Definition and research guide
This page combines a MeSH definition, publication statistics and selected research abstracts. It is a starting point for reading the literature, not a medical textbook or a systematic evidence review.
Content available: 3 complete abstracts (589 words), 9 references. Full article text is not stored or reproduced here; follow the PMID, DOI or PMC links to read the original sources and their access terms.
Definition
The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.
Definition: NLM Medical Subject Headings (MeSH) scope note (Public domain (U.S. National Library of Medicine); attribution requested). View the MeSH record.
Also known as: Soils; Peat; Humus.
Where it fits in the MeSH classification
- Broader topics
- Complex Mixtures; Geological Phenomena; Environment
- Narrower topics
- Clay; Humic Substances; Sand; Permafrost
- See also
- Soil Erosion
Research landscape
PubMed indexes 117,213 records tagged with the MeSH heading “Soil” (counts retrieved 2026-10-31). 54,844 of them (46.8%) were published from 2020 onward, and the busiest period so far is 2020 onward with 54,844 records.
Reviews account for 6,654 records (5.7%) and meta-analyses for 992. Randomized controlled trials number 126 (0.1%) as a share of all records on the topic. Randomized trials make up only a small share of this literature, so much of what is known comes from laboratory, observational or descriptive work.
Show the data
| Period | Records |
|---|---|
| through 1999 | 5,215 |
| 2000-2009 | 16,524 |
| 2010-2019 | 40,630 |
| 2020 onward | 54,844 |
Publication-type chart data
| Type | Records | Share |
|---|---|---|
| Reviews | 6,654 | 5.7% |
| Meta-analyses | 992 | 0.8% |
| Randomized controlled trials | 126 | 0.1% |
Method: PubMed query "Soil"[MeSH Terms] with publication-type and date filters, retrieved 2026-10-31.
Reading the evidence in public health and nutrition
Population and nutrition studies mostly observe what people eat, breathe or are exposed to and then look for links with health, which shows association and not proof of cause. Self-reported diet is imprecise, people who eat or live differently also differ in other ways, and effects measured across a population may not apply to one person. Check the study design, how exposure was measured, what else was accounted for and the size of the effect, not only whether it was statistically significant.
Evidence from open-access studies
These open-access studies come from PubMed’s best-match results for this heading (papers whose main topic it is), ranked here by citation count, with one recent addition. Each abstract is reproduced in full under its recorded open licence so that you can read the authors’ own words. They illustrate the literature; they are not a systematic summary of it. Citation counts measure attention, not reliability or clinical benefit.
| Study / authors | Year | Source label / design | Europe PMC citations | Licence / source |
|---|---|---|---|---|
| Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition | 2026 | Research article Design not recorded in structured metadata | 2 | cc by PMID 42297767 · DOI · PMC13270027 |
| Depth-resolved transcriptional activity of antibiotic resistance genes in deep permafrost of the Qinghai-Tibet Plateau | 2026 | Research article Design not recorded in structured metadata | 2 | cc by PMID 42373864 · DOI · PMC13683339 |
| Divergent patterns of richness and density in the global soil seed bank | 2026 | Research article Design not recorded in structured metadata | 1 | cc by PMID 42632859 · DOI · PMC13499811 |
Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition [1]
Abstract reading summary — source excerpts
- Opening excerpt
- Soil organic matter (SOM) decomposition by microorganisms is a major uncertainty in predicting terrestrial carbon-atmosphere feedbacks, partly because we lack understanding of the microbial diversity involved in depolymerizing different carbon pools across environmental gradients.
