Sugarcane’s Hidden Underground Clock: Phosphorus Swings Reshape Soil Fungi Across the Crop Cycle

On the humid lowland plantations of South Sumatra, Indonesia, a quiet drama unfolds beneath the rows of sugarcane that never makes it into the harvest ledger. A new multi-site study of tropical Ultisols — the acidic, phosphorus-hungry soils that dominate the Indonesian uplands — reveals that the chemical, physical and biological condition of the soil shifts in a strikingly coordinated way across a single ratoon crop cycle, and that the star of the show is available phosphorus. The findings, published in Discover Soil, offer one of the most complete snapshots yet of how a major industrial crop reshapes its own underground environment over eleven months of growth.

The research team, led by soil scientists at Universitas Sriwijaya, sampled twenty plots across three commercial plantations at four crop stages: three, five, seven and eleven months after ratooning. Because following the same plots destructively through a full cycle is impractical at commercial scale, the researchers used a space-for-time chronosequence design, sampling different plots at each stage while modelling site effects statistically. At every plot they measured a battery of indicators: soil pH, organic carbon, Bray-1 extractable phosphorus, aggregate stability expressed as mean weight diameter, bulk density, arbuscular mycorrhizal fungal spore density, root colonization, genus-level diversity and stalk height, with cane yield and sucrose content recorded at harvest.

The single largest contrast in the entire dataset concerned phosphorus. Plots sampled at three months held a mean of 66.1 milligrams of available phosphorus per kilogram of soil — a figure that collapsed to 11.7 milligrams at five months and hovered between 15 and 18 milligrams thereafter. The statistical effect size was extraordinary, with crop stage explaining more than 99 percent of the variance in available phosphorus. Yet the authors are careful to note that the cause of this dramatic early-season spike cannot be established from their observational data. A simple mass balance shows that crop removal alone cannot explain the decline: total phosphorus uptake by a whole cane crop is typically only 20 to 40 kilograms per hectare, whereas the measured difference corresponds to roughly 148 kilograms of extractable phosphorus per hectare in the top twenty centimetres.

That leaves several open explanations, including sorption of phosphorus onto the aluminium and iron oxides that make Ultisols such notorious phosphorus fixers, differences in fertiliser rate or timing among fields, the position of sampling points relative to banded fertiliser applications, and variation in rainfall and leaching. None of the fertiliser records were available to the researchers, a gap they identify as the most important single limitation for interpreting the phosphorus results. Intriguingly, available phosphorus was also higher at seven months than at five months — a rebound that simple depletion and sorption dynamics do not readily explain on this timescale, and which further suggests that management interventions between the fifth and seventh months may have played a role.

The mycorrhizal story is where the data become genuinely compelling. Arbuscular mycorrhizal fungi are ancient symbionts that trade photosynthate from their plant hosts for phosphorus scavenged from beyond the root depletion zone by networks of microscopic hyphae. The symbiosis is famously sensitive to soil phosphorus: when phosphorus is plentiful, host plants cut carbon supplies to the fungus and colonization declines, a response now traced to phosphate-starvation signalling pathways at the molecular level. The Sumatran sugarcane fields appear to obey this rule in the field. Root colonization was lowest, at 14.6 percent, in the phosphorus-replete three-month plots, surged to 62.3 percent at five months as phosphorus was drawn down, and moderated thereafter. Spore density followed the same trajectory, peaking at 57.3 spores per 100 grams of soil at five months.

The inverse relationship between available phosphorus and root colonization was the strongest correlation in the study, with a Pearson coefficient of minus 0.97. But the authors subject their own headline result to a searching critique. The pooled correlation is, in statistical terms, a contrast between two separated clusters — the six phosphorus-rich three-month plots and the fourteen later ones — rather than a within-field dose-response curve. When the earliest stage is excluded, the correlation weakens substantially, and within individual stages the coefficient is unstable and even changes sign. Root-system age is also perfectly confounded with crop stage in a ratoon system, since colonization is scored on progressively older roots, and percentage colonization commonly rises with root age irrespective of soil phosphorus. The authors present phosphorus suppression and root ontogeny as competing explanations of equal standing, to be disentangled only by manipulative experiments.

