Machine learning assessment of molecular trophic diatom index (mTDI) using planktonic eDNA for water quality in freshwater ecosystems

Two rivers situated in Central Poland, the Bzura and the Pilica, were selected for analysis of their water quality using benthic diatom species as indicators. The Bzura River has previously been strongly contaminated with organic pollutants, while the Pilica River has been classified as having good water quality. Samples were collected from nine sites along the Bzura in April 2003 and seven sites along the Pilica in April 2006. The main aims of the study were to determine the dominant diatom species present in the rivers and to assess their usefulness as biological indicators. Water quality of the rivers was estimated on the basis of the SPI - Specific Pollution sensitivity Index (CEMAGREF 1982) and the GDI - Generic Diatom Index (Coste, Ayphassorho 1991) while trophic status was estimated using TDI - Trophic Diatom Index (Kelly, Whitton 1995). Indices determining saprobic water pollution (SPI, GDI) indicated water quality of class III and IV for the Bzura River and class II and III for the Pilica River. The trophic status determined on the basis of the TDI index revealed the Bzura water to be classified in the eutrophic-to-hypertrophic zone and that of the Pilica River to the oligo-mesotrophic-to-eutrophic zone. The diatom taxa that dominated in the Bzura River were species that are generally considered to be tolerant and resistant with respect to organic water pollution, including: Cyclotella meneghiniana Kützing, Gomphonema parvulum (Kützing) Kützing, Nitzschia palea (Kützing) W. Smith, Nitzschia paleacea Grunow, Sellaphora pupula (Kützing) Mereschkovsky, Stephanodiscus hantzschii Grunow, Ulnaria ulna (Nitzsch) Compere. In the Pilica River diatoms from groups that are sensitive and tolerant to organic pollution were seen to dominate, such as: Achnanthidium minutissimum (Kützing) Czarnecki, Aulacoseira granulata (Ehrenberg) Simonsen, Cocconeis neodiminuta Krammer, Cocconeis placentula Ehrenberg, Cocconeis placuntula var. lineata (Ehrenberg) Grunow, Cyclotella radiosa (Grunow) Lemmermann, Fragilaria crotonensis Kitton, Geissleria decussis (Øestrup) Lange-Bertalot et Metzeltin, Melosira varians Agardh, Navicula reichardtiana Lange-Bertalot, Planothidium frequentissimum (Lange-Bertalot) Lange-Bertalot, Pseudostaurosira brevistriata (Grunow) Williams & Round, Rhoicosphenia abbreviata (Agardh) Lange-Bertalot and Staurosira pinnata Ehrenberg.

Diatoms are siliceous micro-algae and have been used with increasing frequency as bioindicators in aquatic ecosystems. Typically, European diatom indices have been modified and augmented with data on taxa endemic to and commonly found in other parts of the world. In order to further test the application of diatom indices, water quality and diatom sampling were performed in the Bloukrans River system, Eastern Cape Province of South Africa. Nine sites with contrasting water quality were sampled along the length of the river in February, May and July 2018. Multivariate statistical analysis (Canonical Correspondence Analysis) was employed to elucidate spatiotemporal differences in diatom community structure. Canonical correspondence analysis indicated that differences in diatom community assemblages were best explained by dissolved oxygen, temperature, nitrate, conductivity and phosphate. Diatom-based indices incorporated in OMNIDIA software were also applied to assess the integrity of the water quality as indicated by diatom communities. Several foreign indices (e.g. the trophic diatom index (TDI), biological diatom index (BDI)) and the South African Diatom Index (SADI) were used in the study. The SADI demonstrated that the Bloukrans River was impacted and had significant correlations with water quality variables (p < .05). We therefore recommend the wider use of the SADI as an indicator of water quality conditions in South African lotic systems.

