Institutes & CentersInstitute for Alpine Environment - Projects - MICROVALU

MICROVALU

Evaluating microbiodiversity in Alpine pastures

The project MICROVALU, funded by the Euregio Science Fund, aims to identify the main drivers of microbial and faunal diversity in the soil of alpine pastures. We collect data on abiotic/climatic factors (such as soil moisture, soil organic matter content, temperature, number of days of snow cover), as well as biotic interactions between the microbiota of soil, rhizosphere and above and below ground fauna (including invertebrates, small mammals and livestock). MICROVALU will evaluate the interactions of these soil components along an altitudinal gradient, in order to predict how such interactions may be affected by climate change.

Project duration: April 2019 - March 2023
Project status:
Funding:
Public institutions (Other projects /Project)
Institute: Institute for Alpine Environment

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biodiversity ecosystems environmental monitoring

Scientific Publications

Journal article2024

Comparison of commonly used software pipelines for analyzing fungal metabarcoding data

Rzehak T, Praeg N, Galla G, Seeber J, Hauffe HC, Illmer P

Julia Seeber

Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.

DOI Source

DOI: 10.1186/s12864-024-11001-x

Journal article2024

Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem

Galla G, Praeg N, Rzehak T, Sprecher E, Colla F, Seeber J, Illmer P, Hauffe H C

Julia Seeber

Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY–NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.

DOI Source

DOI: 10.1038/s41598-024-59086-4

Journal article2023

Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem

Galla G, Präg N, Colla F, Rzegak T, Illmer P, Seeber J, Hauffe HC

Julia Seeber

Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Currently available protocols for metataxonomy assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. It has been suggested that the addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases during processing and support direct comparisons of microbiota composition, but the impact of MC on diversity estimates of samples is unknown. Here, large and small aliquots of pulverized bovine fecal samples were extracted with no, low or high doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We demonstrated that sample diversity estimates were distorted only if MC dose was high compared to sample mass (i.e. when MC > 10% of sample reads). We also showed that MC was an informative in situ positive control, permitting an estimation of the sample 16S copy number, and detecting sample outliers. We tested this approach on a range of sample types from a terrestrial ecosystem, including rhizosphere soil, whole invertebrates, and wild vertebrate fecal samples, and discuss possible clinical applications.

DOI Source

DOI: 10.1038/s41598-023-30916-1

All Publications

Comparison of commonly used software pipelines for analyzing fungal metabarcoding data
Rzehak T, Praeg N, Galla G, Seeber J, Hauffe HC, Illmer P (2024)
Journal article
BMC Genomics

More information: https://bmcgenomics.biomedcentral.com/articles/10.1186/s ...

https://doi.org/10.1186/s12864-024-11001-x

Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem
Galla G, Praeg N, Rzehak T, Sprecher E, Colla F, Seeber J, Illmer P, Hauffe H C (2024)
Journal article
Scientific Reports

More information: https://www.nature.com/articles/s41598-024-59086-4

https://doi.org/10.1038/s41598-024-59086-4

Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem
Galla G, Präg N, Colla F, Rzegak T, Illmer P, Seeber J, Hauffe HC (2023)
Journal article
Scientific Reports

More information: https://www.nature.com/articles/s41598-023-30916-1

https://doi.org/10.1038/s41598-023-30916-1

Our partners

Edmund Mach Foundation

Leopold Franzens University Innsbruck

Project Team

Julia Seeber

Michael Steinwandter

Helene Blasbichler

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