Diatom Samples Research Articles

The Effects of Cattle Grazing on the Composition of Diatom Assemblages in the Peatland Pools of the Southeastern Alps (Italy, Adamello-Brenta Nature Park)

Mires are significant C-sinks and important habitats for biodiversity conservation. Particularly in the Alpine peatlands, grazing and trampling cause mires to degrade, causing changes in plant communities that increase bulk density, peat erosion, and nutrient excesses. We took sixteen samples of epipelic and epiphytic diatoms from mire pools subjected to varying degrees of grazing in the Adamello-Brenta Nature Park (Trento, Italy). We identified >100 diatom species (ca. 70% included in Red List threat categories). We used nMDS to identify groups of diatom species. Their statistical significance was checked with an ANOSIM and, to identify the species that contributed most to the difference between the two groups, a BEST-SIMPER procedure was carried out. The multivariate analyses allowed us to identify significant differences among the most and least grazed sites, and to select the species that contributed most to this distinction. We confirmed that some species were more frequent and abundant in the most grazed sites and behaved as opportunists in the presence of a greater nutrient input, to the detriment of rare and sensitive species, which were more numerous and abundant in the less grazed sites. We provided useful information on grazing effects, underlining the importance of managing and protecting habitats of unique environmental value.

A high-efficiency local and global detector for diatom-based drowning diagnosis

Detection and classification of diatoms has been considered as the most effective method for the drowning diagnosis in forensic practice. However, challenges (such as limited samples, complex background interference, and detecting multiple objects) remain during detection and classification. To address these challenges, we propose a MDMS (multi-scale dynamic multi-head self-attention)-based deep learning network for the diatom-based drowning diagnosis. This framework uses TFFT (two-stage full fine-tuning training strategy) to solve the challenges of limited diatom samples and detecting multiple objects, and builds a multi-scale dynamic multi-head self-attention module to extract the local and global features of diatom images. In the meantime, we introduce an online hard example mining strategy to attenuate the complex background interference. The experimental results show that the proposed framework can effectively reduce the missing and false detection rates of diatom objects, with the mAP (mean Average Precision) reaching 92.434%, which is better than the result using the mainstream methods.

Assessment of river ecological status in the French West Indies based on diatom flora

The Water Framework Directive (WFD) requires member states to routinely assess the river ecological status using community-based indices. However, there is still a lack of published WFD-compliant methods for the French West Indies, especially using diatom-based indices. Martinique and Guadeloupe exhibit diverse landscapes shaped by their complex geological history and tropical climatic conditions. These strong particularities make the existing indices developed for the European mainland unusable. Based on diatom sampling from to 2013 (607 samples) and through multivariate analyses, we developed the Indice Diatomique des Antilles (IDA). We first identified the key abiotic factors influencing diatom communities on both islands, and then characterized taxon sensitivity by considering their presence probability along a pressure gradient.. The index was based on the presence and relative abundance of these taxa in each sample. The last step consisted of using new data from the 2014–2022 sampling surveys (457 samples) as a validation dataset to verify IDA accuracy. Our results suggest that the IDA methodology is well designed to assess the ecological status of rivers in the West Indies.

Determination of water quality and trophic level by using epilithic diatoms in Büyükçekmece Reservoir

In this study, the composition, distribution, and seasonal changes of epilithic diatoms were investigated to reveal the water quality and trophic level of Büyükçekmece Reservoir, which is one of the essential freshwater sources for İstanbul, Türkiye. Water and diatom samples were collected on the same day from all stations, and sampling was only on one day for a specific sampling season. Seventy-six taxa belonging to 30 genera were identified, two of which were centric and 74 were pennate diatoms; 12 of the epilithic species were newly-reported diatoms for the Büyükçekmece Reservoir. The highest number of epilithic diatom species was obtained in November, and the lowest was in February. According to relative abundance, Gomphonella olivacea was abundant in February, Cymbella lange-bertalotii in May, and Cocconeis placentula in August and November. According to the diatom-based water quality indices, the Büyükçekmece Reservoir belongs to I (very good, oligotrophic) and II (good, meso-oligotrophic) water quality classes. Redundancy analysis was used to reveal the association of epilithic diatom species with ecological variables, and it was determined that Silicate-Si, Ammonium-N, and temperature were the most effective variables in the distribution of epilithic diatoms.

