Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes

Premke, Katrin; Wurzbacher, Christian; Felsmann, Katja; Fabian, Jenny; Taube, Robert; Bodmer, Pascal; Attermeyer, Katrin; Nitzsche, Kai Nils; Schroer, Sibylle; Koschorreck, Matthias; Hübner, Eric; Mahmoudinejad, Termeh Hesam; Kyba, Christopher C. M.; Monaghan, Michael T.; Hölker, Franz

doi:10.1016/j.envpol.2022.119627

Cited by 11 publications

(8 citation statements)

References 63 publications

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“…Ultimately, the DNA was stored at À80 C for long-term storage. We also tested benthic samples from surface waters derived from Premke et al (2022) or the local river Isar, Germany. DNA extracts from cultures of the fungal genera Candida, Tetracladium, Clavariopsis, and Dichotomacladium, as well as an undescribed strain of Chytridiomycota and a bacterium (Aquabacterium) were atested as outgroups.…”

Section: Sample Collection and Dna Extractionmentioning

confidence: 99%

“…To evaluate the 5.8S primer set even further, we tested two DHS samples and four environmental aquatic samples collected by Premke et al (2022), who already confirmed the presence of Cryptomycota by metabarcoding in these samples (S 5), for Illumina sequencing of the 5.8S amplicon. All samples showed the expected amplicon length (Figure 1; environmental samples 4 to 8), and we subjected them to Illumina sequencing.…”

Section: Evaluation Of Environmental Ampliconsmentioning

confidence: 99%

“…Furthermore, cultivation-based investigation often fails, as substrates or hosts are yet to be discovered. Typical trophic roles of aquatic fungi involve the degradation of allochthonous plant material, like leaf litter, and the parasitemediated mineralization of microscopic organisms (Wurzbacher et al, 2010). This biotrophic or saprotrophic lifestyle on organic particles results in a nondescript cell morphology, including zoospores, round-shaped sporangia, and cysts (Jobard et al, 2010), increasing the possibility of misidentification solely based on morphological characteristics (Lefèvre et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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Quantification of the dark fungal taxon Cryptomycota using qPCR

Stüer‐Patowsky,

Lilje,

Wurzbacher

2024

Environ Microbiol Rep

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Fungi are present in a wide variety of natural environments, and in the last years, various studies have shown that they are quite abundant in aquatic ecosystems. In addition, a whole new highly diverse phylum, the Cryptomycota, was discovered. Nevertheless, research on aquatic fungi and a detailed evaluation of their functions and distribution are still sparse. One of the main reasons is a limitation in reliable identification and quantification methods. To bridge part of the research gap, this study aims to implement a quantitative PCR method to detect and quantify the newly discovered phylum. We developed and validated a Cryptomycota‐specific qPCR primer pair targeting the 5.8S region that detects the majority of Cryptomycota, but Microsporidia. The resulting amplicon is 102 bp long. We used different environmental samples to evaluate the primer pair, various fungal sequences as negative control and positive control sequences. Obtained amplicons were sequenced using Illumina, and the obtained ASVs were all classified as Cryptomycota. The qPCR method works reliably and specifically for the quantification of Cryptomycota in environmental samples.

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Section: Sample Collection and Dna Extractionmentioning

confidence: 99%

Section: Evaluation Of Environmental Ampliconsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Quantification of the dark fungal taxon Cryptomycota using qPCR

Stüer‐Patowsky,

Lilje,

Wurzbacher

2024

Environ Microbiol Rep

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“…R. Soc. B 378: 20220360 community shifts towards microbial taxa that benefit from nocturnal light [17,67]. Short-wave light appears to be particularly prone to triggering such effects on periphyton communities developing near lit water surfaces (less than 15 cm) [110], where spectral attenuation of short wavelengths can be expected not to be pronounced.…”

Section: (F ) Novel Communitiesmentioning

confidence: 99%

Light pollution of freshwater ecosystems: principles, ecological impacts and remedies

