MEB Seminar | Dr. Nicole Ratib

Dr. Nicole Ratib
Post-Doc, USC, MEB (PI: Dr. Cameron Thrash)
Research Profile

Genomic and physiological characterization of Escherichia coli evolving in long-term batch culture

Tuesday, March 10, 12 PM, AHF 153 (Torrey Webb Room)

Abstract: In most natural environments, bacteria spend much of their time under conditions of starvation and stress. Long-term batch cultures are an excellent laboratory system to study adaptation during nutrient stress because cells are incubated for relatively long periods of time, months to years, without the addition of nutrients. During long-term batch culture cells adapt to acquire energy from cellular detritus creating a complex and dynamic environment for mutants of increased relative fitness to exploit. To characterize the population dynamics and identify beneficial alleles, we analyzed the genomes of 1117 clones isolated from a single long-term batch culture inoculated with a single clone and incubated for 1200 days. A total of 679 mutations were identified including single nucleotide polymorphisms, indels, movement of mobile genetic elements, large deletions up to 64kbp and amplifications up to ~500kbp. During the 3.3-year incubation, two main lineages diverge and continuously evolve. There is evidence of at least two instances of a fixed mutation reverting back to the wild type allele, suggesting beneficial mutations may later become maladaptive. Most of the mutated genes encode proteins involved in metabolism, transport, or transcriptional regulation. Clones from the two lineages are physiologically distinct based on outgrowth in fresh medium and competition against the parental strain. Similar population dynamics and mutated genes were detected in three parallel populations sequenced through day 60 providing evidence for positive selection. These data provide new insight into the population structure and mutations that may be beneficial during periods of starvation in evolving bacterial communities.

Wrigley Sonosky Sustainability summer fellowship

The USC Wrigley Institute is now accepting applications for the 2020 Sonosky Sustainability Summer Fellowship. Applications due March 11. Notice is attached.

   Sonosky 2020 Announcement by uscbiscgrad on Scribd

MEB Seminar | Dr. Leslie Babonis

Dr. Leslie Babonis
Research Assistant Scientist, University of Florida, Whitney Lab for Marine Bioscience
Research Profile

Understanding biodiversity, one cell at a time

Thursday, February 6, 12 PM, AHF 153 (Torrey Webb Room)

Abstract: I study novelty. Specifically, I am interested in understanding the factors that drive the origin and diversification of novel cell types. More than just taxon-specific oddities, novel cell types can promote niche specialization and facilitate speciation events; thus, studying novelty is critical for understanding the evolution of biodiversity. One of my favorite projects focuses on understanding the mechanisms driving morphological and functional specialization of cnidocytes (stinging cells) across cnidarians (corals, jellyfish, and their kin). Using a combination of observational and functional techniques, I have constructed a cnidocyte gene regulatory network that I use to test hypotheses about the evolutionary origin of this truly bizarre lineage of cells. Surprisingly, the fate of this novel cell lineage seems to have been acquired through recycling and reorganization of an old gene regulatory network, rather that the origin of a novel regulation strategy.

MEB Seminar | Dr. Allie Graham

Dr. Allie Graham
NSF PRFB Fellow, Oregon State University
Research Website

From the Mountains to the Sea: Comparative Genomics of Mechanisms Underlying the Physiological Response to Low Oxygen

Tuesday, January 28, 12 PM, AHF 153 (Torrey Webb Room)

Abstract: Environmental variables can exert a considerable selective pressure across the entire organism – from their genome to their physiology. Organisms living in extreme environmental conditions provide excellent systems to investigate numerous basic questions about the limits of an organism's ability to adapt, to understanding the inherent repeatability of molecular adaptation, and thus the origins of biodiversity, by examining both phenotypic and genotypic novelty. My work uses both integrative and comparative approaches to understand the mechanisms underpinning the response to such environmental variables, with a focus on oxygen availability (i.e. hypoxia). This talk will journey through my previous work on high-altitude adaptation in Andean duck species, to my current work on hypoxia in copepods (and other crustaceans), and conclude with how my discoveries opened up numerous exciting avenues for future work in aquatic invertebrates.

