Basic ecological questions that drive this research include: (1) How do diversity and function vary between natural and human impacted environments? (2) How are the bacterial, archaeal and eukaryotic communities linked to each other and to what extent do they interact at the gene level? (3) What role does history (order of species arrival) play in community assembly? This is a cross-cutting theme of my research that I have been pursuing in a variety of projects and site-based science locations including pH/heavy-metal extreme environments, the rapidly-warming waters off the western Antarctic Peninsula, microbial communities on plastic marine debris from around the world (what I have termed the "Plastisphere"), fish microbiomes, and anaerobic phototrophic microcosms derived from freshwater and marine environments. While much of this work has targeted "sun-lit" waters due to accessibility, much of my work in Spain's Rio Tinto and elsewhere has been with heterotrophs and chemoautotrophs, and I am equally fascinated with the dark ocean and applying some of these questions to this under-sampled marine biome.
This theme explores natural and anthropogenic changes and their impact on microbial biodiversity. Projects include the impact of flooding and sewage overflow due to storms, as well as other factors such as thermal pollution and temperature increases on microbial communities in rivers, lakes, and coastal waters. Another project is examining the connection between harmful algal bloom dynamics and bacterial diversity and succession patterns in coastal waters. Very fine scale sampling at different points along the bloom period using automated samplers, in combination with machine-learning algorithms is helping us determine whether microbial community diversity and structure pre-bloom can be modeled to help predict bloom onset or termination. Harmful algal blooms are an increasing problem worldwide and threaten marine food resources. In addition to the automated plankton samplers used in this study, I have also worked with instrument manufacturers to develop technology to allow fine scale in situ measurements within microbial biofilms.
This research has been on-going in my laboratory since my postdoctoral studies of pH extreme environments and has continued in a variety of site-based locations including coral reefs on the tropical island of Moorea in French Polynesia, local estuaries, globally-distributed open ocean sites, and the biotic and abiotic surfaces of macroalgae and microplastics in the sea. I employ both marker gene surveys and metagenomic assessments of microbial diversity using next-generation sequencing methodologies with an eye towards understanding larger scale biogeographic patterns and the mechanisms behind them. A recent addition to my biodiversity studies has been holopelagic species of the brown alga Sargassum and its associated communities. My lab is developing population genomic markers with which to study recent strandings of these floating ecosystems in the Caribbean and most recently Brazil.
The fish model system is a promising one because fish depend heavily on their microbial-influenced innate immune system and readily lend themselves to experimental microcosms involving pathogens. My lab is studying how pathogens emerge in nature using Vibrio and Legionella as a model systems. We are employing genomics in combination with transcriptomics of Vibrio that colonize plastic and other substrates in the marine environment. Vibrio's ability to rapidly colonize the surface of plastic and be transported large distance in the ocean make it a good model for understanding its role as an emerging pathogen in aquaculture.
This research theme connects my research interests and those of my organic geochemistry colleagues at NIOZ-Texel and Brown University in the US. We have been comparing laboratory paleotemperature proxies with in situ measurements and are developing new proxies for application to lacustrine and estuarine paleothermometry for quantifying climate history. As part of this research focus, my laboratory has contributed to documenting the diversity of alkenone-producing haptophytes at lacustrine sites across the world, performing laboratory manipulations to identify the environmental controls for production of certain classes of alkenones, and most recently, exploring biosynthetic pathways of alkenone production. The study of alkenone metabolic pathways is an area of on-going interest in my laboratory.