Mangrove forests are often portrayed as unstoppable carbon factories: fast-growing trees rooted in tidal mud, capturing atmospheric carbon dioxide and burying it in oxygen-poor sediments for centuries. Yet a new study suggests that the identity of the mangrove itself may determine whether that carbon becomes long-term climate storage or remains vulnerable to decomposition and loss. Researchers report that the native mangrove Kandelia obovata stores substantially more soil carbon than the introduced Sonneratia apetala, despite the exotic species’ high productivity. The difference, they argue, is not simply a matter of how much plant material enters the soil. It is driven by a hidden biological partnership beneath the roots, where plant metabolites select particular microbial communities and reshape the chemical conditions that control carbon persistence.

The study, published in Plant and Soil, examined rhizosphere sediments associated with the two mangrove species. The rhizosphere is the narrow zone of soil directly influenced by roots, root exudates and microbial activity. It is one of the most chemically dynamic environments in an ecosystem. Plants release sugars, amino acids, organic acids, flavonoids and other compounds into this zone, effectively creating a selective nutritional landscape for microorganisms. The researchers integrated microbiomics, metabolomics and ecoenzymatic stoichiometry to investigate how these processes differed between K. obovata and S. apetala. Their results indicate that the native species exerted stronger “host selection,” filtering the surrounding microbial pool and favoring organisms with traits associated with nutrient retention, mineral transformation and the formation of stable microbial residues.

The carbon contrast between the two mangroves was pronounced. Sediments beneath K. obovata contained higher concentrations of total soil organic carbon, microbial biomass carbon and mineral-associated organic carbon, or MAOC. Microbial biomass carbon represents the carbon contained in living microbial cells, while MAOC refers to organic compounds that become attached to reactive minerals, especially iron-bearing minerals. This mineral-bound fraction is widely considered one of the more persistent forms of soil carbon because physical and chemical associations can shield organic molecules from microbial enzymes. By contrast, carbon that remains dissolved, particulate or only weakly protected is more exposed to oxidation, transport and decomposition. The findings therefore suggest that the native mangrove supports not just greater carbon accumulation, but a pathway that moves carbon toward more durable storage pools.

A central element of that pathway was the chemistry of the root environment. The researchers identified plant-associated metabolites, including ginkgetin, that correlated with stronger microbial selection under K. obovata. Ginkgetin is a biflavonoid compound, and although the precise ecological function of this metabolite in mangrove sediments requires further testing, its association with microbial community structure is significant. Root-derived compounds can act as carbon sources, chemical signals or selective inhibitors. They may favor microorganisms capable of tolerating particular redox conditions, using complex substrates or forming close associations with plant tissues. In this case, the metabolite profile of K. obovata appeared to be linked to a microbial community less dominated by rapid opportunists and more enriched in organisms adapted to efficient resource use and chemically demanding sediment environments.

The study interprets this community difference through the ecological concept of r- and K-selected microbial strategies. R-strategists are generally fast-growing organisms that exploit abundant, easily available resources. They can rapidly consume labile carbon, but their growth may be accompanied by substantial respiration and nutrient loss. K-strategists tend to grow more slowly, use resources more efficiently and invest in persistence under competitive or nutrient-limited conditions. Sediments associated with S. apetala were enriched in bacteria interpreted as r-strategists, whereas K. obovata favored a greater abundance of K-strategists. The distinction is not an absolute division between two microbial groups, but a functional framework describing how microbial life-history traits influence carbon processing. A community dominated by fast growth may accelerate carbon turnover, while one characterized by efficient biomass production and persistence may channel more carbon into microbial residues and protected soil organic matter.

Nitrogen cycling appeared to be one of the mechanisms connecting microbial strategy with carbon storage. Beneath K. obovata, the researchers found stronger associations with bacteria involved in iron and sulfur oxidation as well as enhanced potential for dissimilatory nitrate reduction to ammonium, known as DNRA. In DNRA, nitrate is reduced to ammonium rather than converted into gaseous nitrogen compounds. This process conserves nitrogen within the sediment because ammonium can remain available for plant and microbial uptake. In nitrogen-limited mangrove soils, that retention may have major consequences. Microbes require nitrogen to build proteins, nucleic acids and cellular machinery; when nitrogen is scarce, they may be unable to convert incoming carbon into biomass efficiently. By conserving nitrogen, DNRA could support microbial biosynthesis, increase microbial biomass carbon and promote the production of microbial residues that ultimately contribute to soil carbon storage.

