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Diatoms.org: Supporting taxonomists, connecting communities
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. Diatoms.org 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 diatoms.org , document key elements of the project, examine ongoing challenges and consider the unexpected emergent properties, including the value of diatoms.org 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 diatoms.org is in a key position to serve as a hub of training and continuity for the study of diatom biodiversity and aquatic conditions.
Morphology and evolutionary significance of Adoneis pacifica gen. et sp. Nov. (Fragilariaceae, Bacillariophyta), a marine araphid diatom from Chile
A new marine diatom genus and species, Adoneis pacifica G.W. Andrews and P. Rivera, has been identified in Chilean coastal waters. This taxon shows obvious affinities to the genera Rhaphoneis and Delphineis , but cannot be classified in either, as they are currently construed. Adoneis pacifica resembles Rhaphoneis in outline and to some degree in the pseudocelli, whereas it resembles Delphineis in the structure of the vela and the positioning of the apical rimoportulae. However, distinctive characters of this new monotypic genus are: (1) the usual positioning of a single rimoportula near the centre of each lateral margin of the valve, and (2) the occurrence of well organized apical pore fields (pseudocelli), in which the pores are much smaller than elsewhere on the valve. These appear to be primitive traits for the araphid diatom family Fragilariaceae, and they suggest that Adoneis pacifica may be a conservative species important in the study of the evolution of the family.
The middle Eocene araphid diatom Rhaphoneis atlantica sp. Nov.: morphology and evolutionary significance
A middle Eocene deposit near the base of the continental slope 205 km east of Rehoboth Beach, Delaware, contains an assemblage of abundant diatoms, including a species herein described as Rhaphoneis atlantica. This species is substantially older than the better known species of Rhaphoneis of Miocene and younger age, and it shows morphological features that appear to be primitive for the genus. Rhaphoneis atlantica provides clues to the evolutionary history of the genus Rhaphoneis as well as other genera in the araphid subfamily Fragilarioideae.
Cymbella langii, a new miocene diatom from the Espanola area, Rio Arriba county, New Mexico, U.S.A
A distinctive new fossil freshwater diatom species, Cymbella langii McLaughlin & Andrews, is described from a diatomaceous earth deposit in the Chamita Formation of the Santa Fe Group near Espaiiola, central New Mexico. This deposit is dated by K-Ar and mammalian biostratigraphy as Hemphillian or late Miocene in age.
Late Quaternary paleoceanography of the Pervenets Canyon area of the Bering Sea: Evidence from the diatom flora
Sediments from three gravity cores from an east-west shelf-to-slope transect along the axis of Pervenets Canyon in the northern Navarin basin, Bering Sea were analyzed for diatoms. The diatom floras present in the cores were divided into four assemblages following Sancetta (1981). The Bering Basin (deep water open ocean) and Sea Ice (ice cover at least six months per year) Assemblages were dominant in each core. The taxa that comprise the Bering Shelf Assemblage (continental shelf) indicate that downslope transport plays only a minor part in the development of the thanatocenoses. The presence (up to 10% of the total valve count) of the Productivity Assemblage, which consists mainly of poorly silicified, easily dissolved taxa, indicates that nutrient flux is relatively high in the region. Several taxa can be used as proxy indicators for specific water masses. Neodenticula seminae (Simonsen & Kanaya) Akiba & Yanagisawa is indicative of Holocene open marine (deep water) conditions. Nitzschia cylindra (Grunow) Hasle and N. grunowii Hasle are both associated with sea ice and are thought to indicate late Pleistocene conditions. The relative downcore abundance of these taxa was used to approximate the Pleistocene- Holocene boundary (recognized in Core 80–65 at a depth of about 75 cm).
Comparative ultrastructure of two closely related thalassiosira species: Thalassiosira vulnifica (gombos) fenner and T. fasciculata Harwood et Maruyama
The distinctive morphology and relatively short geological range (3.25 to 2.5 Ma) of Thalassiosira vulniflca (Gombos) Fenner make it especially useful for Pliocene biostratigraphic studies in the Antarctic region. Thalassiosira fasciculata Harwood et Maruyama has a geological range (4.5 to 0.75 Ma) that overlaps that of T. vulnifica and it resembles this taxon in possessing prominent fultoportulae on the valve face, strongly fasciculated areolae, and distinctive marginal fultoportulae. However, the greater spacing between rows of areolae and the larger distinctive fultoportulae present in T. vulnifica clearly separate it from T. fasciculata. The importance of accurate identification is discussed as it relates to ongoing Antarctic glacial sediment studies.