Marine & Environmental Biology Seminar | Dr. Phillip Cleves

Dr. Phillip Cleves
Post-Doctoral Research Fellow, Stanford University
Research Profile |

Molecular and cellular bases of cnidarian-dinoflagellate symbiosis and its breakdown

Tuesday, January 21, 12 PM, AHF 153 (Torrey Webb Room)

Abstract: The symbiosis between corals and dinoflagellate algae is essential to the energetic requirements of coral-reef ecosystems. However, coral reefs are in danger due to elevated ocean temperatures and other stresses that lead to the breakdown of this symbiosis and coral "bleaching". Despite the importance of coral reefs, the molecular basis of how corals maintain a healthy symbiosis and avoid bleaching is poorly understood, in part because of the lack of a tractable genetic model system. The small anemone Aiptasia is symbiotic with algal strains like those in reef-building corals but has many experimental advantages, making it an attractive laboratory model for cnidarian symbiosis.  To explore the transcriptional basis of heat-induced bleaching, we used RNAseq to identify genes that are differentially expressed during a time course of heat stress of symbiotic and aposymbiotic Aiptasia strains. We observed a strong upregulation of hundreds of genes at times long before bleaching begins in symbiotic anemones. The putative promoters of these early stress-response genes are enriched for binding sites for the NFB and HSF1 transcription factors, suggesting that many of these genes share core transcriptional control. The overall expression patterns were similar between the symbiotic and aposymbiotic anemones, indicating that many of the expression changes are not specific to the presence of the algae. Nonetheless, reducing HSF1 activity with a pharmacological inhibitor resulted in more severe bleaching, suggesting that this symbiont-independent stress response is protective against bleaching.
           
Genetic tools are needed to allow rigorous functional testing of the roles of candidate genes in symbiosis and bleaching. Recently, we have developed methods for knocking down and overexpressing genes of interest in Aiptasia. Meanwhile, we have successfully used the CRISPR/Cas9 technology to create genetic changes in embryos of the coral Acropora millepora. We used this technology to knock out HSF1 and demonstrated its role in coral heat tolerance. Through the establishment of both gain-of-function and loss-of-function methods in both Aiptasia and corals, it will be possible to exploit the year-round spawning of Aiptasia to perform initial tests of gene function in cnidarian-algal symbiosis and then further test the discoveries made using similar technologies in corals.

MEB Seminar | Dr. Casey Mueller

Dr. Casey Mueller
Assistant Professor, CSUSM, Biology
Lab Website

Thermal physiology: exploring themes of development and variability in different animal models

Tuesday, Dec. 3, 12 PM, AHF 153 (Torrey Webb Room)

Abstract: Dr. Mueller will present some of her lab’s data on copepods, as well as some work on chorus frogs and possibly rainbow trout.  Many of the ideas can be applied to marine organisms.

MEB Seminar | Dr. Jeff Bowman

Dr. Jeff Bowman
Assistant Professor, UCSD, Scripps Institute of Oceanography, Integrative Oceanography Division
Lab Website

Trials, tribulations, and transcriptomes: Understanding microbial ecosystem processes along the western Antarctic Peninsula

Tuesday, Nov. 5, 12 PM, AHF 153 (Torrey Webb Room)

Abstract: The western Antarctic Peninsula (WAP) is a dynamic marine environment defined by contrasting onshore and offshore water masses, rapidly shifting sea ice conditions, and strong season cycles of light and temperature.  The region is well known for its charismatic megafauna, but the charisma of its marine microbes is just beginning to emerge.  I’ll describe some of our efforts over the last several years to understand the dynamics of marine microbial communities along the WAP, culminating in our ongoing effort to use metatranscriptomics to understand the carbon and energy transfers associated with the winter-spring seasonal transition.  This transitional period is dominated by lipid metabolisms among a surprisingly diverse group of marine phytoplankton.  Given the variability in timing of the annual sea ice retreat, and the importance of lipid-rich phytoplankton in regional foodwebs, we anticipate implications for metabolic energy budgets across trophic levels.

MEB Seminar | Dr. Alyson Santoro

Dr. Alyson Santoro
Assistant Professor, UCSB, EEMB
Lab Website

Nitrification as a window on the mesopelagic

Tuesday, October 7
12 PM
AHF 153 (Torrey Webb Room)

Abstract: The mesopelagic ocean--often called the “twilight zone”--is a critical area for the microbial processing of sinking organic matter. Our lab studies some of the most abundant members of the mesopelagic microbial community, the ammonia-oxidizing archaea and nitrite-oxidizing bacteria. Together, these organisms carry out the biogeochemical process of nitrification and are responsible for producing the vast deep ocean nitrate reservoir. They also play an underappreciated role in carbon and trace metal cycling. My talk will describe combining laboratory cultures with field rate measurements to understand the critical role of nitrifiers in the intertwined geochemical cycles of carbon, nitrogen, and trace metals in the dark ocean.