The alternative pattern emerged under S. apetala. Its sediments showed stronger associations with denitrification, a process that transforms nitrate into gaseous products such as nitrous oxide and dinitrogen. Denitrification is an essential component of the global nitrogen cycle, but in a nutrient-limited rhizosphere it can remove biologically useful nitrogen from the soil system. The researchers propose that intensified denitrification beneath the exotic mangrove may contribute to nitrogen loss, restricting microbial anabolism and reducing the amount of carbon incorporated into microbial biomass. This interpretation is consistent with the broader principle that microbial carbon storage depends not only on carbon supply, but also on the balance of carbon and nutrients. A tree may produce abundant litter and root material, yet the resulting carbon stock can remain low if microorganisms rapidly respire the carbon or lack sufficient nitrogen to convert it into stable cellular and extracellular products.

Iron and sulfur chemistry provided a second major explanation for the divergence in carbon fate. In waterlogged mangrove sediments, iron can cycle between oxidized and reduced forms. Reactive iron oxides are especially important because they can bind organic molecules, creating iron-associated carbon that is less accessible to decomposers. Microbial iron reduction, however, can dissolve these minerals and release their associated carbon. Sulfate reduction creates another route through which sediment chemistry can shift. The study found that S. apetala sediments were enriched in iron- and sulfate-reducing bacteria. According to the authors, their activity may encourage the formation of low-reactivity iron sulfides, effectively locking iron into mineral forms that are less capable of binding organic carbon. Once reactive iron is sequestered as iron sulfide, fewer mineral surfaces remain available to capture and protect organic compounds, potentially limiting MAOC formation.

Under K. obovata, by contrast, the enrichment of iron- and sulfur-oxidizing bacteria may help maintain or regenerate reactive mineral phases. Oxidation can transform reduced iron into iron oxides with greater capacity to interact with organic matter. This does not mean that oxidation always increases carbon storage; iron cycling is strongly dependent on water levels, pH, sulfide concentrations, tidal exchange and the chemical composition of organic matter. However, the findings point to a microbial “iron gate” that may regulate whether carbon is physically and chemically protected in the sediment. When the gate remains open, reactive minerals can bind organic compounds. When microbial reduction and sulfide production close it, carbon protection may weaken. The native mangrove’s stronger host selection may therefore influence carbon storage through both biological nutrient retention and geochemical mineral preservation.

The implications extend beyond a comparison of two tree species in one mangrove system. Mangrove restoration and blue-carbon accounting often emphasize planting density, aboveground biomass and growth rate, but these measures may not predict the durability of buried carbon. The study suggests that restoration decisions should also consider plant–microbe interactions, root metabolite profiles, nitrogen-cycling pathways and the availability of reactive minerals. Introducing a fast-growing species may increase canopy cover without producing equivalent gains in stable soil carbon. Conversely, a slower-growing native species could generate stronger microbial selection and greater long-term carbon protection. The authors propose that targeted microbial regulation or mineral amendments might eventually improve restoration outcomes, although such interventions would require careful field testing because altering iron, sulfur or nitrogen cycling could also affect greenhouse-gas emissions and ecosystem function.

The researchers caution, implicitly, that the results describe linked ecological processes rather than a single proven cause-and-effect chain. Metabolites correlated with microbial selection, microbial groups correlated with nitrogen and iron transformations, and those transformations correlated with carbon pools. Demonstrating causation will require experiments that manipulate specific compounds, microbial functions or mineral conditions under controlled tidal environments. Even so, the study offers a new way to understand why visually similar mangrove stands can differ greatly in their climate value. Soil carbon fate is not determined solely by how much carbon enters a wetland. It depends on who consumes that carbon, which nutrients remain available, how microbes allocate carbon between respiration and biomass, and whether minerals can protect the resulting organic matter. Beneath the roots of native Kandelia obovata, the researchers found a tightly coordinated biological and geochemical system that appears to favor carbon retention. Beneath exotic Sonneratia apetala, a faster and less selective microbial regime may send more carbon—and potentially more nitrogen—back into circulation.

Subject of Research: Microbial community assembly, nitrogen and iron–sulfur cycling, and soil organic carbon stabilization in native and exotic mangroves

Article Title: Host selection-driven microbial community assembly and functional differentiation determine mangrove soil carbon fate

Article References: Duan, F., Zhao, X., Tan, F. et al. “Host selection-driven microbial community assembly and functional differentiation determine mangrove soil carbon fate.” Plant and Soil (2026). https://doi.org/10.1007/s11104-026-09015-3

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09015-3

Keywords: Mangrove restoration, soil organic carbon, host selection, microbial community assembly, mineral-associated organic carbon, Kandelia obovata, Sonneratia apetala, DNRA, denitrification, iron–sulfur cycling

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