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Diatom Species Abundance Data from LTER Caribbean Karstic Region (CKR) study (FCE) in Yucatan, Belize and Jamaica during 2006, 2007, 2008
Several studies have shown that within the Florida Coastal Everglades, periphyton mat properties, (incuding biomass, nutrient and organic content, and community composition) vary predictably in response to water quality.The Florida Coastal Everglades (FCE) wetland system is very similar with respect to climate, geology, hydrology and vegetation, to wetlands found in Jamaica, the Yucatan region of Mexico and parts of Belize. This study was therefore conducted to ascertain (i) the level of similarity between the periphyton diatom communities from karstic wetland sites in Belize, Mexico, Jamaica and comparable sites within the FCE, (ii) the relationship between periphyton biomass, TP levels and diatom community composition at these sites, and (iii) the feasibility of employing diatoms as indicators of water quality at these sites, using models relating diatom community composition to water quality from comparable sites within the FCE. Multiple wetland sites in Jamaica, the Yucatan region of Mexico and parts of Belize were visited between 2006 and 2008, during wet and dry seasons. At each site physico-chemical data were collected along with periphyton samples. The periphyton samples were processed in accordance with standard methods to obtain biomass, organic content and TP measures, and to identify and enumerate diatom and soft algae species. Various aspects of the diatom communities were then compared to previously compiled data on diatom communities from various parts of the FCE. SIMI analysis was used to determine the level of similarity between the systems and Non-Metric Multidimensional Scaling was used to identify relationships between diatom communities and water quality.
Relative Abundance Diatom Data from Periphyton Samples Collected from the Greater Everglades, Florida USA from September 2005 to November 2014
This data package contains relative diatom taxon abundances collected annually during the wet season between 2005 and 2014 from sites distributed throughout the greater Everglades ecosystem. This project is part of the Comprehensive Everglades Restoration Program's Monitoring and Assessment Plan intended to document baseline variability in periphyton attributes for assessing the effectiveness of restoration projects. A total of 200 primary sampling units (PSU) of 800 m x 800 m are nested in 32 landscape units and each year, random coordinates are 'drawn' within each PSU and one sampleable draw is visited in each. Sampled periphyton is processed for diatoms, slides are prepared, and 500 frustules are enumerated and identified to the lowest possible taxonomic resolution per slide. Taxon abundances are then relativized to the total count. These data accompany environmental, periphyton biomass, and soft algal abundance datasets. Post-2014 data are available upon request to the project PI, Evelyn Gaiser.
Unravelling winter diatom blooms in temperate lakes using high frequency data and ecological modeling
<p>This repository contains the dataset and the R script of the lake ecological model linked to the following publication:</p> <p>Article title: Unravelling winter diatom blooms in temperate lakes using high frequency data and ecological modeling</p> <p>Journal title: Water Research</p> <p>Article Number: 116681</p> <p>Abstract: In temperate lakes, it is generally assumed that light rather than temperature constrains phytoplankton growth in winter. Rapid winter warming and increasing observations of winter blooms warrant more investigation of these controls. We investigated the mechanisms regulating a massive winter diatom bloom in a temperate lake. High frequency data and process-based lake modeling demonstrated that phytoplankton growth in winter was dually controlled by light and temperature, rather than by light alone. Water temperature played a further indirect role in initiating the bloom through ice-thaw, which increased light exposure. The bloom was ultimately terminated by silicon limitation and sedimentation. These mechanisms differ from those typically responsible for spring diatom blooms and contributed to the high peak biomass. Our findings show that phytoplankton growth in winter is more sensitive to temperature, and consequently to climate change, than previously assumed. This has implications for nutrient cycling and seasonal succession of lake phytoplankton communities. The present study exemplifies the strength in integrating data analysis with different temporal resolutions and lake modeling. The new lake ecological model serves as an effective tool in analyzing and predicting winter phytoplankton dynamics for temperate lakes.</p>
NAAMES_IFCB_diatoms_image_features
