December 21, 2014

Ecosystem Modeling Course For Non Programmers

A two week Brown-MBL course, “ENVS 2680 Ecosystem Modeling for Non-Programmers” was taught by MBL Senior Scientist, Dr. Ed Rastetter, to Brown University graduate and undergraduate students between January 6th- Jan 17th 2014 at MBL in Woods Hole. The two week hands-on course introduced five students to the uses and construction of ecosystem models.

Ecology is a relatively young science that grew from the largely descriptive discipline of Natural History. As the science has matured, it has begun to develop a firm quantitative foundation. For the most part, this foundation has been statistical (regression, correlation, analysis of variance, and ordination). The purpose of this course was to introduce the students to the other component of this quantitative foundation –  dynamic simulation modeling of ecological processes.

The students will use what they learned in the two week intensive class and over the course of the semester to develop their own simulation model of an ecosystem.  The model will be completed by the end of the term.

The course is usually offered every two years. For more information on the course view the following link:  ENVS 2680 modeling course and schedule-1

2013 Brown MBL Partnership Retreat

Mai Tran, a Brown MBL graduate student demonstrates imaging equipment at the Brown MBL Retreat in Woods Hole, MA.

Mai Tran, a Brown MBL graduate student demonstrates imaging equipment at the Brown MBL Retreat in Woods Hole, MA.

The annual Brown MBL Program Retreat took place on Friday and Saturday November 8 and 9, 2013 at MBL Speck Auditorium in Woods Hole. Over 70 participants from Brown University and MBL attended the two day event. It featured a student poster session and social on Friday evening, a mini-symposium on “Imaging Across Biology” which featured invited talks on novel science on biological imaging across scales from molecules to microbes to remote sensing and a display of microscope and imaging equipment used at MBL in the past and present. In addition, the Brown MBL Program hosted 36 undergraduates from Brown University on a tour of MBL that highlighted summer internship and semester opportunities for students to engage in research in Woods Hole. The undergraduates had a private tour of MBL facilities including the Marine Resources Center and a field trip to a salt marsh restoration and research project on South Cape Beach, Waquoit Bay National Estuarine Research Reserve.

For more information on the event a complete agenda can be seen here:  2013BrownMBLRetreatAgenda

Brown MBL Student Lindsay Brin Defends PhD Dissertatation and Receives a NSF Postdoc Fellowship in Canada

Brown-MBL student Lindsay Brin successfully defended her PhD dissertation on September 6th, 2013 at Brown University. Lindsay, a student in the Department of Ecology and Evolutionary Biology at Brown University, conducted her doctoral research in the labs of Brown University Assistant Professor Jeremy Rich and MBL Ecosystems Center Senior Scientist Anne Giblin.

Brin’s research focused on the relationship between environmental factors and microbially-mediated nitrate reduction processes in coastal sediments, particularly denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA). The rates and relative importance of these processes affect how much nitrogen (N) is available in coastal ecosystems for primary productivity and eutrophication, and are linked to climate through global marine N cycling. Understanding the controls on these processes is essential for predicting the effects of climate change and other environmental alterations on coastal ecosystems.

Brin illustrated the role of temperature, organic matter and nitrate in determining rates of nitrate reduction in New England coastal sediments, providing some of the first seasonal data on these processes and the first measurements of anammox and DNRA in these sediments. She demonstrated that warming and changes in organic matter availability could affect positive feedbacks on primary productivity by altering fluxes of N between the sediments and the water column, and further showed that DNRA may be an important unappreciated process in temperate continental shelf sediments.

During her graduate studies, Brin’s research was supported by a National Defense Science and Engineering Graduate Fellowship, a Stanley Watson Graduate Fellowship in Environmental Studies, and a Sounds Conservancy Grant.

In October, Lindsay will begin a National Science Foundation Postdoctoral Research Fellowship in Biology at the Potato Research Centre in Fredericton, NB, Canada, to study the effects of climate change, particularly altered snow cover, on N cycling in agricultural soils. Through a two year field study she will address the question of how does altered snow cover affect soil N cycling and microbial communities in the winter and through the following growing season.

Former Brown MBL Student, Pedro Flombaum, Publishes Article in Oecologia

Former Brown-MBL student Dr. Pedro Flombaum recently published a new journal article entitled Interactions among resource partitioning, sampling effect, and facilitation on the biodiversity effect: a modeling approach.  Pedro was a 2008 graduate student in the Brown University EEB Program and a former student of Dr. Ed Rastetter at MBL.  He now works at the Centro de Investigaciones del Mar y de la Atmósfera (CIMA) in Buenos Aires, Argentina.  His journal article can be found here.

