Department of Biological Sciences Newsletter Volume 8, No. 2; Spring, 2013

The sea is emotion incarnate. It loves, hates, and weeps. It defies all attempts to capture it with words and rejects all shackles. No matter what you say about it, there is always that which you can't. C. Paolini

Once again, spring is here. Classes are in full swing, flu season is hitting many, flip-flopping like a newly caught flounder, and days are short. Most of us look forward to the flowers, blooms and improving weather, knowing that the summer heat is soon upon us. But it is also a time to ramp up our intellectual “juices” with seminars, talks and meetings. Enjoy the spring, and nature’s renewal. The Editor (W.O. Smith) Faculty Moment: Bongkeun (BK) Song My starting point in becoming a denitrifying and characterized began the moment that their taxonomic and physiological I met Dr. Norberto Palleroni at Rutgers diversity using traditional and modern University in 1995. Dr. Pallernoi is systematics. Whole genomic DNA- known as the father of Pseuodmonas. DNA hybridization techniques were He was my first teacher applied to reveal the genetic diversity and taught me from the basics of and the degree of genomic variation in bacterial cultivation to the advance the bacterial isolates. After receiving techniques in moloecular systematics. my Ph.D in Environmental Science, I Under his supervision I conducted the conducted a postdoctoral research at taxonomic characterization of toluene Dr. Bess Ward’s laboratory from 2000 degrading denitrifying bacteria and got to 2004. The four years working with a Masters degree in Environmental Dr. Ward were a critical time period in Science. We published two papers my professional career in becoming a reporting the taxonomic classification marine microbial ecologist and of Azoarcus and Thauera spp. capable molecular biologist with a special of degrading toluene under interest in the cycle. I started denitrifying conditions. After working on genes encoding for completing my MS degree, Dr. Max dissimilatory nitrite reductases Häggblom agreed to be my Ph.D (nirS/nirK), critical enzymes in adviser with Dr. Palleroni. He led me to , to determine the play with dirt and to find denitrifying diversity and community structure of bacteria capable of degrading denitrifying bacteria in aquatic halogenated (chlorinated) compounds. environments. I also examined I isolated a large number of transcriptional regulation of nitrate

- 1 - reductase and nitrate transporters communities This study aimed to genes involved in nitrate uptake of reveal the alteration of sedimentary N various marine . While I cycling pathway response to sea level was with Ward, I was awarded an NSF rise by employing molecular and Postdoctoral Research Fellowship, stable isotope analyses, microsensor which allowed me to explore the techniques, and N network modeling. genetic diversity of denitrifying bacteria involved in aromatic carbon degradation and arsenic trans- formation. I was hired as an assistant professor at the University of North Carolina Wilmington (UNCW) in 2004. At UNCW, I collaborated with Dr. Craig Tobias to investigate the importance of anaerobic ammonium oxidation () in estuarine and coastal environments. ANAMMOX, the anaerobic oxidation of NH4 to N2 using NO2 as an oxidant, has been of special interest to me since it was discovered in 1995. We developed highly specific molecular tools to detect and quantify ANAMMOX bacteria as well as highly sensitive 15N-isotope techniques to measure their activities in small amounts of sediments. We found for the first time an endemic distribution of diverse ANAMMOX bacteria along the salinity gradient of the Cape Fear B.K. collecting those elusive River Estuary. Continuing this microbes from the sediments. research, I received an NSF grant to In addition to the ANAMMOX studies examine the linkage between diversity in NC estuaries, I examined anammox and function of ANAMMOX, communities in deep-sea sediments denitrifying and nitrifying communities with Drs. Martin Palmer and Rachel in the Cape Fear River Estuary. We Mill at University of Southampton, UK. developed in situ sediment transplant I also worked with Drs. Richard Smith experiments to determine how and John K. Böhlke at USGS to diversity affects the functional stability determine the importance of of ANAMMOX, denitrification and ANAMMOX in the subsurface N cycle. nitrification. I was also awarded a These are some examples illustrating grant to study the effect of salinity my research emphasis on microbial N increase on sedimentary N and N O 2 2 cycles in various . production mediated by ANAMMOX, denitrifying, nitrifying and DNRA

