In the water above natural oil seeps in the Gulf of Mexico, where oil and gas bubbles rise almost a mile to break at the surface, scientists from the Georgia Institute of Technology, Columbia University and Florida State University have discovered something unusual: phytoplankton, tiny microbes at the base of the marine food chain, are thriving.
The oil itself does not appear to help the phytoplankton, but the low concentration of oil found above natural seeps isn’t killing them, and turbulence from the rising oil and gas bubbles is bringing up deep-water nutrients that phytoplankton need to grow, according to a study appearing January 25 in the journal Nature Geoscience. The result is phytoplankton concentrations above oil seeps that are as much as twice the size of populations only a few kilometers away.
“This is the beginning of evidence that some microbes in the Gulf may be preconditioned to survive with oil, at least at lower concentrations,” said Ajit Subramaniam, an oceanographer at Columbia University’s Lamont-Doherty Earth Observatory and co-author of the study. “In this case, we clearly see these phytoplankton are not negatively affected at low-concentrations of oil, and there is an accompanying process that helps them thrive. This does not mean that exposure to oil at all concentrations for prolonged lengths of time is good for phytoplankton.”
The research shows that the effects of oil and gas at the sea surface can be very different from the impacts of events such as the Deepwater Horizon spill, said Joseph Montoya, a professor in Georgia Tech’s School of Biology and another of the paper’s co-authors. The research could lead to a reconsideration of the response made to spills.
“There may be different responses by different organisms as we look at different regions of the spill itself,” said Montoya.
The study is the first to demonstrate this kind of teleconnection between the sea floor, subsea floor and microbial processes in the upper ocean, said Andy Juhl, an aquatic ecologist at Lamont and co-author. It also provides insight into how microbes and oil interact under water.
The researchers, along with colleagues in the Ecosystem Impacts of Oil and Gas Inputs to the Gulf (ECOGIG) consortium, began studying interactions around oil seeps after the Deepwater Horizon oil well disaster in 2010 to better understand what happens to the oil during catastrophic gushers and to find ways to better respond to similar disasters in the future. The natural seeps, found in many parts of the Gulf of Mexico, are tiny compared to an oil well blowout. An oil slick from a natural seep lasts between one and seven days and reaches between 1 and 100 square kilometers. In comparison, the surface oil from the Deepwater Horizon well covered about 11,200 square kilometers and persisted for months, Subramaniam said. But natural seeps still produce enough oil and gas that the scientists can smell it at the surface and see the oil bubbles burst.
In the lab, Juhl has been conducting experiments to understand how different concentrations of oil affect different types of phytoplankton. He has found no amount of oil on its own that has a positive effect on phytoplankton. “The direct effect of oil is usually negative, but in some cases small amounts of oil can be outweighed by the positive effect of the nutrients that are tagging along,” Juhl said.
Nigel D’Souza, then a post-doctoral researcher at Lamont, discovered the phytoplankton response to oil seeps while on a ship in the Gulf of Mexico monitoring chlorophyll fluorescence – energy that is emitted as light by compounds inside phytoplankton cells used for photosynthesis. Each time the ship crossed over a known oil seep, he noticed a spike in phytoplankton abundance. It was a Eureka moment, Juhl said. The evidence backed up what Susan Phan, a co-author and Columbia University student working on her senior thesis with Subramaniam, had previously noticed in remote sensing data. The scientists were able to compile multiple lines of evidence through chlorophyll fluorescence, water sampling and satellite images that all supported the idea that phytoplankton were benefitting from something connected with the seeps, even though the seeps were thousands of feet below.
The biggest impact was seen a few hundred feet deep in the water column, at the point where phytoplankton have enough light from above to still grow, and are receiving the most nutrients rising from below. Over oil seeps, D’Souza – who is now at Georgia Tech – found that the population was about double the usual amount. The measurements also showed increases in phytoplankton abundance at the surface.
There are still many questions. For example, scientists don’t yet know which types of phytoplankton are thriving over the seeps, or if some types of phytoplankton in the community are negatively affected by the rising oil. Previous studies have subjected phytoplankton to oil in laboratories to test their sensitivity and found differences in the impact on oceanic versus coastal phytoplankton and differences when phytoplankton were in nutrient-rich or nutrient-poor water, as well as damage to some phytoplankton cells at various concentrations of oil.