- Closing excerpt
- Our results show that a substantial portion of ostensibly stable SOM remains vulnerable to microbial decomposition, a mechanism not captured in current Earth System Models.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (195 words)
Soil organic matter (SOM) decomposition by microorganisms is a major uncertainty in predicting terrestrial carbon-atmosphere feedbacks, partly because we lack understanding of the microbial diversity involved in depolymerizing different carbon pools across environmental gradients. We address this gap using a continental-scale dataset pairing shotgun metagenomes with high-resolution SOM chemistry, assembling 0.76 Tbp of prokaryotic MAGs (828 genomes) and identifying 66,727 SOM molecules from 47 standardized U.S. soil cores selected using respiration rates from 106 soils. Integrating these datasets reveals widespread microbial potential for depolymerizing chemically-recalcitrant SOM previously considered stable. We uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels, suggesting coordinated decomposition of complex SOM through distinct but complementary biochemical strategies. The metabolic potential for depolymerization of chemically-recalcitrant compounds is supported by the abundance of these molecules across the soils, as indicated by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), and by flux balance analysis of metabolic models. Our results show that a substantial portion of ostensibly stable SOM remains vulnerable to microbial decomposition, a mechanism not captured in current Earth System Models.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42297767 · DOI · PMC13270027
Depth-resolved transcriptional activity of antibiotic resistance genes in deep permafrost of the Qinghai-Tibet Plateau [2]
Abstract reading summary — source excerpts
- Opening excerpt
- The Qinghai-Tibet Plateau harbors permafrost ecosystems containing diverse antibiotic resistance genes (ARGs), yet their transcriptional activity and depth-resolved patterns remain poorly understood.
- Closing excerpt
- Overall, this study provides evidence of ARG transcripts in permafrost layers, offering a baseline for future investigations of resistome dynamics under thaw conditions.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (200 words)
The Qinghai-Tibet Plateau harbors permafrost ecosystems containing diverse antibiotic resistance genes (ARGs), yet their transcriptional activity and depth-resolved patterns remain poorly understood. Here, we performed meta-transcriptomic profiling of two permafrost cores (40-m and 100-m) from the Tuotuo River Basin. Within each core, permafrost layers exhibited higher relative ARG transcript abundance and diversity than overlying active layers. β-Lactam, multidrug, and puromycin resistance transcripts were enriched in permafrost, whereas aminoglycoside resistance predominated in the active layer. Antibiotic inactivation mechanisms were more prevalent in permafrost, while target modification dominated in the active layer within the analyzed cores. Plasmid-associated ARGs were detected, and mobile genetic elements (MGEs) showed stratified distributions, with integrative and conjugative elements more abundant in active layers and integrons enriched in permafrost strata. ARG transcript levels were associated with microbial community composition, MGEs, metal tolerance genes, and trace metal concentrations. Neutral community modeling suggested that ARG assemblages are largely consistent with stochastic processes, indicating long-term persistence under environmental filtering. As the analysis is limited to two cores, these observations reflect site-specific transcriptional patterns rather than generalizable regional trends. Overall, this study provides evidence of ARG transcripts in permafrost layers, offering a baseline for future investigations of resistome dynamics under thaw conditions.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42373864 · DOI · PMC13683339
Divergent patterns of richness and density in the global soil seed bank [3]
Abstract reading summary — source excerpts
- Opening excerpt
- Soil seed banks are an important component of plant population and community dynamics, buffering temporal heterogeneity and allowing populations to recover following disturbance.
- Closing excerpt
- Our findings of divergences between species richness and seed density across global biomes, and how they are impacted by habitat degradation, give valuable insights to the understanding of plant biodiversity worldwide.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (194 words)
Soil seed banks are an important component of plant population and community dynamics, buffering temporal heterogeneity and allowing populations to recover following disturbance. At the same time, patterns in soil seed banks are likely to reflect scale-dependent patterns in above-ground vegetation, patterns that differ strongly across world regions. Here, we investigate components of diversity in the soil seed bank across global biomes and ecosystems. We find that patterns of species richness in the soil seed bank diverge from patterns of seed density, although our results indicate high levels of uncertainty, especially at smaller spatial scales. Importantly, we show that habitat degradation is consistently associated with lower richness, potentially limiting future ecosystem recovery. Among ecosystems, Mediterranean and tropical regions exhibit high species richness, but seed density m-2 in the soil is highest in wetlands and arable systems. We identify lower seed densities in both high-diversity tropical biomes that are characterised by short-lived seeds, and low-diversity boreal and tundra biomes with more stable established vegetation. Our findings of divergences between species richness and seed density across global biomes, and how they are impacted by habitat degradation, give valuable insights to the understanding of plant biodiversity worldwide.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42632859 · DOI · PMC13499811
Key reviews and meta-analyses
The most cited review-type papers among PubMed’s best-match results for this heading, listed with bibliographic details only. Follow the links for the full text and access terms.
