Intertwined Relationship Between Soil pH and Microbes in Biogeography

Abstract

Soil pH indicates the extent of acidity and alkalinity in terrestrial ecosystems and is one of the most important edaphic properties, greatly influencing nutrient availability, metal mobility, microbial growth, and ecosystem health. It is often considered the “master variable” in soil science because pH changes can cause a series of shifts, for example, the solubility changes of key ions such as phosphorus, aluminum, and calcium, could sequentially affect plant growth and microbial functioning (Weil and Brady 2016). Importantly, soil pH reflects the outcome of long-term interactions between climate, organisms, parent material, topology, and time. In the context of global change, soil pH is also variable. Precipitation regime shifts, warming-induced organic matter decomposition, acid deposition, and fertilization all contribute to pH fluctuations at multiple temporal and spatial scales (Philippot et al. 2023). Though soil pH generally maintains a relatively stable state via buffering systems such as aluminum compounds and carbonates, extreme shifts in pH can override this resilience, leading to cascading impacts on microbial communities and ecosystem stability. Understanding the mechanisms of the regulating factors and ecological consequences of soil pH changes and microbial life is essential for predicting terrestrial responses to climate change.

Over the past two decades, advanced developments in high-throughput sequencing have enabled new insights into the composition and structure of soil microbiomes across global biomes. Early continental-scale surveys demonstrated that soil pH was the best predictor of bacterial diversity and communities compared to other edaphic variables (Fierer and Jackson 2006). A meta-analysis has confirmed that bacterial diversity exhibits strong unimodal or linear relationships with pH, peaking in near-neutral conditions, and found a strong influence of soil pH on bacterial community assembly processes globally (Tripathi et al. 2018). These relationships are commonly observed across spatial scales and ecosystem types, from tundra to tropical forests. Therefore, most studies treat microbial communities as static responders to environmental gradients or changes. Our recent work (Feng et al. 2024) challenges this paradigm by demonstrating that core bacterial communities can serve as bioindicators of soil pH dynamics under future climate scenarios instead of just responders. The Core Bacteria Forecast Model (CoBacFM), integrating data from over 1,200 grassland sites globally, identified the biogeographic distributions of bacterial eco-clusters whose abundance was similarly shifted to environmental variables and forecast pH changes. The model projects that more than 60% of global grasslands will experience pH increases (alkalization) by 2100, particularly in regions like northeastern Asia, Oceania, and Africa. These predictions were supported by 14 global field warming simulation experiments, linking modeling results with ecological observations on a large scale.

In newly published research in Global Change Biology, the role of soil pH in shaping microbial biogeographic patterns is reaffirmed by Duan et al. (2025), who analyzed 207 terrestrial sites across six major ecosystems in China, representing diverse climatic and environmental gradients. Unlike previous studies, this study simultaneously examined soil bacterial and eukaryotic communities. Their findings reveal that soil pH has distinct effects on bacterial and eukaryotic β-diversity, functioning as an ecological filter that operates differently across microorganisms. Specifically, bacterial communities converge under low-pH conditions, that is, more similar or homogenizing, suggesting strong environmental filtering and potential loss of niche diversity. Conversely, eukaryotic communities show increased dissimilarity in acidic environments, possibly due to the strong competitiveness or higher stress tolerance, occupying complex niches. This asymmetric response reflects taxonomic differences, divergent evolutionary histories, and physiological features. For example, bacteria may respond to acidification through functional redundancy and similar resistance strategies, whereas fungi may exhibit more specialized or idiosyncratic responses, resulting in higher spatial turnover (Bahram et al. 2018). These findings highlight the necessity of treating microbial domains independently in biogeographic models and question the assumption that all microbial groups respond uniformly to environmental gradients. Moreover, the soil pH impact depends on spatial scaling, and integrative frameworks need to consider both local environmental filtering and regional dispersal limitations. These two driving forces have been central to plant and animal biogeography for long periods and are now equally relevant to microbial distribution patterns.