Endictya hendeyi sp. nov., a new coastal diatom species from North America
Endictya hendeyi E. Hemphill-Haley sp. nov. is described from Recent and Quaternary, estuarine and marine deposits along the west coast of the United States. This taxon is distinguished by its 1) consistently small valves; 2) areolae of uniform size on the valve face in linear tangential rows; 3) prominent, external spatulate extensions of the rimoportulae at the valve face/mantle junction; 4) externally projecting hyaline rim or flange at the interior edge of the mantle; and 5) discontinuous pattern of pores on the basal siliceous layer. The new species is compared to the generitype, E. oceanica Ehrenberg, as well as E. minor A. Schmidt and E. margaritifera A. Mann.
Taxonomy and distribution of the genus Muelleria frenguelli
Navicula gibbula Cleve and its allies have a number of morphological characters which are visible under the light microscope and distinguish them from taxa included in Navicula Bory sensu stricto. These include proximal raphe ends which are sharply and unilaterally hooked and often extend beyond the central area, as well as two apparently thickened longitudinal ribs which extend the length of the valve on either side of the raphe. With the use of the SEM additional well-defined characters of the N. gibbula complex become apparent. Distal raphe ends are bifurcate and the valve face and mantle possess bipartite walls similar to those in Neidium Pfitzer. Furthermore, the apparently thickened longitudinal ribs are actually hollow canals, a feature reminiscent of the longitudinal canals of Diploneis Ehrenberg. Characters of the group are particularly well-defined and distinct from those of other genera, justifying separation from Navicula . Based on the valve morphology of N. gibbula and all other members of the section Naviculae fistulatae McCall, we separate these taxa from Navicula and resurrect the genus Muelleria Frenguelli to include them.
Planktonic marine diatom record of the past 18 m.y.: Appearances and extinctions in the pacific and southern oceans
Recently published diatom biochronologies provide accurate (to 0.1 m . y .) determination of the ages of appearances and disappearances of planktonic diatoms during the past 18 m . y . in the equatorial Pacific , North Pacific , and Southern Ocean . Comparisons of these records reveal the age of evolutionary appearance and extinction of species and their region of origin. Extinct planktonic diatom species have a mean longevity of 3.4 ± 2.8 m . y . (SD, n = 53) in the equatorial Pacific , 2.5 ± 2.1 m . y . (n = 52) in the North Pacific , and 2.9 ± 2.3 m . y . (n = 38) in the Southern Ocean . The relatively large standard deviations are likely due to the inclusion of taxa that probably could be subdivided into two or more species. In the equatorial Pacific , evolutionary turnover of diatom species was relatively high between 18 .0 and 6.0 Ma compared with the period after 6.0 Ma, presumably reflecting changing oceanic circulation and evolving water masses. In the North Pacific , evolutionary turnover speaked between 10.0 and 4.5 Ma, with increasing high-latitude cooling and enhanced provincialism. In the Southern Ocean , evolutionary turnover of endemic diatoms was greatest between 5.0 and 1.6 Ma, which provides evidence for the strong provincial character of Pliocene diatom assemblages. Taken as a whole, oceanic diatom assemblages became increasingly provincial in character during the late Miocene and Pliocene, as pole-to-equator thermal gradients increased and oceanic frontal systems were strengthened.
Morphology, ecology and biogeography of Stauroneis pachycephala P.T. Cleve (Bacillariophyta) and its transfer to the genus Envekadea
Stauroneis pachycephala was described in 1881 from the Baakens River, Port Elizabeth, South Africa. Recently, it was found during surveys of the MacKenzie River (Victoria, Australia), the Florida Everglades (USA) and coastal marshes of Louisiana (USA). The morphology, ecology and geographic distribution of this species are described in this article. This naviculoid species is characterised by lanceolate valves with a gibbous centre, a sigmoid raphe, an axial area narrowing toward the valve ends, and capitate valve apices. The central area is a distinct stauros that is slightly widened near the valve margin. The raphe is straight and filiform, and the terminal raphe fissures are strongly deflected in opposite directions. Striae are fine and radiate in the middle of the valve, becoming parallel and eventually convergent toward the valve ends. The external surface of the valves and copulae is smooth and lacks ornamentation. We also examined the type material of S. pachycephala . Our observations show this species has morphological characteristics that fit within the genus Envekadea. Therefore, the transfer of S. pachycephala to Envekadea is proposed and a lectotype is designated.
