Assessing ecological status in karstic lakes through the integration of phytoplankton functional groups, morphological approach and environmental DNA metabarcoding

Hanžek, Nikola; Udovič, Marija Gligora; Kajan, Katarina; Borics, Gábor; Várbíró, Gábor; Stoeck, Thorsten; Žutinić, Petar; Orlić, Sandi; Stanković, Igor

doi:10.1016/j.ecolind.2021.108166

Cited by 12 publications

(4 citation statements)

References 53 publications

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“…The highest production rates correspond to years of highest chironomid abundances, and the same goes for the years with lowest rates. Lake Kozjak is known to normally fluctuate between these two trophic states [43,61]. This study shows that in years of high chironomid emergence, up to 4400 mg m −2 y −1 of chironomid biomass is available to terrestrial animals either directly as prey or indirectly as carcasses that decay on the soil surface [62].…”

Section: Magnitude Of Chironomid Emergencementioning

confidence: 82%

Long-Term Chironomid Emergence at a Karst Tufa Barrier in Plitvice Lakes National Park, Croatia

Dorić,

Pozojević,

Baranov

et al. 2024

Insects

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Chironomids are found in all types of freshwater habitats; they are a ubiquitous and highly diverse group of aquatic insects. Plitvice Lakes National Park is the oldest and largest national park in Croatia and consists of numerous and diverse freshwater habitats, making the area an ideal location for long-term research into the chironomid emergence patterns and phenology. The main objectives of this study were to identify the composition of the chironomid community, determine the phenology of the identified species, and assess the main factors influencing their emergence in Plitvice Lakes. During 14 years of research, more than 13,000 chironomids belonging to more than 80 species were recorded. The most abundant species was found to be Parametriocnemus stylatus. The highest abundance of chironomids was recorded in lotic habitats with faster water current over substrates of moss and algae and pebbles. Water temperature and the availability of organic matter were found to be the main factors that drive chironomid emergence at the tufa barrier studied. In the last years of this study, a prolonged flight period was observed. Although this is not statistically significant (at this stage of the study), it could be due to a higher water temperature in winter.

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Section: Magnitude Of Chironomid Emergencementioning

confidence: 82%

Long-Term Chironomid Emergence at a Karst Tufa Barrier in Plitvice Lakes National Park, Croatia

Dorić,

Pozojević,

Baranov

et al. 2024

Insects

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“…In addition, the use of environmental DNA (eDNA) as a biomonitoring method that can be used for the sampling of diatoms, macroinvertebrates, and multiple taxonomic groups from aquatic ecosystems in a non-destructive framework [137] arises mainly due to the limitations and bottlenecks described above (sampling bias, taxonomy skills, and time inefficiency) [30]. Furthermore, the eDNA method has been used to propose many objectives for diversity measurements in multiple taxa [138][139][140], integration of ecological status assessments [141], invasive alien species monitoring [108], and hypotheses such as the rivers being a kind of "biodiversity conveyor belts" across terrestrial and aquatic ecosystems [142].…”

Section: Omics In Freshwater Biomonitoring: a Multifaceted Frameworkmentioning

confidence: 99%

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Machuca-Sepúlveda

Miranda

Lefin

et al. 2023

Biology

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Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.

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“…Environmental DNA metabarcoding technology is used for qualitative and quantitative analysis of organisms through collection of environmental samples, enrichment, DNA extraction, selection of molecular markers, design of universal primers for their amplification, and high-throughput sequencing. In recent years, eDNA technology has been used in various applications such as species diversity monitoring (Plough et al, 2018;Webster et al, 2020;Zou et al, 2020;Jia et al, 2021;DiBattista et al, 2022;Knudsen et al, 2022), invasive species detection, and biomass assessment (Tillotson et al, 2018;Fraija-Fernandez et al, 2020;Wang et al, 2020;Hanzek et al, 2021). The method has been used to detect target species (Baudry et al, 2021;Matthias et al, 2021;Brand et al, 2022;Ruppert et al, 2022), for example, in 2021 to detect giant catfish in the Mekong River (Osathanunkul, 2022).…”

Section: Introductionmentioning

confidence: 99%

Optimization of pore size and filter material for better enrichment of environmental DNA

Liu,

Tan,

Wang

et al. 2024

Front. Environ. Sci.

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In the study of environmental DNA (eDNA), the rate of water filtration and the amount of DNA obtained are of general interest to researchers. We compared the PCTE filters with different pore sizes in enriching total DNA and fish eDNA from water samples. We also designed and tested a new filter device with a PET pad (5 µm) superimposed on a PCTE membrane (3 µm) and compared it to a pure PCTE filter. A comprehensive evaluation of filtration time, eDNA concentration, fish DNA quantification, and fish species detected showed that the shortest average filtration time was obtained with the 8 μm pore size (2 min 9 s) and the longest average filtration time was obtained with the 0.2 μm pore size (32 min 6 s). The highest average DNA concentration was 3.785 ng/μL for the 0.2 μm filter and the lowest was 0.577 ng/μL for the 8 μm filter; meanwhile, the concentrations of fish DNA measured by quantitative PCR were 5.02E+02(8 μm), 4.79E+02(3 μm), 1.63E+03(1.2 μm), 5.95E+03(0.2 μm) copies of fish DNA per µl and there was no significant difference in the results between them (p > 0.05). The sequencing results showed that 17 fish species were detected in the 0.2 μm filter, 10 species in the 1.2 μm filter, 12 species in the 3 μm filter and 11 species in the 8 μm filter. Comparing to 3 μm and 0.2 um, the average filtration time in stacked-filter was reduced by 4 and 24 min, respectively, while the average concentration was 2.46 and 1.55 times higher than the former. The qPCR results showed that the number of eDNA copies of the samples enriched with the 3 µm and stacked-filter was 4.79E+02 and 1.53E+04, respectively. 3 μm and stacked-filter showed significant differences (p < 0.05), while 0.2 µm and stacked-filter did not show significant differences (p > 0.05). Sixteen fish species were detected by the stacked-filter. The number of eDNA obtained and the number of fish species detected were higher than those of the pure PCTE filter, while clogging during filtration was effectively avoided. We recommend using the stacked-filter to enrich eDNA from water samples.

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Assessing ecological status in karstic lakes through the integration of phytoplankton functional groups, morphological approach and environmental DNA metabarcoding

Cited by 12 publications

References 53 publications

Long-Term Chironomid Emergence at a Karst Tufa Barrier in Plitvice Lakes National Park, Croatia

Long-Term Chironomid Emergence at a Karst Tufa Barrier in Plitvice Lakes National Park, Croatia

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Optimization of pore size and filter material for better enrichment of environmental DNA

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