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Diatom Laboratory

Research

Diatom Taxonomic Certification

Become a diatom taxonomist, certified by the Society for Freshwater Science.

The Level 1 Diatom Taxonomic Certification indicates an up-to-date working knowledge of the diagnostic characteristics of accepted North American inland diatom genera, providing a practical base for proficiency in performing taxonomic identifications of inland diatoms at the genus level. This certification serves as the first step to certification at the species level.

The Society of Freshwater Science Taxonomic Certification Program was implemented to certify that trained and skilled people are providing aquatic identifications in North America. The Stroud Water Research Center currently administers the Taxonomic Certification Program for SFS. The successful completion of the taxonomic certification process results in a certificate of proficiency in performing taxonomic identifications of inland diatoms that stands for 3 years. The program also helps promote undergraduate and graduate training of new taxonomic experts, training of taxonomic technicians through workshops, development of new manuals for identifying aquatic invertebrates and algae, and taxonomic excellence in other disciplines and other parts of the world. Study materials are available here:

David Burge (foreground) and Meredith Tyree (background) working on microscopes at INSTAAR, University of Colorado.

 

Working Together: the US Geological Survey Cooperative Agreement

Our lab partners with INSTAAR’s Center for Water, Earth Science, and Technology (CWEST) and the US Geological Survey to further the research of diatom autecology and taxonomy. We analyze samples of rivers and lakes from across the country to determine the biotic condition, based on diatoms. We have been working on regional studies of rivers in the southeast, northeast, Pacific northwest and California along urban and agricultural gradients. By identification of diatom species in rivers, we are able to determine the condition and impact of stressors to aquatic environments. Our work emphasizes the development of repeatable taxonomy across different analysts and laboratories.

 

Scanning electron micrograph of the center part of the diatom Neidium hitchcockii, a taxon with a page on the Diatoms of North America site.

Diatoms of North America: Online

Our lab is part of a collaborative project to document the diversity of diatom species in North America (diatoms.org). The project aims to provide accurate information on diatom identification, ecology, and geographic distribution. Identification of diatoms is crucial to measuring the biotic integrity of lakes and streams. Before the Diatoms of North America project, inconsistent taxonomy threatened accurate assessment of biotic condition. As a result of this project, diatom data has become both more consistent and more correct. Diatoms of North America has been developed in part with the generous funding and support of US EPA, USGS, the Institute of Arctic and Alpine Research at University of Colorado and other organizations.

 

An example of part of the Southeast Regional Survey Voucher Flora. Each voucher consists of three parts. Part one is an excel file containing OTU codes and their corresponding species identification. Part two is a pdf file of the entire flora, with searchable OTU codes. Part three is a compressed folder of numerous .tif files by diatom genera. Each image is identified by an INSTAAR accession number.

Transparent Data Archives for Taxonomy

In the past, there have been difficulties in merging data sets from different labs. In the INSTAAR Diatom Lab, we developed a process for verifying taxonomic decisions and comparing data from different sources. At the core, are “voucher floras”, which are image catalogs of diatoms organized into unique operational taxonomic units (OTUs), specific to regions or projects. The images within the flora represent the range of entities encountered in a project, because they are derived from each study rather than from a flora from some other geographic region. These floras help to document the size and morphological range of each diatom species, while allowing for transparency of the analysis process. When analysts are able to refer to OTUs and their morphological “meaning” through images that are project specific, data reproducibility is improved. Moreover, understanding of the size diminution series, or “morphological space” throughout a species’ life history for each taxon, is shared by analysts. A process for incorporating newly encountered taxa and sharing them is an important component of the process. The voucher floras are archived and made accessible so that future work to merge data sets is clear and straightforward.

2018 Northeast Lakes Voucher Flora Future Edition

2018 Northeast Lakes Voucher Flora Voucher Edition

2016 USGS Pacific Northwest Regional Survey River Voucher Flora

2015 USGS Southeast Regional Survey River Voucher Flora

2014 USGS Northeast Regional Survey River Voucher Flora

 

Diatoms of Northeast Lakes

Our lab recently completed a project with US EPA Region 1 and participating states (Maine, New Hampshire, Vermont, Connecticut, Rhode Island, New York and New Jersey). The objective of the work was to analyze diatoms in surface sediments of 120 lakes and develop a regional diatom flora for use by states in their assessment programs. Meredith Tyree coordinated the work, including developing a consistent taxonomy and rigorous QA/QC protocol across three laboratories. The northeast lakes were extremely diverse, with nearly 1200 operational taxonomic units (OTUs) recognized and placed in a voucher flora. The project included a workshop at the Academy of Natural Sciences of Drexel University, in which students, taxonomists and ecologists used the resources of the herbarium to identify diatom species.

 

Gabriela Fernandez, intern in the Diatom Lab with the 2018 RESESS program. Gabriela examined 3.5 m of pure diatomite deposited in Nebraska 5 million years ago, and concluded that a shallow lake and wetland habitat formed in a temperate climate.

Development of North American Grasslands, Diatom Evolution and Climate

The late Miocene was a time of global cooling, trending toward the modern climatic regime of the present day. As global temperatures cooled, mid latitude terrestrial environments became increasingly more arid, resulting in a decrease in woodlands and the expansion of silica-rich grasslands. The early Miocene lacustrine diatom diversity greatly expanded, potentially in response to expansion of grasslands. Recent work suggests that the silica fraction of grasses, phytoliths, play an important role in the delivery of dissolved silica to freshwater lakes. However, these ideas require examination. In order to understand the connection of grasslands, diatom stratigraphic markers and climate, Gabriela Fernandez is examining a lacustrine diatomite core from the Ogallala Formation in Nebraska. Gabriela is an intern with the Research Experiences in Solid Earth Science for Students (RESESS http://resess.unavco.org/).  She is examining the diatom record to reconstruct lake and environmental history in the grasslands of Nebraska during the late Miocene.

 

Didymosphenia geminata

A Native Invader – Didymosphenia geminata

Within the past 25 years, Didymosphenia geminata, a large, freshwater, stalk-forming benthic diatom, has transformed from a rare taxon to a nuisance species, overwhelming nutrient-poor lotic systems in its native range in the Holarctic as well as new southern habitats, most notably in New Zealand, Chile and Argentina. Much of the research regarding D. geminata and its emergent ecological role takes a rather limited view, focusing on solving the “problem” of blooming behavior and estimating the cause and extent of ecologic and economic impact. However, consideration of the life history, and in particular, population level growth dynamics and sexual reproduction, has received little attention. In fact, the life history of D. geminata and its role in the success of this species is largely unknown. In the past, studies of diatom life history have been based on small numbers of cells, because of the labor-intensive nature of measuring individual valves in the light microscope. Now, novel observational and analytical methods using the Fluid Imaging FlowCam allow us to gain new knowledge of this species, its size distribution dynamics, and diatom size dynamics more broadly.

 

Diatoms of North America Archived Webpages

The Diatoms of North America website (diatoms.org) is frequently updated with changes in taxonomy and concept. The previous versions are posted here:

Contact Information

(Phone) 303 492-5361
SEEC S173