This study aimed to assess the impact of land use patterns on water quality and benthic diatom community structure and to test the applicability of diatom indices developed in other regions of the world to a small temperate southern African river system. Sampling was conducted at eight study sites along the length of the river on four separate occasions. Multivariate data analyses were performed on the diatom community dataset to specify the main gradients of floristic variation and to detect and visualize similarities in diatom samples in relation to land-use patterns within the catchment. One hundred and twelve (112) diatom species belonging to 36 genera were recorded during the study. Canonical correspondence analysis (CCA) demonstrated that variations in the benthic diatom community structure were best explained by ammonium, nitrate, conductivity, pH, temperature, resistivity and water flow. OMNIDIA was used for calculation of selected diatom water quality indices. A number of the indices, e.g., the trophic diatom index (TDI), eutrophication/pollution index and biological index of water quality (BIWQ), either under- or over-estimated the water quality of the system. With few exceptions, there were no significant correlations (p> 0.05) between the diatom indices’ values and the nutrient variables. The absence of any significant correlations between the diatom indices’ values and selected physico-chemical variables suggests that indices developed in other regions of the world may not be suitable for temperate southern African rivers. Keywords : biomonitoring, diatom indices, diatom community, Kowie River, nitrogen, multivariate analysis, point-source pollution, water quality

Benzing DH. 2000. Bromeliaceae: Profile of an adaptive radiation(with contributions by B. Bennett, G. Brown, M. Dimmitt, H. Luther, I. Ramirez, R. Terry, W. Till). 690 pp. Cambridge: Cambridge University Press. £75 (hardback).

The study attempts to assess water quality in Abu-Zirig Marsh which used epiphytic Diatom community for assessing water quality. Many of Diatom indices {Trophic diatom index (TDI), Diatom index (DI), Generic diatom index (GDI) have been used to give qualitative information about the status of the freshwater ecosystem(good, moderate, high pollution). In this study, the epiphytic diatoms on both host aquatic plants Phragmites australis and Typha domengensis were collected from Abu-Zirig Marsh within Thi-Qar Province at three sites in Autumn, 2018 and winter, 2019. Epiphytic diatoms were Identified by the preparation of permanent slides method, some species of epiphytic diatom showed dominance such as Cyclotella meneghiniana, Gomphonema angustatum, Cocconies placentula, Cymbella affinis, Navicula cryptoephala, Nitzschia linearis, N. dissipata, Surirella ovalis. Abundant diatoms indicated trophic conditions of the Marsh. The results of diatom indices revealed that IPS (10-12.5) is a moderate pollution condition of marsh, DI (2.9-3.4) range from high to moderate pollution condition, TDI (47.2-60.8) indicates trophic condition ranging from (oligo-mesotrophic to eutrophic) condition of marsh while GDI a range between (11.6-13.7) moderate pollution condition, the aim of the study that is about evaluating water quality of Abu-Zirig Marsh by using Diatom indices (IPS,DI,TDI and GDI), as well as due to scarce local previous studies of epiphytic diatoms and used as bio-indicator of water quality in Abu-Zirig Marsh, therefor suggested this study .

The objective of this study was to determine the effects of land-use patterns on both diatom community composition and water quality in tropical streams during the dry season. Benthic diatom collections and water quality sampling were done 4 times at 10 sites. A suite of environmental variables that varied with human land-use pattern was assessed to find the combination of variables that best explained patterns of diatom community composition. Canonical Correspondence Analysis (CCA) was used to determine environmental gradients along which species were distributed. A clear relationship between both benthic diatom communities and water quality and land-use pattern was observed with species richness, diversity and evenness, decreasing significantly from the agricultural and forest area to the urban area. Upstream, forested, agricultural sites, with good water quality (BOD5 = 0.9 to 2.6 mg∙ℓ-1, DO = 6.8 to 8.2 mg∙ℓ-1, phosphate = >2 to 4.7 μg∙ℓ-1), were characterised by Thalassiosira weissflogii, Orthoseira dentroteres, Meridion anceps, Melosira varians, Diatoma spp, Diadesmis contenta, Eunotia papillo, E. bilunaris, E. intermedia, E. sudetica, Aulacoseira alpigena, A. ambigua, Cymbopleura naviculiformis and Stauroneis phoenicenteron. Urban sites, with medium to bad water quality (BOD5 = ~7 mg∙ℓ-1, DO = ~7 mg∙ℓ-1, phosphate = 12.6 to 83.1 μg∙ℓ-1), were characterised by Diadesmis dissimilis, Frustulia rhomboids, Nitzschia scalaris, Nitzschia linearis, Cyclotella pseudostelligera Neidium ampliatum, N. affine, Encyonema silesiacum, E. neomesianum,Aulacoseira granulata, Navicula cryptotenella, Pinnularia legumen, P. gibba, P. divergens, Surirella linearis, S. robusta, and Achnanthidium minutissimum. Downstream urban sites, with very bad water quality (BOD5 = 19.5 to 26.2 mg∙ℓ-1, DO = 0.4 to 1.9 mg∙ℓ-1, phosphate = 142.5 to 248.7 μg∙ℓ-1), were characterised by Gomphonema parvulum, G. accuminatum, Nitzschia palea, Nupela praecipua, Sellaphora pupula, Planotidium lanceolata, Fallacia monoculata and Pinnularia subcapitata. Diatom communities demonstrated potential for acting as indicators of changes in water quality due to changes in catchment land-use patterns.Keywords: land-use, benthic diatoms, environmental gradient, agricultural, forests, urban

