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Consistent identification of diatoms is a prerequisite for studying their ecology, biogeography, and successful application as environmental indicators. However, taxonomic consistency among observers has been difficult to achieve because taxonomic information is scattered across numerous literature sources, presenting challenges to the diatomist. Firstly, literature is often inaccessible because of cost or its location in journals that are not widely circulated. Secondly, taxonomic revisions of diatoms are taking place faster than floras can be updated. Finally, taxonomic information is often contradictory across literature sources. These issues can be addressed by developing a content creation community dedicated to making taxonomic, ecological, and image-based data freely available for diatom researchers. represents such a content curation community, providing open, online access to a vast amount of recent and historical information on North American diatom taxonomy and ecology. The content curation community aggregates existing taxonomic information, creates new content, and provides feedback in the form of corrections and notices of literature with nomenclatural changes. The website not only addresses the needs of experienced diatom scientists for consistent identification but is also designed to meet users at their level of expertise, including engaging the lay public in the importance of diatom science. The website now contains over 1000 species pages contributed by over 100 content contributors, from students to established scientists. The project began with the intent to provide accurate information on diatom identification, ecology, and distribution using an approach that incorporates engaging design, user feedback, and advanced data access technology. In retrospect, the project that began as an ‘extended electronic book’ has emerged not only as a means to support taxonomists, but for practitioners to communicate and collaborate, expanding the size of and benefits to the content curation community. In this paper, we outline the development of, document key elements of the project, examine ongoing challenges and consider the unexpected emergent properties, including the value of as a source of data. Ultimately, if the field of diatom taxonomy, ecology, and biodiversity is to be relevant, a new generation of taxonomists needs to be trained and employed using new tools. We propose that is in a key position to serve as a hub of training and continuity for the study of diatom biodiversity and aquatic conditions.
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Diatom Research
ISSN: (Print) (Online) Journal homepage: supporting taxonomists, connecting
Sarah A. Spaulding, Marina G. Potapova, Ian W. Bishop, Sylvia S. Lee, Tim S.
Gasperak, Elena Jovanoska, Paula C. Furey & Mark B. Edlund
To cite this article: Sarah A. Spaulding, Marina G. Potapova, Ian W. Bishop, Sylvia S. Lee,
Tim S. Gasperak, Elena Jovanoska, Paula C. Furey & Mark B. Edlund (2021)
supporting taxonomists, connecting communities, Diatom Research, 36:4, 291-304, DOI:
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Published online: 11 Jan 2022.
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Diatom Research, 2021
Vol. 36, No. 4, 291–304, supporting taxonomists, connecting communities
1U.S. Geological Survey/INSTAAR, Boulder, CO, USA
2The Academy of Natural Sciences of Drexel University, Philadelphia, PA, USA
3Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
4U.S. Environmental Protection Agency, Office of Research and Development, Center for Public Health and Environmental Assessment,
Washington, DC, USA
5Strange Attractor LLC, Boulder, CO, USA
6Department of Palaeoanthropology, Senckenberg Research Institute, Frankfurt am Main, Germany
7Department of Biology, St. Catherine University, St. Paul, MN, USA
8Science Museum of Minnesota, St. Croix Watershed Res. Station, Marine on St. Croix, MN, USA
Consistent identification of diatoms is a prerequisite for studying their ecology, biogeography, and successful application as environmen-
tal indicators. However, taxonomic consistency among observers has been difficult to achieve because taxonomic information is scattered
across numerous literature sources, presenting challenges to the diatomist. Firstly, literature is often inaccessible because of cost or its
location in journals that are not widely circulated. Secondly, taxonomic revisions of diatoms are taking place faster than floras can be
updated. Finally, taxonomic information is often contradictory across literature sources. These issues can be addressed by developing a
content creation community dedicated to making taxonomic, ecological, and image-based data freely available for diatom researchers. represents such a content curation community, providing open, online access to a vast amount of recent and historical infor-
mation on North American diatom taxonomy and ecology. The content curation community aggregates existing taxonomic information,
creates new content, and provides feedback in the form of corrections and notices of literature with nomenclatural changes. The website
not only addresses the needs of experienced diatom scientists for consistent identification but is also designed to meet users at their level
of expertise, including engaging the lay public in the importance of diatom science. The website now contains over 1000 species pages
contributed by over 100 content contributors, from students to established scientists. The project began with the intent to provide accurate
information on diatom identification, ecology, and distribution using an approach that incorporates engaging design, user feedback, and
advanced data access technology. In retrospect, the project that began as an ‘extended electronic book’ has emerged not only as a means
to support taxonomists, but for practitioners to communicate and collaborate, expanding the size of and benefits to the content curation
community. In this paper, we outline the development of, document key elements of the project, examine ongoing challenges
and consider the unexpected emergent properties, including the value of as a source of data. Ultimately, if the field of diatom
taxonomy, ecology, and biodiversity is to be relevant, a new generation of taxonomists needs to be trained and employed using new tools.
We propose that is in a key position to serve as a hub of training and continuity for the study of diatom biodiversity and
aquatic conditions.
Keywords: website, online flora, taxonomic consistency, content curation community, North America
The discovery and documentation of life on the planet
Earth remain a vast endeavour. The challenge is far
too large for the small number of formally trained sci-
entists and far too complex for traditional publication
(Wilson 2003,Jetzetal.2012, Parr et al. 2014, Meyer
et al. 2015). The internet empowers extended, dispersed
scientific communities to collaborate over broad spa-
tial scales, nearly instantaneously (Borgman 2007). The
Encyclopedia of Life (EOL), a model content curation
Correspondence author: Sarah A. Spaulding E-mail:
Associate editor: Rebecca Bixby
(Received 27 January 2021; accepted 22 September 2021)
community (Rotman et al. 2012), is at the forefront of
collaboration and provides open access and engagement
of the public in science (Wilson 2003). EOL facilitates
access to knowledge about Earth’s life, in all of its forms,
and thus, makes science more egalitarian. Data on the
many aspects of organisms (e.g., names, distribution, life
cycle, food webs) can be gathered together and served via
platforms such as EOL. Microorganisms such as diatoms,
which require high-powered microscopes for observation,
present additional challenges. However, knowledge of the
This work was authored as part of the Contributor’s official duties as an Employee of the United States Government and is therefore a work of the United States Government. In
accordance with 17 U.S.C. 105, no copyright protection is available for such works under U.S. Law.
This is an Open Access article that has been identified as being free of known restrictions under copyright law, including all related and neighbouring rights (https:// You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
Published online 11 Jan 2022
292 Sarah A. Spaulding et al.
basic biology and diversity of diatoms continues to be lim-
ited, even by specialists, and even within North America.
Yet, knowledge of diatoms has great utility in environmen-
tal sciences (Smol & Stoermer 2010), as does an EOL-type
resource that is specific for diatom specialists.
Since Ehrenberg (1854) first recognized the distinct
diatom flora of western North America, floristic zones
of the eastern, southeastern and northwestern parts of
the U.S. have been noted (Kociolek & Spaulding 2000,
Potapova & Charles 2003, Morales 2005, Kociolek 2006,
Ponader & Potapova 2007). Yet, while there are a number
of recent regional floras, including the Arctic (Antoni-
ades et al. 2009a), Cape Cod (Siver et al. 2005), Montana
(Bahls 2005,2010,2013), Great Smoky Mountains (Furey
et al. 2011), and the Atlantic Coastal Plain (Siver & Hamil-
ton 2011), floras are limited in terms of geographic and
taxonomic scope and become outdated because of the rapid
pace of revisions in classification that follow advance-
ments in understanding phylogenic relationships (Nakov
et al. 2014,2015, Ruck et al. 2016a,b). Furthermore, it was
estimated that 20–25% of the species within the U.S. have
yet to be described by science (Potapova & Charles 2003),
an estimate that has increased over the past decade (Bishop
et al. 2017a). While a number of publications address
uncovering and describing new species or documenting
species distributions (e.g., Spaulding et al. 2002, Potapova
& Ponader 2004, Potapova & Winter 2006, Antoniades
et al. 2009b, Kumar et al. 2009, Kociolek & Thomas 2010,
Potapova et al. 2019a, Stone et al. 2020), many more taxa
remain to be described.
