Deepwater Horizon and the Rise of the Omics

University of South Florida Scholar Commons C-IMAGE Publications C-IMAGE Collection 3-25-2020 Deepwater Horizon and the Rise of the Omics Joel E. Kostka Georgia Institute of Technology Samantha Joye University of Georgia Rita Collwell University of Maryland Follow this and additional works at: https://scholarcommons.usf.edu/cimage_pubs Part of the Marine Biology Commons Scholar Commons Citation Kostka, Joel E.; Joye, Samantha; and Collwell, Rita, "Deepwater Horizon and the Rise of the Omics" (2020). C-IMAGE Publications. 6. https://scholarcommons.usf.edu/cimage_pubs/6 This Article is brought to you for free and open access by the C-IMAGE Collection at Scholar Commons. It has been accepted for inclusion in C-IMAGE Publications by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. MICS 28 Eos // APRIL 2020 DEEPWATER HORIZON AND THE RISE OF THE Microbial genomics techniques came of age following the Deepwater Horizon spill, offering researchers MICSunparalleled insights into how ecosystems respond to such environmental disasters. By Joel E. Kostka, Samantha Joye, and Rita Colwell Photograph of oil beneath the surface of the Gulf of Mexico following the Deepwater Horizon spill (background). In the inset, microscopic speci- mens of Candidatus Macondimonas diazotrophica are visible both inside and around the edges of oil droplets (large round shapes) in this micro- scope image. Credits: Rich Matthews/AP images (photo); Shutterstock/CoreDESIGN (DNA illustration); and Shmruti Karthikeyan (inset) SCIENCE NEWS BY AGU // Eos.org 29 lmost everywhere scientists gas) that enters the marine environment The DWH spill have looked on or near through natural mechanisms like seeps was also the first Earth’s surface—from ice- [Leahy and Colwell, 1990]. major environ- buried Antarctic lakes to As researchers began unveiling the com- mental disaster for arid, ultraviolet- baked des- plexity of microbial communities and illu- which genomics erts and ecosystems ranging minated fundamentals of how they operate technologies had from pristine to heavily polluted—they have in recent decades, though, much remained matured to such Afound abundant and often highly diverse unclear about their structure and function- an extent that they populations of microorganisms. Microor- ing in nature. The reason for this was in part could be deployed ganisms, or microbes, are everywhere; they because of a shortage of techniques for to quantify micro- are adaptable, and they play key roles in ele- studying them. Because of their small size, bial responses ment cycling and ecosystem functioning in microbes evade easy observation, and most over large spatial nearly every environment on Earth. cannot be cultured in the laboratory. At the and temporal Microbes are the great decomposers in time of the Exxon Valdez oil spill in 1989, for scales. As a result, ecosystems, breaking down dead and dying example, environmental microbiology was a the field of envi- organic matter and recycling major nutrients relatively nascent field. But in the past ronmental for use by plants. And by reacting rapidly and decade, a variety of so-called omics tech- genomics matured adapting to changing conditions, they act as niques, focused on parsing the genetic during the past first responders in helping restore balance makeup of cells, have emerged and offered decade in parallel and stability to ecosystems after such distur- researchers powerful new ways to study with the DWH bances as pollution or catastrophic storms. microbial communities and the roles played response. Techni- Microbes are, for example, intimately by specific groups of microbes. cal advances in involved in ecosystem responses to oil spills. genomics enabled Like organic matter derived from Omics Emerge direct, compre- modern- day primary production, oil The 2010 Deepwater Horizon (DWH) oil spill hensive analyses formed over geologic time can act as a car- in the Gulf of Mexico is the largest acciden- of the microbes in bon source that fuels microbial growth and tal oil discharge into a marine environment their natural habi- metabolism. Hydrocarbon- degrading for which a proportional emergency tat, be it oil-contaminated or uncontami- microbes have been studied for decades response effort was mounted. In contrast to nated seawater or sediments. Researchers and are thought to be ubiquitous and the Valdez spill, the last major spill affect- studying the effects of the DWH spill pre- diverse and to have adapted to consuming ing the United States before 2010, the DWH sided over an explosion of microbial oil over millions of years [Head et al., 2006]. discharge occurred in deep water, with genomics data that enabled major advances And biodegradation mediated by indige- extraordinarily large