Laboratory conditions can change the complexity and composition of the natural aquatic mycobiome on Alnus glutinosa leaf litter

Carl, Steffen; Mohr, Silvia; Sahm, René; Baschien, Christiane

doi:10.1016/j.funeco.2022.101142

Cited by 4 publications

(6 citation statements)

References 73 publications

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“…The DNA extracts (described in the previous paragraph) were used to perform NGS according to the protocol of Carl et al (2022). For each of the studied communities (P1-3, V1 and 2, and W1-3), three levels of fungicides (0, 30, and 300 μg/L, excluding 3 μg/L) and nutrients (very low, low, and high) were evaluated, omitting the low fungicides and medium nutrient concentrations, respectively.…”

Section: Fungal Community Compositionmentioning

confidence: 99%

“…Preparation of leaf samples for sequencing on the Illumina MiSeq device is described in Carl et al (2022), with detailed information provided in the Supporting Information, SA.2.3. Amplicon libraries of the fungal ITS2 rDNA gene were generated using a mix of five forward primers (ITS3tagmix) and one reverse primer (ITS4ngs; Tedersoo et al, 2014Tedersoo et al, , 2015.…”

Section: Fungal Community Compositionmentioning

confidence: 99%

“…From this, PIPITS created an operational taxonomic unit (OTU) table for every sample, which was assigned according to the "Species Hypothesis" of the UNITE database (Nilsson et al, 2019). Classification of OTUs was curated as described in Carl et al (2022). In brief, (1) classification assigned to OTUs was reblasted against the US National Center for Biotechnology Information reference databases (nucleotide collection of GenBank BLAST ® ; megablast within "blastn" web application; National Institutes of Health, 2023; (2) the classification was corrected, if necessary, as detailed in Carl et al (2022); and (3) OTUs assigned to the same species hypothesis were merged to one taxon to lessen the marker bias of the internal transcribed space (ITS) region, and OTUs leading to the same species curation were merged/sample.…”

Section: Fungal Community Compositionmentioning

confidence: 99%

“…Classification of OTUs was curated as described in Carl et al (2022). In brief, (1) classification assigned to OTUs was reblasted against the US National Center for Biotechnology Information reference databases (nucleotide collection of GenBank BLAST ® ; megablast within "blastn" web application; National Institutes of Health, 2023; (2) the classification was corrected, if necessary, as detailed in Carl et al (2022); and (3) OTUs assigned to the same species hypothesis were merged to one taxon to lessen the marker bias of the internal transcribed space (ITS) region, and OTUs leading to the same species curation were merged/sample. The criteria used for the curation of each OTU were: (1) significant similarity to any BLAST-hit of a fungal taxon (≥95%); (2) reasonable coverage of sequence (≥95%); (3) highest e-value (ratio between coverage and similarity of the sequence); and (4) reliably published sequence (reference database, isolate voucher, publication yes/no) of the fungal ITS rDNA region (Heeger et al, 2018; Supporting Information, Table S7).…”

Section: Fungal Community Compositionmentioning

confidence: 99%

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Elevated Fungicide and Nutrient Concentrations Change Structure but not Function of Aquatic Microbial Communities

Gonçalves,

Feckler,

Pollitt

et al. 2024

Enviro Toxic and Chemistry

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Leaf decomposition is a key process in stream ecosystems within forested catchments; it is driven by microbial communities, particularly fungi and bacteria. These microorganisms make nutrients and energy bound in leaves available for wider parts of the food web. Leaf‐associated microorganisms are subjected to anthropogenic pressures, such as the increased exposure to nutrients and fungicides associated with land‐use change. We assessed the sensitivity of leaf‐associated microbial communities with differing exposure histories, namely, from pristine (P) streams, and streams impacted by wastewater (W) and agricultural run‐off (vineyards; V). In the laboratory, microbial communities were exposed to elevated nutrient (NO3‐N: 0.2–18.0 mg/L, PO4‐P: 0.02–1.8 mg/L) and fungicide concentrations (sum concentration 0–300 µg/L) in a fully crossed 3 × 4 × 4‐factorial design over 21 days. Leaf decomposition and exoenzyme activity were measured as functional endpoints, and fungal community composition and microbial abundance served as structural variables. Overall, leaf decomposition did not differ between fungicide treatments or exposure histories. Nonetheless, substantial changes in the fungal community composition were observed after exposure to environmentally relevant fungicide concentrations. Elevated nutrient concentrations assisted leaf decomposition, and the effect size depended on the exposure history. The observed changes in the fungal community composition support the principle of functional redundancy, with highly efficient decomposers maintaining leaf decomposition. Environ Toxicol Chem 2024;00:1–12. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

