ArticleeLife2020
Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms.
Article in eLife, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed.
- Gnotobiotic growth and phosphorus limitation of Arabidopsis thaliana and co-occurring microbes on phosphated iron oxides.Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine · 2026Article
- Lives in a gram of soil: linking life cycle biology to soil ecology.The ISME journal · 2026Review
- Synthetic soils for ecological and synthetic biology applications.FEMS microbiology reviews · 2026Review
- Investigating the effects of soil microstructures on bacterial growth via microfluidic channels and an agent-based model.Scientific reports · 2025Article
- Fluid mechanics within mycorrhizal networks: exploring concepts, traits, and methodologies.The New phytologist · 2025Review
- Article
- A roadmap to understanding and anticipating microbial gene transfer in soil communities.Microbiology and molecular biology reviews : MMBR · 2025Review
- Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground.PNAS nexus · 2025Article
- Soil-mimicking microfluidic devices reveal restricted flagellar motility of Bradyrhizobium diazoefficiens under microconfinement.Communications biology · 2025Article
- Coarse-graining bacterial diffusion in disordered media to surface states.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Surfactin facilitates establishment of Bacillus subtilis in synthetic communities.The ISME journal · 2025Article
- Mini Winnies: scaled down and transparent Winogradsky columns for microscopy in microbiology education.Journal of microbiology & biology education · 2024Article
- Synthetic microbiology in sustainability applications.Nature reviews. Microbiology · 2024Review
- Simultaneous Two- and Three-Photon Deep Imaging of Autofluorescence in Bacterial Communities.Sensors (Basel, Switzerland) · 2024Article
- Linking methanotroph phenotypes to genotypes using a simple spatially resolved model ecosystem.The ISME journal · 2024Article
- Fabricated devices for performing bacterial-fungal interaction experiments across scales.Frontiers in microbiology · 2024Review
- The Meioflume: A New System for Observing the Interstitial Behavior of Meiofauna.Integrative organismal biology (Oxford, England) · 2024Article
- Construction and characterisation of a structured, tuneable, and transparent 3D culture platform for soil bacteria.Microbiology (Reading, England) · 2024Article
- ReducingAnalytical chemistry · 2023Article
- Establishment of a transparent soil system to study Bacillus subtilis chemical ecology.ISME communications · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil's opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.
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What OpenQuestion 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 OpenQuestion graph.