THE RELATIONSHIP BETWEEN ORGANIC MATERIAL CONTENT IN SEDIMENTS AND THE ABUNDANCE OF EPIPELIC DIATOMS IN THE INTERTIDAL ZONE OF THE WATERS OF DUMAI CITY, RIAU PROVINCE

This research was conducted in March 2023, located in Koneng Beach, Dumai City. The purpose of this study was to determine the organic matter content and abundance of epipelic diatoms vertically and to analyze the relationship between the organic matter content in sediments and the abundance of epipelic diatoms vertically in the intertidal area of Dumai City Waters. The method used is the survey method. The sampling point is determined using a purposive sampling method. Sampling of epipelic diatoms was carried out using a modified corer, which was then brought to the laboratory to identify and calculate the abundance of diatoms and the sediment samples to calculate the content of organic matter and sediment fractions. Water quality measurements accompanied sampling with a brightness value of 0.57 m, temperature of 33 °C, current speed of 0.33 m/s, salinity of 28 ppt, and pH of 8.13. The results of the analysis of organic matter are 2.55 – 13.38%. The results of the sediment fraction analysis show that the research location is dominated by sandy silt. Nineteen genera of epipelic diatoms were found in the waters of Koneng Beach, Dumai City, with abundance values between 5,291–39,983 ind/cm2. The one-way ANOVA test results obtained an average value of 0.000, meaning there is a significant difference in the abundance of epipelic diatoms between the sediment layers. The results of the linear regression test showed that the effect of sediment organic matter on the abundance of epipelic diatoms was 50.85%.

Two-stage channels can enhance local biodiversity in agricultural landscapes

Field drainage causes habitat loss, alters natural flow regimes, and impairs water quality. Still, drainage ditches often are last remnants of aquatic and wetland habitats in agricultural landscapes and as such, can be important for local biodiversity. Two-stage channels are considered as a greener choice for conventional ditches, as they are constructed to mimic the structure of natural lowland streams providing a channel for drainage water and mechanisms to decrease diffuse loading. Two-stage channels could also benefit local biodiversity and ecosystem functions, but existing information on their ecological benefits is scarce and incomplete. We collected environmental and biological data from six agricultural stream systems in Finland each with consequent sections of a conventional ditch and a two-stage channel to study the potential of two-stage channels to enhance aquatic and riparian biodiversity and ecological functions. Biological data included samples of stream invertebrates, diatoms and plants and riparian beetles and plants. Overall, both section types were highly dominated by few core taxa for most of the studied organism groups. Riparian plant and invertebrate communities seemed to benefit from the two-stage channel structure with adjacent floodplains and drier ditch banks. In addition, two-stage channel sections had higher aquatic plant diversity, algal productivity, and decomposition rate, but lower stream invertebrate and diatom diversity. Two-stage channel construction did not diversify the structure of stream channels which is likely one explanation for the lack of positive effects on benthic diversity. However, both section types harbored unique taxa found only in one of the two types in all studied organism groups resulting in higher local gamma diversity. Thus, two-stage channels enhanced local biodiversity in agricultural landscapes. Improvements especially in aquatic biodiversity might be achieved by increasing the heterogeneity of in-stream habitat structure and with further efforts to decrease nutrient and sediment loads.

Simple approaches for evaluation of OTU quality based on dissimilarity arrays

An accurate and complete taxonomic description of the diversity present in an environmental sample is out of reach at this time. Instead, metabarcoding is used today and it is expected that OTUs represent a category relevant for biodiversity inventories on a molecular basis. However, artefacts in the production of OTUs can occur at different stages and may impact ecological conclusions. We propose to evaluate the quality of OTUs in a sample by characterising the deviation of each OTU’s dissimilarity array from that of an ideal OTU where all sequences are at distances smaller than the barcoding gap. We consider two deviations: the creation of composed OTUs, corresponding to the artificial merging of several OTUs and the creation of noisy OTUs that contain some sequences that are loosely associated with the core sequence of the OTUs and that do not form a compact subgroup. We propose a simple and automatic 2-step method that successively categorises the OTUs of a sample as composed or single and then identifies OTUs with noise amongst the single ones. The associated code is available at https://forgemia.inra.fr/alain.franc/otu_shape. We applied the method on 32 samples of diatoms from Arcachon Bay (France) that represent contrasted environmental conditions and we obtained good agreement with expert categorisation of OTUs. We suggest that single OTUs without noise can be used as such for further ecological studies. Composed OTUs should be post-treated with classical clustering or community detection tools. The quality of single OTUs with noise remains to be further tested via supplementary studies on a diversity of organisms.