Furthermore, advances are being made to expand the
research potential of specimens in programmes such as
the Extended Specimen Network (Lendemer et al. 2020),
which link data types including genetic, phenotypic, and
environmental data. Taxonomic and ecological data are
crucial for water quality monitoring and assessment pro-
grammes and biodiversity inventories, including those
overseen by federal agencies [e.g., U.S. Environmental
Protection Agency (U.S. EPA), U.S. Geological Survey
(USGS)], state and local agencies, tribal governments,
and academic researchers. Taxonomy is the framework
upon which biodiversity science relies (Ebach et al. 2011,
Sluys 2013), yet taxonomy and taxonomists are as vulner-
able to extinction as the organisms they study. The decline
of taxonomy as a field of study is well-documented (Lück-
ing 2008,Wheeler 2010, Sluys 2013), and taxonomy often
is portrayed as ‘a science in crisis’ (Agnarsson et al. 2007,
Rodman 2007). If is a means to continue the
science of taxonomy, that outcome would be an immense
At the same time, trends to privatize and monetize
science and scientific publishing, in general, are still
strong (Jones et al. 2014, Ellwood et al. 2015,Heise
& Pearce 2020) and such trends limit public access to
science. When knowledge and data are more accessible
to everyone, science becomes more equitable (Rotman
et al. 2012, Parr et al. 2014). Information on diatoms
should not be held only within expensive journals, books,
and scientific societies. In the case of U.S. Government-
funded programmes, there are requirements to make data
available online wherever practical and to make the infor-
mation accessible for use by the public (OMB 2009,2013).
Meeting these requirements for diatom data collected with
federal funding are indeed practical to the extent of mak-
ing information fully discoverable in a convenient open
format for a wide range of users. Furthermore, infor-
mation can be more appealing to all types of students
through the use of intentional design and compelling
In this paper, we provide an example of an open, online
diatom flora following the model of a content curation
community (Rotman et al. 2012). The flora is created
through an aggregation of taxonomic, ecological, and dis-
tribution information that is curated by an Editorial Review
Board. We outline the development of, docu-
ment key elements, and examine ongoing challenges. With
nearly one million page views each year, we consider the
website a success. Yet, the project is not often cited as
a source in journal articles and our contributors have not
received a commensurate citation and professional recog-
nition by academia. The purpose of this publication is to
document the functioning of, its outcomes,
and future potential.
The primary audience of includes those who
need to identify diatoms or those who seek detailed sci-
entific information about their ecological roles in aquatic
systems. This audience, which includes students and pro-
fessionals in academic, consulting and public agency roles,
may work as diatom analysts, academic professionals or
graduate students in training. A typical diatom taxonomist
spends time working at a microscope equipped with a dig-
ital camera and imaging software. Many of these users are
tasked with identifying diatom species as data elements
for research and monitoring projects, for which consistent
taxonomic treatment is imperative. Consistent taxonomy
across analysts and labs is particularly difficult because the
information needed for identification (including images,
dimensions, and descriptions) is dispersed across a large
number of scientific publications and taxonomic volumes.
Kociolek & Spaulding (2000) observed that taxon names
applied to studies typically reflect the resources available
to a particular person or laboratory rather than an accu-
rate flora of the study region. In addition, the
site serves as the standard for taxonomic accreditation
by the Society for Freshwater Science genus certifica-
tion programme (Alers-Garcia et al. 2021), with a species
certification programme in progress.
The secondary audience, which includes people who
spend little or no time at a microscope, includes scientists 293
or managers who wish to access the information associ-
ated with diatom species, such as the water conditions in
which a species grows, or the definition of a term from
the glossary. Students (primary and secondary school, uni-
versity) and other public users form part of this audience.
The site attracts over 70% of its visits from the lay pub-
lic, such as people searching on the phrase ‘what is a
diatom?’ Thus, opens the world of diatoms
to a diverse, international audience by conveying biologic
information in non-specialist terminology. Although we
label this audience ‘secondary’, the outcomes from visits
from this audience may be even more consequential. Bio-
diversity is crucial to society, and it is this audience that
has the ability to effect species conservation and ecosystem
management (Jetz et al. 2013, Meyer et al. 2015, Navarro
et al. 2017).
The website project is intended to fill a gap in the
formal scientific literature by serving diatom taxonomists,
ecologists, and water quality managers. Each taxon page
represents a synthesis of information that is otherwise time-
consuming, or resource-prohibitive, for an individual user
to obtain. The resource is based on (1) early efforts to pri-
oritize design elements and (2) ongoing attention to the
careful curation of content. Electronic floras have sev-
eral advantages over traditional floras (i.e., books). Firstly,
content can be continually improved through updates that
incorporate new knowledge, expertise, and refinement
of nomenclature based on systematics. When they are
detected, errors can be corrected, and revisions to pages
can be archived and tracked. The digital format also allows
flexibility in the way that content can be displayed.
Taxa included within were initially drawn
from lists developed through the U.S. Geological Sur-
vey National Water Quality Assessment program. In the
process of developing species pages for the project, how-
ever, nomenclatural errors and inconsistent identifications
emerged in the list. Furthermore, the project began with
a bias towards taxa reported from streams and rivers. As
contributors have worked on projects on lakes, wetlands,
and estuaries, the habitat coverage has expanded. Now,
contributors use, improve, and update the list of taxa simul-
taneously with new taxon pages and updates to taxon
Operating principles
The project adopted many of the principles outlined
in the EOL for curating online taxonomic content
(Parr et al. 2014). An open process was established to
include contributors, develop taxon pages, develop site
design, manage reviews, and respond to notification of
errors. Editorial Review Board members regularly hold
meetings, workshops, and requests for feedback. Commu-
nity listening sessions have included the biennial North
American Diatom Symposium and International Society
for Diatom Research (Edlund et al. 2019). The operat-
ing principles cover project oversight, taxon designation,
specimen access, species concept, funding priorities, and
scientific review.
Project oversight
The process for the inclusion of new pages and activities of
the Editorial Review Board aims to be transparent and to
avoid top-down management. Feedback from the scientific
community, as well as forums for participation by water
managers provide differing views on priorities and needs
(Lee 2019).
Taxon designation
The project adheres to the International Code of Nomencla-
ture (ICN) for algae, fungi, and plants (Turland et al. 2018)
and does not bypass formal scientific publication in a peer-
reviewed journal. Beginning in 2012, the ICN included
electronic publication as constituting valid publication,
under certain parameters:
29.1. Publication is effected, under this Code, by distribu-
tion of printed matter (through sale, exchange, or gift) to
the general public or at least to scientific institutions with
generally accessible libraries. Publication is also effected by
distribution on or after 1 January 2012 of electronic material
in Portable Document Format (PDF; see also Art. 29.3 and
Rec. 29A.1) in an online publication with an International
Standard Serial Number (ISSN) or an International Standard
Book Number (ISBN).
While could serve as an outlet for formal tax-
onomic publication, it has not included new descriptions to
Specimen access
One of the requirements of is that light and/or
scanning electron micrograph images are from specimens
deposited in a public herbarium. Thus, anyone should be
able to obtain the physical specimen of any image in Applied taxonomic names should be validly
published and correct. We recognize, however, that there
will be errors in the application of names. Those errors
are corrected through updates, as they are determined. For
example, the taxon page for Encyonema stoermeri Spauld-
ing, Pool & Castro was published (Spaulding et al. 2010,
Spaulding 2010a), but the type had been previously pub-
lished as Encyonema temperei Krammer (Krammer 1997).
The scientific community reported the error, and an update
was made to correct the name to E. temperei.
294 Sarah A. Spaulding et al.
Species concept
We propose a common philosophy recognizing species
as “morphologically distinct groups”, however, morpho-
logical species may not, in many instances, align with
molecular concepts of species or phylogenetic species. We
adopt a morphological species concept as an operational
definition. In cases of questionable taxonomic affiliation,
a ‘sort it out’ philosophy will prevail because it is easier
to subsequently combine taxonomic errors resulting from
splitting morphological specimens too finely, rather than
being able to recover coarser groups. As we are learning,
it is expensive and difficult to recover and rectify errors
when different entities are combined that should have been
treated separately (Lee et al. 2019).
Funding priorities
The selection of taxa for the development of taxon pages
has been prioritized based on relative abundance, indica-
tor status, and difficulty in identification for USGS and
U.S. EPA monitoring programmes (Stoddard et al. 2005,
Lee et al. 2019). To date, the funded development of con-
tent for species pages has followed two models, (1) direct
funding of an expert for a specified group of taxa and
(2) travel funding for contributors to work in collabo-
ration, using the resources of the Diatom Herbarium at
the Academy of Natural Sciences of Drexel University,
Philadelphia, Pennsylvania, USA. Contributions have been
made based on other motivations, including (1) personal
research and exceptional dedication (e.g., the hundreds of
species pages contributed by Loren Bahls, University of
Montana), (2) production of pages by students, such as
more than 100 species pages contributed by students in the
Ecology and Systematics of Diatoms course at Iowa Lake-
side Laboratory, and (3) outcomes linked to research grant
requirements for broader impacts (Furey et al. 2011).