<p>This text file (NAAMES_IFCB_diatoms_image_features.txt) contains data on all Imaging FlowCytobot (IFCB) images identified as diatoms (either individual cells or chains) during the North Atlantic Aerosol and Marine Ecosystem Study (NAAMES). Data are from the western North Atlantic, 2015-2018; see Behrenfeld et al. (2019) <em>Frontiers in Marine Science </em>for expedition details. The images were collected using an IFCB deployed onboard the ship and connected to the flowing sea-water system with intake at ~5 m depth. The images were classified and the data here identified as diatoms using a convolutional neural network with 90% accuracy. See https://github.com/emmettFC/selected-projects/blob/master/plankton_vision/README.md for details of the neural network development and testing. Data are used in the manuscript "Plankton Imagery Data Inform Satellite-Based Estimates of Diatom Carbon", Geophysical Research Letters, 49, e2022GL098076. https://doi. org/10.1029/2022GL098076. Additional data from the NAAMES expedition are available at https://seabass.gsfc.nasa.gov/naames.</p>
Seismic profiles, diatom and microfossil assemblages, and radiocarbon ages for constructing a post-glacial sea level curve from Fiordland, New Zealand
Two research cruises (12PL027 and 13PL018) were conducted aboard the University of Otago RV Polaris II in 2012 and 2013 to collect marine sediment cores and 2d seismic data as part of a collaborative research effort to study late-Pleistocene and Holocene environmental change in New Zealand. Data includes 4 Boomer seismic profiles, 4 CHIRP seismic profiles, seismic line GPS tracks, diatom assemblages (raw counts and relative abundances) and microfossil assemblages (raw counts and relative abundances), and radiocarbon ages from 4 marine sediment cores. The data used to construct a post-glacial sea level curve for Fiordland, New Zealand are also included, as well as data from published literature plotted for global comparisons. These data accompany the publication: Dlabola. E.K., Wilson, G.S., Gorman, A.R., Riesselman, C.R., and Moy, C.M. 2015. A post-glacial sea-level curve from Fiordland, New Zealand. Global and Planetary Change, 131, 101-114. https://doi.org/10.1016/j.gloplacha.2015.05.010
Metacommunity simulations for diatom assemblages residing in benthic cyanobacterial mats in Fryxell Basin in Taylor Valley in the McMurdo Dry Valleys, Antarctica
Here, we use MCSim, a spatially explicit metacommunity simulation package for R, to test alternative hypotheses about the roles of dispersal and species sorting in maintaining the biodiversity of diatom assemblages residing in black and orange mats in Fryxell Basin in Taylor Valley in the McMurdo Dry Valleys of Antarctica. The spatial distribution and patchiness of cyanobacterial mat habitats was characterized by remote imagery of the Lake Fryxell sub-catchment in Taylor Valley collected in January 2015. The available species pool for diatom metacommunity simulation scenarios was informed by the Antarctic Freshwater Diatoms Database, maintained by the McMurdo Dry Valleys Long Term Ecological Research program, representing samples collected between January 1994 and January 2013. We used simulation outcomes to test the plausibility of alternative community assembly hypotheses to explain empirically observed patterns of freshwater diatom biodiversity in the long-term record. The most plausible simulation scenarios suggest species sorting by environmental filters, alone, was not sufficient to maintain biodiversity in the Fryxell Basin diatom metacommunity. The most plausible scenarios included either (1) neutral models with different immigration rates for diatoms in orange and black mats or (2) species sorting by a relatively weak environmental filter, such that dispersal dynamics also influenced diatom community assembly, but there was not such a strong disparity in immigration rates between mat types. The results point to the importance of dispersal for understanding current and future biodiversity patterns for diatoms in this ecosystem, and more generally, provide further evidence that metacommunity theory is a useful framework for testing hypotheses about microbial community assembly. This dataset supports the paper: Sokol, E. Et al, 2020. Evaluating Alternative Metacommunity Hypotheses for Diatoms in the McMurdo Dry Valleys Using Simulations and Remote Sensing Data
Diatom composition and environmental data from the Greater Everglades, Florida, USA (2013-2020)
Environmental and diatom data were collected from sites in the Big Cypress National Preserve (BICY) by the South Florida/Caribbean Inventory and Monitoring Network of the National Park Service and from sites in the Everglades Protection Area (EPA) as part of the Monitoring and Assessment Program of the Comprehensive Everglades Restoration Plan. Samples from years 2012, 2013, 2019, 2019, and 2020 are included in this dataset. Environmental data include drier variables that have been found to influence diatom assemblage composition in the greater Everglades ecosystem, including periphyton mat total phosphorus (a proxy for phosphorus in the environment), water column pH, water column conductivity, water depth, days since last dry, and hydroperiod. Diatom data include diatom species composition as percent relative abundances. Code included is pertinent to the methods described in "Robust species optima estimates from non-uniformly sampled environmental gradients" by Solomon et al. 2025, Journal of Paleolimnology.
