Dr. Irena Kaczmarska

Professor

"Diatom flora and paleoecological analysis of Eemian profile in freshwater deposits at Imbramowice near Wroclaw"

1972 - M.Sc. (Biology), Jagellonian University, Cracov, Poland

"Late-Glacial diatom flora at Knapowka near Wloszczowa (South Poland)"

I am interested in all things diatomological

- past, present and future

Three main projects currently in progress are:

1. Evolution and ecology of marine planktonic diatoms

   The long-term objective of my program is to investigate diatom evolution, both through the study of the reproductive process and the structure of the components involved. First, I study how diatoms overcome the effect of cell size diminution, a common consequence of their mode of vegetative propagation. Sexual reproduction is the most common means of restoring size and I study factors that affect the onset and the success of various sexual stages. The ultimate goal is to further the understanding of planktonic diatom breeding systems, a subject that is still in its infancy. Second, I focus on the relationship between sex cell structure, ontogeny and molecular phylogeny inferred from ssu rRNA gene sequence comparisons. Two cell components are of interest: the auxospore cell wall and portulae.

2. Non-indigenous species

   This project is a part of the Canadian Aquatic Invasive Species Network (CAISN, NSERC). We are examining temporal changes and genetic variability of diatom aquatic invasive species (AIS) brought to Canada in ship ballast waters. We aim to identify factors affecting their survival and establishment in new environments.

3. DNA barcoding of diatoms

   Compared to terrestrial plants and complex animals, species diversity of diatoms is relatively poorly known. The purpose of this project is to demonstrate that DNA barcoding can be successfully applied to diatoms. The practice of using a small portion of an animal, plant or macroscopic algae as the DNA-source is not applicable to microorganisms. Normally, monoclonal cultures are used instead. Because establishing cultures is labor intensive and many cells prove intractable (potentially biasing results), we also aim to develop protocols to enable the generation of DNA sequences from field-sampled colonies and individual cells to facilitate future research.

4. Domoic acid producing phytoplankton species and their impacts on Atlantic salmon

   A number of diatoms belonging to the genus Pseudo-nitzschia have gained notoriety due to their production of domoic acid (DA), resulting in the accumulation of toxins in consumers higher up the food web, including fish and mammals. In the Bay of Fundy, one of these diatoms, P. pseudodelicatissima, shows variable toxicity. There is thus a great need to establish a genetic identity of the species present in the Bay so that future toxicity events can be attributed to a specific genotype of a particular diatom. This project assesses the genetic variability of DA producing clones isolated from areas carrying salmon farming operations and evaluates thresholds of each of the Pseudo-nitzschia clones at which mortalities or stresses in Atlantic salmon occur under controlled laboratory conditions.

We seek applications for a Masters Graduate Student or Technician in molecular taxonomy of diatoms (barcoding of diatoms). The successful candidate will contribute to an ongoing research program assessing the correspondence of certain gene sequences to biological boundaries of species in diatoms using clonal isolates primarily from the Canadian Maritimes.

The ideal candidate will have experience with microbial cultures (preferably diatoms) and standard molecular methodologies (DNA extraction, PCR, etc.). To apply, please send a resume, transcript, thesis abstract (if applicable) and contact information for three references to:

Dr. Irena Kaczmarska
Department of Biology
Mount Allison University
63B York Street
Sackville, NB
E4L 1G7 Canada

e-mail: iehrman@mta.ca

Review of applications starts immediately and continues until the position is filled. The initial appointment will be for one year, with continuation of support pending on satisfactory performance, with the possibility of further extension by collaborating on future research proposals, including international programs.

Books and book chapters:

• Przybyłowska-Lange, W., I. Kaczmarska, B. Marciniak, & J. Siemińska. 1989. Gromada Chrysophyta, Klasa Bacillariophyceae. In: Budowa geologiczna Polski. III. Atlas skamieniałości przewodnich i charakterystycznych. 3b. Kenozoik, Czwartorzed. Wydawnictwa Geologiczne. Warszawa. pp. 183-213. 14 PL.
• Kaczmarska, I. & S.R. Rushforth. 1984. The diatom flora of Blue Lake Warm Springs, Utah, USA. Bibliotheca Diatomologica 2(l): 1-49.
• Fugladda, N., I. Kaczmarska & S.R. Rushforth. 1984. A contribution to the freshwater diatom flora of the Hawaiian Islands. Bibliotheca Diatomologica 2(2): 1-55.

