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Current Projects

Sediment sampling from Soutar boxcorer for bulk foraminiferal collections, July 2017. J. M. Bernhard (left) and C. Hansel (right) (image by G. Farfan)

Collaborative Research: Physiological plasticity and response of benthic foraminifera to oceanic deoxygenation

NSF BIO IOS,  J.M. Bernhard (WHOI), C. Hansel (WHOI), S.D. Wankel (WHOI), F. Gomaa (WHOI / Harvard), Y. Zhang (URI)

With the expansion of dysoxia in the world’s oceans, the capacity for organisms to adapt and persist in depleted oxygen conditions or anoxia will be essential to sustain life. Foraminifera present a unique and environmentally relevant model organism in which to study the physiological response of such external forcing. Further, given their demonstrated metabolic plasticity under changing geochemical environments together with the fact that fossil foraminifera are used so extensively for paleoclimate interpretations, an improved understanding of such physiological responses to environmental change will bolster our abilities to predict future climate-change responses in the ocean. We are identifying how the integrative genetic, metabolic, and physiological response of foraminifera allows for their survival under climate-change induced fluctuations in oxygen.

Half models printed from microCT-scanned benthic foraminifera. Left is half model of Melonis barleeanus for the Artic; right is half model of Astrammina triangularis from the Antarctic (image by JB Martin / JM Bernhard).

Collaborative Research: Does calcification by paleoceanographically relevant benthic foraminifera provide a record of localized methane seepage?

NSF OCE Marine Geology & Geophysics,  J.M. Bernhard, V. Le Roux (WHOI), J.B. Martin (Univ. Florida)

Since ground breaking research on foraminiferal isotope ratios in the 1950s, isotopic compositions of fossil foraminiferal tests (shells) have been used to infer past climate and oceanographic histories. While much is known regarding temporal and spatial distributions of extant and extinct foraminifera, vastly less is known about their physiologies or the relationship between their physiology and incorporation of environmental isotope signatures into their mineralized, and fossilizable, remains. Yet this relationship is the crux of many paleoenvironmental interpretations.  Nearly each time the cell structure of foraminifera from “extreme” environments is investigated, novel adaptations are found.  This multidisciplinary project represents one of the first efforts to evaluate relationships between isotope compositions in the test, foraminiferal viability and physiology, and diagenetic status of the carbonate test.

Sample curation on the shore of Green Lake in May 2017, from left: C. Elleman (artist / scientific illustrator); J.M. Bernhard (WHOI), P.T. Visscher (UConn), L. Fisher (UConn) (image by P. Forte).

Collaborative Research: Alteration of microbially-produced carbonate rock by unicellular predators to better understand early Earth’s dominant ecosystem

NSF EAR GeoBiology Program. Pieter Visscher (University of Connecticut), Joan Bernhard (WHOI) and Veronique Le Roux (WHOI)

Microbialite abundances and morphologies over time document complex interplays between biological, geological and chemical processes. Details of microbialite diagenesis are poorly understood and the drastic decline in stromatolite occurrence and diversity in the late Precambrian has long been a conundrum. This project considers possible connections between stromatolite decline, thrombolite origin, and the rise of complex life. Bridging knowledge of extant microbialite communities through early diagenesis and, ultimately, to the microbialite fossil record is integral to improving our understanding of the evolution of life on early Earth. We are using state-of-the-art approaches to study living analogs and relict materials to expand our understanding of these salient components of life on ancient Earth.

Past Projects

Impact of multiple stressors

The oceans are changing in multiple ways: Earth is warming, the oceans are acidifying, and certain oceanic regions are becoming stagnant. We are studying the impact of these stressors, singly and in concert, on an important group of marine meiofauna, benthic foraminifera.

(Presentation material from an invited talk at the U.S. Ocean Acidification Principal Investigators' meeting, September 2013, Washington, D.C.)


For this project, the ROV Jason was used to collect sediment samples from very specific locations in Deep Hypersaline Anoxic Basins (DHABs) in the Mediterranean Sea. Image by Joan M. Bernhard (WHOI).

