Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Ságová-Marečková, Markéta; Boenigk, Jens; Bouchez, Agnès; Cermakova, Kristina; Chonova, Teofana; Cordier, Tristan; Eisendle, Ursula; Eleršek, Tina; Fazi, Stefano; Fleituch, Tadeusz; Frühe, Larissa; Gajdošová, Magdalena; Graupner, Nadine; Haegerbaeumer, Arne; Kelly, Anita M.; Kopecký, Jan; Leese, Florian; Nõges, Peeter; Orlić, Sandi; Panksep, Kristel; Pawłowski, Jan; Petrusek, Adam; Piggott, Jeremy J.; Rusch, Johannes C.; Salis, Romana K.; Schenk, Janina; Šimek, Karel; Šťovíček, Adam; Strand, David; Vasquez, Marlen I.; Vrålstad, Trude; Zlatkovic, S.; Zupančič, Maša; Stoeck, Thorsten

doi:10.1016/j.watres.2020.116767

Cited by 132 publications

(53 citation statements)

References 253 publications

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“…However, the multidimensional and noisy data sets are common in the high-throughput sequencing data. To explore the ecological signal from background noise, machine learning algorithms (such as RF model) have been attempted to prove correlations between high-throughput sequencing data and environmental stressors ( Sagova-Mareckova et al, 2021 ). We identified microeukaryote taxa at the order level that were discriminant of lake salinity using the RF model, therefore it is likely that this model allows for generalization of predictability across continental scales compared with lower-resolution taxonomic levels ( Edwards et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Salinity Is a Key Determinant for the Microeukaryotic Community in Lake Ecosystems of the Inner Mongolia Plateau, China

Liu

Jiang

et al. 2022

Front. Microbiol.

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The arid and semiarid areas experienced remarkable lake shrinkage during recent decades due to intensive human activities and climate change, which would result in unprecedented changes of microeukaryotic communities. However, little is known about how climate change affects the structure and ecological mechanisms of microeukaryotic communities in this area. Here, we used an 18S rRNA gene-based high-throughput sequencing approach to explore the structure, interspecies interaction, and assembly processes of the microeukaryotic community in lake ecosystems of the Inner Mongolia Plateau. As a direct result of climate change, salinity has become the key determinant of the lacustrine microeukaryotic community in this region. The microeukaryotic community in this ecosystem can be divided into three groups: salt (Lake Daihai), brackish (Lake Dalinuoer) and freshwater lakes. Co-occurrence network analysis revealed that salinity shapes the interspecies interactions of the microeukaryotic community. This causes interspecies interactions to change from antagonistic to cooperative with an increase in salinity. Phylogenetic-based β-nearest taxon distance analyses revealed that stochastic processes mainly dominated the microeukaryotic community assembly in lake ecosystems of the Inner Mongolia Plateau, and salinity stress drove the assembly processes of the microeukaryotic community from stochastic to deterministic. Overall, these findings expand the current understanding of interspecies interactions and assembly processes of microeukaryotic communities during climate change in lake ecosystems of the Inner Mongolia Plateau.

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Section: Discussionmentioning

confidence: 99%

Salinity Is a Key Determinant for the Microeukaryotic Community in Lake Ecosystems of the Inner Mongolia Plateau, China

Liu

Jiang

et al. 2022

Front. Microbiol.

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“…Their integration to environmental assessment using high-throughput sequencing and metabarcoding technologies is thus promising, providing a more holistic overview of the response of aquatic ecosystems to environmental changes. This is even more relevant as the science is moving toward ecosystem-wide food web modelling 20,51,63 , and protists, as key players of the microbial food-web, serve an important function of recycling carbon and energy in lakes.…”

Section: Discussionmentioning

confidence: 99%

“…This includes the reconstruction of the long-term dynamic of micro-organisms 18 which represent the largest source of biodiversity and ecological functions, but have long been omitted from debates concerning the response of the global biodiversity, in part due to the lack of data 19 . As such, sed-DNA offers new opportunities to reconstruct a more holistic view of the long-term response of lakes to environmental changes 18,20 . For instance, through the implementation of new paleoindicators, sed-DNA can allow to reconstruct the long-term dynamic of overlooked communities such as the communities of the microbial loop that play a key role in the functional ecology of lakes.…”