MEB Seminar | Dr. Rebecca Albright

Dr. Rebecca Albright
California Academy of Sciences, Invertebrate Zoology
Research Profile

Coral Reefs in a Changing Climate: Challenges and Reasons for Hope

Tuesday, October 1
12 PM
AHF 153 (Torrey Webb Room)

Abstract: Already under severe pressure from a number of stressors, including overfishing and pollution, coral reefs are also among the most vulnerable ecosystems to climate change and ocean acidification: We have lost an estimated 50% of the world's coral reefs over the last several decades and are projected to lose more than 90% by 2050. While acute disturbances such as temperature-induced coral bleaching are largely responsible for accelerated reef decline in recent years, chronic disturbances like ocean acidification erode a reef’s capacity to recover by slowing growth and reproduction. In this talk, I will give an overview to the challenges that reefs are currently facing, focusing on the impacts of changing seawater chemistry on various aspects of coral reef biology, ecology, and biogeochemistry.  We will also explore some of the novel and exciting ideas that are emerging to address the coral reef crisis. We'll highlight strengths and limitations of current approaches and discuss next steps towards saving these valuable ecosystems.

MEB Seminar | Dr. Eric Boyd

Dr. Eric Boyd
Associate Professor, Montana State Univ., Microbiology and Immunology
Lab Website

Tuesday, September 24
12 PM
AHF 153 (Torrey Webb Room)

Abstract: Feedbacks between biological and geological processes drove the co-evolution of life and the environment. Yet, little is known of the nature of these feedbacks and the time scales over which they occurred. Here we describe a series of geobiological feedbacks that have played out over the past ~1.1 to 0.8 Ga and that shaped the co-evolution of thermoacidophiles and their acidic hot spring habitats. Future experimentation will evaluate kinetic controls on the acid-generating reactions and the physiological adaptations that allowed microbes to exploit these reactions to fuel their metabolisms.

MEB Seminar | Dr. Randie Bundy

Dr. Randie Bundy
Assistant Professor, University of Washington, Chemical Oceanography
Lab Website

The impact of organic compounds on the cycling of trace metals in the ocean

Tuesday, September 10, 2019
12 PM
AHF 153 (Torrey Webb Room)

Abstract: Trace metals such as iron are essential nutrients for phytoplankton and bacteria, impacting primary productivity in many regions of the ocean. Our understanding of the iron cycle has improved dramatically since the dawn of the international GEOTRACES program, with the chemical speciation of iron emerging as a key control on the oceanic inventory of iron. The speciation of dissolved iron in seawater is dominated by complexation to a diverse pool of organic compounds which impact the bioavailability and reactivity of this scarce nutrient, yet the identity of these compounds are largely unknown. In this talk I will discuss how we determine the identity of these compounds in seawater with novel analytical tools, and why these organic ligands are important for trace metal cycling.

MEB Seminar | Dr. Matthew Church

Dr. Matthew Church
Associate Professor, University of Montana, Flathead Lake Biological Station
Lab Website | Abstract

Eddy-driven variability in nitrification in the subtropical North Pacific Ocean

Tuesday, September 3
12 PM
AHF 153 (Torrey Webb Room)

Abstract: Nitrification is a key step in the marine nitrogen cycle, controlling oxidation of reduced nitrogen in the ocean. Mesoscale eddies, which vertically perturb isopycnal surfaces within the main pycnocline, are thought to play important roles in upper ocean biogeochemical processes; however, potential impacts of eddies on microbial nitrogen cycling in the dimly-lit mesopelagic waters remains largely unknown. In this talk I will summarize on-going work examining how eddies influence the export of particulate nitrogen (PN), rates of nitrification, and the abundances and spatial distributions of nitrifying Archaea (using the ammonia-monooxygenase gene [amoA] as a biomarker) in the oligotrophic waters of the North Pacific Ocean. Eddies influence upper ocean nutrient pools and fluxes, shape the distributions of nitrifying microorganisms and rates of nitrification in the mesopelagic waters. These results suggest that eddy-mediated changes to the upper ocean can have important roles in modifying nitrogen transformation in the interior waters of the ocean.