The study combined sampling from surface vessels with remote sensing from space.
“Satellite radar data have given us a detailed picture of where natural seeps are concentrated across deep seafloor of the Gulf of Mexico,” said co-author Ian MacDonald, an oceanographer and professor at Florida State University. “Building on this, the present, novel results show biological effects near the ocean surface in areas where seeps are most prolific.”
The research also demonstrates the importance of oceanographic field research in understanding complex ecosystem issues.
“There has been a tendency to rely on autonomous samplers in place of researchers out at sea,” Montoya observed. “For this project, it was really important to have diverse groups of scientists with broad interests working together both at sea and onshore, to tease the system apart.”
The research team plans two pathways of study next: To analyze the behavior of different types of phytoplankton above seeps to better understand how they interact with oil, and to improve understanding of how oil from deep underwater rises to the surface.
The study was part of the ECOGIG Consortium, a multi-institutional group that studies natural oil seeps in the Gulf of Mexico, funded by the Gulf of Mexico Research Initiative. In addition to those already mentioned, coauthors on the study were Mark Hafez, Alexander Chekalyuk, and Beizhan Yan of Lamont-Doherty Earth Observatory; and Sarah Weber of the Georgia Institute of Technology.
This work is supported by The Gulf of Mexico Research Initiative's (GOMRI) ECOGIG consortium, with additional support from National Science Foundation (NSF) grant OCE-0928495. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
CITATION: N.A, D’Souza, et al., “Elevated surface chlorophyll associated with natural oil seeps in the Gulf of Mexico,” (Nature Geoscience, 2016). http://dx.doi.org/10.1038/ngeo2631
The Torres lab has been awarded a four year, $1.2 million grant by the National Institutes of General Medical Sciences to investigate a newly discovered regulatory mechanism that controls G protein signaling, a process essential for the transduction of extracellular signals (such as hormones, neurotransmitters, and photons of light), and the target of most pharmaceutical drugs.
Spawned by their development and application of a custom bioinformatics software tool (called SAPH-ire) 1, the Torres lab discovered a new way in which G protein signaling is regulated by phosphorylation – an enzyme-driven chemical modification of specific amino acid side chains found in most proteins. The newly discovered phospho-regulatory element, like G proteins themselves, is well conserved throughout eukaryotes, which will enable Torres and his lab to investigate how the element functions across diverse organisms such as budding yeast and humans. The National Institutes of Health grant will also provide funding to determine the biochemical mechanism of G protein phosphorylation – including the enzymes that activate the regulatory element in coordination with other cellular processes including cell division and stress. Through these and other approaches, Torres hopes to determine whether his lab has discovered a protein mechanism that is not only fundamental to the process of G protein signaling in all eukaryotes, but also a possible alternative target for pharmaceutical drug therapies.
Dewhurst, H. M., Choudhury, S. & Torres, M. P. Structural Analysis of PTM Hotspots (SAPH-ire)--A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families. Mol. Cell. Proteomics 14, 2285–97 (2015).
Dr. Frank Stewart in the School of Biology was recently awarded a grant from the Georgia Improving Teacher Quality (ITQ) Grants Program to renew the Summer Workshop in Marine Science (SWiMS). Coral reef collapse, oil spills, and sea level rise are among the most pressing science topics facing policymakers, researchers, and the general public. Understanding these and other issues affecting our oceans is critical to the preservation of marine resources and to a broad education in science. The goal of SWiMS is to use marine science research at Georgia Tech to enhance standards in middle and high school Life and Earth Science education.