Scientific review
Members of the Editorial Review Board and recognized
national and international specialists serve as referees for
the online taxon pages. The review process follows the
model of scientific peer-review, except that the referees
are not anonymous. The curation of scientific content by
contributors and reviewers is acknowledged throughout
the site. The recognition is meant to support openness,
to document contributions by reviewers, and for contrib-
utors, reviewers, and editors to share the responsibility for
accurate information.
Ideally, the organizational framework and navigation of would be based on a consensus phylogenetic
tree of diatoms. However, there are such large uncertain-
ties around diatom relationships that current phylogenies
(Theriot et al. 2010, Williams & Kociolek 2010)aretoo
broad to provide an effective organizational structure. As
a result, the higher-level organization is artificially par-
titioned into morphological groups. Advances are being
made in using phenotypic data from species descriptions
to develop phylogenetic matrices (Cui et al. 2010, Endara
et al. 2018) and we are testing computer-ready versions of species descriptions as a source of phyloge-
netic data (T. Nakov, pers. comm., University of Arkansas,
2019). Within the morphological group framework, the
project implements visual and nomenclatural cues and a
search function to aid practitioners in reaching a correct
identification. Species pages serve as the core of the project
and are organized in a specific manner.
Visual and nomenclatural cues and search
Clearly, websites offer greater flexibility in the display
of information than books. With, genera and
species can be displayed by name, or by an iconic image,
facilitating recognition based on the shape and size of the
taxon. Genus member species may be filtered by valve
length, stria density, or both, allowing practitioners to nar-
row a search to a smaller number of taxa. also
incorporates composite guide images that direct practition-
ers to the features that diagnose one taxon from all others.
Finally, the Compare feature allows users to make direct,
visual comparisons of similar taxa, as well as taxa that are
often confused in surveys. The Compare feature allows a
side-by-side examination of diatom images at a common
magnification, a feature not possible with books, or other
online floras.
The Genus Considered field communicates anticipated
nomenclatural transfers. For example, Navicula hodgeana
R.M. Patrick & Freese lacks the features of the genus
Navicula Bory(Hamilton & Manoylov 2021) and instead,
appears to be more aligned with the genus Fallacia Stickle
& D.G. Mann in Round et al.Genus Considered field
allows the taxon to be included in both Navicula and
Fallacia genus pages until a formal nomenclatural act is
published. As evolutionary relationships among diatoms
are uncovered (Theriot et al. 2010, Nakov et al. 2014,2015,
Ruck et al. 2016a), nomenclatural changes follow (Ruck
et al. 2016a,b,Raricketal.2017). However, in many
instances, there is a time lag between the publication of
phylogenies and nomenclatural change in the literature.
The Genus Considered field allows a species to be included
within its validly published genus, as well as listed under
the ‘anticipated’ genus. Thus, the site allows the greater
ability for practitioners to follow changing nomenclature.
Furthermore, the Search feature allows users to find a
taxon under nomenclatural synonyms. For example, Luti-
cola goeppertiana (Bleisch) Mann ex Rarick et al. (Rar-
ick 2017) can be searched as its current name, or its
other validly published names (i.e., Navicula goeppertiana 295
(Bleisch) H.L. Smith, Navicula mutica var. goeppertiana
(Bleisch) Grunow).
Species pages
The species page represents the core of the
project, with sections dedicated to particular data formats.
The current, correct, and complete scientific name of the
taxon is included in the Description section, along with
objective, or homotypic, synonyms. In the early develop-
ment of the online flora, we learned that users sometimes
knew a diatom by a name that had been applied incor-
rectly. That experience inspired the creation of a Reported
As field as a way to acknowledge a previous record, even
if a name other than the current name was used. For
example, Kociolek (2011) noted that Thalassiosira lacus-
tris (Grunow) Hasle had been reported as Thalassiosira
bramaputra (Ehrenberg) Håkansson & Locker, a taxon
that had not been verified in North America (Smucker
et al. 2008). If a user enters ‘bramaputra’ in the search
field, the species page for T. lacustris is returned. Thus,
the Reported As field allows a user to search on a name
that may be commonly in use, but which may not be cor-
rect, and still arrive at the species page showing the current,
correct name.
The Description section includes a size series of high-
resolution light micrographs. A minimum of five images
of the taxon illustrates the size range and morphologi-
cal variability from collections in North America, each
with a reference by accession number to public herbar-
ium. Images must be of good resolution, obtained on a
high-quality microscope [minimum of 1.3 numerical aper-
ture (NA) oil immersion objective and 1.3 NA condenser].
Contributors include metadata, including cell dimensions,
herbarium slide number, collection location, and voucher
slide number. A distinct symbol identifies images of a
nomenclatural type (holotype, isotype, lectotype, isolecto-
type, and neotype). Scanning electron microscope images
are included when possible, including the ongoing addi-
tion of images by other practitioners, pending approval of
the original taxon page author.
Historically, as in foundational studies in limnol-
ogy, European (primarily German) authors dominated the
diatom literature and, arguably, continue to do so to the
present day. In the absence of North American floras,
European names were applied to North American species,
often in error. In response to the previous blind appli-
cation of European names, we strictly adhere to a rule
that images and observations included in are
based on North American specimens. Contributors pro-
vide written descriptions of the morphology and provide
accurate dimensions of the taxa they observe and other
verified North American records. An advantage of this
flora is that the taxon dimensions may be updated when
a practitioner documents a wider morphological range.
Species descriptions can expand or become modified to
reflect new insights. Species descriptions include diagnos-
tic features of the taxon, such as features of the striae,
raphe, and valve shape. Contributors include notes on the
specimens illustrated and how they compare to the range
of variation of the taxon in North America. Contributors
also include important nomenclatural history. For example,
species pages for Aulacoseira ambigua (Grunow) Simon-
sen and Aulacoseira granulata (Ehrenberg) Simonsen
includes examples of such nomenclatural notes (Potapova
& English 2010a,b).
A diagnosis, or the features in which each taxon differs
from closely related or similar taxa, is included in num-
bered elements of the Guide feature modelled on visual
keys in popular bird identification guides. The diagnosis
is further expanded in the Compare portion of each page.
The intent is that these sections provide a concise diagnos-
tic treatment of the key characters of each taxon, and those
taxa with which it can be confused. The diagnosis guides
practitioners on distinguishing closely related taxa, such as
‘Species 1 has an oval central area, while Species 2 has
a rectangular central area’. Each diatom Guide includes a
composite image with numbered points that direct the user
to the named features. This feature, one of the most impor-
tant parts of the page, is where the contributor informs the
community on how to distinguish a species from similar,
or often confused, species. The Compare section, another
unique feature of, allows users to view sim-
ilar species at the same magnification to facilitate visual
The Autecology section includes data on the basic
information of the habits of each species. Although it was
not emphasized at the outset of the project, ecological data
are one of the most requested sections by users of the site.
Since 2016, all new pages have included text or images in
this section, and we continue to work to include ecologi-
cal content in the balance of species pages. Additionally,
the Autecology section includes tags that designate partic-
ular features of species such as size, motility, habitat types,
attachment, and distribution. These tags were primarily
conceived as a way to let analysts browse other taxa that
may occur in the same region in lieu of a more complicated
distribution map. Powerful means to combine or concate-
nate attributes may be used for browsing or searching. For
example, a user may wish to construct a query such as ‘I
wish to see taxa that are non-motile, unattached, and occur
in California’. Other websites that are ‘metadata-heavy’,
such as stock photography sites, were the inspiration for
this faceted search. Efforts are being made to enhance these
The Original Description section includes text in the
language of original publication and iconotype, if avail-
able. These original descriptions and illustrations are often
burdensome to locate in journal articles and books, or
are even inaccessible outside of academic libraries and
296 Sarah A. Spaulding et al.
databases. Illustrations of specimens of the nomenclatural
type are especially valuable data and are marked and called
out in image metadata. In some cases, the original descrip-
tion may be ambiguous (particularly for early authors, such
as Ehrenberg and Kützing) and further work would be nec-
essary to establish the identity of the type. In other cases,
the original description may be clear but may not be a con-
vincing match to the North American specimens. Thus,
the Description text may note potential discrepancies for
future revision.