MEB Seminar | Dr. Sheila Kitchen

Dr. Sheila Kitchen
Post-Doc, California Institute of Technology, PI: Dr. Joseph Parker
Research Website

Adaptive potential and limits in Caribbean acroporid corals

Tuesday, August 27
12 PM
AHF 153 (Torrey Webb Room)

Abstract: Reef-building corals are currently threatened by rapid changes in local and global stressors, and hybridization offers a potential shortcut for rapid adaptation and evolutionary rescue in these species. The sympatric corals Acropora palmata and A. cervicornis form the hybrid, A. prolifera, whose abundance has continued to increase while the parental species decline. Previous work indicates that weakened prezygotic isolation mechanisms in A. cervicornis but not A. palmata could allow for continuous unidirectional gene flow between the two species. Furthermore, asymmetric introgression from A. palmata to A. cervicornis has been recorded in three nuclear loci. In contrast, we found evidence for bidirectional introgession across three hybrid zones, although the frequency of hybrids and backcrosses differs across the range. Genome assemblies of A. palmataand A. cervicornis were compared to other corals to identify orthologs uniquely shared by the Caribbean acroporids. Genomic sequence data from the two parental species and their hybrids was used to further characterize the patterns of genomic synteny, divergence and introgression across hybrid zones. Combined, these approaches elucidate genomic hotspots of introgression and parallel evolution with implications for how hybridization may shape adaptation in these important foundation species across the Caribbean and North-West Atlantic.

Host: Dr. Carly Kenkel

MBBO Ph.D. Dissertation Defense | Erin McParland

Erin McParland
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. Naomi Levine)

The dynamic regulation of DMSP production by marine phytoplankton

Wednesday, May 8, 2019
10 AM
AHF 153 (Torrey Webb Room)

Abstract: Dimethylsulfoniopropionate (DMSP) is a labile sulfur and carbon metabolite that significantly contributes to both the cycling of marine dissolved organic carbon and the balance of Earth’s albedo. DMSP is produced by the majority of eukaryotic marine phytoplankton and by many prokaryotes, but despite decades of research, the cellular mechanism and environmental drivers of DMSP production remain unknown. My thesis confirms that the cellular mechanism of DMSP is differentiated by the cellular concentrations of DMSP in different producers, where high DMSP producers (e.g. dinoflagellates and haptophytes) constitutively produce DMSP and low DMSP producers (e.g. cyanobacteria and diatoms) actively regulate DMSP production in response to environmental stress. However, with natural community experiments and global model predictions, my thesis demonstrates that variability of in situ DMSP production is driven by the biomass of high producers. My thesis highlights the potential for predicting in situ DMSP concentrations with a high DMSP producer marker gene and demonstrates the importance of accurately capturing the sub-dominant community for prediction of DMSP, or other similar metabolites produced by a small fraction of the marine microbial community.

MBBO Ph.D. Dissertation Defense | Pingping Qu

Pingping Qu
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. David Hutchins)

Thermal Acclimation and Adaptation of Key Phytoplankton Groups and Interactions with Other Global Change Variables

Wednesday, May 1, 2019
11 AM
AHF 153 (Torrey Webb Room)

Abstract: Marine phytoplankton play critical roles in global primary productivity, carbon export and biogeochemistry. The relationships between environmental forcing and key phytoplankton groups in marine ecosystems need more attention, especially under global change scenarios. Among many other environmental changes, phytoplankton communities in the euphotic zone are anticipated to be most sensitive to concurrent ocean acidification, warming, more thermal variability and reduced nutrient supplies.

Marine diatoms play critical roles in global primary productivity, carbon export and the food web. Marine diazotrophic cyanobacteria are equally important as a source of new nitrogen through nitrogen fixation. In order to better understand the possible responses of marine diatoms and diazotrophs to a changing ocean environment, my studies focused on the synergistic effects of multiple climate change variables on an important diatom, as well as the responses of two keystone diazotrophs to thermal variability and to long-term selection by warming.

In my first chapter, the physiological responses of the widespread centric diatom Coscinodiscus sp. to interactions between three climate-change variables (elevated CO2, warming, and nitrate availability) were investigated to better understand the interactions of multiple global changes on large, carbon-exporting diatoms. The second one examined how short-term thermal variability affects the growth and physiology of the diazotrophic cyanobacterium Trichodesmium erythraeum GBRTRLI101, as well as the interaction between temperature variation and phosphate availability. The third chapter tested the physiological responses and compared and contrasted acclimation and  adaptation of Trichodesmium erythraeum IMS101 and Crocosphaera WH0005 under long-term experimental selection at different temperatures, exploring possible ecological and biogeochemical implications of ways that these two representative diazotrophic cyanobacteria may cope with future warmer conditions.