- 2 - Student Moment: Jon Lefcheck I’m a fourth year Ph.D. candidate groundfish assemblage using data working with Dr. Emmett Duffy. I from the ChesMMAP survey. This earned my B.A. in Biology in 2009 from project not only united students in the Colby College, and came to VIMS Biological and Fisheries departments, shortly thereafter. Thankfully, it wasn’t but also students from 15 institutions my first rodeo: I was an REU intern at from all over the world, including VIMS in the summer of 2008, so I knew China, Kenya, Chile, and Brazil. This what I was in for. As an intern, I novel educational model brought worked with Emmett, Paul Richardson, student representatives (including 4 and the other members of the Marine from VIMS) together 5 times over the Lab on a tank experiment. course of two years to discuss project Long days, blazing sun, cranky ideas, future directions in the field, plumbing (daily trips down the ferry and to collaborate and share analytical pier to backwash the sand filter)…who skills [http://www.dbdgs.org]. The knows why it spoke to me, but it did. I second was a working group for the was resolute on returning to the lab for Life Survey, a my Ph.D. In fact, VIMS was the only network of divers performing surveys place I applied. of hard substrate marine communities When I first came to VIMS, I crafted a from Tierra del Fuego to Svalbard and research plan around invasion biology everywhere between. For this, I had to that I ultimately scrapped to focus on fly to Tasmania and sequester along emerging concepts in biodiversity, with 30 other researchers on a tiny specifically using organismal traits island penal colony with 1 electrical and phylogenetic relationships to outlet and tons of kangaroos. Not only describe community-wide diversity was it a totally awesome experience, and how it relates to but a truly humbling opportunity to processes. My dissertation work has work with some fantastically talented been a combination of manipulative [http://www.reeflifesurvey.com] experiments, investigations of biogeo- researchers. graphic patterns, and mathematical I’ve also been keen on using social simulations, involving epifaunal media and the internet for scientific , small estuarine fishes, outreach and communication. I was large estuarine fishes, and well, fishes recently convinced that actual science everywhere. I certainly didn’t expect to happens on Twitter (yeah, Twitter). I’ll work so much on fishes when I came use this opportunity as a shameless here, but just another example of how plug for my own blog, where in VIMS takes you on strange journeys. addition to musings, I periodically post I have been fortunate during my time snippets of R code that some of you at VIMS to be involved in a number of may find useful projects that have helped me rack up [http://jslefche.wordpress.com/] some serious frequent flyer miles. The During my sophomore year at Colby, first was a distributed graduate I was convinced to take a class on seminar that I co-led at VIMS creative writing. During the first class, investigating different components of we had a writing exercise that began diversity in the Chesapeake Bay with the prompt: “You open the door

- 3 - to your basement and walk down the Jon at the penal colony searching for stairs, and see…” I spent 20 minutes the elusive electric plug. describing the dusty boxes, etc. that are pretty much a staple of all basements. My peers, on the other hand, turned the basement into a metaphor for their sister’s depression and one guy was particularly taken with the basement as an allegory for the use of recreational drugs during Elizabethan England. Clearly, these people were cut from a different, darker cloth than I. Suffice it to say, I dropped the class immediately and asked my advisor what to do to fill up the credits. She suggested I talked to the resident marine ecologist to see if he needed any help with research. I spent a lovely semester marking intertidal snails with Testor’s model paint, and the rest is history!