Periphyton Abundance and Structural Traits, Diatom Taxa Relative Abundance, and Associated Environmental Data from Samples Collected from the Greater Everglades, Florida, USA from September 2005 - ongoing
This data package contains benthic algae (periphyton) and environmental data collected annually during the wet season between 2005 and 2021 from sites distributed throughout the greater Everglades ecosystem. This project is part of the Comprehensive Everglades Restoration Program's Monitoring and Assessment Plan (CERP MAP) intended to document baseline variability in periphyton attributes for assessing the effectiveness of restoration projects. A total of 200 primary sampling units (PSU) of 800 m x 800 m are nested in 32 landscape units (LSU) and each year, random coordinates are 'drawn' within each PSU and one draw is visited in each sampleable PSU. Sampled periphyton is processed for aggregate structural traits (i.e., biomass, chlorophyll-a, organic content, and phosphorus concentration) and for diatom taxa. For diatoms, slides are prepared, and at least 500 frustules are enumerated and identified to the lowest possible taxonomic resolution per slide. Taxon abundances are then relativized to the total count. These data accompany environmental and spatial data for each sampled draw. In addition to the CERP MAP data, this dataset also includes data on the same variables collected from up to 21 primary sampling units in the Broward County Water Preserve Area beginning in 2020. The data in this package replace and supersede those in package knb-lter-fce.1210 (https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-fce&identifier=1210).
Green algae, cyanobacteria and diatom concentrations from the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) Project
SALTEx (Seawater Addition Long-Term Experiment) is a field experiment designed to simulate saltwater intrusion in a tidal freshwater wetland to predict how chronic (Press) and acute (Pulse) salinization will affect this and other tidal freshwater ecosystems. The SALTEx experiment was initiated in 2012 and consists of 31 field plots , each 2.5 m on a side. There are three treatments (Press, Pulse, and Fresh) and two types of controls (with and without sides), each consisting of six replicates. The Press treatment plots receive regular (4 times each week) additions of a mixture of seawater and fresh river water. Pulse plots receive the same mixture of seawater and river water during September and October, which is historically a time of low flow in the river when natural saltwater intrusion occurs. The Fresh treatment plots receive regular additions of fresh river water. Treatment water is added during low tide to facilitate its infiltration into the soil, and all plots are inundated by astronomical tides at high tide. We are measuring the abundance of benthic algae with a BenthoTorch as one of the response variables for the SALTEx project.
Hubbard Brook Stream Ecology Record: Diatom Species Richness and Voucher Flora, 2018-2022
This dataset contains species richness data for epiphytic diatom communities collected from weir ponds in seven headwater streams within the Hubbard Brook Experimental Forest (HBEF) in New Hampshire between 2018 and 2021. Diatom samples were gathered using artificial bryophyte substrates, deployed in weir ponds to mimic natural diatom habitats. Species richness was quantified by identifying diatom taxa to the lowest possible taxonomic level, with 86 taxa spanning 43 genera recorded. This dataset represents the first comprehensive classification of diatom communities at HBEF, providing a baseline for future studies in this ecosystem. Environmental variables, including light availability, dissolved organic carbon, total dissolved nitrogen, and pH, were concurrently measured to assess their influence on diatom community composition. The light (lux) data used in this study is openly available in the EDI Data Portal at https://doi.org/10.6073/pasta/0f40b75b299494d736645d940fa2b5a4. The chlorophyll-a data and analysis methodology are available at https://doi.org/10.6073/pasta/7fa32d94240fc7780d62cb7e65eafdb2. Reach characteristics were sourced from the EDI Data Portal at https://doi.org/10.6073/pasta/3e4b95149245341d522383bba51de7c7. This study provides valuable insights into the relationships between environmental factors and diatom diversity in northern hardwood forest streams, aiding ecological monitoring and bioindicator studies. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Rio Mameyes diatoms in the Rio Mameyes from 1998 to 2001
Survey expeditions of the diatoms of Puerto Rico and other Caribbean islands were conducted briefly in the late 1800's and early 1900's,. However, until now no intensive study of changes in freshwater diatom community over time has been undertaken. In conjunction with other measures of quality of water in the Rio Mameyes, i.e. pH, conductivity, temperature, nutrients, periphytic diatoms have been collected monthly for two years in an effort to detect the effects of disturbances such as hurricanes and human demands on a river ecosystem. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