• Thaler M. & I. Kaczmarska. 2009. Gyrosigma orbitum (Bacillariophyta), a new species from a Bay of Fundy salt marsh. Botanica Marina 52: 60-68.
• Allaway, H., V. Lloyd & I. Kaczmarska. 2008. Whole mount in situ immunofluorescent hydridization of diatoms. Diatom Research 23: 1-9.
• Kaczmarska, I. & J.M. Ehrman. 2008. Poloniasira fryxelliana Kaczmarska and Ehrman, a new thalassiosiroid diatom (Bacillariophyta) from the Early Oligocene diatomites in Polish Flysch Carpathians, southeast Poland. Nova Hedwigia, Beihefte 133: 217-230.
• Kaczmarska, I., C. Reid, J.L. Martin & M.B.J. Moniz. 2008. Morphological, biological, and molecular characteristics of the diatom Pseudo-nitzschia delicatissima from the Canadian Maritimes. Botany 86: 763-762.
• Kaczmarska, I., N.A. Davidivich & J.M. Ehrman. 2007. Sex cells and reproduction in the diatom Nitzschia longissima (Bacillariophyta): discovery of siliceous scales in gamete cell walls and novel elements of the perizonium. Phycologia 46: 726-737.
• Kaczmarska, I., J.L. Martin, J.M. Ehrman, & M.M. LeGresley. 2007. Pseudo-nitzschia species population dynamics in the Quoddy Region, Bay of Fundy. Harmful Algae 6: 861-874.
• Kaczmarska, I., C. Reid & M. Moniz. 2007. Diatom taxonomy: morphology, molecules and barcodes. Proceedings of the 1^st Central-European Diatom Meeting 2007. Kusber W.-H. & Jahn R. (eds), Botanic Garden and Botanical Museum Berlin-Dahlem, FU-Berlin. pp. 69-72
• Davidovich, N.A., I. Kaczmarska, & J.M. Ehrman. 2006. The sexual structure of a natural population of the diatom Nitzschia longissima (Bréb.) Ralfs. In: A. Witkowski (ed.), Proceedings of the 18th International Diatom Symposium, 2004, Miedzyzdroje, Poland, pp. 27-40, Biopress Ltd., Bristol.
• Kaczmarska, I., M. Beaton, A.C. Benoit & L.K. Medlin. 2006. Molecular phylogeny of selected members of the Order Thalassiosirales (Bacillariophyta) and evolution of the fultoportula. Journal of Phycology 42: 121-138.
• Trites, M., I. Kaczmarska, P.W. Hicklin, J.M. Ehrman & J. Ollerhead. 2005. Benthic diatoms from two mudflats in Chignecto Bay, Upper Bay of Fundy. Hydrobiologia 544: 299-319.
• Ehrman, J.M. & I. Kaczmarska. 2004. A virtual instrument metaphor for object identification: an example application using toxic diatoms. Limnology and Oceanography Bulletin 13: 1-4.
• Medlin, L.K. & I. Kaczmarska. 2004. Evolution of the diatoms: V. morphological and cytological support for the major clades and a taxonomic revision. Phycologia 43: 245-270.
• Ehrman, J.M. & I. Kaczmarska. 2002. A 90-degree-tilt rotary adapter for SEM. Microscopy Today 2-2: 24-26.
• Ehrman, J.M. & I. Kaczmarska. 2001. A simple transmitted electron detector for SEM. Microscopy Today 1-5: 12-14.
• Kaczmarska, I., J.M. Ehrman & S.S. Bates. 2001. A review of auxospore structure, ontogeny, and diatom phylogeny. In: Economou-Amilli, A. (ed.) Proceedings of the 16th International Diatom Symposium pp. 601: 153-168, University of Athens Press, Athens, Greece.
• Hiltz, M., S.S. Bates & I. Kaczmarska. 2000. Effect of light : dark cycles and cell apical length on the sexual reproduction of the pennate diatom Pseudo-nitzschia multiseries (Bacillariophyceae) in culture. Phycologia 39: 59-66.
• Kaczmarska, I., T.A. Clair, J.M. Ehrman, S.L. MacDonald, D. Lean & K.E. Day. 2000. The effect of UV-B on phytoplankton populations in clear and brown temperate Canadian lakes. Limnology and Oceanography 45: 651-663.
