KRuMBS-Kyphosid Ruminant Microbial Biodigestion of Seaweeds
Collaborators: Neil Sims (lead) @ Kampachi Farms, Eric Allen, Pieter Dorrestein @ UCSD, Linda Wegley Kelly @SDSU, Lieve Laurens @ NREL, Steven Singer and Michael Schluppenhauer @ LBNL, Pieter Dorrestein @ UCSD
Student Trainee: Wesley Sparagon
Summary: Marine agronomy, or seaweed farming - the oceanic analogy to terrestrial cropping - offers an opportunity to capture carbon from ocean waters without imposing additional burdens on earth’s available arable land, limited fresh water, or energy and fertilizer resources. Macrolgae are a highly attractive source of raw materials for production of biofuels (or precursors thereof), along with a range of other potentially marketable products. This research proposal is therefore founded on the premise that we can use nature as a model for more efficient fermentation of macroalgae into fuel. The fish family Kyphosidae may offer the best prospects for this: they are common, active-swimming herbivorous grazers of macroalgae that are renowned for their digestive efficiency, and fine flesh quality. Equipped with a highly complex ruminant digestive system, they are able to convert macroalgae into high-quality fish flesh, kinetic energy and biowaste. Our plan is to define the role that microbial gut flora – the microbial consortium that has been refined by natural selection processes - play in the kyphosids’ remarkable digestive efficiency, and then co-opt their microbial assemblages to serve our own ends: to yield fuels and useful byproducts, in a zero-carbon, environmentally beneficial, massively scalable system. The potential also exists to harvest energy-rich lipids and single cell proteins (SCPs) that remain after the fermentation process. Kyphosids are perhaps crucial to monetizing macroalgae, and may thus be key to mankind’s sustainable use of the earth’s environment. Securing such sustainability may, by this method, be accomplished without slowing the progress of industrial development or global progress.
Setting Nutrient Thresholds to Coral Reef Health (National Fish and Wildlife Foundation 2014-2016)
Collaborators: Michael Fox @ WHOI, Tom Oliver @ NOAA, Nyssa Silbiger @ CSUN, Megan Donahue @ UH Manoa, Hollie Putnam @ URI
Student Trainees: Krissy Remple, Zachary Quinlan
Summary: Existing numeric water quality thresholds do not consider effects of land based source pollution (LBSP) on corals or coral ecosystems and narrative thresholds that consider corals only include reference to coral disease or mortality, only triggering mitigation after potentially irreversible consequences have occurred. In some coral reef areas, the EPA has been supporting shifting to biological criteria, and while ʻbiocriteria’ may outperform many traditional numeric thresholds, disease or mortality is a lagging indicator of LBSP effects that may be difficult to reverse. We aim to link water quality thresholds directly to coral physiological responses adaptable to a diversity of tropical high island biogeochemical contexts. We propose to develop a methodology that can be used in adaptive watershed LBSP mitigation to monitor coral physiology at timescales relevant to management objectives. Specifically, we propose to:(1) Develop a coral/microbial nutrient response gene expression panel, (2) Document water quality gradients in 4 Hawaiian islands that span a range of island ages, soil chemistry and land use practices, (3) Assay nitrogen and phosphorus response genes in coral samples from field gradients and (4) Establish coral and microbial response thresholds to varying levels of N and P related to measured N and P concentrations.
Establishing a Hawaiian Watershed as a Model Microbiome Mesocosm
Collaborators: Margaret McFall-Ngai (lead), Nicole Hynson, Joanne Yew, Anthony Amend and Camilo Mora @ UH Manoa
Summary: The next frontier in microbiome research is to understand from where our microbes derive. Importantly, the environment and host should be considered as a holistic entity whereby the function of a host cannot be understood without knowledge of the microbiome of the ecosystem in which it resides. Here we propose to address fundamental gaps in our basic understanding of the assembly and function of environmental microbial communities with the goal of defining the compositions and functions that support healthy hosts and environments. To accomplish this goal, it is critical that host and environmental microbiomes are studied within a well-characterized ecosystem. We will establish a Hawaiian watershed as a model ecosystem that encompasses a wide range of organisms and habitats in which we can contextualize the processes that shape microbiomes and link microbiome composition to function. To accomplish this, we will use complementary approaches based on field studies within a carefully monitored natural landscape, and experiments within a lab setting where we can control environmental conditions to mechanistically link microbiome structure to physiological effects. From these efforts, we will build predictive probabilistic models that describe the conditions (biotic and abiotic) that support healthy microbiomes at the ecosystem scale.