Relationships between diatoms and tidal environments in Oregon and Washington, USA
A new regional dataset comprising 425 intertidal diatom taxa from 175 samples from 11 ecologically diverse Oregon and Washington estuaries illustrates the importance of compiling a large modern dataset from a range of sites. Cluster analyses and detrended correspondence analysis of the diatom assemblages identify distinct vertical zones within supratidal, intertidal and subtidal environments at six of the 11 study sites, but the abundance of some of the most common species varies widely among and within sites. Canonical correspondence analysis of the regional dataset shows relationships between diatom species and tidal exposure, salinity and substratum (grain size and organic content). Correspondence analyses of local datasets show higher values of explained variation than the analysis of the combined regional dataset. Our results emphasize that studies of the autecology of diatom species require many samples from a range of modern environments to adequately characterize species–environment relationships.
Fossilized diatoms of siliceous hydrothermal deposits in Yellowstone National Park, USA
The study of eukaryotic extremophiles is relatively novel, and, therefore, documentation of the structure and function of micro-organisms in continental hydrothermal systems globally is limited. In this study, we investigate fossil diatoms in siliceous hydrothermal deposits of the Upper Geyser and Yellowstone Lake hydrothermal basins in Yellowstone National Park, and utilize preserved diatom assemblages to infer local environmental conditions. Siliceous sinter from both the Upper Geyser Basin and Yellowstone Lake contains evidence of in-situ diatom growth within these environments. At Upper Geyser Basin, the assemblage consisted of species that could grow on moist siliceous sinter and was dominated by Rhopalodia gibberula . Diatom valves were found in various preservation states, ranging from nearly pristine to highly diagenetically altered. Diatoms collected from siliceous spires in Yellowstone Lake consisted largely of tychoplanktonic and benthic species that were almost certainly growing on the outside of the structure, with an assemblage indicative of relatively shallow, alkaline waters. What remains unclear without access to material for high-resolution dating is whether diatoms colonized the spires during hydrothermal activity or after activity ceased. Our results indicate that diatom frustules can, to some extent, survive alteration in low-temperature (<76°C) hydrothermal environments.
Planktonic marine diatom record of the past 18 m.y.: Appearances and extinctions in the Pacific and Southern Oceans
Recently published diatom biochronologies provide accurate (to 0.1 m.y.) determination of the ages of appearances and disappearances of planktonic diatoms during the past 18 m.y. in the equatorial Pacific, North Pacific, and Southern Ocean. Comparisons of these records reveal the age of evolutionary appearance and extinction of species and their region of origin. Extinct planktonic diatom species have a mean longevity of 3.4 ?? 2.8 m.y. (SD, n = 53) in the equatorial Pacific, 2.5 ?? 2.1 m.y. (n = 52) in the North Pacific, and 2.9 ?? 2.3 m.y. (n = 38) in the Southern Ocean. The relatively large standard deviations are likely due to the inclusion of taxa that probably could be subdivided into two or more species. In the equatorial Pacific, evolutionary turnover of diatom species was relatively high between 18.0 and 6.0 Ma compared with the period after 6.0 Ma, presumably reflecting changing oceanic circulation and evolving water masses. In the North Pacific, evolutionary turnover peaked between 10.0 and 4.5 Ma, with increasing high-latitude cooling and enhanced provincialism. In the Southern Ocean, evolutionary turnover of endemic diatoms was greatest between 5.0 and 1.6 Ma, which provides evidence for the strong provincial character of Pliocene diatom assemblages. Taken as a whole, oceanic diatom assemblages became increasingly provincial in character during the late Miocene and Pliocene, as pole-to-equator thermal gradients increased and oceanic frontal systems were strengthened.
Nitrogen deposition effects on diatom communities in lakes from three National Parks in Washington State
The goal of this study was to document if lakes in National Parks in Washington have exceeded critical levels of nitrogen (N) deposition, as observed in other Western States. We measured atmospheric N deposition, lake water quality, and sediment diatoms at our study lakes. Water chemistry showed that our study lakes were ultra-oligotrophic with ammonia and nitrate concentrations often at or below detection limits with low specific conductance (−1 year −1 and were variable both within and across the parks. Diatom assemblages in a single sediment core from Hoh Lake (Olympic National Park) displayed a shift to increased relative abundances of Asterionella formosa and Fragilaria tenera beginning in the 1969–1975 timeframe, whereas these species were not found at the remaining (nine) sites. These diatom species are known to be indicative of N enrichment and were used to determine an empirical critical load of N deposition, or threshold level, where changes in diatom communities were observed at Hoh Lake. However, N deposition at the remaining nine lakes does not seem to exceed a critical load at this time. At Milk Lake, also in Olympic National Park, there was some evidence that climate change might be altering diatom communities, but more research is needed to confirm this. We used modeled precipitation for Hoh Lake and annual inorganic N concentrations from a nearby National Atmospheric Deposition Program station, to calculate elevation-corrected N deposition for 1980–2009 at Hoh Lake. An exponential fit to this data was hindcasted to the 1969–1975 time period, and we estimate a critical load of 1.0 to 1.2 kg N ha −1 year −1 for wet deposition for this lake.