Developed by Dr. Stewart in partnership with Gustavia Evans at the Center for Education Integrating Science, Mathematics, and Computing (CEISMC), SWiMS is open to local middle and high school science teachers from high need local education agencies of Fulton County and Clayton County. Through lectures by faculty, discussion and lesson planning sessions, and hands-on lab and field exercises, the 5-day SWiMS course disseminates teaching modules developed around cutting-edge marine science by Georgia researchers. SWiMS modules consist of lesson plans and laboratory exercises that address key marine topics, such as ocean food webs, coral reef decline, and ocean acidification in response to global change. SWiMS 2016 will be held at Georgia Tech from June 27 to July 1. Teachers will leave with enhanced content knowledge as well as lesson plans and schedules for module implementation and evaluation. Each participant will receive 5 professional learning units and a $500.00 stipend. Additional details can be found at https://swimsgatech.wordpress.com/ Details about the ITQ program can be found at https://coe.uga.edu/outreach/programs/teacher-quality
Assistant professor Chong Shin and members of her lab discovered Fhl1b as a novel target of Bone morphogenetic protein (Bmp) signaling. Bmp signaling has been shown to play an essential role in inducing the liver at the expense of pancreas in different animal models. Nevertheless, the identity of downstream gene regulatory networks of Bmp signaling that specify the liver to the detriment of pancreas remains elusive. Moreover, the key question of whether Bmp signaling suppresses pancreas gene program keeping progenitors competent to differentiate into the liver or directly induces the liver gene program has not yet been answered.
Using transcriptome profiling and single-cell level functional analyses in a zebrafish model, Shin and colleagues have discovered Fhl1b as a Bmp2b signaling target that may actively suppress the pancreas gene program to properly modulate liver induction, lineage allocation, and β-cell regeneration.
These findings of Bmp2b regulation of Fhl1bsuggest a new paradigm of how Bmp signaling regulates the cell fate choice of liver versus pancreas and β-cell mass. Furthermore, these results give profound insight into why effective Bmp signaling suppression is critical for the induction β-cells in human pluripotent stem cells (hESCs). Accordingly, a comprehensive understanding of how lineage-specific multipotent progenitors make a developmental choice will shed light on the re/programming of stem/progenitor cells into specific cell lineages, enabling us to generate functionally relevant cells for clinical utility.
This research was supported by the National Institute of Diabetes and Digestive and Kidney Diseases (K01DK081351), the Regenerative Engineering and Medicine Research Center (GTEC 2731336 and GTEC 1411318), the National Science Foundation (1354837), and the School of Biology (Georgia Institute of Technology).
Citation: Xu J, Cui J, Del Campo A, Shin CH (2016) Four and a Half LIM Domains 1b (Fhl1b) Is Essential for Regulating the Liver versus Pancreas Fate Decision and for β-Cell Regeneration. PLoS Genet 12(2): e1005831. doi:10.1371/journal.pgen.1005831
A study from School of Biology Professor Greg Gibson’s group just published in the American Journal of Human Genetics argues that we should be looking not just at the structural parts of genes, but also the regulatory regions around them. The paper demonstrates that there is a burden of rare genetic variants in these regions that associates with abnormal gene expression. It does not show that they cause birth defects, but does suggest that they need to be seriously considered as WGS technology develops.
Gibson explains it in the form of a metaphor about building a house. He says there are two critical components: the bricks and mortar, and the plans for where to put them. If there is a defect in the glass or a crack in a piece of wood, then sooner or later the structure may fall apart. This is what current approaches focus on, the so-called protein coding-regions. But if the architect’s plans call for more windows than the beams can support, or the contractor doesn’t deliver enough concrete, then the consequences can be just as bad.
We now know that a lot more of the genetic component of differences in the way we look and behave, or of what makes us susceptible to different diseases, is in the planning than the structural components. This insight is based on studies of common polymorphisms, namely the millions of genetic differences that we all share. The new study argues that it will also be true of rare genetic variants including new mutations that are specific to a single person.
Graduate student Jing Zhao sequenced the regulatory regions of almost 500 genes from 500 participants in the Georgia Tech-Emory Predictive Health Institute study, and added up the number of rare mutations in people whose expression of those genes was toward the extremes. The result is what she calls a smile plot, because the curve has a high number at either end and low number in the middle. It means that the plans can be off in either direction, making too little or too much transcript for each gene. Explains Gibson, it is as if all the houses with crooked window frames are that way not because of the wood quality, but because each builder made different mistakes when putting the frames in.