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Section: Fungal Community Compositionmentioning

confidence: 99%

Section: Fungal Community Compositionmentioning

confidence: 99%

Section: Fungal Community Compositionmentioning

confidence: 99%

Section: Fungal Community Compositionmentioning

confidence: 99%

See 2 more Smart Citations

Elevated Fungicide and Nutrient Concentrations Change Structure but not Function of Aquatic Microbial Communities

Gonçalves,

Feckler,

Pollitt

et al. 2024

Enviro Toxic and Chemistry

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“…Fisher was first isolated and described in 1991 as an endophyte from alder roots (Dartmoor National Park, UK; Marvanová and Fisher 1991 ). Since then, this species has been reported in microbial ecology studies worldwide such as in India ( Rajashekhar and Kaveriappa 2003 ), Germany ( Carl et al 2022 ), South Korea ( Mun et al 2019 ), and Portugal ( Duarte et al 2015 ). The strain F. fistucella CCM F-13091 is the ex-type of the species and was obtained from Ludmila Marvanová of the Czech Collection of Microorganisms (CCM).…”

Section: Introductionmentioning

confidence: 98%

Comparative genome analysis of the freshwater fungus Filosporella fistucella indicates potential for plant-litter degradation at cold temperatures

Vasconcelos Rissi,

Ijaz,

Baschien

2023

G3: Genes, Genomes, Genetics

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Freshwater fungi play an important role in the decomposition of organic matter of leaf-litter in rivers and streams. They also possess the necessary mechanisms to endure lower temperatures caused by habitat and weather variations. This includes the production of cold-active enzymes and antifreeze proteins. To better understand the physiological activities of freshwater fungi in their natural environment, different methods are being applied, and genome sequencing is one in the spotlight. In our study, we sequenced the first genome of the freshwater fungus Filosporella fistucella (45.7 Mbp) and compared the genome with the evolutionary close-related species Tricladium varicosporioides (48.2 Mpb). The genomes were annotated using the carbohydrate-active enzymes database where we then filtered for leaf-litter degradation-related enzymes (cellulase, hemicellulase, laccase, pectinase, cutinase, amylase, xylanase, and xyloglucanase). Those enzymes were analyzed for antifreeze properties using a machine-learning approach. We discovered that Filosporella fistucella has more enzymes to participate in the breakdown of sugar, leaf, and wood than Tricladium varicosporioides (855 and 719, respectively). F. fistucella shows a larger set of enzymes capable to resist cold temperatures than T. varicosporioides (75 and 66 respectively). Our findings indicate that in comparison with T. varicosporioides, F. fistucella has a greater capacity for aquatic growth, adaptability to freshwater environments, and resistance to low temperatures.

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Mass lysis of bacterial predators drives the enrichment of antibiotic resistance in soil microbial communities

Saha,

Kalathera,

Sumi

et al. 2023

Preprint

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While studies on anthropogenic activities and antibiotic resistance are numerous, the impact of microbial interactions on resistance in complex communities remains uncertain. Here we demonstrate a correlation between the presence ofMyxococcus xanthusin natural soil communities and the abundance of antibiotic-resistant bacteria. Further, introducingM. xanthusisolates also enriches antibiotic resistance. This is due to the mass lysis ofM. xanthuscells, which results in a toxic environment that fosters the proliferation of pre-existing resistant bacteria rather than de novo resistance evolution. Metagenomic analysis revealed that this enrichment is not limited to the tested antibiotics in culture-based methods, indicating its broader relevance. Crucially, these findings go beyond laboratory settings, showingM. xanthusintroduction enriches resistant isolates in natural soil communities. Finally, we demonstrate that the mass lysis ofM. xanthuscells during starvation-induced development—key aspect of the lifecycle ofM. xanthus—also results in the enrichment of antibiotic resistance in soil communities. Together, we demonstrate how life-history traits in bacterial predators, likeM. xanthus, significantly impact antibiotic resistomes in nature. This study also highlights the complex dynamics at play in the evolution and maintenance of antibiotic resistance, emphasizing the role of interspecies interactions in shaping antibiotic resistance profiles.

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Laboratory conditions can change the complexity and composition of the natural aquatic mycobiome on Alnus glutinosa leaf litter

Cited by 4 publications

References 73 publications

Elevated Fungicide and Nutrient Concentrations Change Structure but not Function of Aquatic Microbial Communities

Elevated Fungicide and Nutrient Concentrations Change Structure but not Function of Aquatic Microbial Communities

Comparative genome analysis of the freshwater fungus Filosporella fistucella indicates potential for plant-litter degradation at cold temperatures

Mass lysis of bacterial predators drives the enrichment of antibiotic resistance in soil microbial communities

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