Original species descriptions data are included in to aid in making species diversity information
globally available to people for the purposes of teach-
ing, scholarship, and research. Indeed, the ICN (Turland
et al. 2018) states that effective publication of species
includes widespread distribution. The Citations & Links
section provides references to original descriptions and
other relevant publications related to the taxon. When
available, links to resources such as Index Nominum
Algarum (Silva 2009), Diatombase (Kociolek et al. 2019),
GenBank (Benson et al. 2013), and the Diatom New
Taxon File at the Academy of Natural Sciences (Potapova
et al. 2019b) are included.
Nomenclature, at least as relating to genus and species
names, requires continuous updates and revisions to refine
content, reflect nomenclatural changes, and correct errors
(Vaidya et al. 2018). The Update section is reserved for
changes to a page that would alter the concept of that taxon
(e.g., addition or removal of particular images, change in
size dimensions) or aspect of the name (e.g., transfer from
one genus to another). Each update includes text describing
the reason for the change, the date of the change, and the
person who made the change. Previous versions of the page
are archived and available within the Practitioners section
of the site.
Discussion is built by practitioners, for practitioners. The
project fills a gap in the resources that we, as diatom tax-
onomists, ecologists, and water quality managers, need
in order to do our work. For the advanced practitioner,
each taxon page represents a synthesis of information that
is otherwise time-consuming, or resource-prohibitive, for
an individual to obtain. represents a grow-
ing scientific body of knowledge strengthened by revision,
correction, and updates as science advances. Yet, the refer-
ence has its greatest reach for the general public, providing
answers to basic questions and inviting people to learn
more about microbial life on Earth.
Based on metrics for the audience, the
project is already successful, not only in North America,
but internationally. Data (via Google Analytics) show that
over the two most recent years (June 2018–June 2020),
nearly two million pages were accessed by 226,000 users
Table 1. Data tracked by Google Analytics for 1
June 2018–31 May 2020.
Total number of page views 1,886,000
Number of users (unique computers) 225,600
Number of sessions 424,780
Pages per session 4.4
Average session duration (minutes) 6.1
Table 2. Data tracked by Google
Analytics for 1 June 2018–31 May
Country Users % Users
USA 99,112 44.0
India 16,762 7.4
Canada 12,809 5.7
UK 9138 4.1
China 5978 2.7
Japan 5583 2.5
Australia 5314 2.4
Indonesia 4667 2.1
Philippines 4265 2.0
Mexico 3722 1.7
(i.e., unique computers) (Table 1). The site visitation met-
rics are comparable, or greater, than the visitation of fifteen
major botanical (primarily higher plant) web resources
(Jones et al. 2014). Not only is site-traffic high, but a
core set of users access information with high intensity.
The average time spent on most websites is measured in a
few seconds, while the average time spent on
page is over six minutes, demonstrating that people engage
with the content, i.e., they study it. The site is accessed
most within the United States (44%), as compared to other
countries (Table 2) with California having the greatest
number of users within the United States (Table 3). The
most commonly accessed page is the
page, followed by (Table 4),
indicating broad reach to a public audience.
Much of the site traffic of is by sec-
ondary school and college students, based on feedback
from teachers. As students gain experience, they have
the opportunity to contribute their knowledge, furthering
the growth of Students in the Ecology and
Systematics of Diatoms course at Iowa Lakeside Labora-
tory have contributed over 100 pages since 2011. As a
result, undergraduate and graduate students gain experi-
ence with peer-review and gain a citation for their resumé.
The project serves as a pedagogical tool that integrates stu-
dent involvement; students learn the practice of science
and the dissemination of knowledge. Student created pages
are an important contribution to the project. For exam-
ple, the student page for Gyrosigma acuminatum (Kützing)
Rabenhorst (Chabut 2014) was accessed over 2000 times
in the past two years. 297
Table 3. Data tracked by Google Analyt-
ics for 1 June 2018–31 May 2020.
State Users Pages/session
California 12,446 2.9
Illinois 12,297 1.6
Texas 6224 4.3
Florida 6008 4.3
New York 5135 3.1
Washington 4006 4.5
Virginia 3909 3.0
Pennsylvania 3177 9.9
Ohio 3156 5.3
Massachusetts 3125 2.5
Georgia 2692 5.0
North Carolina 2562 2.5
Michigan 2372 6.6
Colorado 2343 6.0
New Jersey 2199 4.4
Minnesota 1864 5.5
Oregon 1828 3.9
Wisconsin 1519 4.7
Arizona 1316 4.9
Maryland 1312 2.6
Tennessee 1306 3.1
Louisiana 1244 5.8
Indiana 1151 6.8
Connecticut 1107 3.1
Iowa 1107 9.2
Missouri 1013 2.3
Alabama 914 2.4
South Carolina 911 3.0
Utah 850 11.2
Finally, the curation of diatom text, images, and associ-
ated data has led to impacts of beyond its use
as a taxonomic flora. First, the project has led to increased
use of the primary literature by exposing a large audi-
ence to original species descriptions. We, the Editorial
Review Board, have noted increases in requests for orig-
inal publications following the posting of species pages
on Second, the project provides detailed dis-
tribution records of species. For example, the project
facilitated modelling of the hydrologic, climatic, and land-
scape processes that drive the distribution of Didymosphe-
nia geminata (Lyngbye) M. Schmidt (Kumar et al. 2009,
Spaulding 2010b). Third, the project has fostered taxo-
nomic publication. For example, posting of Planothidium
biprorum (M.H. Hohn & Hellerman) Lange-Bertalot led
to the description of a new species, P. incuriatum Wetzel
et al. (Wetzel et al. 2013). The taxon Gomphonema caper-
atum Ponader & Potapova was known under a provisional
laboratory name for many years, but once it was described
(Ponader et al. 2017) and published on,it
was recognized in new regions by additional analysts.
In another instance, the species page for Planothidium
rostratum (Østrup) Lange-Bertalot was found to include
a species that had not been recognized in North Amer-
ica (Wetzel et al. 2019). The new taxon, P. potapovae
Table 4. Data tracked by Google Analytics for 1 June
2018–31 May 2020.
Rank Page Page views
1 /what-are-diatoms 150,360
2 /genera 126,724
3 /home 69,670
4 /morphology 63,766
5 /species 42,718
6 /morphology/centric 34,000
7 /morphology/araphid 31,959
8 /genera/navicula 25,189
9 /morphology/monoraphid 24,598
10 /morphology/symmetric_biraphid 23,264
11 /genera/nitzschia 20,379
12 /morphology/symmetrical_biraphid 20,275
13 /genera/gomphonema 16,169
14 /morphology/nitzschioid 13,086
15 /genera/cymbella 12,818
16 /genera/fragilaria 12,768
17 /genera/achnanthidium 12,752
18 /morphology/asymmetric_biraphid 12,416
19 /genera/aulacoseira 12,368
20 /morphology/asymmetrical_biraphid 11,007
21 /practitioners 10,873
22 /genera/eunotia 9834
23 /genera/pinnularia 9829
24 /genera/cyclotella 9532
25 /glossary 9106
26 /morphology/eunotioid 8761
27 /genera/synedra 8547
28 /genera/surirella 8162
29 /genera/planothidium 8141
30 /genera/encyonema 8015
31 /morphology/epithemioid 7924
32 /genera/sellaphora 7801
33 /genera/cocconeis 7550
34 /morphology/surirelloid 7385
35 /genera/amphora 7132
36 /genera/achnanthes 7112
37 /genera/stephanodiscus 6671
38 /genera/grid 6173
39 /genera/stauroneis 6150
40 /genera/diatoma 6069
41 /genera/epithemia 5991
42 /genera/ulnaria 5986
43 /news/where-do-diatoms-live 5955
44 /about 5942
45 /genera/diploneis 5694
46 /news/what-is-diatomaceous-earth 5580
47 /genera/pseudostaurosira 5497
48 /news/how-big-are-diatoms 5310
49 /genera/staurosira 5208
50 /genera/staurosirella 4875
C.E. Wetzel & Ector, was described from the original P.
rostratum species page. In the process of preparing con-
tent for species pages, issues concerning identification,
nomenclature and systematic position of species prompted
further publications. For example, students participated as
co-authors in publications on nomenclatural changes and
298 Sarah A. Spaulding et al.
species revisions (Spaulding et al. 2010, Rarick et al. 2017,
Edlund et al. 2017, Williams et al. 2021).
Finally, news and project pages serve as public outreach
and broader impacts for the National Science Founda-
tion, National Park Service, U.S. EPA, and USGS funded
efforts, with links to the taxa in each research programme.