The Harshest Habitats on Earth

  • We studied the microbial eukaryote communities of haloclines in Deep Hypersaline Anoxic Basins that lie in > 3km of water in the Mediterranean Sea. My lab is dedicated to studies of the benthic protists; Virginia Edgcomb’s lab is studying the plantkic microbial communities and certain aspects of the benthos.  Read more about our collection expedition.
  • Additionally, we investigated metazoan occurrences in the deep halocline / brines of these DHABs. Do animals truly inhabit hypersaline anoxic environments?
  • Oceanus Magazine -The Harshest Habitats on Earth: Life blooms in Deep Hypersaline Anoxic Basins
  • See our publications from these projects:
  • Edgcomb, V.P., M.G. Pachiadaki, P. Mara, K.A. Kormas, E.R. Leadbetter, J.M. Bernhard (2016) Gene expression profiling of microbial activities and interactions in sediments under haloclines of E. Mediterranean deep hypersaline anoxic basins.  ISME Journal, 10(11): 2643-2657.
  • Bernhard, JM, CR Morrison, E Pape, DJ Beaudoin, MA Todaro,  MG Pachiadaki, KAr Kormas, VP Edgcomb (2015) Metazoans of redoxcline sediments in Mediterranean deep-sea hypersaline anoxic basins. BMC Biology 13: 105; doi 10.1186/s12915-015-0213-6.
  • Kormas, K.A., M.G. Pachiadaki, H. Karayanni, E.R. Leadbetter, J.M. Bernhard, V.P. Edgcomb (2015) Inter-comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins. Extremophiles 19: 949-960, doi: 10.1007/s00792-015-0770-1.
  • Bernhard, JM, K Ar Kormas, MG Pachiadaki, E Rocke, DJ Beaudoin, C Morrison, PT Visscher, A Cobban, VR Starczak, VP Edgcomb (2014) Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments, Frontiers in Microbiology, 5: art. 605; doi: 10.3389/fmicb.2014.00605.

A fluorescently labeled living benthic foraminifer living in a Bahamian stromatolite (photomicrograph by Joan M. Bernhard, WHOI).

What Doomed the Stromatolites?

Oceanus Magazine - What Doomed the Stromatolites? Scientists find key clue to an ancient enigma

See our publications from this project:

Edgcomb, VP, JM Bernhard, RE Summons, W Orsi, D Beaudoin, PT Visscher (2014) Active eukaryotes in microbialites from Highborne Cay, Bahamas, and Hamelin Pool (Shark Bay), Australia. ISME Journal, 8: 418-429;  doi:10.1038/ismej.2013.130.

Grabenstatter, J., S. Méhay, A. McIntyre-Wressnig, J.-L. Giner, V. Edgcomb, D. Beaudoin, J.M. Bernhard, R. E Summons (2013) Identification of 24-n-propylidenecholesterol in a member of the Foraminifera. Organic Geochemistry, 63:145-151; doi: 10.1016/j.orggeochem.2013.08.010.

Bernhard, J.M., V.P. Edgcomb, P.T. Visscher, A. McIntyre-Wressnig, R.E. Summons, M.L. Bouxsein, L. Louis, M. Jeglinski (2013) Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas. PNAS, 110: 9830-9834; doi:10.1073/pnas.1221721110.

Edgcomb, V.P., J.M. Bernhard, D. Beaudoin, S. Pruss, P.V. Welander, F. Schubotz, S. Mehay, A.L. Gillespie, R.E Summons (2013) Molecular indicators of microbial diversity in oolitic sands of Highborne Cay, Bahamas.  Geobiology, doi: 10.1111/gbi.12029.

Recirculating seawater system used to maintain living benthic foraminifera in J Bernhard’s environmental cold room. Image by J.K. Blanks (WHOI).

