The differential expression of Chironomus spp genes as useful tools in the search for pollution biomarkers in freshwater ecosystems

Surveillance spilled Chironomidae (Diptera) larvae from drinking water treatment plants in South Korea using morphogenetic species analysis and eDNA metabarcoding

Chironomid larvae (Diptera: Chironomidae) are tremendous indicator species that can tolerate a broad range of environmental conditions, from polluted to unimpaired water ecosystems. These species are ubiquitously observed in all bioregions and can even be found in drinking water treatment plants (DWTPs). Detection of chironomid larvae in DWTPs is a critical issue because their presence may be indicative of the water quality in the supply of tap water for human consumption. Therefore, the aim of the present study was to identify the chironomid communities that reflect the water quality of DWTPs and develop a biomonitoring tool to detect biological contamination of the chironomids in DWTPs. To do so, we investigated the identity and distribution of chironomid larvae in seven DWTP areas using morphological identification, DNA barcoding, and sediment environmental DNA (eDNA) analysis. A total of 7924 chironomid individuals encompassing three subfamilies and 25 species of 19 genera were identified in 33 sites within the DWTPs. The Gongchon and Bupyeong DWTPs were dominated by Chironomus spp. larvae, which were correlated with low levels of dissolved oxygen in the water. In the Samgye DWTP and Hwajeong DWTP, Chironomus spp. were almost absent, and instead, Tanytarsus spp. were abundant. Additionally, the Gangjeong DWTP was dominated by a Microtendipes sp., and two species of Orthocladiinae (a Parametriocnemus sp. and a Paratrichocladius sp.) were found only in the Jeju DWTP. We also identified the eight most abundant Chironomidae larvae found in the DWTPs. Furthermore, eDNA metabarcoding of DWTP sediment indicated the presence of different eukaryotic fauna and confirmed the presence of chironomids in DWTPs. These data provide useful morphological and genetic information regarding chironomid larvae that can be used for the water quality biomonitoring of DWTPs to support the supply of clean drinking water.

Sex-specific alterations in adaptive responses of Chironomus columbiensis triggered by imidacloprid chronic and acute sublethal exposures

The use of imidacloprid is a common pest control practice in the Neotropical region. However, the imidacloprid unintended sublethal effects on Neotropical aquatic non-target arthropods and undesirable consequences for aquatic environments remain unclear. Here, we assessed the susceptibility of Chironomus columbiensis (Diptera: Chironomidae) larvae to the neonicotinoid imidacloprid and evaluated whether sublethal exposure types would trigger sex-dependent adaptive responses (e.g., emergence, body mass, reproduction, wing morphology). We conducted a concentration-mortality curve (96 h of exposure) and established chronic and acute sublethal exposure bioassays. While chronic sublethal exposures consisted of exposing individuals during their entire larval and pupal stages, the acute sublethal exposures represented a single short duration (24 h) exposure episode during either the first or fourth larval instar. Our results revealed that chronic sublethal exposure reduced the body mass of males, while acute sublethal exposures during the first instar resulted in heavier males than those that were not exposed to imidacloprid. Chronic exposure also reduced the reproduction of males and females, while the acute sublethal exposure only affected the reproduction of individuals that were imidacloprid-exposed on their later larval instar. Chronic and acute sublethal exposures did differentially affect the wing properties of C. columbiensis males (e.g., increased size when chronically exposed and highly asymmetric wings when acutely exposed in early larval phase) and females (e.g., highly asymmetric wings when chronically and acutely exposed). Collectively, our findings demonstrated that imidacloprid can cause unintended sublethal effects on C. columbiensis, and those effects are dependent on sex, exposure type, and developmental stage.

Analysis of Differential Gene Expression of the Aquatic Insect Protohermes costalis (Walker) (Megaloptera: Corydalidae) in Response to Cadmium Exposure

Heavy metal pollution in freshwater ecosystems is a serious threat to aquatic organisms. Species of Megaloptera are important predators of aquatic invertebrates and have been widely used as bioindicators in assessing the quality of freshwater ecosystems. In this study, we determined the differential gene expression profile of Protohermes costalis (Walker) (Megaloptera: Corydalidae) in response to cadmium (Cd) exposure by using transcriptome analysis. A total of 60,627 unigenes were obtained in the transcriptomes of 150 mg/liter (PL), 1,000 mg/liter (PH) CdCl2 treatment, and the no Cd control (PC). Differential expression gene (DEG) analysis by pairwise comparison identified 2,794 DEGs after filtering the noninsect genes and repetitive counts. 606 DEGs were shared in comparisons of PL versus PC and PH versus PC, with 165 DEGs consistently up-regulated and 441 down-regulated by both PL and PH. Six heat shock proteins (HSPs) in the HSP70 family were identified in P. costalis and PcosHSP68 was up-regulated by both PL and PH. Real-time quantitative polymerase chain reaction (RT-qPCR) confirmed that the expression levels of PcosHSP68 in PL and PH were higher than that of PC by 31 and 197%, respectively. These results showed that exposure to Cd altered the gene expression profiles of P. costalis and the transcriptome data presented in this study provide insight into future studying on molecular mechanisms of Cd toxicity to these insects.

Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review

While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment.

Improved Chironomid Barcode Database Enhances Identification of Water Mite Dietary Content

Chironomids are one of the most biodiverse and abundant members of freshwater ecosystems. They are a food source for many organisms, including fish and water mites. The accurate identification of chironomids is essential for many applications in ecological research, including determining which chironomid species are present in the diets of diverse predators. Larval and adult chironomids from diverse habitats, including lakes, rivers, inland gardens, coastal vegetation, and nearshore habitats of the Great Lakes, were collected from 2012 to 2019. After morphological identification of chironomids, DNA was extracted and cytochrome oxidase I (COI) barcodes were PCR amplified and sequenced. Here we describe an analysis of biodiverse adult and larval chironomids in the Great Lakes region of North America based on new collections to improve chironomid identification by curating a chironomid DNA barcode database, thereby expanding the diversity and taxonomic specificity of DNA reference libraries for the Chironomidae family. In addition to reporting many novel chironomid DNA barcodes, we demonstrate here the use of this chironomid COI barcode database to improve the identification of DNA barcodes of prey in the liquefied diets of water mites. The species identifications of the COI barcodes of chironomids ingested by Lebertia davidcooki and L. quinquemaculosa are more diverse for L. davidcooki and include Parachironomus abortivus, Cryptochironomus ponderosus. Parachironomus tenuicaudatus, Glyptotendipes senilis, Dicrotendipes modestus, Chironomus riparius, Chironomus entis/plumosus, Chironomus maturus, Chironomus crassicaudatus, Endochironomus subtendens, Cricotopus sylvestris, Cricotopus festivellus, Orthocladius obumbratus, Tanypus punctipennis, Rheotanytarsus exiguus gr., and Paratanytarsus nr. bituberculatus.

Multi-Level Gene Expression in Response to Environmental Stress in Aquatic Invertebrate Chironomids: Potential Applications in Water Quality Monitoring

In freshwater ecosystems, aquatic invertebrates are influenced continuously by both physical stress and xenobiotics. Chironomids (Diptera; Chironomidae), or non-biting midges, are the most diverse and abundant invertebrates in freshwater habitats. They are a fundamental link in food chains of aquatic ecosystems. Chironomid larvae tolerate stress factors in their environments via various physiological processes. At the molecular level, environmental pollutants induce multi-level gene responses in Chironomus that regulate cellular protection through the activation of defense processes. This paper reviews literature on the transcriptional responses of biomarker genes to environmental stress in chironomids at the molecular level, in studies conducted from 1991 to 2020 (120 selected literatures of 374 results with the keywords "Chironomus and gene expression" by PubMed search tool). According to these studies, transcriptional responses in chironomids vary depending on the type of stress factor and defensive responses associated with antioxidant activity, the endocrine system, detoxification, homeostasis and stress response, energy metabolism, ribosomal machinery, apoptosis, DNA repair, and epigenetics. These data could provide a comprehensive overview of how Chironomus species respond to pollutants in aquatic environments. Furthermore, the transcriptomic data could facilitate the development of genetic tools for water quality and environmental monitoring based on resident chironomid species.

Developmental/reproductive effects and gene expression variations in Chironomus riparius after exposure to reclaimed water and its fortification with carbamazepine and triclosan