- Research article Water, sanitation, hygiene, and soil-transmitted helminth infection: a systematic review and meta-analysis [4]
- Research article Effect of sanitation on soil-transmitted helminth infection: systematic review and meta-analysis [5]
- Research article Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality [6]
- Research article A meta-analysis of experimental warming effects on terrestrial nitrogen pools and dynamics [7]
- Research article Efficacy of recommended drugs against soil transmitted helminths: systematic review and network meta-analysis [8]
- Research article Microbial carbon use efficiency promotes global soil carbon storage [9]
References
- Song YC, Shi C, Stratton KG, Ayala-Ortiz C, Stohel I, Freire-Zapata V, et al.. Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition. . 2026. PMID 42297767 · DOI · PMC13270027
- Sajjad W, Kang S, Yin X, Wu X, Deng F, Williamson C, et al.. Depth-resolved transcriptional activity of antibiotic resistance genes in deep permafrost of the Qinghai-Tibet Plateau. . 2026. PMID 42373864 · DOI · PMC13683339
- Auffret AG, Ladouceur E, Haussmann NS, Keil P, Daouti E, Elumeeva TG, et al.. Divergent patterns of richness and density in the global soil seed bank. . 2026. PMID 42632859 · DOI · PMC13499811
- Strunz EC, Addiss DG, Stocks ME, Ogden S, Utzinger J, Freeman MC. Water, sanitation, hygiene, and soil-transmitted helminth infection: a systematic review and meta-analysis. PLoS Med. 2014. PMID 24667810 · DOI · PMC3965411
- Ziegelbauer K, Speich B, Mäusezahl D, Bos R, Keiser J, Utzinger J. Effect of sanitation on soil-transmitted helminth infection: systematic review and meta-analysis. PLoS Med. 2012. PMID 22291577 · DOI · PMC3265535
- Zhou Z, Wang C, Luo Y. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat Commun. 2020. PMID 32555185 · DOI · PMC7300008
- Bai E, Li S, Xu W, Li W, Dai W, Jiang P. A meta-analysis of experimental warming effects on terrestrial nitrogen pools and dynamics. New Phytol. 2013. PMID 23550663 · DOI
- Moser W, Schindler C, Keiser J. Efficacy of recommended drugs against soil transmitted helminths: systematic review and network meta-analysis. BMJ. 2017. PMID 28947636 · DOI · PMC5611648
- Tao F, Huang Y, Hungate BA, Manzoni S, Frey SD, Schmidt MWI, et al.. Microbial carbon use efficiency promotes global soil carbon storage. Nature. 2023. PMID 37225998 · DOI · PMC10307633
About this article
- Sources
- NLM Medical Subject Headings (definition, synonyms); NCBI PubMed (counts, identifiers); Europe PMC (open-access abstracts and citation counts).
- Verification
- Every reference was resolved against PubMed on 2026-11-04; title, year and DOI matched.
- Review state
- automated source verified; no human expert review has been recorded yet.
- Version
- 1, last updated 2026-11-04.
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Evidence strength
EvidenceHelix's computed view of the study designs behind this topic: how common meta-analyses, randomized trials and reviews are, how recent the literature is, and a plain-language reading. It describes the design mix of the literature. It is not a quality appraisal of any study, and it is not medical advice.