Hölker,

Jechow,

Schroer

et al. 2023

Phil. Trans. R. Soc. B

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Light pollution caused by artificial light at night (ALAN) is increasingly recognized as a major driver of global environmental change. Since emissions are rapidly growing in an urbanizing world and half of the human population lives close to a freshwater shoreline, rivers and lakes are ever more exposed to light pollution worldwide. However, although light conditions are critical to aquatic species, and freshwaters are biodiversity hotspots and vital to human well-being, only a small fraction of studies conducted on ALAN focus on these ecosystems. The effects of light pollution on freshwaters are broad and concern all levels of biodiversity. Experiments have demonstrated diverse behavioural and physiological responses of species, even at low light levels. Prominent examples are skyglow effects on diel vertical migration of zooplankton and the suppression of melatonin production in fish. However, responses vary widely among taxa, suggesting consequences for species distribution patterns, potential to create novel communities across ecosystem boundaries, and cascading effects on ecosystem functioning. Understanding, predicting and alleviating the ecological impacts of light pollution on freshwaters requires a solid consideration of the physical properties of light propagating in water and a multitude of biological responses. This knowledge is urgently needed to develop innovative lighting concepts, mitigation strategies and specifically targeted measures. This article is part of the theme issue ‘Light pollution in complex ecological systems’.

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“…The lack of database for freshwater ‐omics data can be explained by the reduced amount of data sets produced so far, especially, in comparison with large oceanic expeditions such as Tara Ocean. However large‐scale initiatives are multiplying with, for example, studies on microbial biogeography with hundreds of freshwater ecosystems studied at the national scale (e.g., New Zealand, Germany, Tibet, Mongolia [Liu et al, 2022; Pearman et al, 2022; Premke et al, 2022; Tandon et al, 2020]) or at the European scale (Boenigk et al, 2018; Ortiz‐Álvarez et al, 2020, 2018) as well as long‐term time series (Linz et al, 2017; Mondav et al, 2020). We therefore developed a manually curated database focused on freshwater ecosystems (FreshOmics), including all types of sequence‐based ‐omics data from bacteria, archaea, microbial eukaryotes, and viruses by compiling, and organizing most available data and knowledge from published literatures and associated repositories.…”

Section: Introductionmentioning

confidence: 99%

FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

Biderre‐Petit

Charvy

Bronner

et al. 2022

Molecular Ecology Resources

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Freshwater is a critical resource for human survival but severely threatened by anthropogenic activities and climate change. These changes strongly impact the abundance and diversity of the microbial communities which are key players in the functioning of these aquatic ecosystems. Although widely documented since the emergence of high‐throughput sequencing approaches, the information on these natural microbial communities is scattered among thousands of publications and it is therefore difficult to investigate the temporal dynamics and the spatial distribution of microbial taxa within or across ecosystems. To fill this gap and in the FAIR principles context we built a manually curated and standardized microbial freshwater –omics database (FreshOmics). Based on recognized ontologies (ENVO, MIMICS, GO, ISO), FreshOmics describes 29 different types of freshwater ecosystems and uses standardized attributes to depict biological samples, sequencing protocols and article attributes for more than 2487 geographical locations across 71 countries around the world. The database contains 24,808 sequence identifiers (i.e., Run_Id / Exp_ID, mainly from SRA/DDBJ SRA/ENA, GSA and MG‐RAST repositories) covering all sequence‐based ‐omics approaches used to investigate bacteria, archaea, microbial eukaryotes, and viruses. Therefore, FreshOmics allows accurate and comprehensive analyses of microbial communities to answer questions related to their roles in freshwater ecosystems functioning and resilience, especially through meta‐analysis studies. This collection also highlights different sort of errors in published works (e.g., wrong coordinates, sample type, material, spelling).

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Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes

Cited by 11 publications

References 63 publications

Quantification of the dark fungal taxon Cryptomycota using qPCR

Quantification of the dark fungal taxon Cryptomycota using qPCR

Light pollution of freshwater ecosystems: principles, ecological impacts and remedies

FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

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