Culturing studies of environmental controls on benthic foraminiferal shell chemistry

Tom Chandler (University of South Carolina); Tim Shaw (University of South Carolina); Dan McCorkle (WHOI G&G); Christopher Hintz (USC postdoc); Jessica Blanks (USC MS student); Helena Filipsson (Goteborg University, Sweden); Sara Lincoln (MIT PhD student)

Colleagues and I culture deep-water calcareous benthic foraminifera. Culturing methods provide ways to study environmental and physiological (vital) influences on the foraminifers shell chemistry. Our past efforts resulted in growth and reproduction of Bulimina aculeata, an infaunal species common on the NW Atlantic continental margin, under controlled conditions in artificial-sediment culture chambers.

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The stable isotopic and trace element compositions of these cultured B. aculeata were determined, and the foraminiferal *13C, *18O, Cd/Ca, and Ba/Ca values were compared with the water chemistry of the culture system, and with the shell chemistry of free-range B. aculeata (see Hintz et al. 2004 Limnology & Oceanography Methods; Hintz et al. in press Geochimica et Cosmochimica Acta for more detailed discussion of results). This study demonstrated that foraminiferal cultures that reproduce and calcify can be maintained under tightly constrained carbonate chemistry and trace element concentrations and that the cultured foraminifera show reproducible, interpretable compositional patterns that are consistent with field-based understanding of foraminiferal ecology and shell chemistry. Presently, we are conducting experimental studies designed to isolate the influence of single factors (e.g., carbonate ion concentration; trace element composition; temperature) that influence benthic foraminiferal shell chemistry. In addition to these culturing studies, related field-based studies of in situ foraminiferal life positions and shell composition are also being conducted. This material is based upon work supported by the National Science Foundation under Grant No. 0437366. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Aside from the trace metal and carbonate ion work funded by NSF Marine Geology & Geophysics; initial temperature experiments were funded by WHOI's Ocean & Climate Change Institute, which led to additional (ongoing) funding from NSF Marine Geology & Geophysics. These temperature experiments are being done in collaboration with Helena Filipsson (Goteborg University, Sweden) and Sara Lincoln (MIT). See a recent article from Oceanus magazine about this project: Cell-sized Thermometers.

Cores, incubated in situ with a fluorogenic probe, are offloaded from the MBARI ROV Tiburon. These cores were collected as part of a DOE-funded project (with Jim Kennett, UCSB) on the effects of carbon dioxide sequestration on deep-sea foraminifera.

Effects of carbon dioxide disposal on deep-sea foraminifers

Jim Kennett (University of California, Santa Barbara); Jim Barry (Monterey Bay Aquarium Research Institute)

One potential mechanism to alleviate global warming due to greenhouse gases is to sequester carbon dioxide in the deep sea, but the effects of such disposal on the resident fauna are not well understood.

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Along with colleagues (Jim Kennett, University of California Santa Barbara; Jim Barry, Monterey Bay Aquarium Research Institute), my lab is funded by the Department of Energy to determine the effects of deep-sea CO2 disposal on benthic foraminifera. A month-long CO2-release experiment was conducted using MBARI?s ROV Tiburon from December 2004 to January 2005. Because necrotic foraminiferal cytoplasm can remain in a foraminiferal shell for weeks (see Bernhard 2000 Micropaleontology for review), which is the time frame of our experiment, we used a fluorescent labeling approach to identify live foraminifera. Cores were incubated in a fluorogenic probe that is dependent on hydrolytic enzyme activity (Cell Tracker Green CMFDA, Molecular Probes, Eugene OR). To avoid any potential negative effects from temperature and pressure changes associated with collection, incubations were executed on the seafloor prior to core collection and fixation, and approach that has not previously been attempted. Although samples are still being analyzed, we know the incubations worked. Laboratory experiments on foraminiferal survival in response to elevated CO2 and decreased pH were conducted by Liz Mollo-Christensen, an undergraduate from Colby College, and Nadine Eisenkolb, an undergraduate from the University of Hawaii. A manuscript describing initial results was recently submitted for publication. If you are interested in this project, check back soon-- we may be looking for a new graduate student to conduct laboratory experiments to determine the effect of predicted increases in pCO2 on Scandinavian, temperate and tropical benthic foraminiferal survival and shell morphology. 