Staff Stuff: Betty Neikirk It’s hard to believe that I’ve started taxonomist. I was also the lab my 29th year of employment here at manager and supervisor to some “well VIMS! [Editors Note: 29 years is known” graduate students. Little did I greater than the mean age of graduate know that one of them was going to students] I must say that if you had end up being my husband 12 years asked me then where I thought I may later, Chip Neikirk, and I’d end up be working in 29 years, I never would being his boss once again! Another have guessed I’d be in the same place. worm picker named Willy Reay went This speaks for what a fine place VIMS on to bigger things as well. Who knew is to work, at least in my opinion. that picking worms would pave the I started working at VIMS in 1983, way for Chip to become the Deputy having just graduated with a B.S. in Chief of Habitat at VMRC and Willy the Biology Randolph-Macon College in Director of the CBNERRVA here at Ashland, VA. I found myself in Bob VIMS. Diaz’s lab literally starting at the Although I enjoyed my benthic “bottom” and picking worms for experience, I had the opportunity to minimum wage ($2.65/hour). It seems move into the seagrass beds in 1985 as though picking worms is a rite of when I accepted a position with Ken passage at VIMS, as there have been Moore and Dick Wetzel in what was many of us that started this way. formerly known as the Wetlands Within five months I landed my first Department. After about seven years full time job! I went from picking of working at VIMS and assisting worms to becoming a polycheate numerous graduate students with their

- 4 - theses and dissertations, the writing certifications to drive boats, trailer was on the wall. I realized that if I was boats, drive forklifts or operate fire ever going to advance I needed to go extinguishers. Many students and back to school and get a master’s faculty have come and gone, many degree myself. Ken and Dick allowed buildings have been razed, and many me the opportunity to take educational departments have changed, but a leave and pursue coursework at VIMS. critical change was becoming a I still had job obligations, but never mother to Will (now 14) and Kate (10). would have been able to pursue an I’m very lucky to have never had to fill advanced degree otherwise. Soon out a job application or update my after, Iris Anderson joined VIMS. I resume in 29 years! Yep, if you had invited Iris to share my office and the ever told this girl from the mountains close quarters allowed us to get to of Virginia that she would operate know each other. Iris soon became boats, scuba dive and back a trailer, I my co-major professor. Of course this would’ve thought you were talking to meant that my thesis work would someone else. involve nitrogen cycling in salt marsh systems and more mud! I don’t regret Betty doing one of her jobs over 29 going back to school for a minute and years. feel fortunate to have been given the opportunity to pursue an advanced degree. As time has passed, I enjoy my job more and more. I am now a Marine Scientist Supervisor and oversee the Shallow Water Monitoring Program for Ken Moore. Ken is also the Research Coordinator for CBNERRVA at VIMS which has allowed me to be heavily involved with their water quality monitoring efforts with Willy Reay. I couldn’t ask for a better group of people in Biological Sciences and CBNERR to work with. I still get plenty of field work in and would have it no other way. As a supervisor I feel that one of the most important things I can do is stay involved at this level. During my tenure here at VIMS many things have changed. Back in the “old days” we didn’t have to have

The Talking Head: Department Chair Comments The New Year of 2013 is upon us and while a new year usually brings thoughts of change and anticipation for the future, we tend to work on a slightly different calendar here, with fall and the arrival of new students being one of our major harbingers of change. Currently, most of our students have had at least one semester here and the “First Years” are busily working on research ideas and