Brown MBL student Cassandra Bilogan successfully defends her dissertation

Cassandra Bilogan defends her dissertation at Brown University

Cassandra Bilogan defends her dissertation at Brown University

Cassandra Bilogan successfully defended her dissertation on August 5th, 2013 at Brown University in Providence, RI.  Cassandra described her doctoral research that was completed in Dr. Marko Horb’s lab at the MBL’s Bell Center for Regenerative Biology and Tissue Engineering. Cassandra’s research focused on elucidating the molecular mechanisms involved in endoderm development and pancreatic organogenesis in Xenopus laevis. Specifically, she identified a novel role for a well-conserved RNA-binding protein during endoderm development. This research provided new insights into a previously unappreciated role of the spatial-temporal regulation of germ layer patterning during gastrulation. During her graduate studies Cassandra published two first author papers and a second author review paper.

Cassandra is also the first Ph.D. student to graduate from the Bell Center. Her research was supported by grants to Dr. Horb from the National Institutes of Health and a Canadian Institute of Health Research fellowship to Bilogan.

In October, Cassandra will start a postdoctoral fellowship at the Cleveland Clinic in the lab of Dr. Takuya Sakaguchi.

For more information on Cassandra click here

New Harvests for Research on Agricultural Intensification

CN Mbola 17-01-12091 compress

Photo by Chris Neill

Agricultural activities are changing globally in response to increased demand for foods and other goods, but how are these changes occurring and affecting people and ecosystems differently across the planet?

From 14-16 January 2013, postdoc Rebecca Ryals of the Marine Biological Lab (MBL) and the Brown Environmental Change Initiative (ECI) convened a workshop at MBL for faculty, researchers and graduate students working in Brazil, Africa, China and North America to share recent findings from research on agricultural change, spanning natural and social science fields.  Participants hailed from numerous ECI-affiliated departments at Brown, including Ecology and Evolutionary Biology, Geological Sciences, and Sociology, the Marine Biological Laboratory (MBL), the Woods Hole Research Center (WHRC) and institutions across the country, including The Earth Institute at Columbia University and the Cary Institute of Ecosystem Studies in New York, and the University of Virginia.

Researchers presented projects on facets of agricultural intensification from Brazil, East Africa, North America and China.  For Brazil, presented research showed surprising dynamics of the fate and transport of fertilizer-added nitrogen and phosphorus through soils, differing seasonal variations in soil moisture across land use areas, impacts of riparian forest buffers on stream water quality, innovative satellite remote sensing techniques for studying extents and patterns of double-cropping, and relationships between national currency valuation, markets, social dynamics and agricultural production.  For East Africa, preliminary results demonstrated relationships between seasonal patterns in nitrogen transport dynamics through soils , new multi-satellite-based approaches for mapping land cover in complex, small land-holder dominated landscapes, and impacts of fertilizer use on soil microbial diversity.  Research in North America focused on range and livestock management impacts for watershed biogeochemistry, and web tools for increasing public awareness of how personal food choices connect to ecosystem nitrogen losses.  Research in North America and China highlighted relationships between fertilizer rates, and CO2 and N2O losses from soils to the atmosphere.

Together, presentations highlighted that agricultural intensification, the increased use of technology (e.g. fertilizers, mechanization, new cultivars) to improve crop yields per unit area, has progressed in starkly contrasting patterns between places such as Brazil and East Africa.  Environmental and social consequences such as fertilizer-applied nitrogen losses and local food security were shown to matter differently across continents. Discussions stressed that factors from a region’s economic development status before intensification occurs, to soil texture, must be considered integrally for scientists across disciplines to pursue appropriate future research.  The workshop produced outlines for interdisciplinary research papers, watershed-scale research projects, conference proposals, and new senses of camaraderie among participants.

Brown-MBL Student Research on Phosphorous Budgets in Soybean Agriculture in Bioscience and Science Daily

Brown-MBL student Shelby Hayhoe-Riskin’s work on phosphorous uptake and release in soils and associated environmental impacts in the three largest soybean growing regions of the world will be published in an upcoming issue of Bioscience.  Brown-MBL joint faculty Stephen Porder and Chris Neill are co-authors on the paper as are Meagan Schipanski of Pennsylvania State University and Elena Bennett of McGill University. Science Daily reported on the research on December 17th. Read more…

Brown-MBL Graduate Student Priya Dutta Defends Dissertation

Anupriya Dutta. Photo by Jessica Mark Welch

On December 5, 2012, Brown-MBL Graduate Student, Anupriya Dutta, successfully defended her PhD dissertation, ‘Recognizing microRNAs (miRNAs) in Microinvertebrates and Confirming their Absence.’

