The research team, led by Mahlatse Ellias Moremi of the South African Sugarcane Research Institute alongside colleagues from the Agricultural Research Council, followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to sift through the literature. An initial database search across Scopus, Web of Science, PubMed and ScienceDirect yielded 536 records, which the authors narrowed down through independent screening to 42 eligible studies. From these, they catalogued a remarkable 146 bacterial genera and 95 fungal genera, classifying each according to three functional roles: nutrient solubilisation, pathogen suppression, and plant pathogenicity. This functional lens matters because the balance among these groups ultimately determines whether a soil supports crop growth or harbours disease.

The review arrives at a critical moment for a crop with enormous global significance. Sugarcane underpins more than 75 percent of world sugar production and roughly 40 percent of biofuel output, with Brazil, China and India dominating the supply. African nations contribute 5.6 percent of global production, led by South Africa, where the crop supports employment and food security while contributing to several United Nations Sustainable Development Goals, including Zero Hunger and Affordable and Clean Energy. Yet conventional practices such as pre-harvest burning, intensive tillage and long-term monocropping have been linked to soil degradation, nutrient imbalances and declining yields. The new synthesis provides the most comprehensive picture yet of how these pressures ripple through the microbial world.

Among the bacterial genera, a clear set of dominant players emerged. Sphingomonas, reported in 17 field studies, topped the list, followed by Bradyrhizobium with 14 reports, Bacillus with 13, and Gemmatimonas with 10. Streptomyces and Acidothermus each appeared in nine studies. These taxa are far from random arrivals: Sphingomonas, Bradyrhizobium and Bacillus are well documented for their roles in nitrogen fixation, nutrient cycling, disease suppression and plant growth promotion. On the fungal side, Talaromyces, Fusarium, Curvularia and Mortierella dominated the field-study records, while Fusarium, Trichoderma and Penicillium were the most frequently reported genera in greenhouse experiments. Notably, this roster spans the full functional spectrum, from beneficial solubilisers to notorious pathogens.

One of the most striking revelations concerns a mismatch between what lives in sugarcane soils and what the biotechnology industry sells. Commercial phosphorus-solubilising products are overwhelmingly built around Bacillus strains and the arbuscular mycorrhizal fungus Funnelformis. Yet the review shows that indigenous sugarcane soils are naturally dominated by a different suite of potent solubilisers, most notably Sphingomonas and Bradyrhizobium. The authors argue that this native phosphorus-mobilising potential represents a largely untapped resource, and that next-generation biofertilisers tailored to sugarcane systems might do better to harness these locally adapted taxa rather than relying on exotic inoculants that face fierce competition from established native communities.

The review also exposes how strongly experimental context shapes results. When the authors compared microbial responses across field and greenhouse settings, they found that Sphingomonas was the only genus consistently reported in both environments for intercropping studies—and even then, its response flipped, increasing in field conditions while decreasing in the greenhouse. The explanation likely lies in the stability of controlled environments, which favour microbial colonisation and metabolite production, versus the environmental variability of real fields, where moisture extremes, nutrient heterogeneity and resource competition constrain colonisation. The practical implication is sobering: greenhouse results cannot be straightforwardly extrapolated to the field, and robust conclusions demand integration across experimental scales.

Soil compartment added another layer of complexity. Under some treatments, such as nitrogen, phosphorus and potassium fertilisation combined with straw return, genera like Bryobacter, Bradyrhizobium and Sphingomonas showed consistent abundance patterns in both bulk soil and the rhizosphere, the narrow zone of root influence. Under other conditions, including sugarcane-wheat rotations and sugarcane-peanut intercropping, the same genera diverged sharply between compartments. Time mattered too: Fusarium abundance remained unaffected by organic amendments at 50 days but declined significantly after 100 days, indicating that some management effects only emerge after prolonged soil-microbe interactions. Any single snapshot, the authors caution, risks missing the true dynamics of these communities.

Crop genotype proved to be a decisive moderating factor throughout the synthesis. The widely grown variety ROC22 suppressed bacterial genera such as Acidothermus and Gemmatimonas while enriching fungal genera like Talaromyces and Mortierella, whereas the newer variety Z9 produced the opposite trend for Trichoderma. In one study, the effects of intercropping on Sphingomonas, Acidothermus and Gemmatimonas were completely reversed when comparing wild-type and genetically modified sugarcane. Arbuscular mycorrhizal fungal communities likewise shifted in a variety-specific manner under green cane harvesting. Because most genera responded to the interaction between variety and management rather than to either factor alone, the authors conclude that breeding strategies and microbiome research must be developed hand in hand.