-5- anticipating of their research projects. Soon VIMS itself will be celebrating its 75th anniversary in 2015, which suggests that it may have begun to reach a state of senior status in the world of . Having just returned from a workshop discussing the potential effects of changing climate on the Pacific Northwest, it struck me how different scientists and citizens view patterns in time. For those of us who think about recent patterns in the environment, a 20 or 30 year pattern is almost background noise. Fifty to 100 year trends are more understandable and longer trends or cycles become much more believable. Most non-scientists, I think, tend to view things within the framework of their lifetime, extending 10 to 50 or 60 years. Concepts like “Climate Change” extending over 50 or 100 years or more may be too abstract to comprehend within the daily demands of living a life. However, when change is rapid enough to be viewed in the lifetime context, its awareness is greatly heightened. For example, a significant loss of seagrasses in the Chesapeake Bay occurred within only one or two decades, and certainly many older people can remember how things “use to be” when they were younger. Therefore, recognition, focus and support for seagrass research and restoration activities have been high. While we as scientists tend to look at the longer view, we too, our influenced by our view of the world. When VIMS first started, most scientists worked on the effects of overharvesting or disease on fisheries, which were then declining quite rapidly within the span of a human lifetime, with little focus on habitat change. The next group (my generation) beginning in the 1970s became focused on “anthropogenic impacts” (commonly referred to pollution), habitat loss and generally those things mankind does locally or regionally to degrade the natural environment. People could see the changes occurring within their lifetimes that were affected by human population growth and development, and so this focus became important. Climate was usually not mentioned except in how seasonal or yearly climate differences affected man’s impacts on the environment. Today, hardly any one of our proposals or scientific papers does not at least mention the potential results of the research as they relate to “Climate Change”. Again, recent climate induced changes have reached a point where we can see alterations in populations or habitats within our lifetime view of the world. Who has not seen and been impressed by pictures of glaciers disappearing over the span of recent decades? Yet the effects of “pollution”, fisheries overharvesting and other factors are still there. However, as important as the changing climate to research is now, what might be the focus of research efforts by marine scientists in future decades? Might the warming climate have increased “invasive species” impacts to the point where most research proposals must include at least some mention of how the results of that study will help to understand this currently paramount issue? For those of you just beginning your careers…stay tuned.

Selected Recent National and International Presentations by Biological Sciences’ Personnel Brush, M.J. 2012. Standing on the shoulders of a giant: Scott W. Nixon’s contributions to coastal systems ecology. Atlantic Estuarine Research Federation Fall meeting, Chincoteague, VA.

-6- Friedrichs, M.A.M., 2012. Using multiple models for management in the Chesapeake Bay: A shallow water pilot project. CBP Management Board Meeting. Annapolis, MD, November, 2012. Lake, S.J. and M.J. Brush. 2012. Modeling the formation of periodic in a tributary estuary: the York River, Virginia. Atlantic Estuarine Research Federation Fall meeting, Chincoteague, VA. Marieke M van Katwijk, Anitra Thorhaug, Nuria Marbà, Chris Pickerell, I Althuizen, E Balestri, G Bernard, ML Cambridge, A Cunha, CM Duarte, C Durance, C Gadoullet, W Giesen, Q Han, S Hosokawa, G Kendrick, W Kiswara, T Komatsu, C Lardicci, KS Lee, A Meinesz, M Nakaoka, RJ Orth, EI Paling, A Ransijn, JJ Verduin. 2012 Revegetation of seagrass beds worldwide. A review of actions and possible keys to success. ISBW, Brazil, November. Orth, R. J. 2012. Eelgrass and bay scallop restoration on the seaside of Virginia’s eastern shore. Virginia Coastal Partners Workshop. Richmond, VA. December. Orth, R. J. 2012.Eelgrass restoration: The Chesapeake Experience: Lessons Learned, Challenges Ahead. Eelgrass Workshop, Odense, Denmark. November. Smith, W.O. Jr, X. Liu, N.H. Doan, K.W. Tang and N.L.Nguyen. Giantism in the harmful species Phaeocystis globosa. Intern. Conf. “Bien Dong 2012”, Institute of Oceanography, Nha Trang, Viet Nam; September, 2012. Smith, W.O. Jr, X. Liu, N.H. Doan, K.W. Tang and N.L.Nguyen. Giantism in the harmful algal bloom species Phaeocystis globosa. Intern. Conf. “Bien Dong 2012”, Institute of Oceanography, Nha Trang, Viet Nam; September, 2012. Smith, W.O. Jr, X. Liu, N.H. Doan, K.W. Tang and N.L.Nguyen. Giantism in the harmful algal bloom species Phaeocystis globosa. International Conference on Harmful Algae, Changwon, Korea; October, 2012. Smith, W.O. Jr, E.M. Olson, and D.J. McGillicuddy, Jr Phaeocystis antarctica ghost colonies: a previously unknown component of Phaeocystis blooms in the Ross Sea. International Conference on Harmful Algae, Changwon, Korea; October, 2012. Truitt, B. T., B. W. Lusk, R. J. Orth, M. Luckenbach, J. A. Wesson, K. McGlathery, L. McKay. 2012. Marine Restoration, Ecosystem State Changes, and Resiliency in the Coastal Bays of Virginia. Natural Areas Conference, Norfolk, October.

