Linda Amaral Zettler Lab Updates

1) Marine Biodiversity and Conservation on the High Seas

This past spring semester, Amaral-Zettler joined colleagues at the Sea Education Association in Woods Hole to develop a new curriculum in Marine Biodiversity and Conversation (MBC) funded through the NSF Transforming Undergraduate Education in Science (TUES), Technology, Engineering and Mathematics program. The twelve-week semester engaged 17 students from 15 US universities plus one international college to integrate scientific study of marine biodiversity with conservation planning for the high seas. The course began with five weeks of class work on the shore campus in Woods Hole where students took classes in policy, read and discussed the literature on key issues in conservation biology and honed their skills in molecular and morphology-based approaches to marine biodiversity. At sea, students worked as teams on original research projects designed to document the biodiversity of the Sargasso Sea. Their voyage began in St. Croix, US Virgin Islands on the SSV Corwith Cramer that sailed on a transect north through the Sargasso Sea and terminated in Woods Hole, MA 5 weeks later, stopping in Bermuda for one week midway to learn about Bermudian culture and conservation efforts centered around the Blue Halo project, an effort to establish a no-take marine reserve within Bermuda’s Exclusive Economic Zone.

Figures, L to R: Images from the MBC semester research cruise spanning over seven orders of magnitude (1 micrometer bacterial cell to 15 meter whale).  Petri plate with marine bacterial colonies, plastic marine debris, viper fish, and humpback whale.

Figures, L to R: Images from the MBC semester research cruise spanning over seven orders of magnitude (1 micrometer bacterial cell to 15 meter whale). Petri plate with marine bacterial colonies, plastic marine debris, viper fish, and humpback whale.

While on shipboard, the students logged many hours at the microscope identifying 6 species of Sargassum hydroids, 15 species of deep-water myctophid fishes, and over 50 morphotypes of microbes belonging to the genus Vibrio. Other student projects examined the population genetic variability in the larvae of spiny lobsters, North-American and European eel larvae, Sargassum shrimp, and the Sargassum macroalgae that constitute the hallmark of the Sargasso Sea itself. Their data will be added to the International Ocean Biogeographic Information System (iOBIS) database, the database that served the former Census of Marine Life (, and the Encyclopedia of Life ( Additional voucher samples will help promote conservation efforts via the Ocean Genome Legacy by preserving a variety of Sargasso Sea species for later downstream genetic barcoding. The efforts of the microbes student group are also helping to contribute directly to a separate NSF-funded project examining the diversity, function and fate of microbes on plastic marine debris in the open ocean.

In addition to traditional morphological identifications, for the first time aboard these sailing school vessels, students extracted genomic DNA from their samples and used molecular biology techniques taught on shore to target marker genes of interest for their individual projects. Their samples were sequenced at the W. M. Keck Sequencing Facility in the Josephine Bay Paul Center at the Marine Biological Laboratory in Woods Hole. Upon returning from sea, students were trained in bioinformatics to apply their new molecular findings to the questions developed in their independent research projects. The course culminated in a final symposium that brought an expert panel of policy makers, conservation biologists and leaders in biodiversity research to provide feedback to the student-lead presentations of conservation plans to protect the Sargasso Sea. Through a unique blend of hands-on research science and policy education, future MBC students will have an opportunity to narrow the gap between science and policy makers while helping to affect change in the protection of the High Seas. Major elements of this curriculum are transportable to regional biodiversity and conservation topics in a number of environments and will be the focus of a phase-II grant submission to the TUES program.


2) Microbial Influences on Harmful Algal Blooming Alexandrium populations

Harmful algal blooming (HAB) species of the dinoflagellate genus Alexandrium are responsible for the syndrome known as Paralytic Shellfish Poisoning (PSP), a life-threatening neurological illness that is brought on by consumption of contaminated shellfish with the algal-derived saxitoxin. On Cape Cod, salt ponds or kettle holes located in the Nauset Marsh System (NMS) area in Orleans and Eastham host annual blooms of this toxin-producing alga in the early spring. These isolated salt ponds provide unique “natural laboratories” for the investigation of bloom onset, development and termination of Alexandrium fundyense, the dominant blooming species in that region. In collaboration with Anderson Laboratory at the Woods Hole Oceanographic Institution and through the Woods Hole Center for Oceans and Human Health, the Amaral-Zettler laboratory has been studying the association of A. fundyense with specific bacterial communities during pre-, peak- and post- bloom conditions. Bacteria have the potential to influence bloom formation via the stimulation of growth but they may also influence timing of bloom decline via cell lysis or cyst induction. The importance of determining how general and predicable bacterial-HAB associations are in nature calls for assessments of bacterial community structure studies associated with the different stages of a bloom.

PPS deployment at Salt Pond with Nauset Marsh Visitor’s Center in the background.

Our field sampling capitalized on an automated sampling technology called the Phytoplankton Sampler (PPS; McLane Research Laboratories) outfitted with a modified filter holder to collect high-frequency samples compatible with DNA preservation during the spring Alexandrium bloom in 2012 from Mill and Salt Ponds in the NMS. We successfully deployed the PPSs 3 times in the two ponds with the final recovery in mid-May following the end of the Alexandrium bloom. During this time, the two PPSs collected replicate automated samples at high tide (twice per day) every other day for a total of 144 samples. In mid-May, we redeployed both PPSs in Salt Pond to sample once a day through the end of June to catch a second bloom. DNA extraction from these samples is currently underway and amplicon sequencing to determine bacterial community structure on the Illumina HiSeq or MiSeq next-generation sequencing platform is planned for the fall. Once the data are in hand we will combine high-resolution microbial community structure data coupled with high-resolution hydrodynamic data within the study area to interpret microbial network data and Alexandrium population structure in an environmental context. In collaboration with Martin Polz and Eric Alm at MIT, we will apply a suite of supervised learning methods as part of the SLiME software package to identify both species-species interactions and species-environment associations across independent samples and over a time series. We will use these proposed associations to fit a predictive model of microbial species dynamics as a critical test of our understanding of the driving forces underlying microbial community structure. We will test to what extent A. fundyense blooms: (i) are linked to specific types of microbial populations across samples and ponds, and, importantly, (ii) contain identifiable indicator populations that precede the onset of blooms and may thus serve as predictors.

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