Bdelloid rotifers are aquatic microinvertebrates that have several outstanding qualities among metazoans. They make up the only ancient asexual animal lineage. Bdelloid rotifers are also incredibly robust to DNA damage, which is a necessary adaptation for life in desiccation-prone environments.  During desiccation, they are capable of incorporating foreign DNA into their genome. An investigation of a class of noncoding small RNAs, called microRNAs (miRNAs), reveals that the unique characteristics of bdelloid rotifers are reflected in their miRNA repertoire. miRNAs are involved in post-transcriptional gene regulation and have been implicated in numerous cellular processes. Some miRNAs are believed to be indispensable due to their integration into many gene regulatory networks.  For this reason, many miRNAs are easy to identify across diverse animal phyla. However, the  conserved miRNA repertoire of  bdelloid rotifers is exceptional in this regard. The surprising miRNA repertoire of bdelloid rotifers not only provides important clues to understanding the asexual evolution of bdelloid rotifers, but also reveals new insights into miRNA evolution in animals.

Brown-MBL PhD Student Susanna Theroux Defends Dissertation

Susie Theroux defends her dissertation on November 28, 2012. Photo by Kalitamara Moody.

Speaking to a live audience in Providence and over videolink to Woods Hole, Susanna Theroux defended her dissertation on November 28th, 2012. Theroux described her doctoral research that was completed in collaboration between the labs of Dr. Yongsong Huang at Brown University’s Department of Geological Sciences and Dr. Linda Amaral-Zettler at the MBL’s Bay Paul Center.

Theroux’s research focused on haptophyte algae that produce organic biomarkers used for paleoclimate reconstruction. Specifically, she identified novel species of haptophyte algae in lake environments that were responsible for producing alkenone lipids that record the temperature of the lake water going back through time. By combining field studies in Greenland and North Dakota, culture studies and DNA sequencing in Woods Hole and organic analyses in Providence, the project was able to identify novel species of algae and their individual lipid signatures. This research also provided new insights into haptophyte bloom dynamics in lake environments and will impact how future geologic records of haptophyte biomarkers are interpreted. This research was supported by grants to Huang and Amaral-Zettler from the National Science Foundation and the Brown SEED fund and an American Association of University Women fellowship to Theroux.

In January, Theroux will be starting a postdoctoral fellowship at the Department of Energy’s Joint Genome Institute.

Student Research Highlight: Microbial Communities in Antarctica

Catherine Luria is finishing her second year in the Brown-MBL Graduate Program, advised by Hugh Ducklow (Ecosystems Center, MBL) and Jeremy Rich (Dept. of Ecology and Evolutionary Biology, Brown University). She recently returned from her first field season on the Antarctic Peninsula, where she participated in the Palmer Station Long Term Ecological Research (LTER) Project.

The peninsular region is one of the most rapidly warming regions on earth, with a 4-6°C increase in midwinter temperatures over the last 50 years and a 40% decline in winter sea ice extent. These changes are having profound impacts on all levels of the ecosystem, from marine diatoms to Adelie penguins.

Catherine is examining not only how microbial communities in this region change across study sites, seasons, and years, but also what factors drive microbial seasonal succession against a backdrop of rapid climate change. She is particularly interested in the effects of annual sea ice advance and retreat on microbial communities. As sea ice forms during the austral fall, bacteria and phytoplankton are entrained in the ice and often persist through the winter. In the spring, the sea ice melts releasing organic matter as well as bacteria and phytoplankton. This water column “seeding” may have dramatic impacts on microbial community composition within the water column and trigger phytoplankton blooms that help support this productive ecosystem. Although previous studies have examined the effects of sea ice extent and duration on primary production, zooplankton, and seabirds, little is known about the impact of sea ice advance and retreat on microbes and how microbes will respond to climate-driven declines in sea ice extent and duration. Catherine is exploring this question through a combination of environmental sampling and incubation experiments. She is excited to return to the Antarctic in September 2012 for further research.

 by Catherine Luria, May 2012