The taxa in several of these projects on paleolimnology
and freshwater assessment (Spaulding et al. 2015, Bishop
et al. 2017a,b, Tyree et al. 2020a,b) are supported
by documentation in species pages. conveys
the relevance of diatoms through citizen science, actively
engaging the public in contributing to the project (e.g.,
Edlund 2017).
Challenges and future directions
While now includes over 1000 species pages,
the website has not reached a point of development to be
able to serve as a primary resource for analysts. Many
taxa remain to be documented, including some common
taxa that are frequently encountered. Many of the taxa
included to date are those with relatively few problematic
taxonomic issues. Over the past several years, hundreds
of taxon pages for common taxa have been initiated by
contributors, but work was suspended when complex tax-
onomic issues were uncovered. Thus, we know that these
additional pages require a greater amount of both time and
expertise to complete. Perhaps our biggest challenge is to
better support analysts by expanding the resource. A cur-
rent goal is to expand the platform to better
support analysts and researchers and train the next gen-
eration of taxonomists. Over the past five years funding
has supported contributors’ efforts to research taxa. Efforts
made by 3–5 graduate students or postdoctoral researchers
over the next five years would bring to the
point of including 80% of the taxa encountered in North
American freshwaters.
Moreover, in the light of the climatic and environmen-
tal upheaval of earth’s species diversity and ecological
systems, there is an urgent need for to expand
its reach to a diverse generation of young people, few of
whom have access to microscopes. We regularly receive
inquiries and requests to expand into a global
resource by linking to other freshwater diatom floras and
databases, as well as including marine and fossil taxa.
We need to expand the roles for everyone, including stu-
dents and citizen scientists, across geographic provinces
(Ellwood et al. 2015,2018). Expansion of roles, along
with the expansion of content, requires greater coordi-
nation of resources. While infrastructure is in place that
supports the connection of databases across global hubs
(Meyer et al. 2015), a clear plan and funding are required to
implement those connections. Finally, despite the immense
impact of web content, there is little recognition by
academia of the value of web contributions; the legitimacy
of online curation remains to be established and matched
in accordance with its influence (Rotman et al. 2012, Parr
et al. 2014). As the scientific value of online contribu-
tions becomes more recognized, contributors and editors
should gain institutional recognition for activities such as
site maintenance and editorial oversight of lineages, or
groups, of taxa.
The further design could involve developing the ability
for practitioners to create customized floras. For example,
a user might require smaller floras of taxa from lakes in
the northeastern US, fens in the midwestern US, or Psam-
mothidium Bukhtiyarova & Round species across North
America. Additionally, now that the number of species
pages has surpassed a critical threshold of being required in
task agreements (e.g., U.S. EPA National Lakes Survey),
we have the opportunity to investigate diatom biology
through meta-analyses of the site itself. For example, we
can query not only geographic distributions but also size
distributions of species. For example, the data now allows
comparing the morphological range of species within a
genus, or species that live in the most pristine streams, or
downloading large sets of images for use in artificial intel-
ligence. This opportunity to query allows us to
begin using big morphological data. Are there underlying
evolutionary, physiological, or ecological factors that drive
these different allometric patterns? Using data contained
within the website, we can explore the biogeography of
species on a continental scale, improving the understand-
ing of rates of evolutionary change, stochastic processes
associated with dispersal limitation, and spread of invasive
Technological advances themselves are likely to offer
opportunities for scientific progress. For example, in com-
bination with, data from national lake surveys,
such as U.S. EPA National Lake Survey and National Eco-
logical Observatory Network (, allowed
analysis of species distributions and environmental mod-
elling (Kumar et al. 2009). Additionally, image recognition
software may facilitate automated diatom identification
(Spaulding et al. 2012, Bishop et al. 2017b, Cristóbal
et al. 2020, Kloster et al. 2020), allowing taxonomists
to focus on uncovering biodiversity. Through develop-
ment of associated voucher floras (Tyree et al. 2020a,b)
and improved coordination of analysts, can
streamline workflows and encourage productive outcomes.
As a result, there is potential for understanding diatom bio-
geography with verified data that has not been possible
before. provides a hub for the toolset that
diatomists need to work efficiently. For many groups
of organisms, monitoring is compromised by taxonom-
ically biased efforts (Navarro et al. 2017), a problem
that has been solved for diatoms (Bishop et al. 2017a,
Tyree et al. 2020a,2020b). adapted rapidly
to communicating developments in analysis, taxonomy,
harmonization, and taxonomic certification by hosting
the widely viewed online seminars of the Diatom Web 299
Table 5. Consideration of issues across (1) books and other non-digital literature, (2), and (3) the future of
Issue Books Future of
Audience Narrow range of specialists and
experienced professionals
Wide range – lay public to experienced
Broader public education; enhanced community involvement
through online teaching and discussion
Cost to Audience Very high (US $100-1200) per
No cost; important to keep no cost to
promote fair science
No cost; important to keep no cost to promote fair science
Cost to Public No cost In-kind content by contributors, federal and
academic support
Support from user communities through grants; adoption
by a professional society; or establishment of a non-profit
Access Limited to those with academic
or federal affiliations through
Open access through the internet Expand workshops, courses, and discussions to all
experience levels of audience
Contributors Specialists; experienced
Specialists; experienced taxonomists Increase training for students; continue and expand
participation through Diatom Web Academy workshops
Reviewers Not reviewed; limited editorial
Scientific and editorial standard met through
peer review; reviews are not anonymous
to further responsibility for content
Expansion of review process to include early-career
scientists to review content as part of their training
Advancement of
High at time of publication,
potential decrease in impact
over time
Value increases with each contribution;
updates are timely so that practitioners
can stay informed
itself provides data that advances science; data
are served through queries; functions to drive scientific
inquires; opens new avenues of inquiry; the project
provides a means to continue taxonomic training and
expertise into the future
Content Flexibility Fixed to time of publication Can be updated or corrected with new
Incorporation of displays in response to practitioner need
Display Flexibility Fixed to time of publication Flexible in terms of updates, search,
organized by morphology (text or shape),
filter by size or striae
With advances in uncovering diatom relationships, phylogeny
can become the organizational structure
Number of Taxa Fixed to time of publication Continually added but currently limited by
Expand with support from user communities through grants;
expand through the Society for Freshwater Research
Taxonomic Certification Program
Taxon Comparison "flipping’ between pages of interest Selection fixed by editors Develop further flexible format for practitioners to view taxa
of interest
Aids to Identification Descriptive text, comparison tables Descriptive text, iconic images, guide
images, comparison feature
Users add their own images; access to high-resolution scans
of entire microscope slides
Taxonomic Coverage Limited to geographic region or
taxonomic group, or both
Limited to North America; freshwater Practitioners and funders include 2000–3000 North
American taxa; include worldwide freshwater, distribution;
expand to marine genera and species
300 Sarah A. Spaulding et al.
Academy (
1), an especially valuable role in fostering community and
communication during the global pandemic. In addition,
the project provides an archive of diatom data and infor-
mation in a way that the larger scientific community can
view, verify, and utilize content to infer patterns and pro-
cesses, using statistical and meta-analyses. The activities
supported and promoted by provide a means
for documentation of a chain of inference forming a taxo-
nomic standard of practice. Thus, provides a
structured approach for working with diatoms as data ele-
ments. Next steps should include linkage of images and
voucher floras (Bishop et al. 2017a, Tyree et al. 2020a)to
standardized formats, such as those of the Humboldt Core
for biological inventories (Guralnick et al. 2018).
The project began as a version of an extended elec-
tronic book in the form of Diatoms of the United States.
Over time, the interaction of contributors, content, users,
courses, students, workshops, reviewers, artists, and online
seminars blossomed into something else (Table 5). By way
of these interactions, facilitated by strong a visual for-
mat, the project fosters human relationships and allows
new means for the international diatom community to learn
from one another. We think that this ‘something else’ can
be expressed as a type of relational ecology, and that there
is a strong link among human relationships, the content on
the site, and the engagement of a community. Indeed, it is
the emergence of human connections that adds value to the
endeavour of This relational ecology encom-
passes a broad swath of research objectives and social
behaviour. The establishment of an emergent intelligence
opens doors to continued conversations and to interac-
tions that ‘poke’ at science to further its advancement. The
project needs to remain nimble enough to take advantage
of new technologies to address issues, including the human
interplay between the parts and the whole of the project. It
may be that the original core of the project, the species and
genus pages, are actually the least of Across
the various pages, there is now enough data to provide
science outcomes from querying the data. is
now, in itself, a source of data.