Alongside the mycorrhizal dynamics, the physical condition of the soil improved steadily with crop age. Mean weight diameter of water-stable aggregates rose from 1.14 millimetres at three months to 1.61 millimetres at eleven months, while bulk density fell from 1.36 to 1.25 grams per cubic centimetre. Soil organic carbon concentration climbed from 14.0 to 15.7 grams per kilogram, although when converted to fixed-depth carbon stocks the difference shrank to just over three percent, a reminder that concentration-based comparisons can exaggerate real changes in carbon storage. Aggregate stability correlated strongly with organic carbon but not with spore density, leading the authors to decline the tempting inference that fungal hyphae and glomalin-related soil protein were driving the aggregation — neither was measured directly, and unmeasured contributors such as root exudates, particulate organic matter and oxide chemistry may have been equally important.

The mycorrhizal community also became more diverse as the crop matured, with the Shannon diversity index rising from 1.41 to 2.47 across the chronosequence. Because different fungal genera differ in hyphal architecture, phosphatase activity and carbon demand, the authors suggest this shift may represent a broadening of functional capability rather than a mere change in abundance — though genus-level morphology cannot resolve species turnover, and spore-based diversity is known to be biased toward taxa that sporulate readily. Notably, the stage pattern persisted after statistical adjustment for site, and no stage-by-site interaction was detected for any of the nine variables, suggesting the pattern is not a peculiarity of a single plantation. The authors caution, however, that two of the three sites contributed only one block per stage, so the design supports adjustment for site rather than true site-specific replication.

To condense the coordinated changes into a single number, the team constructed a composite soil quality index from a principal-component-derived minimum data set of five indicators: available phosphorus, organic carbon, aggregate stability, spore density and root colonization. The index scored lowest, at 0.19, at the earliest stage and rose to around 0.8 at later stages. The authors are refreshingly candid that this result is partly determined by construction — the three-month plots held the least favourable value of all five indicators simultaneously — and that scoring phosphorus as less-is-better makes the index a measure of conditions favourable to the symbiosis rather than of agronomic fertility. When phosphorus was instead scored against an agronomic optimum band of 16 to 35 milligrams per kilogram, the earliest stage still ranked lowest under every threshold combination tested, but the identity of the best-scoring stage shifted. At harvest, cane yields ranged from 96 to 102 tonnes per hectare with apparent sucrose of 10.2 to 10.8 percent, though with only four harvested plots these figures are descriptive.

The practical upshot is a hypothesis rather than a prescription. The data show that the crop stage with the highest available phosphorus was also the stage with the least mycorrhizal colonization, and it is reasonable to ask whether reducing or splitting early-season phosphorus applications might allow the symbiosis to develop more fully, with possible benefits for phosphorus acquisition and soil structure. But no fertiliser regime was manipulated in this study, no yield response to any phosphorus treatment was measured, and inadequate early phosphorus carries its own risks to crop establishment. What the study delivers instead is a rigorous, unusually self-critical demonstration that chemical, physical and biological soil indicators move together in a real production landscape — and a clear, testable rationale for field experiments on phosphorus timing that could help tropical agriculture squeeze more fertility from its most stubborn soils while conserving the fungal partners that have quietly farmed them for millions of years.

Subject of Research: Long-term sugarcane cultivation effects on phosphorus availability, arbuscular mycorrhizal colonization and soil quality indicators in tropical Ultisols

Article Title: Long term sugarcane cultivation on tropical Ultisols drives changes in available phosphorus and arbuscular mycorrhizal colonization and soil quality indicators

Article References: Long term sugarcane cultivation on tropical Ultisols drives changes in available phosphorus and arbuscular mycorrhizal colonization and soil quality indicators. (n.d.). https://doi.org/10.1007/s44378-026-00345-3

Image Credits: AI Generated

DOI: 10.1007/s44378-026-00345-3

Keywords: sugarcane, tropical Ultisols, arbuscular mycorrhizal fungi, available phosphorus, soil quality index, aggregate stability, soil organic carbon, root colonization, ratoon cropping, South Sumatra, soil fertility, phosphorus fixation