• Kaczmarska, I. & L.L. Dowe. 1997. Reproductive biology of the red alga Polysiphonia lanosa (Ceramiales) in the Bay of Fundy, Canada. Marine Biology 128: 695-703.
• Kaczmarska, I. & G.A. Fryxell. 1996. Alveus, gen. nova (Bacillariaceae, Bacillariophyta), a heavily silicified diatom found in the Equatorial Pacific. Microscopy Research and Technique 33: 2-11.
• Kaczmarska, I. & G.A. Fryxell. 1995. Micro-phytoplankton of the Equatorial Pacific: 140°W meridianal transect during the 1992 El Niño. Deep-Sea Research 42: 535-558.
• Kaczmarska, I., N.E. Barbrick, J.M. Ehrman & G.P. Cant. 1993. Eucampia Index as an indicator of the Late Pleistocene oscillations of the winter sea-ice extent at the ODP Leg 119 Site 745B at the Kerguelen Plateau. Hydrobiologia 269/270: 103-112.
• Kaczmarska, I. & J.M. Ehrman. 1990. Pyritized diatoms in the sediments of the ODP Leg 116 to the distal end of the Bengal Fan. In: Cochran, J.R. and Stow, D.A.V. et al. 1990. Calif. Univ. Scripps Instit. Proceedings of the ODP, Scientific Results 116: 243-247.
• Cochran, J.R., D.A.V. Stow, C.A. Auroux, K. Amano, P.S. Balson, J. Bouleque, G.W. Brass, J. Corrigan, S. Gartner, S.A. Hall, S. Iaccarino, T. Ishizuka, I. Kaczmarska, H. Kassens, G. Leger, F. Proto Decima, V.C. Raman, N.N. Seger, K. Takahashi, T. Thompson, J.-J. Tiercelin, M. Townsend, A. Wetzel, N. P. Wijayananda & C. Williams. 1987. India-Asia collision studies in the Equatorial Indian Ocean. Nature 330(6148): 519-521.
• Gasse, F., J.C. Fontes, J.C. Plaziat, P. Carbonel, I. Kaczmarska, P. de Deckker, I. Soulie-Marsche, Y. Callot & P.A. Dupeuble. 1987. Biological remains, geochemistry and stable isotopes for the reconstruction of environment and hydrological changes in the Holocene Lakes from North Sahara. Paleogeography, Paleoclimatology, Paleoecology 60: 1-46.
• Kotlarczyk, J. & I. Kaczmarska. 1987.The two horizons with the Oligocene and Lower Miocene diatoms from the Polish Outer Carpathians. Ann. Sci. Geol. Poloniae 57(3-4): 143-189.
• Kaczmarska, I., G.A. Fryxell & T.P. Watkins. 1986. Effect of the Gulf Stream Warm Core Rings on distributional patterns of the genus Nitzschia. Deep-Sea Research 33(1-2): 1843-1868.
• Fontes, J.C., F. Gasse, Y. Callot, P. Carbonell, P.S. Dupeuble & I. Kaczmarska. 1985. Freshwater to marine-like environments from Holocene lakes in Northern Sahara. Nature 317(6038): 608-610.
• Kaczmarska, I. 1985. The diatom flora of Miocene lacustrine diatomites from the Harper Basin, Oregon, USA. Acta Paleobotanica 25(1-2): 33-100.
• Kaczmarska, I. & S.R. Rushforth. 1984. Diatom associations in Blue Lake Warm Springs, Tooele County, Utah, USA. VII International Symposium on Living and Fossil Diatoms Proceedings, Koeltz Sci. Books. pp. 345-358.
• Rushforth, S.R., I. Kaczmarska & J. Johansen. 1984. The subaerial diatom flora of Thurston Lava Tube, Hawaii. Bacillaria 7: 135-157.
• Kaczmarska, I. 1982. Diatoms of the Lower Oligocene diatomites from the Polish Carpathian Flysch. Acta Geol. Sci. Hungariae 24(1-2): 368-372.
• Kaczmarska, I. 1977. Comments on the flora of diatoms (Bacillariophyceae) from Eemian freshwater sediments at Imbramowice near Wroclaw. Acta Paleobotanica 18(2): 35-60.
• Kaczmarska, I. 1976. Diatom analysis of Eemian profile in freshwater deposits at Imbramowice near Wroclaw. Acta Paleobotanica 17(2): 3-33.
• Kaczmarska, I. 1973. Late-Glacial diatom flora at Knapowka near Wloszczowa (South Poland). Acta Paleobotanica 14(3): 179-193