David Lubinski developed the original concepts, structure, and
technical design. Over a decade’s worth of students in the Ecol-
ogy and Systematics of Diatoms course at Iowa Lakeside Lab-
oratory served to stimulate the teaching aspects of the project.
The authors appreciate the ongoing support of Jane Shuttle-
worth and Friends of Lakeside Lab. Past members of Editorial
Review Board (Sam Rushforth, Rex Lowe, and Pat Kociolek)
were instrumental in advancing the foundation of the web flora.
Frequent, dedicated, undercover contributors (Loren Bahls, Rob
Kimmich, Rosalina Stancheva, and Ionel Ciugulea) work quietly
and productively. The authors thank anonymous reviewers who
provided both feedback and new ideas that greatly improved the
manuscript. Students at the University of Colorado (Alec Camp,
Tanya Hannis, and Janey Le) cleaned up endless files. The project
could not have been completed without Diane McKnight, Mered-
ith Tyree, Nicholas Schulte, David Burge, Teofil Nakov, Mitchell
Kimbrough, Nicolas Bottari, and Michiko Swiggs. Eugene F. Sto-
ermer provided the inspiration to take on a seemingly impossible
The views expressed in this article are those of the authors
and do not necessarily represent the views or the policies of the
U.S. Environmental Protection Agency. Any use of trade, firm,
or product names is for descriptive purposes only and does not
imply endorsement by the U.S. Government.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Funding from the U.S. EPA Office of Water and Office of Sci-
ence and Technology supported the direct development of content
by contributors, as well as through formal taxonomic work-
shops. The U.S. Geological Survey under Cooperative Agree-
ment #G15AC00104 with the Institute of Arctic and Alpine
Research (INSTAAR) at the University of Colorado supported
web design and development.
Sarah A. Spaulding
Marina G. Potapova
Ian W. Bishop
Sylvia S. Lee
Paula C. Furey
Mark B. Edlund
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... A few studies are available on the use of sponges as a proxy in paleoenvironmental studies (Docio et al., 2021), taxonomy, geographic distribution, and critical review of the fossil freshwater sponges (Pronzato et al., 2017;Łukowiak, 2020), and more recently the terminology of sponge spicules (Łukowiak et al., 2022). This stands in contrast to those available for other siliceous microfossils such as diatoms and phytoliths (e.g., Neumann et al., 2019;Spaulding et al., 2021). ...
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Freshwater sponges (Porifera: Spongillida) are sessile invertebrates with skeletons composed of siliceous elements termed spicules. Sponge spicules (megascleres, microscleres, and gemmuloscleres) are characterized by widely varying sizes and shapes. These spicules are well-preserved in lacustrine, wetland, and riverine sediments and hold significant ecological and limnological information that can be applied as diagnostic tools in reconstructions of Quaternary environments. However, problems with taxonomy and the absence of systematic guidelines and standards of identification represent major challenges to utilizing freshwater sponges as a paleo-proxy. Here, we present a well-illustrated extraction protocol and morphological guide to the Neotropical freshwater sponge fauna. This guide is intended to introduce researchers and students to the study of freshwater sponges and their use as a diagnostic tool in paleoecology and paleolimnology.
... A few studies on biofilm are limited to estuaries [9,10], but studies on the productivity of the river biofilm, especially on benthic diatoms, are almost missing (see [11]). Diatoms, a major component of phytobenthos in rivers and the most diverse group of protists, are unicellular algae with silica cell walls, responsible for 20% of O 2 production, and are important indicators of water quality [12]. As primary producers, their growth depends on nutrient concentrations and light, contributing immensely to primary biofilm productivity, an important ecosystem function. ...
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The biodiversity–ecosystem functioning (BEF) relationship has been studied extensively for the past 30 years, mainly in terrestrial plant ecosystems using experimental approaches. Field studies in aquatic systems are scarce, and considering primary producers, they mainly focus on phytoplankton assemblages, whereas benthic diatoms in rivers are considerably understudied in this regard. We performed a field study across nine rivers in Greece, and we coupled the observed field results with model simulations. We tested the hypothesis that the diversity–biomass (as a surrogate of ecosystem functioning) relationship in benthic diatoms would be affected by abiotic factors and would be time-dependent due to the highly dynamic nature of rivers. Indeed, geology played an important role in the form of the BEF relationship that was positive in siliceous and absent in calcareous substrates. Geology was responsible for nutrient concentrations, which, in turn, were responsible for the dominance of specific functional traits. Furthermore, model simulations showed the time dependence of the BEF form, as less mature assemblages tend to present a positive BEF. This was the first large-scale field study on the BEF relationship of benthic diatom assemblages, offering useful insights into the function and diversity of these overlooked ecosystems and assemblages.
... The classification of diatoms is based on the system by Round F.E., Crawford R.M., Mann D.G. [70] with additions from later publications [71,72], as well as catalogs of genera and species of diatoms published in print and on the Internet: Fourtanier, Kociolek, [73], Kusber, Jahn, [74], Morphbank, [75], Diatoms of North America [76], AlgaeBase, [77]. ...
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This paper presents the diatom and palynomorph data from a sediment trap deployed in the northern part of the East Barents Sea for an annual cycle from August 2017 to August 2018. The average monthly fluxes of diatoms and dinoflagellate cysts in the photic layer of the northeastern part of the Barents Sea varies from 10.4 × 103 to 640.8 × 103 valves m−2 day−1 and from 0.3 × 103 to 90.0 × 103 cysts m−2 day−1, respectively. Their fluxes are related to the low irradiance of the photic layer during the sea-ice cover period, dominance of southward currents, modern climate, and nepheloid layer conditions. Based on redundancy analysis of the relationship between the fluxes of diatoms and dinoflagellate cysts and organic carbon fluxes, sea-ice covers, and the seasonal cycle of light availability we determined the following. First, sea-ice-associated diatoms and dinocysts are exported to the sediment trap from the melting sea ice with a two-week delay. Second, the appearance of freshwater diatoms and green algae in the sinking material accumulating from March 2018 to July 2018 is also related to the melting of sea ice. And third, the presence of Coscinodiscus radiatus, C. perforatus, Shionodiscus oestrupii and Operculodinium centrocarpum in the diatoms and dinocysts species composition throughout the year indicates the advection of Atlantic waters into the Barents Sea up to 80° N.
... Diatoms are photosynthesizing microalgae with cell walls of transparent opaline silica containing compounds such as pigments, sterols, and fatty acids [3]. Currently, the most commercially important diatom species is Dunaliella salina. ...
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Marine microalgae, diatoms, are considered a source of a wide range of high-value compounds, and numerous studies indicate their biotechnological potential in the food and feed industry, cosmetic industry, nanotechnology, pharmaceutical industry, biodiesel production, fertilizers , and wastewater treatment. The aim of this study was to compare the growth, chemical profiles , and antioxidant activity of the diatom Skeletonema grevillei cultivated in a bioreactor and an incubation-shaking cabinet at different growth phases (after 192 and 312 h). Growth was monitored by evaluating cell density with the Sedgewick Rafter chamber, and the collected biomass was extracted with 70% ethanol assisted by ultrasound. Extracts were evaporated to dryness and compounds were identified in derivatized form by gas chromatography and mass spectrometry (GC-MS) analysis, while antioxidant capacity was evaluated by DPPH and ORAC. Significantly faster growth was observed in the bioreactor than in the incubation-shaking cabinet. Oleamide, palmitelaidic acid, glycerol monostearate, myristic acid, cholesterol, eicosapentaenoic acid, 1-monopalmitin, and 24-methylene cholesterol were identified as the major compounds in both systems. Among them, oleamide was the dominant compound in both systems. It is also shown that prolonging the cultivation period had a direct effect on increasing the extract yield. The highest DPPH inhibition (11.4 ± 1%) and ORAC values (93.3 ± 8.4 mM TE) were obtained for the S. grevillei extract recovered from the bioreactor after 312 h. The obtained results contribute to the possibility of using S. grevillei for various biotechnological applications in the future.