Furthermore, there seem to be specific subsets of genes where these events are more or less likely to happen. This is important, because it implies that we may be able to develop algorithms that identify the most likely places for regulation to go wrong, based on the evolutionary conservation of different parts of genes.
Projects such as the President’s Precision Medicine initiative aim to use genomics to help us decipher individual causes of disease. In the next few years, Gibson expects that much larger datasets of tens and eventually hundreds of thousands of people, in many different tissues, will appear. The challenges are as much in the bioinformatics than the technology.
A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood.
Zhao J, Akinsanmi I, Arafat D, Cradick TJ, Lee CM, Banskota S, Marigorta UM, Bao G, Gibson G.
Am J Hum Genet. 2016 Feb 4;98(2):299-309. doi: 10.1016/j.ajhg.2015.12.023. PMID: 26849112
On April 20, 2010, an explosion on the Deepwater Horizon (DWH) oil rig released a torrent of oil at the seafloor of the Gulf of Mexico, discharging close to 5 million barrels of oil in 87 days. It was the largest accidental oil spill in U.S. history.
Six years hence, the visible signs of the DWH disaster are fading, and the public may be lulled into assuming that all is fixed and well. In fact, many questions remain, and scientists continue to work tirelessly to address them. They include the team of Joel E. Kostka, a professor of biology in Georgia Tech’s College of Sciences. The hope is to develop effective spill mitigation and remediation technologies by understanding the effects of oil spills on marine environments. Kostka’s work on microbial oil degradation seeks to harness natural processes and native microorganisms to address disastrous oil spills.
Kostka’s research is part of the Gulf of Mexico Research Initiative (GoMRI), a 10-year, $500 million independent research program to study the impacts of the DWH oil spill and gain fundamental understanding of the dynamics of such events. Within GoMRI, the Kostka lab is funded under the Center for Integrated Modeling and Analysis of Gulf Ecosystems (C-IMAGE), a research consortium of 19 U.S. and international partners, led by the University of South Florida. Their goal is to advance the understanding of the processes, mechanisms, and environmental consequences of marine oil blowouts.
“We incorporate laboratory experimentation, field-oriented assessments, and modeling to predict the long-term fate and degradation of oil on Gulf ecosystems, especially at the seafloor.” Kostka says. "An especially exciting component of C-IMAGE is that we are comparing the effects of the DWH spill, in the northern Gulf of Mexico, to those of the Ixtoc spill, which occurred in 1979 near Campeche Bay, in the southern Gulf of Mexico." The Ixtoc spill was nearly as large as the DWH spill.
To understand the dynamics and impact of oil spills, the Kostka lab studies the microorganisms that break down oil. “We hypothesize that, similar to the breakdown of natural organic matter, biodegradation mediated by microbes is the ultimate fate of most of the spilled oil that enters the marine environment.” Thus, the Kostka lab studies how fast is, and what controls, the microbial degradation of oil in order to direct the management and cleanup of contaminated ecosystems.
During the DWH discharge in 2010, emergency responders used oil plume models to predict where the oil would go. However, microbial degradation of the oil was not included in most of the models, Kostka observes, “even though we know that a lot of the oil will be eaten by microbes.”
The Kostka lab now has measured how fast the oil was degraded in the deep waters and sediments in the northern Gulf of Mexico. “If there was an oil spill today, we could better predict where oil would go,” Kostka says, “because the model could include our measurements of biodegradation speeds under different oceanographic conditions.”
Working with scientists at Florida State University, Kostka and his team have studied the fate of the DWH oil that landed on Florida beaches and the microbes that degraded the oil. “Since beaches are exposed on shore, we could more easily follow the fate of the deposited oil,” Kostka says. “For the first time, we used state-of-the-art metagenomic techniques to track the oil-eating microbes for a period of more than one year after the oil it was deposited at Pensacola Beach in June 2010.”
Metagenomes are made up of all the genes from all the organisms present in the environment. The genetic sequences in the metagenome reveal the functions of microbes in the sample.