Lecture and lab based courses:

• Biology 2301 - Plant Biology. This course offers an introduction to plant diversity. It includes all forms of organisms capable of oxygenic photosynthesis, both on land and at sea. It is taught in the context of the function of plants in the Earth's ecosystem.
• Biology 3021 - Paleontology. This course provides an overview of the major lineages of plant and animal life known on our planet in the context of the physical, chemical and biotic environment at the time of their evolution and diversification.
• Biology 3351 - Marine Botany. A course that summarizes recent advances in out understanding of plant growth at sea. It focuses on macroscopic plants, mainly from intertidal habitats. Students perform a small field and/or laboratory project presented to the class. The Journal for Algaeholics is a frequent online forum for projects performed by Marine Botany students.

• Biology 4371 - Advanced Marine Science. The topics covered in this course depend on student interest. They may include all or some of the following: marine biology, marine geology, novel methods in ocean science, marine engineering, and biotechnology.
• Biology 4911X - Topics in Biology of Protists. The course is intended for senior undergraduate students interested in microeukaryotes. It allows students in-depth study of one of the 25+ divisions and phyla of protists or a study of one specific aspect of group biology (e.g., evolution of dinoflagellates, geography of invasive protists, etc.). Emphasis will be placed on protists of greatest importance in global ecology, medicine and other applications. Learning specialized methods used to investigate protists may also be included as part of the course. The course will employ a combination of lectures, seminars, discussions and/or independent research projects.
• Biology 4950 - Special Topics in Biology. Students seriously interested in marine botany or ecology conduct an independent study under my supervision. In may involve a small research project or a major literature review. Some examples of such topics are listed below.
• Osborne, N. 2003. The effect of salinity, temperature and water density on cell size reduction in the centric diatom Thalassiosira nordenskioeldii Cleve. Mount Allison University, Sackville, N.B., 58 pp.
• Thompson, Susan. 2000. Role of bacteria in the sexual reproduction of the domoic-acid-producing pennate diatom Pseudo-nitzschia multiseries (Hasle) Hasle. Mount Allison University, Sackville, N.B., 49 pp.

• Biology 4990 – Honours in Biology. Students seriously interested in the biology of diatoms conduct a laboratory and/or field based research project resulting in an Honours Thesis and contributing to a publication. Some recent example theses are listed below.
• MacGillivary, M.L. 2008. Patterns of inheritance in the diatom Tabularia fasciculata (Agardh) Williams & Round. Mount Allison University, Sackville, N.B., 118 pp.
• MacIntosh, K. 2008. Survivorship of phytoplankton in ship's ballast water during a trans-Pacific crossing. Mount Allison University, Sackville, N.B., 77 pp.
• Allaway, H. 2007. Parent specific heritable characteristics, morphological and epigenetic, in the marine araphid pennate diatom Tabularia fasciculata (Agardh). Mount Allison University, Sackville, N.B., 117 pp. A publication in Diatom Research (Allaway et al.,in press [above]) resulted from this thesis project.
• Mills, K.E. 2005. Autogamic sexual behavior and fine structure of sex cells of selected marine centric diatoms. Mount Allison University, Sackville, N.B., 133 pp. A poster on portions of this work, presented at the 44th Northeast Algal Society (NEAS) Meeting, Rockport, ME, April 15-17, 2005 is available here (PDF)

• Biology 5100/5200 - Graduate Topics in Marine Science and Algal Biology. Course subject and scope are tailored to the individual graduate student program. Two examples are listed below.
• Biology 5101 - Biology of Diatoms. This course involves reading of current journal articles on topics such as diatom cell structures and their function, diatom life histories and concept of species in diatoms. Assignments include writing two essays and two critical reviews.
• Biology 5201 - Topics in Biology of Protists. The course is intended for graduate students interested in microeukaryotes. It allows students in-depth study of one of the 25+ divisions and phyla of protists or a study of one specific aspect of group biology (e.g., evolution of dinoflagellates, geography of invasive protists, etc.). Emphasis will be placed on protists of greatest importance in global ecology, medicine and other applications. Learning specialized methods used to investigate protists may also be included as part of the course. The course will employ a combination of lectures, seminars, discussions and/or independent research projects.
• Biology 5202 - Plankton Biology. The course involves reading of current journal articles on topics such as composition and distribution of oceanic phytoplankton communities, chemical antigrazing defenses in phytoplankton and novel technology in phytoplankton research. Students discuss topics with the instructor and/or give an oral presentation to an undergraduate class and write up to three critical reviews or essays.