Cymbella golestanica sp. nov. a new diatom species from Agh Su Waterfall, Golestan National Park, Northeastern Iran

A new species of Cymbella is characterized by morphological, ultrastructural and ecological remarks. The species was found in diatom samples collected from Agh Su waterfall located in western part of Golestan National Park. Cymbella golestanica sp. nov is assigned to the C. leptoceros group based on the areola density, the absence of stigmata and lanceolate shape. The most similar taxa are C. diminuta and C. hustedtii, however in our taxon stria is less dense than the C. diminuta types and more loosely distributed, and apices are completely protracted with ventrally broadened valves and axial area. The most diagnosing features with C. hustedtii are also valve apices and length/width ratio. C. golestanica was also compared with C. subleptoceros and C. designata. Ecologically the newly described species was found as epilithic in alkaline water with low conductivity.

The response of diatom community to small hydropower plant and fish farm

Some of the direct and indirect environmental impacts are related to the construction of fish farms (FFs) and small hydropower plants (SHPs) around the world. Diatom communities are one of the best bioindicators of various pressures like eutrophication, chemical and organic pollution. The main objective of this study was to examine the influence of SHP and FF on diatom community and water quality of the Prištavica River in Serbia. A total of 184 epilithic diatom taxa from 55 genera were identified. Sites after the FF and SHP are distinguished by the same dominant species in each season. Compared to the other sites, species diversity in summer was lower at site after SHP. In terms of spatial dynamics, four groups of taxa are distinguished. Some centric taxa were associated with sites downstream the FF and SHP. Altered physical and chemical parameters were documented at sites downstream of constructions. Water quality of the Prištavica River ranged from high to bad depending on diatom index, season, and sampling site. A greater difference in diatom index values was found at sites upstream and downstream of the FF, than at sites upstream and downstream of the SHP.

EPIPHYTIC DIATOMS IN ENVIRONMENTAL BIOINDICATION: A CASE STUDY OF A SIGNIFICANT NATURAL LAKE IN THE NORTHWEST OF TURKEY

Aim of the study: The Gala Lake, which has a status of National Park and is an under-protection area, is the one of the most important natural stagnant water bodies in the Marmara Region of Türkiye. However, it is under effect of a significant agricultural stress sourced by mainly paddy cultivation. In this research, the epiphytic diatoms of Gala Lake were investigated, and the trophic status of the lake was assessed by applying the Biological Diatom Index (BDI). Material and methods: Epiphytic diatom samples were collected from the submerged macrophytes from 5 selected locations on the lake (G1–G5) with different ecological characters observed to be exposed to different pollution pressures. Results and conclusions: As a result of taxonomic data, 37 diatom species were recorded by identifying a total of 2095 valves, and Cyclotella meneghiniana, Bacillaria paxillifera, and Navicula recens were found as the most dominant species for the Gala Lake. According to the results of bioindication data, Gala Lake was found to be in a "eutrophic state"—"having poor water quality" in terms of applied BDI.

