Microbiomes regulate critical environmental processes like nutrient cycling, toxin production, and organic matter degradation. They often contain thousands of different species, most of which are still unknown to science. In the ocean, microbes perform basic biogeochemical functions that control the flux of carbon, nitrogen, and sulfur into the deep sea and the atmosphere. These processes have important implications for large-scale phenomena like plankton blooms, expanding oxygen minimum zones, and global elemental budgets.
While laboratory experiments can tell us about the biology of individual species, most marine microbes have yet to be cultured. Moreover, lab studies rarely identify their ecological roles or interactions with other organisms. An alternative approach uses environmental DNA ("eDNA") sequencing to characterize entire microbiomes. This community-level eDNA sequencing, also called metagenomics, can answer basic questions about who is there and what they are doing. To perform these analyses, I use a combination of computer science and molecular biology, a field known as bioinformatics. The development of computational tools for analyzing large DNA sequence data sets is another critical field of study undergoing exciting changes with the application of machine learning and powerful statistics designed for microbiome studies. I use metagenomics and bioinformatics to study how marine microbiomes are shaped by resource limitation, respond to perturbations, and impact the health of their environment. I do this in a variety of systems including subsurface marine caverns, sediments, and most recently, in the California Current.
1. Gulf of Mexico Blue Holes
I am part of an interdisciplinary team exploring blue holes in the Gulf of Mexico. Blue holes are subsurface caverns that formed during the last ice age in calcium carbonate, or karst, bedrock. When sea level rose they became undersea structures with unique physical and chemical characteristics compared to the surrounding water column. Our first sampling expedition showed that the holes host high levels of rare and understudied microbes. The genome sequences of these taxa, which I assembled from the environmental DNA, provide important new insight into the ecology of low oxygen marine systems, which are projected to expand substantially with climate change. For more on blue holes check out the PBS Changing Seas episode on our expeditions, and my recent publication in The ISME Journal and accompanying blog post.
While laboratory experiments can tell us about the biology of individual species, most marine microbes have yet to be cultured. Moreover, lab studies rarely identify their ecological roles or interactions with other organisms. An alternative approach uses environmental DNA ("eDNA") sequencing to characterize entire microbiomes. This community-level eDNA sequencing, also called metagenomics, can answer basic questions about who is there and what they are doing. To perform these analyses, I use a combination of computer science and molecular biology, a field known as bioinformatics. The development of computational tools for analyzing large DNA sequence data sets is another critical field of study undergoing exciting changes with the application of machine learning and powerful statistics designed for microbiome studies. I use metagenomics and bioinformatics to study how marine microbiomes are shaped by resource limitation, respond to perturbations, and impact the health of their environment. I do this in a variety of systems including subsurface marine caverns, sediments, and most recently, in the California Current.
1. Gulf of Mexico Blue Holes
I am part of an interdisciplinary team exploring blue holes in the Gulf of Mexico. Blue holes are subsurface caverns that formed during the last ice age in calcium carbonate, or karst, bedrock. When sea level rose they became undersea structures with unique physical and chemical characteristics compared to the surrounding water column. Our first sampling expedition showed that the holes host high levels of rare and understudied microbes. The genome sequences of these taxa, which I assembled from the environmental DNA, provide important new insight into the ecology of low oxygen marine systems, which are projected to expand substantially with climate change. For more on blue holes check out the PBS Changing Seas episode on our expeditions, and my recent publication in The ISME Journal and accompanying blog post.
Conducting biological surveys of the Amberjack Blue Hole rim in September 2018.
2. Marine sediments
Marine sediments contain an order of magnitude more microbes than the water column and are highly spatially structured. They often also exist at a critical interface of oxygen availability in the ocean, where the overlying water is oxygenated but sediments are quickly depleted and become devoid of oxygen in the upper centimeters. These features mean that ecological competition is fierce and unique metabolisms adapted to low-oxygen environments abound in sediments. My Ph.D. thesis focused on the chemical ecology of a group of marine sediment bacteria, a field with applications for drug discovery and microbial evolution. More recently, I compared culture-independent and culture-dependent microbial diversity in marine sediments by combining traditional isolation method with metagenomic sequencing and bioinformatics. This study was recently published in the journal Environmental Microbiology.
Marine sediments contain an order of magnitude more microbes than the water column and are highly spatially structured. They often also exist at a critical interface of oxygen availability in the ocean, where the overlying water is oxygenated but sediments are quickly depleted and become devoid of oxygen in the upper centimeters. These features mean that ecological competition is fierce and unique metabolisms adapted to low-oxygen environments abound in sediments. My Ph.D. thesis focused on the chemical ecology of a group of marine sediment bacteria, a field with applications for drug discovery and microbial evolution. More recently, I compared culture-independent and culture-dependent microbial diversity in marine sediments by combining traditional isolation method with metagenomic sequencing and bioinformatics. This study was recently published in the journal Environmental Microbiology.
3. The California Current
The California Current is a highly productive ecosystem with several ecologically and economically valuable fisheries. Local oceanographic phenomena like upwelling and marine heat waves can impact all levels of the food web; however, the propagation of these effects through trophic levels is largely unknown due to a poor understanding of linkages between microbes, plankton, and metazoans. Using a multi-year eDNA time series, I am assessing how microbiomes correlate with phytoplankton and metazoan community dynamics to generate a more holistic understanding of the marine food web. I use metagenome-assembled genomes and gene functions to characterize microbial communities and connect them to higher trophic level community composition. These combined ‘omics approaches provide a holistic overview of marine ecosystems and may improve biological oceanographic modeling of environmental perturbations in the future.
The California Current is a highly productive ecosystem with several ecologically and economically valuable fisheries. Local oceanographic phenomena like upwelling and marine heat waves can impact all levels of the food web; however, the propagation of these effects through trophic levels is largely unknown due to a poor understanding of linkages between microbes, plankton, and metazoans. Using a multi-year eDNA time series, I am assessing how microbiomes correlate with phytoplankton and metazoan community dynamics to generate a more holistic understanding of the marine food web. I use metagenome-assembled genomes and gene functions to characterize microbial communities and connect them to higher trophic level community composition. These combined ‘omics approaches provide a holistic overview of marine ecosystems and may improve biological oceanographic modeling of environmental perturbations in the future.
Dawn sampling for eDNA on a National Marine Fisheries Service vessel, the NOAA Ship Reuben Lasker, in June 2022.