Choice of biota in stream assessment and monitoring programs in tropical streams: A comparison of diatoms, macroinvertebrates and fish

In the present study, the Biological diatom index (BDI) and the Trophic diatom index (TDI) were calculated for the assessment the ecological status and the water quality of the Sai Gon River in comparison with the physico-chemical variables. In addition, a multivariate method was used to elucidate the main environmental variables driving the diatom community. A total of 87 diatom species were identified and used to calculate the diatom indices. The results of the biological data indicate that ecological status of upstream has a fine water quality; however, the downstream of the river was moderately polluted, and in some cases, of poor status. Canonical correspondence analysis (CCA) permutation tests demonstrated that diatom community was divided into two groups that corresponded to rural and urban characteristics. The BDI and TDI indices showed sensitivity to environmental stressors and served as potential application for bio-monitoring and water quality assessment of surface water in tropical region.

Diatoms are good indicators of water quality in lotic systems. Unlike in the temperate region, the effect of substrate on diatom-based water quality assessment in tropical streams is not fully understood. The purpose of this study was to assess the effect of substrate on diatom-based multivariate water quality assessment. Epilithic, epiphytic, epipsammic and epipelic diatom community and water quality sampling was done four times at 10 sites during the dry season (2008 and 2009). Artificial substrates (brick and glasses) were also placed at the sampling sites during this period and sampled after 1 month. Cluster analysis was performed to show the main differences and similarities in community composition amongst substrates sampled and amongst sampling sites. The IndVal method was used to identify indicator species characterising different substrates. Canonical correspondence analyses (CCAs) were performed to relate the structure of diatom communities from different substrates to predictor variables. A gradient of increasing metal and organic pollution, eutrophication and ionic strength was observed from the agricultural/forested area to the urban area. Diatom community structure closely reflected this gradient, with communities from polluted sites (8, 9 and 10) being different from other communities. Polluted sites were associated with such species as Nitzschia palea, Plantago lanceolata, Achnanthes exigua, Caloneis hyaline, Cyclotella meneghiniana, Gomphonema parvulum, Fallacia monoculata, Luticola goeppertiana, Pinnularia microstauron, Pinnularia subcapitata and Sellaphora pupula. Indicator species analysis showed that common diatom species were not restricted to a single substrate, though preference was generally high for natural (especially macrophytes) compared to artificial substrates. Six CCAs corresponding to six substrates performed to relate diatom community structure to simultaneous effects of predictor variables explained ∼50% of the diatom species variance in all cases and roughly separated highly polluted sites from the rest of the sites. This indicates that the results of diatom-based multivariate water quality assessment based on different substrates may be interchangeable. Only one substrate has to be collected at each site for water quality assessment surveys, thus avoiding unnecessary expensive and time-consuming oversampling. Given the limitations of artificial substrates, sampling of natural substrates is highly recommended.