Diversity and Abundance of Epiphytic Diatoms on Seagrass Leaves (Enhalus acoroides) in Poncan Gadang Island Sibolga City, North Sumatra

The seagrass ecosystem is one of the marine ecosystems that has an important role, namely as a source of life for organisms in the sea. Diatoms are microalgae widely distributed throughout the aquatic environment and are even found in plants, including seagrass leaves. Diatoms greatly influence life in the waters because they play an essential role as a food source for various marine organisms and play a role in the transfer of carbon, nitrogen, and phosphate. This research was conducted in February 2023 on Poncan Gadang Island, Sibolga City, North Sumatra. The study aims to determine the density, relative abundance, abundance, and diversity of epiphytic diatom species on seagrass (Enhalus acoroides) leaves in Poncan Gadang Island. The method used is the survey method, using three stations to take samples. The determination of 3 stations is based on the density of the seagrass beds ecosystem. Sampling of diatoms was carried out by brushing the surface of seagrass leaves about 5x2 cm on the front and back of the leaves. The samples obtained were then analyzed in the laboratory. There were 12 types of diatoms found, consisting of Cocconeis sp., Rhizosolenia sp., Biddulphia sp., Amphipluera sp., Thalassiotrix sp., Nitzchia sp., Synedra sp., Melosira sp., Pleurogosigma sp., Skeletonema sp., Licmiphora sp., and Thalassionema sp. the average value of epiphytic diatom abundance in seagrass leaves ranged from 2160.85 – 4649.94 ind/cm². The epiphytic diatom diversity (H') values ranged from 2.53 to 2.72

New Records for the Turkish Freshwater Algal Flora in Twenty Five River Basins of Türkiye, Part I: Bacillariophyta

The present study aimed to contribute to the algal flora of Türkiye by Bacillariophyta (diatom) as new records for the Turkish freshwater. Phytobenthos and phytoplankton were sampled three times (spring, summer, and autumn) a year between 2017 and 2019. Samples of the phytoplankton were collected with a water sampler from three depths, and samples of diatoms were obtained as epiphytic in the littoral zone of the lakes. However, if macrophytes were absent, epilithic or epipelic diatoms were sampled in lakes. Also, samples of phytobenthos were preferred as epilithic in rivers. However, if stones were absent, epiphytic or epipelic diatoms were sampled. During the studied period, a total of 895 diatom taxa were determined as planktonic (378 taxa) and benthic (860 taxa) in lakes and rivers of 25 river basins of Türkiye, and a total of 39 new records were identified. The highest diatom taxa were determined in the Fırat-Dicle, Konya, Antalya, and Büyük Menderes basins with 11, 11, 10, and 6 taxa, respectively. On the other hand, new records were not detected in 10 basins.

The relationship of organic matter, nitrate, and phosphate content to diatom abundance in the eastern coastal waters of Rupat Island Province

This study was conducted in March 2023 in the coastal waters of the eastern part of the island of Rupat, Riau Province. The method used in this study used the purposive sampling method at 3 station points. Water samples were used to analyze nitrate and phosphate analyzed using Ultraviolet Spectrophotometry, and analysis of water organic matter using the titrimetric method. Diatom sampling using plankton net measuring 25 µm. The results of the study found 14 species from 3 classes of diatoms namely Bacillariophyceae, Cyanophyceae, and Conjugatophyceae. Diatom abundance ranged from 472.22 - 993.05 cells/L. The regression equation for nitrate on diatoms is Y= 929.151-3194.045x. The coefficient of determination (R2) of 0.080 indicates that the effect of nitrate on diatom abundance has a weak close relationship. The effect of phosphate on diatom abundance has a coefficient of determination (R2) of 0.105 and the effect of phosphate has weak proximity. The influence of water organic matter has a coefficient of determination (R2) of 0.033 with a very weak effect. The analysis shows that the concentration of nitrate (NO3) is included in the oligotrophic fertility level, namely the low fertility rate

Using Algal Indices to Assess the Ecological Condition of the Aras River, Northwestern Iran