A phylogenomics resource for the marine diatom Pseudo-nitzschia multistriata
<p>The resource contains phylogenetic trees built from approximately 9000 <em>P. multistriata </em>genes, comparing them to their orthologs (over 2 million sequences) across major taxa of archaea, bacteria and eukaryotes (Basu et al., 2017). For each orthologous group a tree is built twice using two different substitution models. Each sequence within a tree is given a specific ID which is a combination of a unique number along with a taxonomy code, for example "alla_stramenopile|34" signifies </p> <p> </p> <p>1) alla: organism Albugo laibachii.</p> <p>2) stramenopile: broad taxonomic class.</p> <p>3) 34: protein ID for Albugo laibachii DNA topoisomerase 2.</p> <p> </p> <p>The mapping between <em>Pseudo-nitzschia multistriata</em> proteins and the phylogenetic trees is present in the file "p.multistriata_gene_tree.txt". The detailed description of each protein ID given in any phylogenetic tree is present in the file "geneDB.txt". The phylogenetic trees generated using JTT and WAG substitution models of the FastTree program as present in the folders "treeJTT", "treeWAG".</p>
Benthic diatoms of the Ebro Delta coastal wetlands (NW Mediterranean)
<p>This dataset includes 24 sites encompassing diatom counts and associated water chemistry parameters from wide range of wetland habitat types (coastal lagoons, salt and brackish marshes, shallow bays, microbial mats and nearshore marine waters) from the Ebro Delta (Spain). Diatom data represents sediment surface samples collected over three seasons (winter, spring and summer) from 2012-2013 years. The dataset has been formatted following the standards of the Tropical South American Diatom Database (<a href="https://zenodo.org/records/5721364">https://zenodo.org/records/5721364</a>)--a database constituent of Neotoma (<a href="https://www.neotomadb.org/">www.neotomadb.org</a>), a global community-curated database by regional experts for multiple types of paleoecological data--and as part of the project "DiatomS mEEt Databases: resources and practices to enable large-scale ecological research (SEED)" funded by the International Society for Diatom Research (<a href="https://isdr.org/early-career-networking-award/">https://isdr.org/early-career-networking-award/</a>).</p> <p> </p>
Data and script: Reduced enumeration effort, but not coarse taxonomic resolution, is sufficient to represent beta diversity patterns of stream benthic diatoms
<p>This is a dataset on benthic diatom communities sampled in 90 riffles (the local communities) within nine near-pristine subtropical streams (each stream represented a metacommunity) in southeast subtropical Brazil. </p> <p>In addition to the dataset, we also provide the R code used to investigate whether reduced enumeration efforts (i.e., subsets of counted valves per sample) and the identification to the genus level are sufficient to recover patterns in the species composition and in beta diversity of benthic diatom metacommunities.</p>
Slide scans of diatom preparations from river Menne
<p>This archive contains the slide scans used for the deep learning experiments published in Kloster et al. 2022: Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint. The diatom material was sampled at six different locations from the river Menne (Germany), cleaned/oxidized and mounted in Naphrax. Please refer to the manuscript for details.</p> <p>Each scan represents area of ca. 5 × 3.5 mm² scanned by an VS200 slide scanning microscope (Olympus Europa SE & Co. KG, Hamburg, Germany). 61 focal planes were imaged in bright-field mode at a distance of 0.28 µm each using a UPLXAPO60XO 60x/1.42 oil immersion objective. Focus stacking and stitching were performed with the built-in functions of the VS200 ASW software (v3.2.1). Subsequently the RGB color data was reduced to 8bit monochrome grayscale images. This process resulted in the six virtual slide images, each roughly 55,000 × 39,000 pixel.</p> <p>These images depict benthic diatoms Menne river comprising more than 110 different taxa (estimated by identifying a subset of specimens). The sampling of this stream was authorized by the Kreis Paderborn authorities through the 4032-20-450 permit.</p>
Transcriptome assemblies of three diatom and three prymnesiophyte isolates from Station ALOHA and Kaneohe Bay