The study was conducted in March 2019 in three areas subject to impacts of agricultural production, residential areas and landfill in An Giang (Area 1), Kien Giang (Area 2) and Can Tho (Area 3), respectively, to assess relationship between water quality and diversity of phytoplankton. The results showed that water quality at 25 study sites is contaminated with organic matters, suspended solids and coliforms. The study found 422 species of phytoplankton belonging to five phyla of Bacillariophyta, Chlorophyta, Dinophyta, Cyanophyta and Euglenophyta. The density of phytoplankton in the three studied areas ranged from 13 to 77,328 individuals L-1. Among the areas, Area 1 has the highest species composition and density, followed by Area 2 and then Area 3. Among the phytoplankton species occurrence, Melosira granualata, Cyclotella meneghiniana, Cyclotella comta, Trachelomonas sp., Glenodinium beronense, Oscillatoria muticola and Skeletonema costatum dominated and indicated the water environment with high organic matters, nutrient-rich and salty condition. Water quality index (WQI=57-88) indicated water quality ranged from good to medium whereas Shannon-Weiner diversity index (H’=0.71-3.89) showed water quality from medium to heavy pollution. Approximate 56% of the studied sites have similarities in water quality evaluated medium pollution using WQI and H’ although the canonical correspondence analysis (CCA) results indicated that the distribution and abundance of phytoplankton was positively correlated with N-NH4+, P-PO43-, BOD and TSS. It was suggested that H’ is a good water quality indicator for uncontaminated freshwater, but not for saline water or highly complicated contaminating water. The findings revealed that H’ only partially indicates water quality, thus examining physicochemical water quality variables for water quality monitoring is essential.

This study, carried out seasonally between October-2019 and July-2020, aimed to determine the water quality using some water and epilithic diatom indices of the Köprüçay River. It is located in the south of Türkiye and used for tourism, irrigation and drinking water. Ammonium nitrogen (NH4–N), nitrate nitrogen (NO3–N), sulfate (SO4 −2), bicarbonate (HCO3 −), orthophosphate (PO4–P), chloride (Cl−), biochemical oxygen demand (BOD5), temperature (°C), dissolved oxygen, pH, and electrical conductivity were measured. Water quality was determined according to the Surface Water Quality Regulation (SWQR) and Water Quality Index (WQI). The water quality classes of the stream, based on epilithic diatom assemblages, were determined using the Generic Diatom Index (GDI), Saprobi Index (SI), Trophic Index (TI), Swiss Diatom Index (DI-CH), and Trophic Diatom Index (TDI). According to SWQR, the average values of the parameters at all sites were generally in the class I or II (high quality or lightly polluted water). WQI, was calculated based on seasonal and site and all results were determined as “excellent water”. 117 taxa belonging to 51 genera of epilithic diatoms were observed in the Köprüçay River. According to epilithic diatoms, generally all sites were in the range of very slightly polluted or partially polluted (I and II) water quality classes.

Seasonality can play a crucial role in altering water quality in tropical rivers, and as a benthic community, diatom can show seasonal variation and changes in ecological status. During the present study, the Trophic Diatom Index (TDI) and Water Quality Index (WQI) were used to determine the ecological status of a transboundary river, the Sari-Goyain River in Bangladesh. Samplings were carried out from upstream to downstream river sites in wet and dry seasons to observe the seasonal dynamics. The benthic diatom composition and physicochemical parameters showed seasonal variation in ecological water quality assessment. In the River, 42 different diatom species from 19 genera were recorded. The mean TDI values indicated an oligotrophic condition of the river in both seasons. But, the WQI values showed excellent and good water quality in the wet and dry seasons, respectively. So, the WQI was helpful in assessing seasonal variation of ecological water quality status in the Sari-Goyain River. For the long-term monitoring of the ecological status of the river, seasonal variation and WQI-based assessment should be considered.