Diatom enumeration method influences biological assessments of southeastern USA streams
Current fixed-count enumeration methods for benthic diatoms are likely inadequate for most research and monitoring objectives. These methods underestimate taxa richness and may fail to detect losses of species caused by human impacts. Consequently, the full potential of diatoms is not realized in current assessments of biological integrity or species diversity. In this study, we hypothesize that alternative enumeration methods differ in their ability to quantify species composition. Furthermore, we hypothesize that an alternative to the traditional fixed-count method will improve both performance of observed/expected (O/E) indices derived from River Inver- tebrate Prediction and Classification System models and the discrimination of reference-quality and human-modified sites by other standard metrics used in biological assessments. To test these hypotheses, we assessed 1) how well 3 counting methods characterized species richness in a subset of 15 samples of stream benthic diatoms and 2) how counting method affected the performance of O/E indices and metrics by comparing the traditional fixed- count method against the best-performing alternative method. These latter comparisons were based on samples collected from 68 reference-quality streams and 20 streams located along an urban disturbance gradient. We dem- onstrate that traditional fixed counts failed to detect >1⁄2 of species present in most of the 68 reference-quality sites. Instead, timed-presence data produced the O/E index with the best performance and a level of precision similar to published invertebrate O/E indices. Furthermore, the O/E index based on the timed-presence data allowed us to determine which species are most often lost with urbanization. We found that traditional fixed-count and alter- native timed-presence data produce metrics that are nearly equally able to discriminate between reference and dis- turbed sites. This study demonstrates that alternative counting methods improve species detection and require up to ∼30% less effort.
Climate-induced changes in lake ecosystem structure inferred from coupled neo- and paleoecological approaches
Over the 20th century, surface water temperatures have increased in many lake ecosystems around the world, but long-term trends in the vertical thermal structure of lakes remain unclear, despite the strong control that thermal stratification exerts on the biological response of lakes to climate change. Here we used both neo- and paleoecological approaches to develop a fossil-based inference model for lake mixing depths and thereby refine understanding of lake thermal structure change. We focused on three common planktonic diatom taxa, the distributions of which previous research suggests might be affected by mixing depth. Comparative lake surveys and growth rate experiments revealed that these species respond to lake thermal structure when nitrogen is sufficient, with species optima ranging from shallower to deeper mixing depths. The diatom-based mixing depth model was applied to sedimentary diatom profiles extending back to 1750 AD in two lakes with moderate nitrate concentrations but differing climate settings. Thermal reconstructions were consistent with expected changes, with shallower mixing depths inferred for an alpine lake where treeline has advanced, and deeper mixing depths inferred for a boreal lake where wind strength has increased. The inference model developed here provides a new tool to expand and refine understanding of climate-induced changes in lake ecosystems.
A direct immunoassay for detecting diatoms in groundwater as an indicator of the direct influence of surface water
Groundwater under the direct influence of surface water (GWUDISW) is of concern in communities where growing public demand on groundwater resources has resulted in increased withdrawals and hydraulic stress near surface water bodies. Under these conditions, contaminants such as methyl-tert butyl ether (MTBE) and biological materials have been detected in domestic wells. Other contaminants and pathogens associated with surface water are not routinely tested for in groundwater-supplied systems. To address the need for methods to easily identify potentially vulnerable supplies, a direct immunoassay for the quantitative detection of diatoms in raw water samples was developed as a measure of surface water influence on groundwater. Cell wall preparations from Nitzschia palea Kützing, a freshwater diatom found throughout North America, were used to produce a polyclonal antibody that was applied in a direct enzyme-linked immunosorbent assay (ELISA) developed to detect the presence of N. palea cell wall components. The direct immunoassay allows detection at 500 cells L −1 , a level similar to diatom concentrations observed in samples of groundwater collected near the test site. This investigation was the first attempt to utilize an ELISA as an indicator of surface water influence on groundwater. Further research is needed to develop more specific diatom-based monoclonal antibodies, determine cross-reactivity, and optimize sample processing and ELISA procedures for development of a standardized method.