“Specific microbial groups were clearly related to how fast and which oil compounds were degraded,” Kostka says. “If there was an oil spill today, we would be able to tell responders how fast the oil would likely be degraded by microbes.”
On the Florida beaches impacted by the DWH discharge, the Kostka lab has also identified microbial groups that could be used as sentinels, or bioindicators, to tell responders whether important ecosystem services – such as organic matter decomposition and nutrient regeneration – are affected by oil exposure on the beach. “Now that we have established a baseline for the microbes present in beaches by using metagenomics, we could also advise environmental managers as to when the ecosystems are restored to close to the original condition.”
One interesting question that the research has raised is whether the Gulf is really a unique environment for microbes that eat oil.
Scientists had believed that because of the abundance of natural oil seeps in the Gulf, microbes there have adapted to oil and are therefore able to degrade oil quickly, Kostka says. However, comparing the rates at which microbes in the Gulf eat oil with those in other oceans such as the Beaufort Sea in the Arctic Ocean indicates that microbes in different waters degrade oil at similar rates under similar environmental conditions, Kostka’s research has found.
“The finding suggests that oil-eating microbes are present nearly everywhere and are capable of responding to oil spills under the right conditions,” Kostka says. This new hypothesis is supported by recent results showing that the plants of the sea – single-celled marine phytoplankton – naturally produce oil-like chemical compounds, which are eaten by other microbes. Thus, chemicals present in crude oil are naturally produced and consumed all the time nearly everywhere in the world’s oceans.
“The microbial potential for oil cleanup or mitigation appears to be naturally present in the world’s oceans,” Kostka says. “We just need to better understand the controls of that potential to be able to enhance cleanup and predict the fate of spilled oil.”
Biology Professor Jeff Skolnick has been awarded $2.44 million by the National Institutes of Health to study how to repurpose FDA approved drugs to treat genetic diseases. The 5 year project is entitled “Interplay of inherent promiscuity and specificity in protein biochemical function with applications to drug discovery and exome analysis” under the General Medical Sciences section. The project focuses on the gap in how to interpret the information in the enormous number of sequenced human exomes in terms of the functional consequences of the observed variations in amino acids and their connection to human diseases. This gap also underlies the failure to develop drugs, without side effects, to treat these diseases. This failure is exacerbated by the fact that a given drug molecule binds to different proteins involved in numerous cellular processes. This project lays out the details as to how and why these problems occur, and in the context of protein structure, how our existing and proposed progress can help surmount them. Skolnick’s group will first elucidate the design principles underlying protein structure and function and then apply them to repurpose FDA approved drugs to treat Mendelian diseases and to identify the genetic variations underlying such diseases. They will examine whether the stereochemical space of small molecule drugs and endogenous metabolites is complete and also the differences in the properties of drugs and metabolites. From these analyses, they will suggest how binding specificity might emerge from a highly promiscuous background. This might enable the design of better drugs with minimal side effects and a better understanding of how cells work. Employing these insights, they then will develop better structure-based approaches to virtual ligand screening and enzyme function inference. The ability to predict enzymatic function is particularly essential as residue mutations associated with loss of enzymatic function are the most important missense mutations associated with Mendelian disease. These approaches will use the conservation of ligand-protein microenvironments in stereochemically similar ligand binding sites or active sites in different proteins, regardless of their evolutionary relationship. They will explore the biochemical consequences of a class of enzymes that they discovered – dizymes, single domain proteins that perform two different enzymatic activities at two different active sites. For representative cases, They will experimentally test their predictions of ligand binding and enzymatic activity and their influence on cellular biochemical function. All developed tools will be combined in a comprehensive exome annotation approach. First, it will identify disease associated residue variations. Then, it will predict diseases a protein might be associated with and suggest the best protein targets. Finally, it will suggest what might be the best drugs to treat the disease.