• Klein, Georgia. (pending). Biology of non-indigenous diatom species. An NSERC CAISN project. Mount Allison University (supervisor).

My work will include the participation in CAISN, a Canada-wide project on invasive species. Diatoms are among the organisms that will be easily distributed by ship ballast water. Up to now we don't know how fast they adapt to their new environment and if their appearance will have consequences for the existing ecosystem. For example, will they displace or replace the resident organisms? To contribute to the project, we will do qualitative and quantitative analyses of numerous samples collected from ship tanks as well as from port water and sediments.


• Lang, Imke. (pending). Changes in genetic structure of ballast water phytoplankton. An NSERC CAISN project. Mount Allison University (supervisor).

My project is part of the CAISN research program and will include investigations of the change in genetic structure in the populations of diatoms and dinoflagellates taking place during the transoceanic voyages in ballast waters of ships arriving at Canadian ports. The aim is to develop a protocol for the identification of invasive diatoms and dinoflagellates on species and sub-species level. This will include the development of a method for DNA extraction and PCR amplification of single cells, as well as the identification and improvement of molecular markers.


• Villac, Maria Celia. (pending). Composition and abundance of diatoms in the sediments of ship ballast tanks. An NSERC and CAISN project. Mount Allison University (supervisor).

When ships need to take in water from the environment to serve as ballast, organisms and suspended inorganic materials are also picked up. During the voyage, some of the living and of the non-living particulate matter tend to settle to the bottom of the tank(s). Organisms present in their resting stages (cysts, spores) whose structures are often heavier than their vegetative counterparts can further enhance the buildup of such species in the sediment. Some of these species are actually those that can have higher survival rates under adverse conditions. Evidence shows that, even when ballast water is exchanged, the sediment accumulated on the bottom of a ship tank is not completely renewed so that the biota in the sediments is, in fact, a composite of the natural communities of the many regions from where ballast was taken. Data about the assemblages of microalgae present in the sediment of ballast tanks is scanty, although this information is very much needed to ascertain propagule pressure and, as a result, estimate the probability of invasions. This is my challenge: to assess the composition and abundance of diatoms present in the sediments collected in empty ballast tanks of ships that came to Canadian ports during 2007 and 2008.

• Moniz, Monica (pending). Barcoding diatoms. Mount Allison University (supervisor).

The importance of identifying any species reliably, quickly and cost-effectively is of greatest importance in any biological study and may be especially difficult with microorganisms, such as diatoms. Recently, there has been a great enthusiasm in the possibility of barcoding all life. In theory, if we could find a DNA region that evolves fast enough so as to be different in every species, then we have found the necessary tag for species identification. In my Masters thesis, I will first test congruence between molecular, morphological and biological determination of diatom species for a selected number of model diatoms. Once the best model for diatom species identification is found, I will proceed with the barcoding of a wide range of diatom species from locations worldwide.


• MacGillivary, Mike (pending). Does genetic structure of diatom populations change during a transoceanic voyage? Mount Allison University (supervisor).

With recent increases worldwide in the number and size of ocean-going vessels there is a greater potential for alien species to be transported and dispersed worldwide as these ships travel from port to port. Under certain conditions, some of these non-indigenous species may become invasive at the receiving port. As part of the CAISN network, my project aims to detect changes in the genetic structure of populations of diatoms in ballast tank water over the duration of trans-Atlantic voyages. We hypothesize that the change in genetic composition will be non-random, and that we will identify taxonomic and geographic source(s) of the arriving inoculums. By using ITS and rbcL markers in single cell PCR reactions, haplotypic and nucleotide diversity will be estimated within and between each sample day. The most prevalent and/or persistent haplotypes of these species will then be compared to those now present in Canadian receiving port(s) to see whether these haplotypes are already present in these waters. This project will allow us to predict which species and haplotypes are most likely to become invasive species in Canadian ports.

Lab Assistants and Volunteers:

• Laura Mather follows in the footsteps of legends of the likes of Mike MacGillivary and Kayleigh MacIntosh by helping out with all sorts of fascinating activities around the lab. Sometimes this doesn't involve cleaning glassware or the dreaded entry of reprints into the database.