Recent BioSci Peer-reviewed Publications Blake, R.E. and J.E. Duffy. 2012. Changes in biodiversity and environmental stressors influence community structure of an experimental eelgrass (Zostera marina) system. Marine Ecology Progress Series 470:41-54. Luo, Y.-W., H. W. Ducklow, M. A. M. Friedrichs, M. J. Church, D. M. Karl, and S. C. Doney 2012. Interannual variability of primary production and dissolved organic nitrogen storage in the North Pacific Subtropical Gyre. J. Geophys. Res., 117, G03019, doi:10.1029/2011JG001830. Meiners, K.M., M. Vancoppenolle, S. Thanassekos, G.S. Dieckmann, D.N. Thomas, J.-L. Tison, K.R. Arrigo, D. Garrison, A. McMinn, D. Lannuzel, P. van der Merwe, K. Swadling, W.O. Smith Jr., I. Melnikov, and B. Raymond. 2012. Chlorophyll a in Antarctic sea ice from historical ice core data. Geophys. Res. Letters 39, L21602, doi:10.1029/2012GL053478. Sumoski, S, and R. J. Orth. 2012. Biotic dispersal potential in Zostera marina (eelgrass). Marine Ecology Progress Series 471:1-10.

-7- New Grant Activity within the Department  Orth, R. J., K. A. Moore and S. R. Marion. NOVAGRASS, Innovative eelgrass restoration techniques. Danish Council for Strategic Research. $4.49 million; 1-1-13 to 12-31-17.  Friedrichs, M. 2013-2015. Collaborative Research: Impacts of atmospheric nitrogen deposition on the biogeochemistry of oligotrophic coastal waters. NSF. $164,965.  Friedrichs, M. 2013-2016. Primary Productivity Algorithm Round Robin for the Arctic . NASA. $88,000.  Smith, W.O. Jr. Collaborative Research: Penguin foraging reveals phytoplankton spatial structure in the Ross Sea. 9/1/12 - 8/31/14; NSF, $259,767 Departmental Tidbits  Bob Diaz officially retired and was ushered out in a rousing fashion at his house. There is no truth to the rumor of dead polychaetes being used in food the next day.  Mark Brush is serving on the Model Evaluation Group for the Long Island Sound Study Systemwide Eutrophication Model.  Emmett Duffy was one of 12 recipients this year of Virginia’s Outstanding Faculty Award (http://www.wm.edu/news/stories/2013/duffy-receives-virginia-outstanding- faculty-award123.php)  Rachael Blake (PhD 2012) has moved on to a postdoc at Louisiana State University, where she will do the science to fix the BP oil spill once and for all.  VIMS Marine Biodiversity alum James Douglass (PhD 2008) has begun a new faculty position at Florida Gulf University, joining VIMS alums Ai Ning Loh, Aswini Volety, and Dave Fugate who are already on the faculty there – four VIMS alumni in the same department!  The paper by Sarah Sumoski and JJ Orth on biotic dispersal was the featured article in a December issue of Marine Ecology Progress Series.  JJ Orth and Ken Moore were invited to give presentations on their seagrass restoration work and SAV management efforts in Chesapeake Bay to an eelgrass workshop in Nov. in Odense, Denmark.  Jamie Blackburn is now in the Peace Corps and her blog can be found at http://jaime.blogs.wm.edu/2012/12/12/to-build-a-garden-and-entertain-a-village/

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