Bay Paul Center Assistant Scientist Julie Huber, will lead a cruise on the Schmidt Ocean Institute’s research vessel Falkor to the summit of the Axial Seamount. They hope to understand how the viral and microbial communities that live in the rocky outer layer of a submarine volcano interact and alter the flow of carbon and nutrients in the subseafloor crustal ecosystem. The team comprises researchers from the Marine Biological Laboratory (MBL), University of Washington, Oregon State University, NOAA Pacific Marine Environmental Laboratory, University of Massachusetts, Amherst, and J.Craig Venter Institute.
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Location of Axial Seamount and RSN Node. Image credit: Regional Scale Nodes, University of Washington.
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.
The Brown-MBL Graduate Program attracts a diverse group of talented and dedicated students from around the world. Some students spend their first years taking courses at Brown and do not make their base at MBL full-time until their second or third year in the program. Other students remain based in Providence for the duration of their studies but work closely with one or more MBL scientists as they pursue their research. Still other students engage in research that requires them to be at the MBL from the start of their studies. Sixteen graduate students currently are enrolled in the program, ten students have graduated from the program with doctorates and four others have left early with a masters degree.
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.
The Brown-MBL Graduate Program attracts a diverse group of talented and dedicated students from around the world. Some students spend their first years taking courses at Brown and do not make their base at MBL full-time until their second or third year in the program. Other students remain based in Providence for the duration of their studies but work closely with one or more MBL scientists as they pursue their research. Still other students engage in research that requires them to be at the MBL from the start of their studies. Sixteen graduate students currently are enrolled in the program, ten students have graduated from the program with doctorates and four others have left early with a masters degree.
Yuko Hasegawa’s doctoral research focused on developing a new imaging technique to see how microbial communities are organized, particularly inside the body. Her technique allows one to distinguish up to 11 different types of microbes in one fluorescence image, which led her to investigate the spatial distributions of bacterial cells in the gut of mice that were inoculated with bacterial types typically found in the human gut. Hasegawa’s imaging protocols will be useful for characterizing spatial organization of microbial communities in many different types of environmental and clinical samples. Her co-advisors were Gary Borisy (Yuko was his 24th student to graduate with a Ph.D.) and Mitchell Sogin of the Bay Paul Center; she defended her thesis on December 18.
The Brown-MBL Graduate Program attracts a diverse group of talented and dedicated students from around the world. Some students spend their first years taking courses at Brown and do not make their base at MBL full-time until their second or third year in the program. Other students remain based in Providence for the duration of their studies but work closely with one or more MBL scientists as they pursue their research. Still other students engage in research that requires them to be at the MBL from the start of their studies. Sixteen graduate students currently are enrolled in the program, ten students have graduated from the program with doctorates and four others have left early with a masters degree.
Valm, Alex M., Jessica L. Mark Welch, Christopher W. Rieken, Yuko Hasegawa, Mitchell L. Sogin, Rudolf Oldenbourg, Floyd E. Dewhirst, and Gary G. Borisy
(USA) 108: 4152-4157
Bacteria in nature live not as isolated cells, but as members of a community in which many different kinds of bacteria live intermingled in complex associations. The spatial arrangement of bacteria is important because bacteria that are close to each other can exchange DNA, including antibiotic resistance genes, can signal to each other, and can cooperate in digesting complex substrates. Until now, methods for visualizing the spatial organization of microbial communities could reveal only two to three different kinds of bacteria at once. In this paper, MBL-Brown graduate student Alex Valm and his colleagues in the Bay Paul Center developed a method for visualizing and differentiating 15 different kinds of microbes simultaneously. They applied this method to analyze spatial relationships of bacteria in human dental plaque, a microbial biofilm found in the human mouth. Further application of this method may lead to a better understanding of the way oral microbial communities function, with the goal of discovering ways to prevent periodontitis and dental caries. Bay Paul Center scientists Jessica Mark Welch and Gary Borisy and graduate student Yuko Hasegawa plan to apply the method to analyze spatial structure in other microbial communities, such as those in the human gut and, potentially, to microbial communities in soil or on surfaces in the environment.
Interactions of bacterial cells in human dental plaque. Plaque was collected using dental floss and was embedded in plastic resin, sectioned, hybridized with fluorescent probes targeting 15 groups (genera or families) of oral bacteria, and imaged using the Zeiss 780 laser scanning confocal microscope. Each small dot or rod is a single bacterial cell. Bacteria hybridizing to 6 different probes are seen in this image: Pasteurellaceae (dark orange), Streptococcus (yellow), Actinomyces (magenta), Porphyromonas (green), Neisseriaceae (blue), and Fusobacterium (peach). Several kinds of corncob structures, in which dot-like cells surround a central filament, can be seen in the upper part of the image, including multilayer corncobs in which the filament is surrounded by Streptococcus (inner ring) and Pasteurellaceae (outer ring), as well as single-layer corncobs composed of Porphyromonas and of Neisseriaceae. Photo credit: Blair Rossetti.
A paper from Mitch Sogin and Hilary Morrison et al
A microbial community’s functional capability—what it eats, what it produces—is thought by some to be more meaningful than the identities of its members. Functional redundancy in bacterial communities thus allows communities to survive environmental disturbance even if the membership changes. Others believe that microbial communities change both composition and function when perturbed. We found evidence for a third response: resistance. We looked at the microbial community response to nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene (nitrogen metabolism). The community structure was unaffected by significant variations in nutrients at multiple sampling sites despite demonstrable changes in many aspects of marsh ecology. This demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are adaptable to environmental stresses.
Bowen, J. L., Ward, B. B., Morrison, H. G., Hobbie, J. E., Valiela, I., Deegan, L. A., and Sogin, M. L. (2011). “Microbial community composition in sediments resists perturbation by nutrient enrichment.” ISME J.
Publication by Eugene A. Gladyshev, Irina R. Arkhipova
We describe a novel class of single-copy reverse transcriptase (RT)-related genes that do not constitute part of any mobile genetic element, and are clearly distinct from the only known non-mobile RT genes, the telomerases, which maintain chromosome ends in eukaryotes. These RT-like genes are of ancient origin, exhibit patchy distribution across diverse phyla, including animals, fungi, plants, protists, and bacteria, are preserved by natural selection, and are biochemically active. These findings challenge the currently prevailing views on evolution and functional roles of reverse transcriptase-related sequences in living cells.
Fig. 1. Overexpression of a reverse transcriptase-like protein fused to the green fluorescent protein in the fruiting bodies of the model ascomycete fungus Neurospora crassa. Photo credit: Eugene Gladyshev.
