ArticleMicrobiome2018
Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.
Article in Microbiome, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 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
51 citing papers in PubMed, 197 citations in OpenAlex.
- Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces.FEMS microbiology ecology · 2026Article
- Insights into microbial diversity affected by plant cover in athalassohaline ecosystem of el-hamra lake, wadi el-natrun, Egypt.World journal of microbiology & biotechnology · 2026Article
- Tree diversity shapes soil bacterial community structure under low abiotic heterogeneity in the Atlantic forest.Archives of microbiology · 2026Article
- Effects of deep slow-release fertilizer on melon yield, economic benefits and rhizosphere microorganisms.Frontiers in plant science · 2026Article
- Diversity of soil bacterial communities in response to fonio (Digitaria exilis Stapf) genotypes and pedoclimatic conditions in Benin.PloS one · 2026Article
- Land-use intensification reshapes microbial phosphorus cycling, organic matter composition, and phosphorus fractions in Amazonian soils.ISME communications · 2026Article
- Species-specific phylloplane responses to changes in external pH.Journal of experimental botany · 2025Article
- Hydraulic Connectivity and Hydrochemistry Influence Microbial Community Structure in Agriculturally Affected Alluvial Aquifers in the Midwestern United States.Environmental science & technology · 2025Article
- Drivers of fungal and bacterial communities in ectomycorrhizospheres of birch, oak, and pine in a former uranium mining site, Ronneburg, Germany.Environmental science and pollution research international · 2025Article
- Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential.Microbial ecology · 2025Article
- High strain-level diversity of Bradyrhizobium across Australian soils.The ISME journal · 2025Article
- Vertical stratification of P pools in subtropical plantation soils under fertilization and dry-season irrigation: multiomics regulatory strategies.Frontiers in microbiology · 2025Article
- Adaptation and resistance of soil prokaryotic communities to drought intensification in old-growth forests and pastures of southwestern Amazonia.Frontiers in plant science · 2025Article
- Impact of agronomic practices on microbial diversity in brown-desert soil: insights from the Aksu region, Xinjiang.Frontiers in microbiology · 2025Article
- Differential analysis of the quality and soil microhabitat ofFrontiers in microbiology · 2025Article
- Continuous planting American ginseng (Panax quinquefolius L.) caused soil acidification and bacterial and fungal communities' changes.BMC microbiology · 2024Article
- Organic farming systems improve soil quality and shape microbial communities across a cotton-based crop rotation in an Indian Vertisol.FEMS microbiology ecology · 2024Article
- The impact of land-use changes and management intensification on bacterial communities in the last decade: a review.Applied and environmental microbiology · 2024Review
- Lineage-specific evolution ofApplied and environmental microbiology · 2024Article
- Article
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 5 institutions in 4 countries.
Funding
Abstract
backgroundpH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to "spillover effects" on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures.
resultsWe evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical-chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO
conclusionsOur results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and "spillover effects" of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.
Indexed as
Identifiers
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.