volumes of chemical in oil spill science and allowed scientists to nous microbial communities is considered dispersant applied during emergency answer the question, What microbes are the primary fate of most petroleum (oil and response efforts. there?, in complex communities in unprec- edented detail. Metagenomics, the sequencing of all genes for all organisms in a sample, enabled determinations of the full range of microbial species present. It also provided assess- ments of these organisms’ metabolic potential to carry out important ecosystem processes like photosynthesis and the deg- radation of certain carbon compounds. Application of metatranscriptomics, the sequencing of active or expressed genes, provided opportunities to decipher the functions or activities of those same microbes in nature, essentially answering the question, What are they doing? Gene sequences are collected from the environment in fragments. Recent improvements in bioinformatics tools, which use high-performance computing to stitch these fragments back together into the genomes of individual microbial spe- This sand core (left) collected on 30 June 2010 at Pensacola Beach, Fla., contains a pronounced oiled layer cies, have allowed scientists to reconstruct (dark brown). More than 50% of the microbes in that layer belonged to genus Marinobacter (in the Alteromonad- microbial genomes over large scales, reveal- ales order), a known hydrocarbon-degrading microbial group, far more than in sands below and above the oiled ing the incredible diversity and complexity layer. Credit: Markus Huettel of microbial communities. 30 Eos // APRIL 2020 scientific partner- et al., 2011; Yang et al., 2016; Kleindienst et al., ships enabled 2015]. Genomics research revealed that dif- transformative ferent microbial species are adapted to discoveries detail- degrade specific types of hydrocarbon ing how microbes compounds (e.g., natural gases, straight- respond to petro- chain aliphatics, or aromatics) depending leum discharges on environmental conditions like tempera- and facilitate eco- ture and nutrient availability. These dis- system recovery. coveries underscore the natural capacity of Many of these microbes in the Gulf of Mexico and else- partnerships were where to bioremediate petroleum hydro- supported by the carbons. Gulf of Mexico Research Initiative How Oil Affects Ecosystems (GoMRI), created Scientists have long hypothesized that the with a $500 mil- fate and impacts of oil in ecosystems are lion, 10- year com- determined by interplays between the mitment from BP physical and chemical characteristics of the to fund an inde- environment and by hydrocarbon chemistry pendent scientific and biogeochemical processes largely medi- research program ated by microbes. However, the complexity dedicated to of these interactions has impaired our abil- studying oil spill ity to decipher exactly how ecosystem func- impacts and miti- tioning is affected by oil. gation, particu- Oil can be a food source for some larly in the Gulf of microbes, but it can be toxic to others, Jonathan Delgardio and Will Overholt of the Georgia Institute of Technology sam- Mexico. GoMRI has resulting in adverse effects on microbially ple sand layers on 20 October 2010 at Pensacola Beach, Fla., which was heavily funded 17 interna- mediated ecosystem services like the break- polluted by weathered oil after Deepwater Horizon discharge. Researchers used tional consortia down of organic matter and the regenera- genomics to track how microbial communities changed in response to the oil by and thousands of tion of nutrients. Following the DWH comparing oiled sand layers to pristine sands. Credit: Markus Huettel investigators (bit discharge, GoMRI researchers observed .ly/ GoM - Research). through multiple lines of evidence that liq- Armed with genomics tools, Through a systems approach that incor- GoMRI researchers showed that oil- porates genomics along with knowledge and degrading microbes are, indeed, nearly tools from a range of other disciplines (e.g., ubiquitous, found almost everywhere In the wake of the biogeochemistry and oceanography), around the world in low abundance even researchers can now monitor and assess when crude oil is absent. These microbes, Deepwater Horizon spill, ecosystem health—and identify distur- part of the pool of low-abundance species bances that might otherwise go unnoticed— known as the rare biosphere, harbor a spe- multidisciplinary scientific by analyzing microbial populations that cialized metabolic capacity to use oil as a partnerships enabled both act as stewards for and represent bio- food source—a capability that can be rapidly indicators of ecosystems. With these activated upon exposure to oil [Kleindienst transformative

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