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Florida’s coastal salt marshes are vulnerable to both direct and indirect human impacts, including climate change and consequent sea-level rise. For a salt marsh to survive in the face of ongoing sea-level rise, organic and/or mineral sediment must accumulate at a rate equal to or faster than that of sea-level increase. We explored the effects of Late Holocene sea-level variations in the Suwannee River Estuary within the Big Bend region of Florida (USA). We conducted a paleoenvironmental study of a sediment core collected from a salt marsh near Cedar Key, on Florida’s Gulf of Mexico coast. The core spans the last ~ 320 years of sediment accumulation. Carbon isotope (δ13C) data and diatom assemblages indicate the salt marsh was relatively stable during that time frame and was dominated by C3 vegetation, likely Juncus roemerianus, but experienced moderate variations in salinity that likely reflect changes in sea-level, with an increase in salinity and marine incursions between ~ 1850 and 1930 CE. Whereas small vertical changes in sea-level have the potential to inundate large areas of the low-gradient salt marsh, as observed during the interval ~ 1850–1930 CE, the salt-marsh vegetation recovered quickly after 1930 CE, indicating that the rate of aggradation and vegetation growth kept pace with the rate of sea-level rise. Despite the apparent resiliency of Big Bend salt marshes and likelihood that they will persist through accretion and migration, we expect to see major changes in salt-marsh ecology if rates of sea-level rise continue to accelerate.
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Periphyton assemblages from the nearshore environment of the west (California) side of Lake Tahoe, were analyzed to determine their taxonomic composition and community structure across habitats and seasons. Lake Tahoe is the second deepest lake in the US and an iconic oligotrophic subalpine lake with remarkable transparency. It has experienced offshore cultural eutrophication since the 1960s with observations of nuisance nearshore algal growth since the mid 2000s attributed to anthropogenic stressors. Samplings from November 2019–September 2020 provide useful snapshots against which older monitoring may be contextualized. A voucher flora, complete with descriptions, photo-documentation and referencing to species concepts employed, was created as a method of providing reproducible identification and enumeration of algal species, and more seamless reconciliation of detailed taxonomic data with future monitoring projects. The eulittoral zone (0–2 m) is seasonally dominated by elongate araphid (Synedra, Ulnaria) and stalked or entubed diatoms (Gomphonema, Cymbella, Encyonema). The sublittoral zone (>2 m) is dominated by a nitrogen-fixing Epithemia-cyanobacteria assemblage with less seasonal changes in dominance and composition that expanded to impinge on the 2 m depths of the eulittoral zone in the Fall. Sublittoral epipsammic samples, despite their proximity to rocks, had a very distinct diatom composition and high species dominance, similar to what was seen in the Fall eulittoral samples, with high numbers of Staurosirella chains and small biraphid diatoms. The deeper samples at 30 and 50 m contained high numbers of live Epithemia, and indicate a thriving sublittoral assemblage at these greater depths, but with less biomass. The 2019–20 data show many of the same diatom taxa observed in the 1970’s and 1980’s but with changes in species dominance. Notably, there was less of the green alga Mougeotia, when compared to the 1970’s data, and a higher dominance by nitrogen fixing Epithemia in the sublittoral zone, persisting year-round. These new data show roughly double the algal species biodiversity that had been documented previously in the Lake Tahoe nearshore, and is largely attributed to the methods employed. Adopting these new methods in future monitoring efforts should improve harmonization of taxonomic data and help advance our knowledge of the contributions to nearshore cultural eutrophication.
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Siliceous diatom frustules present a huge variety of shapes and nanometric pore patterns. A better understanding of the light modulation by these frustules is required to determine whether or not they might have photobiological roles besides their possible utilization as building blocks in photonic applications. In this study, we propose a novel approach for analyzing the near-field light modulation by small pennate diatom frustules, utilizing the frustule of Gomphonema parvulum as a model. Numerical analysis was carried out for the wave propagation across selected 2D cross-sections in a statistically representative 3D model for the valve based on the finite element frequency domain method. The influences of light wavelength (vacuum wavelengths from 300 to 800 nm) and refractive index changes, as well as structural parameters, on the light modulation were investigated and compared to theoretical predictions when possible. The results showed complex interference patterns resulting from the overlay of different optical phenomena, which can be explained by the presence of a few integrated optical components in the valve. Moreover, studies on the complete frustule in an aqueous medium allow the discussion of its possible photobiological relevance. Furthermore, our results may enable the simple screening of unstudied pennate frustules for photonic applications.
In drowning cases, diatoms provide an insight into ante-mortem and post-mortem evidence as well as aid in determining the geographical location. Diatoms are unicellular aquatic organisms that represent a major taxonomic division of the phytoplankton. The diversity of these diatoms depends on the geographical and environmental conditions as well as on the physico-chemical properties of the habitat. Hence, studying the diversity of diatoms in different water bodies in the Gujarat region will generate a diatomological map of the water bodies, which would assist in forensic analysis. In the present study, 100 water samples were collected from various water bodies, viz. rivers, lakes, ponds, etc., across 33 districts of Gujarat state, divided into 5 geographical regions (Saurashtra, Kutch, North, Central, and South). Identification of the diatoms was carried out by trinocular microscopic techniques. Physico-chemical parameters like pH, temperature, total dissolved solids (TDS), and electrical conductivity (EC) were also analyzed. Heavy metal concentrations were determined using Inductively Coupled Plasma-Mass Spectrometry (ICP-MS). The diversity analysis reveals that each body of water in a different region has its own characteristics of diatoms. The physico-chemical parameters affect the diversity of diatoms by increasing their growth, but higher loads of heavy metals may affect the diatoms by reducing their growth and biochemical compositions. In conclusion, the present study provides an insight into understanding the regional patterns of diatom diversity and formulates reference conditions in these and other water bodies of this region.
Lakes in discontinuous permafrost peatlands are on the front lines of climate change, sensitive to even modest increases in air temperature. The aim of this study was to provide the first limnological characterization of shallow (∼1-2 m depth) lakes in the Scotty Creek basin (Northwest Territories, Canada), a field site of circumpolar significance due to the existence of long-term ecohydrological monitoring going back decades. We use this as a foundation from which to advance our process-based understanding of the potential drivers of lake ecosystem change. Our results showed that dissolved organic carbon (DOC) and lake color were not correlated, a pattern that appears to be an important driver of diatom (siliceous single-celled algae) assemblages in these lakes. Diatoms in the study lakes tended to fall into one of two assemblage clusters. One cluster, comprised of small benthic Fragilariaceae and small Navicula species (sensu lato), was found associated with higher lake color. The second cluster, comprised of Encyonopsis and large Navicula species, was found associated with high DOC, lower color, and the presence of a benthic moss mat. From this, we suggest that DOC quality is a primary control on lake ecology in this region for its role in controlling light penetration to the lake bottom. We hypothesized that the prevalence of nearshore fens and collapse scar wetlands would be important drivers of DOC, but this was not supported in the 9 study lakes for which we had available data to map shoreline features.
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Algal communities act as sensitive indicators of past and present climate effects on northern lakes, but their responses can vary considerably between ecosystems. Functional trait-based approaches may help us better understand the nature of the diverse biotic responses and their underlying ecosystem changes. We explored patterns in diatom (Bacillariophyceae) growth forms and species composition during the Neoglacial in two shallow lakes typical of subarctic regions, including a dark-colored woodland lake and a clear tundra lake. Sediment carbon and nitrogen elemental and isotope biogeochemistry and spectral indices were used to track broadscale changes in lake productivity, the inflow of organic carbon from land, and benthic substratum over the past three millennia. The biogeochemical indices tracked declines in land-lake connectivity as well as lake-water and sediment organic enrichment above and below the subarctic treeline driven by Neoglacial cooling. This broadscale environmental transition was intercepted by periods of elevated primary production associated with transient Neoglacial warm anomalies and, in particular, the twentieth century warming. Although the Neoglacial development of the lakes showed conspicuous similarities, diatom functional and taxonomic responses were not uniform between the lakes pointing to intrinsic differences in the development of benthic habitats and underwater-light regimes. Many of the observed biotic shifts aligned with expectations based on earlier research linking diatom functional traits to changing light and organic levels but the results also point to further research needs, particularly to better differentiate the individual and interactive effects of substratum and light. Despite distinct anthropogenic imprints in the biogeochemical record, the scale of human impact on the lakes’ biota has not, as yet, been profound, but the changes are nonetheless clear when compared to the previous three millennia of natural lake development.
