 to define model ecosystems and standards for combined process rate and molecular data collection needed for effective cross-scale comparisons and enhanced forecasts of ocean deoxygenation (http://www.scor-int.org/SCOR_WGs_WG144.htm).
Today in Scientific Data, two compendia of geochemical and multi-omic
sequence information from Saanich Inlet are provided in support of SCOR 144 activities
and aspirations15,16. Saanich Inlet is a seasonally anoxic fjord on the
east coast of Vancouver Island British Columbia, Canada. A recurring seasonal
development of water column anoxia followed by deep water renewal enables spatiotemporal
profiling across a wide range of water column redox states including conditions
associated with anoxic and sulfidic OMZs17 making Saanich Inlet a model ecosystem for studying microbial
responses to ocean deoxygenation including foundational studies on seasonal
stratification and deep water renewal18,19, trace metal cycling,
The combined use of geochemical and multi-omic sequence information have led to new insights into coupled biogeochemical cycling of C, N and S between key microbial players and the development of a predictive ecosystem model describing the flow of multi-omic sequence information and process rates along eco-thermodynamic gradients11,12,14. Thus, time-series data from Saanich Inlet provides a community-driven framework for observing and predicting microbial community repsonses to ocean deoygenation across multiple scales of biological organization. Readers are encouraged to use this information as a resource for comparative studies and a source of inspiration for developing reproducible hypothesis-driven research in Saanich Inlet and beyond.
How to cite this article: Hallam, S. J. et al. Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone. Sci. Data 4:170158 doi: 10.1038/sdata.2017.158 (2017).
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We thank SCOR Working Group 144 and past and present members of the Hallam Lab for their perennial engagement and support in moving these ideas and information forward into the public domain. We would also like to thank Sydney Brenner for his perspicacity and model systems thinking that has defined both scientific innovations and culture, and inspired us to extend our research beyond neurological networks.
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