Laser Scanning Confocal image (z-stack) of FLEC core showing an anaerobic symbiont-bearing ciliate (magenta arrow) among other microbial eukaryotes and prokaryotes. White arrows point to flagellates; magenta arrows point to oral area of ciliate. See Bernhard et al. (2003) Limnology & Oceanography for more details of the method and other observations. (Joan M. Bernhard, Woods Hole Oceanographic Institution)

Foraminifera and other eukaryotes from sulfidic marine environments

Virgina Edgcomb (WHOI); Samuel Bowser (Wadsworth Center, NY State Department of Health); Katrina Edwards (WHOI MC&G)

One of my long standing interests involves eukaryotes inhabiting oxygen-depleted and anoxic sediments, with or without sulfide enrichment. Over the past 20 years, colleagues and I have studied the fauna in Santa Barbara Basin (Bernhard, Buck, Farmer & Bowser 2000 Nature; Grzymski et al. 2002 L&O; Bernhard, Visscher & Bowser 2003 Limnology & Oceanography), Cariaco Basin (Bernhard 2003 Science), Norwegian Fjords (Bernhard & Alve 1996 Marine Micropaleontol), cold seeps (Bernhard, Buck & Barry 2001 Deep-Sea Research I; Robinson et al. 2004 Marine Ecology), and the Black Sea (JMB unpublished).
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Results indicate that foraminifera commonly dominate these sediments and the dominant eukaryotes typically have putative symbionts. In addition, life position analysis (FLEC, see Bernhard et al., 2003 L&O) indicates complex associations of physiologically diverse microbial communities within a single laminae, suggesting heterogeneous pore-water habitat mosaics exist on the nanoliter scale. Thus, improved nanoscale pore-water chemistry monitoring is needed as well as in situ observations of microbial activity to understand the formation of these unparalleled paleoceanographic records. These studies have been funded by NSF Biological Oceanography, NSF Marine Geology & Geophysics, NSF Microbial Observatories, and NASA Exobiology. Presently, Katrina Edwards and I are modifying the FLEC method to allow simultaneous imaging of specific groups of microbes (labeled with FISH); this pilot study is being funded by WHOI's Ocean Life Institute and NSF. Ginny Edgcomb and I are funded by NSF MIP to identify the symbionts of selected ciliates and flagellates of Santa Barbara Basin sediments. Check back periodically for updates on our progress.

Edge of a chemosynthetic clam bed at a hydrocarbon seep off central California. Sites like this were sampled with ROV Jason for this project. Image © Woods Hole Oceanographic Institution.


Understanding stable isotopic disequilibrium in benthic foraminifera from hydrocarbon seeps

Anthony E. Rathburn (Indiana State University), Jon Martin (University of Florida)

This project seeks answers to the question: What controls the carbon isotopic composition of benthic foraminiferal tests (shells)?

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Answers to this question will be crucial for paleoenvironmental reconstructions in both hydrocarbon seep and non-seep environments. In order to address this question, in July 2007 we will use the ROV Jason to examine environments with "extreme" chemical gradients that accentuate chemical differences between biogenic carbonate and ambient conditions as well as those of "normal" deep-sea conditions. Extreme isotopic gradients present at cold methane seeps provide an ideal habitat to examine the effects of carbon isotopic disequilibrium (up to 40 ?), between foraminiferal calcite and dissolved inorganic carbon (DIC) of ambient water. Recent work suggests that biological factors ("vital effects") and/or ambient isotopic compositions influence carbon isotopic signatures of foraminiferal calcite. The project integrates microbiological techniques and ecological methods with geochemical analyses (pore-water and foraminiferal chemistry) using novel approaches, such as the Fluorescently-Labeled Embedded Core (FLEC) method and epifluorescence microscopic methods to identify live foraminifers. This integrated and detailed approach, specifically examining benthic foraminiferal cytoplasmic ultrastructure for symbiont presence and food composition, along with foraminiferal sub-millimeter distribution and isotope geochemistry, has never been attempted in any natural environment. These techniques will provide new and basic information about the effects of environment, distribution, diet, and symbiont presence/absence on stable isotope signals in foraminiferal tests.