CR: Dissolved Organic Matter Feedbacks in Coral Reef Resilience: The Genomic and Geochemical Basis for Microbial Modulation of Algal Phase Shifts

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National Science Foundation
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Area/s of Research
Ecology and Evolution


Coral reef degradation, whether driven by overfishing, eutrophication, declining water quality,

or other anthropogenic factors, is associated with a phase shift towards a benthic habitat

dominated by fleshy algae (Hughes 1994, McCook 1999, Fabricius 2005). Nearly a decade of research

by our team in coral reef ecosystems of the Pacific has demonstrated that these trajectories

toward increasing algal dominance are restructuring microbial community composition and metabolism

by fundamentally altering the dynamics and quality of dissolved organic matter (DOM). The

resilience of reefs to these phase shifts is a critical question in coral reef ecology, and

managing reefs undergoing these community shifts requires that we develop an understanding

of the role of microbial-DOM interactions in facilitating algal overgrowth and altering reef

ecosystem function. This proposal will integrate DOM geochemistry, microbial genomics and

ecosystem process measurements at ecologically-relevant spatial and temporal scales to test

hypothetical mechanisms by which microbially-mediated feedbacks may facilitate the spread

of fleshy algae on Pacific reef ecosystems. A key product of this research will be understanding

how the composition of corals and algae on reefs interact synergistically with complex microbial

communities to influence reef ecosystem resilience to algal phase shifts.

Intellectual Merit :

A complement of emerging molecular and biogeochemical methods that we have developed and tested

in reef ecosystems will be integrated to investigate mechanisms of microbial-DOM interactions

at multiple spatial and temporal scales. This project will leverage the background environmental

data, laboratory facilities and field logistical resources of the Moorea Coral Reef Long Term

Ecological Research Project in French Polynesia and contribute to that program’s mission of

investigating coral reef resilience in the face of global change. Diel patterns of DOM production

by benthic coral and algae will be quantified along with the composition of chromophoric components

and both free and acid-hydrolyzable neutral monosaccharides and amino acids. Changes in planktonic

and coral-associated microbial communities will be characterized (both taxonomic composition

and gene expression) in response to algal DOM amendments in on-site controlled environmental

chambers using Illumina-sequencing-based phylogenetics and metatranscriptomics, including

tracking algal exudate utilization by specific microbial lineages (stable isotope probing

- tracking exudate 13C into bacterial DNA). Field-deployed 100L tent mesocosms will be used

to examine in situ diel patterns of coupled DOM production and consumption, microbial community

genomics and ecosystem metabolism over representative benthic communities comprising combinations

of algal and coral species. Together these experimental results will guide interpretation

of field surveys of cm-scale spatial dynamics of planktonic and coral-associated microbial

genomics and metabolism at zones of coral-algal interaction, including boundary layer dynamics

of oxygen, bacteria and DOM using planar oxygen optodes, high-throughput flow cytometry and

profiling EEM fluorescence spectroscopy.

Broader Impacts :

This research has implications for managing reef resilience to algal phase shifts by testing

the differential resistance of coral-associated microbial communities to algal DOM and defining

thresholds of algal species cover which alter ecosystem biogeochemistry. This project provides

mentoring across multiple career levels, linking underrepresented undergraduates (through

the C-MORE Scholars native Hawaiian undergraduate research program), two graduate students,

a postdoctoral researcher, a beginning investigator and established PIs. Both UH Manoa and

SDSU are Title III minority-serving institutions, and the PIs are committed to recruiting

from underrepresented groups. Nelson holds a 25% outreach appointment with NOAA Sea Grant

through which this science will be actively translated to Pacific Island communities and reef

management agencies. Datasets will be disseminated through established channels (i.e., BCO-DMO,

MG-RAST) and the results presented in peer-reviewed literature and at national and international

conferences. In addition to training a new generation of reef ecosystem scientists cognizant

of the microbial processes integrated in reef ecology, the results of this work will be synthesized

to provide a new framework for predicting resilience of reef ecosystem biogeochemical processes

to changing benthic communities in the face of global change.