This work is the first in a series, and its purpose is the comprehensive assessment of the ecological state of the Aras River using biological indicators of water quality by diatoms based on species’ ecological preferences, pollution indices, statistics, and ecological mapping. Samples of diatoms and soft algae and measurements of water quality were analyzed at sixteen sampling sites (between 2020 and 2022) along the Aras River. The impact of anthropological activity on the river was monitored concerning water quality, river health, and ecosystem function. The physical and chemical characteristics of the water were measured. The biological properties of the algal periphyton communities, including species composition, were also measured. Based on the studies conducted in this research, 280 species were identified. The most prosperous species were Diatoma vulgaris, Amphora ovalis, Cocconeis placentula, Rhoicosphenia abbre-viatae, Cymbella helvetica, Brevisira arentii, Navicula tripunctata, Nitzschia linearis, Microcystis botrys, Microcystis aeruginosa, Pseudanabaena limnetica, Scenedesmus obliquus, and Pleurosira laevis (a pollution-resistant and salinity-resistant species first found in aquatic habitats in the Aras River). As a result, the empirical data and algal indices showed the river’s lower reaches to be in poor condition. Exploration of the algal assemblage and water chemistry data using computationally unconstrained ordination techniques such as principal component analysis (PCA) and canonical correspondence analysis (CCA) indicated two strong gradients in the data sets. The results support that water body classification is a function of water chemistry and biological and hydrological characteristics, as it is necessary to include pollutant effects on biota since the nature of the receiving waters influences the river’s water quality.

A Voucher Flora of Diatoms from Fens in the Tanana River Floodplain, Alaska.

Climate change and human activities may alter the structure and function of boreal peatlands by warming waters and changing their hydrology. Diatoms can be used to assess or track these changes. However, effective biomonitoring requires consistent, reliable identification. To address this need, this study developed a diatom voucher flora of species found across a boreal fen gradient (e.g., vegetation) in interior Alaskan peatlands. Composite diatom samples were collected bi-weekly from three peatland complexes over the 2017 summer. The morphological range of each taxon was imaged. The fens contained 184 taxa across 38 genera. Eunotia (45), Gomphonema (23), and Pinnularia (20) commonly occurred in each peatland. Tabellaria was common in the rich and moderate fen but sparse in the poor fen. Eunotia showed the opposite trend. Approximately 11% of species are potentially novel and 25% percent matched those at risk or declining in status on the diatom Red List (developed in Germany), highlighting the conservation value of boreal wetlands. This voucher flora expands knowledge of regional diatom biodiversity and provides updated, verifiable taxonomic information for inland Alaskan diatoms, building on Foged's 1981 treatment. This flora strengthens the potential to effectively track changes in boreal waterways sensitive to climate change and anthropogenic stressors.

Response of macroinvertebrate and epilithic diatom communities to pollution gradients in Ecuadorian Andean rivers

Population growth and increasing production demands threaten the highly diverse Andean freshwater ecosystems. Biological indicators constitute a valuable tool for evaluating the ecological quality of freshwater ecosystems under different pressures. Diatom and macroinvertebrate assemblages are the most used bioindicators to assess water pollution, whereby these biotic groups occupy the first and second trophic levels and respond to habitat pollution. Several studies have explored the response of these communities to water pollution in other regions, but no studies have examined their performance in Andean rivers. In this context, this research aimed to evaluate the responses and relationships of both groups of bioindicators in the Upper Guayllabamba basin. We collected macroinvertebrate and diatom samples from nine sites in this basin during the dry and wet seasons, calculated trophic indices for both groups, and related them to environmental characteristics. The results indicated that both bioindicators were sensitive to changes in land use and nutrients. Epilithic diatoms were more sensitive to changes in water chemistry and macroinvertebrates to changes in fluvial habitat and land use. The index based on macroinvertebrates better-detected changes in quality classes between sites and seasons. Therefore, both indices gave complementary information, and their joint use seems suitable in Andean streams.

Diatoms. A viable tool for quantifying surface water pollution

The current work focused on the water quality of the Bega and Timis rivers measured by two methods. One of them is the method by which the water was analyzed from a physical-chemical point of view, and the other aimed at quantifying the degree of water pollution by biological methods. In this sense, diatoms were used. In the study, samples of water and diatoms were taken using specific techniques from the Bega and Timis rivers, starting from near the area of their formation until near the border with Serbia. Four sampling points were chosen on the Timis River plus one sampling point on the Surgani River, which is a tributary of the Timis, and six sampling points on the Bega River. The points were chosen specifically, being located downstream of the major sources of pollution. In order to locate the points, information was collected from the studies carried out as part of an extensive monitoring that spanned several years. The abundance and diversity of diatom species were used to calculate the Biological Diatom Index (BDI) and the Saprobity Index (SI). These two indices provide valuable information about organic or heavy metal pollution of water bodies.