<p><strong>Culture ID/name</strong></p> <p>AT125A – Pseudo-nitzschia sp.</p> <p>AT125C – Pseudo-nitzschia sp.</p> <p>ATCH2 – Chaetoceros sp.</p> <p>Pn B2 – Pseudo-nitzschia sp.</p> <p>KB-HA01 – Chrysochromulina sp. (also called </p> <p>AL-TEMP-12 – Chrysochromulina sp. (also called </p> <p>NF-H275 – Chrysochromulina sp.<br> <br> </p> <p><strong>Growth Conditions</strong></p> <p>All cultures were grown at 27°C, 12:12 light:dark cycle, and with a light intensity of 100 µmol photons m<sup>-2</sup> sec<sup>-1</sup>. AT125C, AT125A, and Pn B2 were grown with Aquil media. ATCH2 was grown with F/20 media with the phosphate concentration modified to a final concentration of 0.5µM. KB-HA01 was grown with F/2 media and AL-TEMP-12 and NF-H275 were grown with K media. None of the cultures were axenic. All cultures were filtered in “light” and “dark” conditions and were in exponential phase when filtered. (Filter types and volumes filtered listed below.) After filtration, all filters were placed into 2mL screwcap tubes, flash frozen with liquid nitrogen, and stored at -80°C.</p> <p><strong>Growth Conditions</strong></p> <p>All cultures were grown at 27°C, 12:12 light:dark cycle, and with a light intensity of 100 µmol photons m<sup>-2</sup> sec<sup>-1</sup>. AT125C, AT125A, and Pn B2 were grown with Aquil media. ATCH2 was grown with F/20 media with the phosphate concentration modified to a final concentration of 0.5µM. KB-HA01 was grown with F/2 media and AL-TEMP-12 and NF-H275 were grown with K media. None of the cultures were axenic. All cultures were filtered in “light” and “dark” conditions and were in exponential phase when filtered. (Filter types and volumes filtered listed below.) After filtration, all filters were placed into 2mL screwcap tubes, flash frozen with liquid nitrogen, and stored at -80°C.<br> <br> [TRANSCRIPTOME SEQUENCING]<br> <br> [QC AND ASSEMBLY]<br> <br> [POST-ASSEMBLY PROCESSING]<br> Diamond v2.0.5.143 was used to blast (e-value: 1e-5) to a cross-kingdom reference sequence database (as described in Coesel et al., 2021). Diamond v2.0.5.143 was used to find the least common ancestor of each contig based upon the blast results. Contigs that were identified as bacteria, archaea, or viruses were excluded from the assemblies.<br> <br> </p>
European river typologies fail to capture trends in diatom, fish, and macrophyte community composition
<p>This repository contains files related to the publication: "European river typologies fail to capture trends in diatom, fish, and macrophyte community composition".</p> <p> </p> <p> </p>
Hyporheic diatom community assemblages from Von Guerard Stream, Taylor Valley, McMurdo Dry Valleys, Antarctica in January 2019
In this data package, we present diatom community assemblages from hyporheic sediments collected in January 2019 from six transects across Von Guerard Stream, Taylor Valley, Antarctica. These samples were collected to address questions about the retention and processing of particulate organic matter in the hyporheic zone of McMurdo Dry Valley streams. The six transects were located at pools, riffles, and meanders (three of each geomorphology type) along Von Guerard Stream and extended across the stream channel to the edges of the wetted zone, ranging from 6.6 to 13.6 m in length. At each sampling location, we collected subsurface sediment sample that was preserved in formalin directly after sample collection. We characterized diatom assemblages by counting a total of 300 diatom valves from each preserved diatom sample. This data package is associated with a complementary data package that contains hyporheic sediment chemistry for the same samples.
Fiddler crab impacts from observational study 2020-21: Aboveground & diatom biomass, plant height, percent N, burrow & mussel density, belowground biomass, and organic matter
The fiddler crab, Minuca pugnax, expanded its range into the Gulf of Maine recently and was first observed in the Plum Island Estuary in 2014. In 2020 and 2021, we investigated the impact of this burrowing crab on benthic microalgal biomass, sediment properties and the above- and belowground biomass of the cordgrass, Spartina alterniflora. To accomplish this, we conducted a control-impact study in plots with and without fiddler crabs in three marshes in the PIE-LTER: Sawyer, Clubhead, and Metcalf. In its historical range (i.e., south of Cape Cod), M. pugnax, enhances Spartina aboveground biomass. In contrast, we found that, on average, when fiddler crabs were present, aboveground biomass was 40% lower in the PIE-LTER. We also found that belowground biomass was 30% lower and benthic microalgal biomass was 45% lower when fiddler crabs were present, which is in line with our expectations. Because fiddler crabs reduced the biomass of foundational primary producers in its expanded range, our results imply that M. pugnax can influence other saltmarsh functions such as carbon storage and accretion as they expand north. More broadly, our results suggest that as species expand or shift their range with climate change, not only can they have profound impacts in their new ranges, but that those impacts can be the inverse of what is seen in their historical ranges.
Figs 86–109 in Four new monoraphid diatom species (Bacillariophyta, Achnanthaceae) from the Maritime Antarctic Region
Figs 86–109. Psammothidium superpapilio Kopalová, Zidarova & Van de Vijver sp. nov. Light and scanning electron micrographs of the type population on Byers Peninsula (Livingston Island). 86–95. LM views of rapheless valves. 96–105. LM views of raphe valves. 106. SEM external view of an entire raphe valve. 107. SEM internal view of an entire raphe valve. 108. SEM external view of an entire rapheless valve. 109. SEM internal view of an entire rapheless valve. Scale bars represent 10 µm.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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