Dr. Sam Brown, Associate Professor of Biology, was just awarded a $600K, 3 year grant from the Simons Foundation for a project entitled “How do quorum-sensing bacteria sense and respond to their social and physical environment?”This project investigates collective decision making in bacteria by exploring how bacteria collectively sense and respond to their environment via a form of cell-cell communication known as quorum-sensing (QS). Despite the widespread interest in QS from molecular mechanisms to social evolution and pathogen control, there is still controversy over the basic evolutionary function of QS – in short, why do bacteria use QS? The standard answer is that cells produce extracellular signals to serve as a proxy for cell density – more signal implies more bacteria. However, inferences to density can be confounded as signal concentration will also vary with changes in the physical environment (diffusion, flow) and other aspects of social organization (spatial patterning, genotypic mixing), leading to a list of alternative hypotheses (e.g. diffusion, efficiency, and genotype sensing).
Current functional hypotheses and mathematical models focus on the limits of inference to physical and/or social environmental variation, given the production and sensing of a single signal type. However, molecular characterization of QS systems often reveals the use of
multiple distinct extracellular signal molecules. To overcome this persistent gap between
functional hypotheses and molecular mechanism we will develop and test theory on the functional roles and limits of multi-signal QS, using the widely studied environmental generalist microbe Pseudomonas aeruginosa (PA). Our central hypotheses are that QS bacteria can (1) simultaneously resolve their social and physical environment, via non-linear processing of multiple signals with differing environmental properties and (2) use simple signal-mediated rules to limit collective behaviors to clonal high density, low diffusion, low flow environments. The proposed research will leverage Georgia Tech’s expertise in spatial math modeling, ‘lab-on- a-chip’ environmental manipulation, high-throughput microbial imaging and evolutionary microbiology.
Biology major June Y. (Austin) Moon has been awarded the Virginia C. and Herschel V. Clanton Jr. Scholarship, for a top pre-medical student in the College of Sciences. Moon participates in undergraduate research with the School of Biology’s Yuhong Fan, in whose lab he studies differentiation of mouse embryonic stem cells. He served as treasurer of the American Red Cross Club at Georgia Tech and is now the advocacy coordinator of the American Medical Student Association at Georgia Tech. A total of six undergraduate awardees in the College of Sciences were announced at the College’s Advisory Board meeting on April 22, 2016, by Associate Dean for Academic Affairs David M. Collard.
Moon was honored along with the five other undergraduate awardees in the campus-wide Student Honors Celebration on April 20, 2016. “That event is an important opportunity in the academic calendar year to recognize the outstanding accomplishments of our students,” says Associate Dean Collard. Moon also joined the College of Sciences Advisory Board Members, Dean Paul M. Goldbart, and guests at the College’s awards presentation and lunch on April 22.
“Introducing our award winners to members of our Advisory Board is a particular honor,” says Associate Dean Collard. “It is something I look forward to each year.”
G. David Williamson, senior science adviser at the Centers for Disease Control and Prevention (CDC), has been elected as a vice president of the American Statistical Association (ASA).
Williamson is senior science adviser and executive director of the Statistical Advisory Group at the CDC and an adjunct professor in the department of biostatistics and bioinformatics in the school of public health at Emory University and at Georgia Southern University. Prior to that, he was the associate director of science at the CDC’s National Center for Injury Prevention and Control; chief science officer in the Office of Surveillance, Epidemiology and Laboratory Services; and director of the Division of Health Studies.
Williamson earned his PhD in biostatistics from Emory University in 1987; two master’s degrees in statistics and biology from Virginia Tech and Georgia Southern, respectively; and an undergraduate degree in biology from the Georgia Institute of Technology in 1973.
Among his appointments with the ASA, Williamson became a fellow in 2004 and was Joint Program Committee chair of JSM in 2000. Active in ASA awards and committees, he also served as vice chair of the Committee on Meetings from 1999–2002; chair (and member) of the Karl Peace Award from 2012–2015; member of the Strategic Initiative on Visibility and Impact in Policy Task Force in 2009–2010; and program chair of the Statistics in Epidemiology Section in 1997.
About the American Statistical Association
The ASA is the world’s largest community of statisticians and the oldest continuously operating professional science society in the United States. Its members serve in industry, government and academia in more than 90 countries, advancing research and promoting sound statistical practice to inform public policy and improve human welfare. For additional information, please visit the ASA website at www.amstat.org.