Faculty Positions at Harbin Institute of Technology

   Nature Index Advertisement%5b1%5d by uscbiscgrad on Scribd

MEB Seminar Series | Nathan Walworth, Ph.D.

Nathan Walworth, Ph.D.
Postdoctoral Researcher, USC, BISC
Prof. Naomi Levine’s Lab

Hitting a moving target: Microbial evolution in a dynamic ocean

Tuesday, October 30, 2018
12 PM
AHF 153 (Torrey Webb Room)

Abstract: Microbes drive global biogeochemistry yet little is known about their microevolutionary rates and processes in response to global change. This is particularly critical in marine systems where long-term trends (e.g. warming) are overlain onto short timescale variability (e.g. eddies) and where advection moves organisms rapidly between ecoregions. The interplay between physical and evolutionary timescales was investigated using a model of adaptation coupled with an eddy-resolving climate model. Fitness increases were encoded by epigenetic modifications under short exposure times to new environments, with beneficial genetic mutations only contributing after extended exposure times. The relationship between microevolutionary and physical timescales is critical for determining future adaptation where assuming instant adaptation may bias model predictions of microbial dynamics. Decoupling between locations of selective pressure and regions of accumulation for adapted individuals was observed. These accumulation zones may act as ‘seed banks’ for novel genotypes and thus evolutionary hotspots under global change.

MEB Seminar Series | Daniel Pondella, Ph.D.

Daniel Pondella, Ph.D.
Professor, Occidental College, Biology; Director, Vantuna Research Group
Research Group Website

More Big Fish, Restoring the Southern California Rocky Reef Ecosystem

Tuesday, October 23
12 PM
AHF 153 (Torrey Webb Room)

Abstract: Southern California has one of the most dynamic and productive marine rocky-reef ecosystems in the world.  Its characteristic giant kelp beds are a visual reminder from the surface of the majestic expanse found below.  Unfortunately, despite its potential we have observed decades of chronic decline in ecosystem health and services. This decline in health for rocky reefs and kelp beds is a result of pollution, habitat loss and overfishing and is particularly problematic for coastal communities where the loss of commercial and recreational fishing opportunities has negatively affected the economy of the region. Traditional management actions can have positive changes, are generally passive (like changing a fishery regulation) but usually work on multi-year to multi-decadal time scales. While my research has highlighted these positive longterm impacts including the return of ‘big fish’ (giant seabass, white seabass, leopard shark, soupfins etc.), my current research is focused on creating solutions that work in short time scales, what I refer to as active management. My colleagues and I are currently developing and implementing a variety of restoration and enhancement techniques to restore the Southern California rocky reef ecosystem using the Palos Verdes Peninsula as the starting point for the region. To support the science behind understanding the efficacy of these technique, I focus on developing ecosystem-based spatial and timeseries models primarily utilizing marine fishes to evaluate and improve our restoration efforts.  Considering the challenges our coastline continues to face, immediately improving the health of our rocky-reef ecosystem and associated fisheries is paramount.

MEB Seminar Series | Anne Dekas, Ph.D.

Anne Dekas, Ph.D.
Assistant Professor, Stanford University
Lab Website

Linking function to phylogeny in marine microbes: two stories from the dark ocean

October 16
12 PM
AHF 153 (Torrey Webb Room)

RESEARCH OVERVIEW
Microorganisms collectively shape the chemistry of our planet, and have for billions of years. Understanding the activity and metabolic capabilities of microbes in the modern environment is therefore critical to understanding the history of the Earth, as well as the future of our climate.
The Dekas Lab focuses on understanding the microbiology and biogeochemistry of the deep sea: the largest and least explored habitat on the surface of our planet. We investigate the diversity, distribution and activity of marine bacteria and archaea driving carbon, nitrogen, and sulfur cycling, with a focus on processes directly and indirectly involved in the production and consumption of greenhouse gases (e.g. CH4, CO2 and N2O). Using techniques from both molecular biology and isotope geochemistry, we answer questions such as: (1) “who” is doing “what” (linking phylogenetic identity to physiological function), (2) what are the biogeochemical controls on metabolic rates, (3) how do specific metabolisms affect global scale biogeochemical cycles and climate, and (4) will these metabolisms act as a positive or negative feedback to climate change?

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