ArticleFEMS microbiology ecology2015
Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils.
Article in FEMS microbiology ecology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 149 citations in OpenAlex.
- Microbial growth rates captured using Raman-SIP reveal a highly active subsurface biosphere fueled by serpentinization.Nature communications · 2026Article
- Model substrate particles uncover dynamics of microbial communities associated with particulate organic matter decomposition in soil.ISME communications · 2026Article
- Lactulose selectively stimulates members of the gut microbiota, as determined by multi-modal activity-based sorting.Gut microbes · 2025Article
- Comparing Raman and NanoSIMS for heavy water labeling of single cells.Microbiology spectrum · 2025Article
- Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground.PNAS nexus · 2025Article
- Raman Microspectroscopy to Trace the Incorporation of Deuterium from Labeled (Micro)Plastics into Microbial Cells.Analytical chemistry · 2025Article
- Distinct microbial communities within and on seep carbonates support long-term anaerobic oxidation of methane and divergent pMMO diversity.The ISME journal · 2025Article
- Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting.Microbiome research reports · 2025Article
- Tracking trash to treasure:RSC advances · 2024Article
- Single-cell measurement of microbial growth rate with Raman microspectroscopy.FEMS microbiology ecology · 2024Article
- Single-cell exploration of active phosphate-solubilizing bacteria across diverse soil matrices for sustainable phosphorus management.Nature food · 2024Article
- Survival and rapid resuscitation permit limited productivity in desert microbial communities.Nature communications · 2024Article
- Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates.The ISME journal · 2024Article
- Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria.The New phytologist · 2023Article
- Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils.Nature food · 2023Article
- Tracking deuterium uptake in hydroponically grown maize roots using correlative helium ion microscopy and Raman micro-spectroscopy.Plant methods · 2023Article
- Article
- Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes.Microbiome · 2023Article
- Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via (15)N2 and (13)C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a (13)C-labeled carbon source and deuterium oxide (D2O, a general activity marker). The described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.
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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.