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Deep convolutional neural networks are emerging as the state of the art method for supervised classification of images also in the context of taxonomic identification. Different morphologies and imaging technologies applied across organismal groups lead to highly specific image domains, which need customization of deep learning solutions. Here we provide an example using deep convolutional neural networks (CNNs) for taxonomic identification of the morphologically diverse microalgal group of diatoms. Using a combination of high-resolution slide scanning microscopy, web-based collaborative image annotation and diatom-tailored image analysis, we assembled a diatom image database from two Southern Ocean expeditions. We use these data to investigate the effect of CNN architecture, background masking, data set size and possible concept drift upon image classification performance. Surprisingly, VGG16, a relatively old network architecture, showed the best performance and generalizing ability on our images. Different from a previous study, we found that background masking slightly improved performance. In general, training only a classifier on top of convolutional layers pre-trained on extensive, but not domain-specific image data showed surprisingly high performance (F1 scores around 97%) with already relatively few (100–300) examples per class, indicating that domain adaptation to a novel taxonomic group can be feasible with a limited investment of effort.
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Although opening up of research is considered an appropriate and trend-setting model for future scientific communication, it can still be difficult to put open science into practice. How open and transparent can a scientific work be? This article investigates the potential to make all information and the whole work process of a qualification project such as a doctoral thesis comprehensively and freely accessible on the internet with an open free license both in the final form and completely traceable in development. The answer to the initial question, the self-experiment and the associated demand for openness, posed several challenges for a doctoral student, the institution, and the examination regulations, which are still based on the publication of an individually written and completed work that cannot be viewed by the public during the creation process. In the case of data and other documents, publication is usually not planned even after completion. This state of affairs in the use of open science in the humanities will be compared with open science best practices in the physical sciences. The reasons and influencing factors for open developments in science and research are presented, empirically and experimentally tested in the development of the first completely open humanities-based PhD thesis. The results of this two-part study show that it is possible to publish everything related to the doctoral study, qualification, and research process as soon as possible, as comprehensively as possible, and under an open license.
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Inconsistency in taxonomic identification and analyst bias impede the effective use of diatom data in regional and national stream and lake surveys. In this study, we evaluated the effect of existing protocols and a revised protocol on the precision of diatom species counts. The revised protocol adjusts four elements of sample preparation, taxon identification and enumeration, and quality control (QC). We used six independent data sets to assess the effect of the adjustments on analytical outcomes. The first data set was produced by three laboratories with a total of five analysts following established protocols (Charles et al., Protocols for the analysis of algal samples collected as part of the U.S. Geological Survey National Water‐Quality Assessment, 2002) or their slight variations. The remaining data sets were produced by one to three laboratories with a total of two to three analysts following a revised protocol. The revised protocol included the following modifications: (1) development of coordinated precount voucher floras based on morphological operational taxonomic units, (2) random assignment of samples to analysts, (3) postcount identification and documentation of taxa (as opposed to an approach in which analysts assign names while they enumerate), and (4) increased use of QC samples. The revised protocol reduced taxonomic bias, as measured by reduction in analyst signal, and improved similarity among QC samples. Reduced taxonomic bias improves the performance of biological assessments, facilitates transparency across studies, and refines estimates of diatom species distributions.
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For more than two centuries, biodiversity collections have served as the foundation for scientific investigation of and education about life on Earth (Melber and Abraham 2002, Cook et al. 2014, Funk 2018). The collections that have been assembled in the past and continue to grow today are a cornerstone of our national heritage that have been treated as such since the founding of the United States (e.g., Jefferson 1799, Goode 1901a, 1901b, Meisel 1926). A diverse array of institutions throughout the United States, from museums and botanical gardens to universities and government agencies, maintain our biodiversity collections as part of their research and education missions. Collectively, these institutions and their staff are stewards for at least 1 billion biodiversity specimens that include such diverse objects as dinosaur bones, pressed plants, dried mushrooms, fish preserved in alcohol, pinned insects, articulated skeletons, eggshells, and microscopic pollen grains. In turn, these collections are a premier resource for exploring life, its forms, interactions, and functions, across evolutionary, temporal, and spatial scales (Bebber et al. 2010, Monfils et al. 2017, Schindel and Cook 2018). Biodiversity collections have historically consisted of physical objects and the infrastructure to support those objects (Bradley et al. 2014). However, the last two decades have witnessed a remarkable wave of digitization that has reshaped the collections paradigm to include digital data and infrastructure (Nelson and Ellis 2018), opening vast new areas for integrative biological research (e.g., a single plant specimen mounted on an herbarium sheet may be analyzed in multitude ways to yield data on flower morphology, DNA for applications from systematic studies to genome sequences, and isotopes for analyses of nitrogen to understand the mechanisms of phenology in relation to nitrogen uptake). In the United States, investment by the federal government through the National Science Foundation's (NSF) Advancing Digitization of Biodiversity Collections (ADBC) program has facilitated the digitization of approximately 62 million US biodiversity specimens since 2011 through 24 thematic collection networks connecting over 700 collections. These networks have helped to develop a collaborative infrastructure connecting specimen data, human resources, research, and education among institutions. The ADBC program has also provided support to iDigBio (the Integrated Digitized Biocollections), which is the central coordinating unit for the digitization effort. The final ADBC grants will be awarded in 2021. During the last several years, the Biodiversity Collections Network has led an effort to gather input from primary stakeholder communities regarding future directions for collections and their use in research and education. The effort culminated in a workshop held from 30 October through 1 November 2018 at Oak Spring Garden in Upperville, Virginia, during which a strategy was developed to maximize the value of collections for future research and education that builds on and leverages the accomplishments of the ADBC program. The strategy that was informed by stakeholders, refined by workshop participants, and vetted through public comment from scientific community is presented in the present article.
While describing the species Tetracyclus hinziae I. Bishop & Spaulding (2015, p. 200), it was noticed that the basionym and type specimens of the similar species Tetracyclus rupestre was unclear. This short note addresses those concerns.
Environmental programs in the United States face technical challenges that inhibit the ability to use diatoms in water quality monitoring and assessment projects. Specifically, inconsistent taxonomy can obscure diatom responses to environmental variables. Problems are the result of (1) limited access to a common set of taxonomic references, especially those that are geographically relevant, (2) inefficient enumeration protocols, (3) lack of complete and transparent documentation of taxa, and (4) limited opportunities for continued education, training, and knowledge sharing. However, robust resources and practices are available to improve diatom data quality and interpretation. Several resources improve diatom data quality, including a publicly accessible taxonomic reference ( and recommended practices. These practices include adoption of the voucher floras, random sample assignment, replicate microscope slides, and improved quality control. Finally, the Society for Freshwater Science Diatom Taxonomic Certification Committee is developing educational materials and certification exams to support practitioner training and to increase the diatom research knowledge base. The resources and practices in this article are broadly applicable to improving basic and applied research on diatoms worldwide.
Modern and fossil populations of a Stephanodiscus Ehrenberg species from June Lake, California (USA) were analysed using light and scanning electron microscopy (SEM). Stephanodiscus valves were a major constituent of almost all analysed samples, often dominating fossil assemblages dating back several thousand years. The most commonly observed Stephanodiscus specimen in the samples bore a striking resemblance to the extinct Late Pliocene species Stephanodiscus klamathensis, particularly under light microscopy. The population size range, ultrastructure, and other defining characteristics closely matched published information on S. klamathensis. However, under SEM, internal views of the specimens from June Lake showed an important difference; specimens lacked valve face fultoportulae, whereas S. klamathensis is characterized by the presence of two valve face fultoportulae, each with three satellite pores near the centre of the valve. Additional differences in valve size range, absence of fultoportulae on the valve face, and the fact that S. klamathensis is an extinct species (observed in diatomites deposited from Late Pliocene to Pleistocene) with no closely related living relatives, necessitates describing this Stephanodiscus as a new species. To date, Stephanodiscus coruscus has been observed only in June Lake, California; most Stephanodiscus that share strong morphological similarities to this species have only been observed in ancient fossil diatomites. Thus, Stephanodiscus coruscus Jeff. R. Stone, Edlund & Streib sp. nov. is not only a new species but also provides a rare glimpse into the likely types of environments that S. klamathensis and other similar ancient Stephanodiscus may have inhabited in the late Pliocene. Character variations between S. coruscus and S. klamathensis reveal potential patterns of evolution in freshwater lineages, such as character loss, over time.
High-resolution images of phytoplankton cells such as diatoms or desmids, which are useful for monitoring water quality, can now be provided by digital microscopes, facilitating the automated analysis and identification of specimens. Conventional approaches are based on optical microscopy; however, manual image analysis is impractical due to the huge diversity of this group of microalgae and its great morphological plasticity. As such, there is a need for automated recognition techniques for diagnostic tools (e.g. environmental monitoring networks, early warning systems) to improve the management of water resources and decision-making processes. Describing the entire workflow of a bioindicator system, from capture, analysis and identification to the determination of quality indices, this book provides insights into the current state-of-the-art in automatic identification systems in microscopy.