The main management practices themselves produced a patchwork of outcomes. Excessive inorganic nitrogen generally suppressed overall microbial abundance, while moderate nitrogen and potassium applications promoted beneficial genera such as Acidothermus, Bradyrhizobium, Bacillus and Nitrospira. Organic inputs like vinasse enriched Burkholderia and Sphingomonas but depleted Bacillus, and combining molasses with urea and potassium chloride enhanced Bacillus while reducing Sphingomonas. Biofertiliser effects were exquisitely sensitive to strain composition, application rate and nitrogen context: a consortium containing Trichoderma asperellum and Bacillus subtilis enriched Bradyrhizobium and Trichoderma, while specialised consortia dominated by Methylobacterium depleted both Bacillus and Burkholderia. Intercropping outcomes depended heavily on the companion crop, with sugarcane-soybean systems enriching Bryobacter, Nitrospira, Penicillium and Trichoderma, and sugarcane-peanut systems promoting Acidothermus and Bradyrhizobium. Meanwhile, green cane harvesting promoted a broader range of beneficial taxa than straw return alone, and the deep-tillage technique known as Fenlong-ridging increased Bradyrhizobium and Talaromyces while reducing Sphingomonas, Penicillium and Curvularia.

Underlying these variable responses, the authors propose a mechanistic framework in which microbiome assembly is governed by chemical nutrient saturation, carbon complexity and spatial compartmentation. High inorganic nitrogen acts as a directional filter, acidifying soil and suppressing oligotrophic diazotrophs like Bradyrhizobium by reducing root carbon allocation, while versatile generalists such as Sphingomonas persist thanks to their protective sphingolipid cell walls. Easily degradable carbon sources trigger blooms of opportunistic copiotrophs, whereas lignocellulosic residues select for robust spore-forming decomposers. The review is candid about its limitations: the evidence base is heavily skewed toward China, which contributed 34 of the 42 studies, most research spans only a single growth cycle, soil classification was often poorly documented, and amplicon sequencing reveals composition rather than function. Still, the overarching message is clear. Soil microbial responses in sugarcane systems are profoundly context-dependent, emerging from interactions among management practices, environmental conditions and crop genotype. Sustainable production, the authors conclude, will require integrated, systems-based approaches that optimise these interactions rather than betting on any single intervention.

Subject of Research: Effects of sugarcane management practices on soil bacterial and fungal communities

Article Title: A scoping review of how various management practices influence bacterial and fungal genera within sugarcane production systems

Article References: Moremi, M. E., Mdlambuzi, T., Mashamaite, C. V., & Elephant, D. E. (2026). A scoping review of how various management practices influence bacterial and fungal genera within sugarcane production systems. Discover Soil, 3(1), Article 127. https://doi.org/10.1007/s44378-026-00283-0

Image Credits: AI Generated

DOI: 10.1007/s44378-026-00283-0

Keywords: sugarcane, soil microbiome, bacteria, fungi, intercropping, fertilisation, straw return, biofertilisers, rhizosphere, pathogen suppression, nutrient solubilisation, sustainable agriculture

The team’s starting point was a simple horticultural trick that foresters have long appreciated. Instead of coaxing seeds through their slow and unreliable germination, one-year-old teak seedlings can be harvested and cut into stumps: a seven-centimetre segment of root joined to a short shoot portion of about 2.5 centimetres, each trimmed to a girth of roughly one centimetre. These stumps are then planted directly into polythene bags filled with red soil, where they resprout into complete young trees. Because every stump is cut from a seedling that has already proven itself vigorous, the method sidesteps the germination problem entirely and produces uniform planting material at a fraction of the cost of tissue culture. What the stumps still lacked, however, was a fast, reliable way to establish themselves in nutrient-poor nursery soil, and that is where the microbes came in.

The researchers assembled a cast of four bacterial strains and two fungal species, all well-known players in the world of plant growth-promoting rhizobacteria, or PGPR, and arbuscular mycorrhizal fungi, or AM fungi. The bacterial lineup included Azospirillum melinis and Azotobacter chroococcum, two free-living nitrogen fixers that can pull atmospheric nitrogen into forms plants can absorb, and Bacillus licheniformis, a phosphate solubiliser that unlocks insoluble phosphorus locked away in soil minerals. On the fungal side, the team worked with Funneliformis mosseae and Glomus sinuosum, two AM fungi that colonise plant roots and build extensive networks of hyphae that extend far beyond the root’s own reach, effectively enlarging the volume of soil the tree can mine for water and nutrients. One month after the stumps had been transplanted into their poly bags, the researchers inoculated them with each microorganism individually and in various combinations, then irrigated and maintained them for three months.

After the three-month nursery phase, the team measured growth, biomass and the concentrations of nitrogen, phosphorus and potassium in the plant tissues. The results were unambiguous. Stumps that had received microbial inoculation grew better and accumulated more biomass than uninoculated control stumps across the board. The effect was strongest when multiple organisms were applied together, a pattern consistent with the idea that the different microbes perform complementary functions: the nitrogen fixers supply one limiting nutrient, the phosphate solubiliser another, and the mycorrhizal fungi knit the whole system together by improving uptake of phosphorus and water through their hyphal networks. Notably, the dual inoculation of the two nitrogen fixers, Azospirillum melinis and Azotobacter chroococcum, performed on par with the full multi-species cocktail, suggesting that a carefully chosen pair of bacteria may deliver most of the benefit without the complexity of managing four or five organisms at once.