In the past few decades, global industrial development and population growth have led to a scarcity of water resources, making sustainable management of groundwater a global challenge. The Water Quality Index (WQI) serves as a comprehensive method for assessing water quality and can provide valuable recommendations at the water quality level, optimizing policies for groundwater management. However, the subjectivity and uncertainty of the traditional WQI have negative impacts on evaluation outcomes, particularly in determining indicator weights and selecting aggregation functions. The proposed water quality index for groundwater based on the random forest (RFWQI) model in this study addresses these issues. It selects water quality indicators based on the actual pollution situation in the study area, employs an advanced random forest model to rank water quality indicators, determines indicator weights using the rank centroid method, scores the indicators using a sub-index function designed for groundwater development, and compares the results of two commonly used aggregation functions to identify the optimal one. Based on the aggregated scores, the water quality at 137 monitoring sites is classified into five levels: “Excellent”, “Good”, “Medium”, “Poor”, or “Unacceptable”. Among the 11 water quality indicators (sodium, sulfate, chloride, bicarbonate, total dissolved solids, fluoride, boron, nitrate, pH, CODMn, and hardness), chloride was given the highest weight (0.236), followed by total dissolved solids (0.156), and sodium was given the lowest weight (0.008). The random forest model exhibits a good prediction capability before hyperparameter tuning (86% accuracy, RMSE of 0.378), and after grid search and five-fold cross-validation, the optimal hyperparameter combination is determined, further improving the performance of the random forest model (94% accuracy, F1-Score of 0.967, AUC of 0.91, RMSE of 0.232). For the newly developed groundwater sub-index function, interpolation is used to score each indicator, and after comparing two aggregation functions, the NSF aggregation function is selected as the most suitable for groundwater assessment. Overall, most of the groundwater in the study area was of poor quality (52.5% of low quality) and not suitable for drinking.

Proper evaluation of water quality is pertinent to estuarine habitat restoration. Identifying the degrading factors of the water environment and predicting the trend of eutrophication are key to restore the habitat. Through trophic level index (TLI), water quality index (WQI), modified Nemerow pollution index (NPI), and the Random Forest (RF) model, water samples collected from various estuaries of Taihu Lake from 2017 to 2019 were evaluated. To predict the water quality development, four scenarios were set viz. S1: add or remove an ecological buffer, S2: increase or reduce the external nutrients, S3: open or close the dam/gate, and S4: increase or decrease the internal release. In Wuli Lake, the nutrient concentrations in the river regions were higher than in the lake regions, while a contrary trend was observed in Gonghu Bay. The estuarine water quality in the dry season (WQI = 40.91, NPI = 1.73) was merely worse than that in the wet season (WQI = 47.27, NPI = 1.67). On the other hand, the eutrophic status in the wet season (TLIWet = 57.93) was worse than that in the dry season (TLIDry = 57.23). The estuarine water quality of Taihu Lake has improved from 2017 to 2019 but still belongs to medium level. The principal component analysis (PCA) revealed that dam construction, land use types, unstable hydrodynamic conditions, and trumpet-shaped estuary were the main factors that aggravated the water quality degradation. The RF model has strong forecasting capabilities for estuarine water quality. When the estuaries are close to residential and industrial districts, controlling the surface runoff and improving sewage treatment efficiency are the most effective measures to improve the water quality. In the estuaries, the sediments are usually disturbed by the wind-waves. Conclusively, reducing sediment disturbance and internal contamination accumulation via biological and engineering measures is the key to estuarine restoration.

This paper examines the efficacy of diatoms as bioindicators of water quality in the upper reaches of the Great Fish River following a period of reduced flow from drought conditions. Of the five sites, three were sampled three times in an 18 month period while the remaining two were sampled once. As a comparison, one headwater site within Mountain Zebra National Park, situated in the same district, was sampled. A total of 166 diatom taxa belonging to 29 genera were identified. Dominant taxa for the Great Fish River were identified as Amphora pediculus; Epithemia sorex; Nitzschia frustulum; Navicula veneta and Craticula buderi. These species, indicative of high nutrient concentrations and moderately saline to brackish conditions can tolerate low flow conditions. The Generic Diatom Index (GDI), the Specific Pollution sensitivity Index (SPI) the Biological Diatom Index (BDI) and the% Pollution Tolerant Valves (%PTV) – part of the UK Trophic Diatom Index (TDI) were used for interpretation of the results. The indices showed that this river is in poor condition. By comparison the headwater site in the Mountain Zebra National Park had Cocconeis placentula var. euglypta, Achnanthidium minutissimum and Cocconeis placentula var. lineata as dominant species and, using the same indices, the river was classified as in moderate to good condition with respect to water quality. When compared to a previous study (2010 – 2012), these sites showed a shift in dominant species indicating a change in water flow conditions and quality.