Section: Introductionmentioning

confidence: 99%

Changes in Ciliate Communities Reveal Modification of Lake Functioning Over the Last Century

Barouillet

Vasselon

Keck

et al. 2021

Preprint

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Ciliates are unicellular heterotrophic organisms that play a key role in the planktonic and benthic food webs of lakes, and represent a great potential as bioindicator. In this study, we used the top-bottom paleolimnological approach to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient using metabarcoding techniques applied on sedimentary DNA (sed-DNA). Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes which are more strongly expose to local human pressure. Analyses of the functional groups indicate important restructuration of the trophic food web and changes that are consistent with several well documented environmental changes such as the widespread increase in deep water anoxia, changes in thermal stability and nutrient cycling. Our study demonstrates the potential offered by sed-DNA to uncover information about past ciliate communities on a wide variety of lakes and the potential of using ciliates as valuable indicators, integrating information from the pelagic to the benthic profundal (and littoral) zones. Through trait-based functional community approach, the ciliates provide additional valuable information on ecosystem functioning, thus offering more a holistic view on the long-term changes of aquatic ecosystems.

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“…Although some researchers also declared that some specific microbes were always inhabited in the polluted environment to improve the tolerance of the ecosystem (Tolkkinen et al, 2015;Garcia et al, 2018), we are still dubious about connecting these specialized microbes to the pollution directly. Sagova-Mareckova et al argued that because of the close biotic interactions including trophic relationships, symbiosis, parasitism or chemical communication in microbial communities, calculation considering the multi-species and community approaches should be more reliable for the microbial index of ecological status (Sagova-Mareckova et al, 2021). To figure out this question, we need more knowledge about the metabolic and physiological properties of these microbes.…”

Section: Microbial Index Of Ecological Status In Sediment Profilementioning

confidence: 99%

Deciphering Historical Water-Quality Changes Recorded in Sediments Using eDNA

Sun

Chen

et al. 2021

Front. Environ. Sci.

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Reservoir sediments harbor abundant bacterial communities that are sensitive to substances transferred from the water column and might record historic water quality in environmental DNA (eDNA). The unique bacterial community along the sediment profile were retrieved based on eDNA in a reservoir to investigate potential links between water quality and the microbial population on a long-time scale. Bacterial communities in sediment samples gathered into three clusters along the depth (depths of 18–38, 8–18, and 1–7 cm). These three sections accumulated during three periods in which water quality was recorded in history (the pristine stage, degraded stage and remediated stage). Sediment samples from the degraded stage had lower microbial community evenness and diversity and higher microgAMBI indices than the other two sections, suggesting that poor water quality during that period was recorded in sedimental eDNA. After decades of biogeochemical cycles, statistical analysis revealed that the main factors affecting the microbial community were bromine, chlorine, and high molecular-weight PAHs in sediments from the degraded stage. The relevant functional groups Dehalococcoidia, Gemmatimonadales, Sva0485, Burkholderiales and Xanthomonadales might be indicators of the historical loading of these pollutants. Amending the microgAMBI index with our functional group of pollution can better illustrate the significant long-term environmental changes caused by historic anthropogenic activities. In sediments from the pristine stage with less pollution input, DIC (dissolved inorganic carbon) from the karst landform was the dominant factor controlling microbial communities. Whereas, the surface sediments, which accumulated during the remediated stage, had more correlation with chemistry, such as sulfate and heavy metals, in the overlying water. Our research revealed that historical changes in the water condition, that can be affected by anthropogenic activities, can be depicted by changes in the bacterial communities stored in the sediment using sedimental eDNA. Assessments of the bacterial communities in the sediments, either by describing their biodiversity or using particular species as indicators, would be potential proxies to describe historical environmental development of microbial communities.

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Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Cited by 132 publications

References 253 publications

Salinity Is a Key Determinant for the Microeukaryotic Community in Lake Ecosystems of the Inner Mongolia Plateau, China

Salinity Is a Key Determinant for the Microeukaryotic Community in Lake Ecosystems of the Inner Mongolia Plateau, China

Changes in Ciliate Communities Reveal Modification of Lake Functioning Over the Last Century

Deciphering Historical Water-Quality Changes Recorded in Sediments Using eDNA

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