Tissue nutrient analysis reinforced the growth story. Levels of nitrogen, phosphorus and potassium were all higher in plants that had received the multiple PGPR inoculations, confirming that the microbes were not merely stimulating growth through hormones or other indirect signals but were genuinely improving the nutritional status of the young trees. This matters for reforestation in a practical sense. Clear-felled forest sites are often depleted in organic matter and available nutrients, and planting stock that arrives with a well-developed internal nutrient reserve and an active microbial partnership is far more likely to survive the shock of transplanting. The mycorrhizal component is particularly significant here, because AM fungi form structures called arbuscules inside root cells, where the plant trades photosynthetic sugars for minerals gathered by the fungus, an ancient symbiosis that underpins nutrient cycling in most terrestrial ecosystems.

The study did not stop at the nursery gate. The improved teak stumps were transplanted into forest lands at Konni in the state of Keralam, India, a region where teak plantations have historically been established on clear-felled forest. Under real field conditions, the inoculated stumps showed good growth and survival, providing the crucial proof of concept that nursery-stage microbial treatment translates into field performance. This last step is where many biofertiliser trials falter, since greenhouse gains often evaporate when plants face drought, competition, herbivory and the heterogeneous soils of an actual plantation. The Konni outplanting, conducted in collaboration with the state forest department, indicates that stump inoculation is not just a laboratory curiosity but a workable component of operational reforestation.

The findings fit into a broader and rapidly growing body of research on microbial symbioses in tropical forestry. Previous work by the same group has shown that AM fungi can improve the establishment of eucalyptus on bauxite mine spoils, that the actinorhizal symbiont Frankia boosts growth in casuarina plantations, and that PGPR inoculation can help trees colonise barren laterite rocks. Studies from other groups have documented similar benefits in acacias in the Sahel, in oil palm under greenhouse conditions, and in sandalwood grown alongside casuarina host plants. Together, these results point toward a paradigm in which the health of a plantation is understood as a property of its soil microbiome as much as of its genetics or its silviculture. The ecological literature has long recognised that above-ground and below-ground biota are tightly linked, and foresters are now learning to exploit those linkages deliberately.

For teak specifically, the implications are considerable. The species commands some of the highest timber prices in the world, and demand from both domestic Indian markets and international buyers has driven extensive plantation programs. India’s timber trade reviews have highlighted the scale of the industry, and teak remains the flagship species for many state forest departments and private growers alike. If stump propagation combined with microbial inoculation can reliably produce vigorous planting stock at low cost, it could reduce dependence on seed orchards and tissue culture labs while shortening the nursery cycle. The economics are attractive: stumps require no specialised equipment, the microbial inoculants can be mass-produced from locally maintained cultures, and the technique is accessible to small-scale nurseries that supply village-level planting programs.

There are also ecological dividends. Reforestation of clear-felled land is one of the most widely deployed strategies for climate mitigation and biodiversity recovery, and its success hinges on early seedling survival. Young trees that establish a mycorrhizal network quickly can access water and nutrients that uncolonised neighbours cannot, giving them a competitive edge during the vulnerable establishment phase. Faster early growth also shortens the period during which plantations are exposed to weed competition and fire risk. By demonstrating that a simple inoculation at the nursery stage can carry through to improved field performance, the Coimbatore team has added a practical tool to the restoration toolkit, one that works with the tree’s own evolutionary history rather than against it.

The study, published in Plant Biosystems as volume 160, article 235, is careful to frame its contributions within the constraints of a single species and a single field site, and the authors declare no competing interests. Further work will be needed to test how the inoculant combinations perform across different soil types, climates and provenances of teak, and to determine whether the dual bacterial treatment identified in the nursery trials remains the optimal choice under field conditions. But the core message is already clear and likely to resonate far beyond Indian forestry: sometimes the cheapest way to grow a better tree is to hand it, at the very start of its life, the microbial partners it would eventually find in a healthy forest soil anyway. In an era when restoration targets are measured in millions of hectares, such elegantly simple interventions may prove to be among the most valuable.

Subject of Research: Use of arbuscular mycorrhizal fungi and plant growth-promoting rhizobacteria to improve growth of Tectona grandis stump cuttings for reforestation in India

Article Title: Arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria promote Tectona grandis root shoot cuttings used in reforestation of clear-felled forest in India

Article References: Arumugam, K., Chacko, J. V. P., Lingam, M., & Nair, S. P. (2026). Arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria promote Tectona grandis root shoot cuttings used in reforestation of clear-felled forest in India. Plant Biosystems, 160(4), Article 235. https://doi.org/10.1007/s44473-026-00243-0

Image Credits: AI Generated

DOI: 10.1007/s44473-026-00243-0

Keywords: teak, Tectona grandis, arbuscular mycorrhizal fungi, PGPR, reforestation, stump cuttings, nitrogen fixation, phosphate solubilisation, biofertilisers, forest restoration, India, plant nutrition