ArticleMicrobiome2022
HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi.
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 92 citations in OpenAlex.
- Exploring agro-ecological significance, knowledge gaps, and research priorities in arbuscular mycorrhizal fungi.Frontiers in microbiology · 2024Pooled it
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- Enhanced soil health and greenhouse gas mitigation potential are linked to microbial network restructuring under long-term organic farming.Fundamental research · 2026Article
- Review
- Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.mSystems · 2026Article
- From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.Plants (Basel, Switzerland) · 2026Review
- Arbuscular mycorrhizal fungi- linked microbial processes in soil nitrogen cycling.FEMS microbiology ecology · 2026Review
- Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.Microbiome · 2026Article
- Arbuscular Mycorrhizal Fungi-Mediated Phytoremediation: Harnessing a Sustainable Approach in Environmental Cleanup of Heavy Metals and Organic Pollutants.Current microbiology · 2026Review
- From soil to sequences: mechanisms and tools unravelling plant-rhizomicrobiome interactions.World journal of microbiology & biotechnology · 2026Review
- SIPdb: a stable isotope probing database and analytical dashboard for linking amplicon sequences to microbial activity using reverse ecology.ISME communications · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Myxobacteria: Versatile cell factories of novel commercial enzymes for bio-manufacturing.Biotechnology advances · 2025Review
- Early-stage reciprocal cooperation between the arbuscular mycorrhizal fungus Rhizophagus irregularis and the phosphate-solubilizing bacterium Rahnella aquatilis is dependent on external phosphorus availability.Communications biology · 2025Article
- Effect of Claroideoglomous etunicatums on rhizosphere bacterial community of tobacco under low nutrient conditions.Advanced biotechnology · 2025Article
- Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere.Microbiome · 2025Article
- Duration of OEnvironmental science & technology · 2025Article
- Comparing field and lab quantitative stable isotope probing for nitrogen assimilation in soil microbes.Applied and environmental microbiology · 2025Article
- Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Mechanisms of cooperation in the plants-arbuscular mycorrhizal fungi-bacteria continuum.The ISME journal · 2025Review
Corrections and comments
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Authors and funding
14 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLinking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling.
resultsOur HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to
conclusionsOur semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.
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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.