ArticlePeerJ2020
Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams.
Article in PeerJ, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 30 citations in OpenAlex.
- Enhancing DNA recovery in low-biomass snow algae samples: a comparative study of extraction methods and their effect on community composition.Applied and environmental microbiology · 2026Article
- Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.Microbiome · 2026Article
- Optimized Method for Efficient DNA Extraction from Agricultural Soils.Methods and protocols · 2026Article
- Spatiotemporal intermittence effect on periphyton microbial communities in a tropical drying river network.ISME communications · 2026Article
- Unearthing the genetic resources of Arabian sea seamount and metagenomic insights into phosphate cycling genes for next generation plant biostimulants.Scientific reports · 2025Article
- Article
- Predicting climate-change impacts on the global glacier-fed stream microbiome.Nature communications · 2025Article
- Article
- Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome.Nature microbiology · 2025Article
- Towards a comprehensive view of wetland benthic communities.Current research in microbial sciences · 2025Article
- The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa.Royal Society open science · 2023Article
- Homogeneous Environmental Selection Structures the Bacterial Communities of Benthic Biofilms in Proglacial Floodplain Streams.Applied and environmental microbiology · 2023Article
- Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters.Microbiology spectrum · 2023Article
- Cross-domain interactions confer stability to benthic biofilms in proglacial streams.Frontiers in microbiomes · 2023Article
- The role of phages for microdiverse bacterial communities in proglacial stream biofilms.Frontiers in microbiomes · 2023Article
- Benthic Biofilms in Glacier-Fed Streams from Scandinavia to the Himalayas Host Distinct Bacterial Communities Compared with the Streamwater.Applied and environmental microbiology · 2022Article
- Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.Global change biology · 2022Article
- Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams.Nature communications · 2022Article
- Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome.The ISME journal · 2022Article
- Spatial patterns of benthic biofilm diversity among streams draining proglacial floodplains.Frontiers in microbiology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.