A biological diatom indices based preliminary assessment of water quality of Thamirabarani river, Southern India

ABSTRACT Diatoms have long been used as bio-indicators for the assessment of surface water quality. This study investigates the biological diatom index (BDI) and water quality index (WQI) for evaluating the water quality impact in the Thamirabarani River, Southern India. Diatom and water samples were taken for the present investigation from ten different locations along the river. The samples were enumerated and the morphometrics valve was documented by light microscopy. In the study area, a total of 70 diatom taxa belonging to 28 genera were recorded. The diatom indices implemented in OMNIDIA software version 6.1 was used to infer the river water quality status. The results showed that based on the BDI and WQI analysis values varied from 6.7 to 17.4 and 48 to 71 were observed. According to the BDI and WQI analysis result during the study period in the river revealed the water quality varied between good (Oligo-mesotrophic) to bad (Eutrophic) ecological conditions. The biological diatom index and water quality index results indicate the respective locations (Site 2, Site 3, Site 7, Site 8, Site 9 and Site 10) represent bad water quality. The result indicated moderate water quality at Sites 4 and Site 6. The diatom indices and water quality index results show the locations Site 1, and Site 5 indicate good water quality. The biological diatom index results from diatom assemblages show more information about the water quality and environmental impact on the river. For the national assessment of water quality better to use diatoms along with physico-chemical parameters variables. Based on the analysis result reveal that the major component of water quality degradation was due to anthropogenic activities, domestic waste and industrial effluents in the study area.

A method for bone marrow extraction of diatoms for forensic science applications.

Diatoms show potential as trace evidence indicators, particularly as evidence of drowning. Often, the diatom test to diagnose drowning is done on soft tissue or bone marrow from a recently deceased individual. This method presented here combines elements from previous forensic literature and methods of diatom isolation in phycology to extract diatoms from bone marrow of skeletal remains for forensic use. This diatom extraction method is time-efficient, minimizes contamination risk, and produces samples of intact diatoms. This method is designed to complete sample preparation within 24 h, sampling the bone for diatoms internally and externally. This method was developed using porcine long bones submerged in water with live diatoms for up to 3 months. Three marrow samples were extracted from each bone so the method was developed using 102 marrow samples. Additionally, 132 surficial bone and environmental samples were collected and prepared during method development. To briefly summarize the method, the bone joints were cut off with an angle grinder in a biosafety hood to expose the marrow, which was removed from the hip, knee, and shaft as separate samples. The marrow was digested with nitric acid at 400°C in glass beakers before being centrifuged with DI water, plated onto microscope slides, and observed with a compound microscope. Observation found good preservation of unbroken diatom cell walls throughout the process. This method can be used to prepare diatoms as forensic trace evidence.

Seasonal Response of Major Phytoplankton Groups to Environmental Variables along the Campeche Coast, Southern Gulf of Mexico

To describe the seasonal response of the major phytoplankton groups to environmental variables along the Campeche coast, southeastern Gulf of Mexico, seven shallow-water (ca. 1 m) stations were monitored from January 2019 to January 2020. Orthophosphate, ammonium, nitrite, nitrate and silicate were measured. Several tests, including ANOVA, the Kolmogorov–Smirnov test, Tukey TSD, Bartlett’s test and canonical correspondence analysis (CCA), were applied. The physicochemical variables (temperature, salinity and pH) recorded are typical for the central coast of Campeche. Seasonal characteristics are affected by the shallowness of the study area. The variation of inorganic nutrient concentrations is likely to be related to specific polluting activities. While the abundance of phytoplankton presented a minimum value of 4.1 × 104 cells L−1 in March, the maximum value of 8.8 × 106 cells L−1 occurred in May; the general average was 5.3 × 105 cells L−1. Based on CCA, the correlation between major phytoplankton groups and physical–chemical variables was high (r ≈ 0.8), indicating a significant relationship. The CCA graphs separated the samples of diatoms by higher values of pH and silicate and separated the samples of cyanobacteria with high values of temperature (>30 °C) from the samples with dinoflagellates and nanoflagellates. Nanoflagellates were abundant in the samples with high values of ammonium and phosphate.