A particularly novel and concerning insight from Duan et al. (2025) is that soil acidification not only alters microbial community composition but decouples the β-diversity trajectories of bacteria and eukaryotes. This decoupling is reflected in the disruption of co-occurrence networks as well. Under low-pH conditions, microbial co-occurrence networks demonstrate the shifts of microbial interactions from cooperative toward competitive or neutral relationships. The increasing proportions of negative correlations in bacterial-eukaryotic interactions suggest reduced ecological integration under low-pH conditions, which could impair nutrient cycling and affect system resilience to further disturbance. This finding aligns with previous work that interdomain interactions were shifted under warming conditions and soil pH and nutrients affect the microbial hierarchical interactions (Zhou et al. 2021). As soil pH shifts, microbial groups that once cooperated may respond in distinct directions, thus affecting biogeochemical processes like decomposition, nutrient turnover, and carbon stabilization. Importantly, these findings imply that the shifts of microbial interactions across dominant domains may play essential roles in functioning stable ecosystems. The study by Duan et al. (2025) contributes a critical insight into the biodiversity-stability relationship, highlighting the microbial interactions from co-occurrence networks as a key indicator of ecosystem stability under environmental stress.

Duan et al. (2025) and our work (Feng et al. 2024) collectively illustrate a microbial feedback loop mechanism in which soil pH and microbial communities regulate each other. Microbial metabolism can directly alter pH through various biogeochemical processes such as ammonification, denitrification, sulfate reduction, and organic acid degradation (Philippot et al. 2023). For example, soil pH can be increased by ammonia-producing bacteria and decreased by the fungal decomposition of organic acids. In turn, soil pH changes could put selective pressure on microbial taxa, leading to shifts in microbial community composition, ecological processes, and ecosystem functions. This feedback loop becomes particularly important under future climate warming, as increased temperatures accelerate microbial metabolism, potentially influencing soil pH. The CoBacFM model captures this complexity by identifying microbial eco-clusters that simultaneously respond to and affect environmental variables. The ecological survey results by Duan et al. (2025) reinforce these dynamics by showing how soil acidification disrupts microbial interactions and ecological stability. Thus, the soil microbiome acts both as a quick responder to environmental change and as an agent influencing living environments, and such a dual role is central to ecosystem resilience under global change.

Despite the growing recognition of microbial importance, most Earth system models still neglect microbiomes or represent them as static or uniform responders. The study by Duan et al. (2025) and our work highlight the integration of microbial traits and feedback into predictive frameworks under global change. This would significantly advance ecological forecasting, bridging the belowground microbial world and aboveground macroscale ecosystems and enabling more accurate projections of carbon cycling, nutrient dynamics, and soil fertility under future climate scenarios. A more holistic modeling approach would integrate not just bacterial dynamics but also those of fungi, archaea, and viruses, considering that each microbial group plays distinct roles in nutrient cycling and ecosystem functions. Furthermore, soil depth profiles and land-use history could expand knowledge about top soils and deep terrestrial ecosystems. The multi-omics data for microbial functional traits and real-time functions should be included to capture the complexity of microbial contributions to biogeochemical cycling. These elements would significantly enhance our ability to simulate ecosystem processes with higher spatial and temporal resolution. As global terrestrial ecosystems face unprecedented pressures from climate change and biodiversity loss, constructing microbe-informed Earth system models becomes a necessary step for designing more robust environmental policies and sustainability strategies. Microbial processes are essential to Earth's ecosystems, and their inclusion will bring the next frontier of ecosystem projections.

The study by Duan et al. (2025) reaffirms the role of soil pH in microbial biogeography. Soil pH is not just an abiotic filter that describes and controls the microbial dynamics under global change but is also dynamic and structured by microbial communities. These findings highlight the intertwined relationship between soil pH and microbiomes on large spatial scales and establish a conceptual bridge to link empirical biogeography with predictive Earth system models. By elucidating how microbial communities respond to and influence pH, these studies would treat the soil microbiome as a central node in ecosystem forecasting. Facing future global changes, recognizing and modeling this intertwined relationship will be crucial for maintaining soil health, biodiversity, and planetary stability.

Kai Feng: writing – original draft, writing – review and editing. Ye Deng: writing – original draft, writing – review and editing.

The authors declare no conflicts of interest.

This article is a Invited Commentary on Duan et al., https://doi.org/10.1111/gcb.70174.