The potential benefits of reclaimed water (RW) uses for environmental enhancement and restoration could become adverse impacts if RW does not meet the quality criteria that ensure wildlife preservation. RW can contain complex mixtures of micropollutants that may accumulate in sediment after environmental uses and affect benthic fauna. Therefore, we designed this study to assess the effects of RW on a sediment insect species used mainly in ecotoxicology (Chironomus riparius). Whole organism effects and gene expression were measured in a water sediment system after spiking RW as overlying water, which was renewed 3 times during the test. Development rate, emergence rate and fecundity were monitored after the 21-day exposure. Endocrine-related genes (EcR, ERR, E75, Vtg), cellular stress genes (hsp70, hsc70, hsp24, hsp10) and biotransformation genes (gp93, GSTd3, GPx, cyp4g) were assessed in larvae after the 10-day exposure. The experimental design also included single or binary fortifications of both test medium and RW, obtained by adding two emerging pollutants: carbamazepine (100 μg/L CBZ) and triclosan (20 μg/L TCS). The chemical characterisation of RW showed that 20 of the 23 screened emerging pollutants fell within the detection limit, 10 exceeded 0.01 μg/L (including CBZ) and three exceeded 0.1 μg/L (hydrochlorothiazide, atenolol, ibuprofen). The analytical measures of sediment (day 21) and overlying water (days 7, 14 and 21) were taken to know the water-sediment distribution of CBZ and TCS added to fortifications. CBZ distributed mainly in overlying water (110-164 μg/L and 73-100 μg/kg), while TCS showed a higher affinity to sediment (2.8-5.1 μg/L and 36-55 μg/kg). RW had significant effects in molecular terms (Vtg, hsp70, hsc70), but had no significant effects on the whole organism. Nevertheless, the single RW fortifications impaired both the development rate and fecundity, while the binary RW fortification impaired only fecundity. The most marked increase in EcR expression was observed for the binary RW fortification. Hsps, GSTd3 and cyp4g showed a similar tendency to that observed for EcR and Vtg in the binary and single RW fortifications. The binary mixture (CBZ and TCS together) in RW was toxic, but not in the medium tests. Therefore, the major concern of RW uses is apparently related to the interactivity between this complex matrix and any other pollutants possibly present in the environment where RW is applied. Our results underscore the need for raising awareness about RW effects, which can be achieved by ecotoxicological testing.

Cadmium-induced developmental alteration and upregulation of serine-type endopeptidase transcripts in wild freshwater populations of Chironomus plumosus

Cadmium, a toxic heavy metal, is a persistent environmental contaminant with irreversible toxicity to aquatic organisms. Chironomus plumosus, a natural species, is the largest sediment-burrowing aquatic midge in freshwater environments. In this study, we evaluated developmental defects in C. plumosus resulting from Cd exposure. In C. plumosus larvae, Cd exposure induced decreased survival and growth rates, reduction of emergence rate and sex ratio, and delayed emergence, as well as elevating the incidence of split tooth deformities. To identify potential biomarker genes to assess environmental pollutants such as Cd, we identified differentially expressed genes (DEGs) in C. plumosus exposed to various Cd concentrations. Among fourteen characterized DEGs, serine-type endopeptidase (SP) and heat shock protein 70 (HSP70) genes exhibited significant upregulation in C. plumosus larvae after Cd exposure. Therefore, we evaluated SP and HSP70 responses in natural C. plumosus populations collected from three sites of a Korean river and analyzed their correlations with eighteen environmental quality characteristics using principal component analysis. The highest expression of SP and HSP70 transcripts was observed in C. plumosus populations from Yeosu in Korea, which has high concentrations of polluting heavy metals. SP transcript expression was positively correlated with concentrations of Cd, Pb, Al, Fe, NO2, and NO3. These results suggested that environmental pollutants such as Cd can impair proteolytic activity in the digestive system of C. plumosus and may ultimately induce developmental alterations. We therefore suggest SP as a potential biomarker to assess the effects of environmental pollutants in aquatic ecosystems.

Environmental benchmarks based on ecotoxicological assessment with planktonic species might not adequately protect benthic assemblages in lotic systems

Freshwater ecosystems face widespread diffuse and point-source contamination. Species Sensitivity Distributions (SSDs) have been used as a tool to determine chemical concentration benchmarks that represent protective levels for most species in the environment. Here we used a SSD approach to assess on the adequacy of standard planktonic organisms to reflect the response of benthic communities, critically supporting the structure and function of lotic ecosystems. For the purpose, SSDs reflecting non-lethal responses of standard planktonic and selected benthic organisms were built based on EC50 values (collected in the literature or estimated following testing herein) regarding three model contaminants: potassium dichromate (PD), 3,5-dichlorophenol (DCP) and lead chloride (LC). The derived HC5 estimates were discriminatory between chemicals and the uncertainty associated with the estimate was remarkably low. The HC5 estimates with corresponding uncertainty were generally within the same order of magnitude for the three chemicals tested, with better discrimination between chemicals regarding their hazardous potential being achieved for benthic organisms: DCP was clearly less hazardous than PD, but LC tends to be as hazardous as PD and DCP (assuming the confidence interval ranges). Moreover, benthic communities were more sensitive to both DCP and PD, in this later case the HC5 being lower by more than one order of magnitude than that found for planktonic communities; for LC, confidence intervals overlapped, preventing a feasible assumption regarding differential sensitivity of the compared communities. Microphytobenthos was highlighted as the most sensitive group to the three tested chemicals in SSDs covering the benthic compartment, while SSDs with planktonic organisms did not consistently show trends in sensitivity ordering. Overall, our results suggest that protective benchmarks retrieved from SSDs built with the responses of standard planktonic organisms (which are the most commonly used for regulation purposes) do not adequately protect benthic communities.