Coral Island Bacterium With Dual Sugar Armor Offers New Hope for Salty, Degraded Soils

On a sun-scorched coral island off the coast of Vietnam, where the soil is little more than porous calcium carbonate laced with salt and starved of nutrients, an unassuming bacterium has been quietly mastering conditions that would kill most living things. Researchers have now decoded the genome of this microbe, a strain of Bacillus velezensis designated DTA1, and found that it carries not one but two complete molecular assembly lines for manufacturing exopolysaccharides, the sticky sugar polymers that bacteria use as armor against hostile environments. The discovery, published in the journal One Ecosystem, offers a tantalizing glimpse of how nature’s own extremophiles could be recruited to repair some of the world’s most degraded agricultural land.

The story begins with a soil sample collected from a coral island in Khanh Hoa Province, Vietnam. Coral island soils are notoriously unforgiving: they are highly alkaline, loose in texture, poor in fertility and cation exchange capacity, prone to drought, and bathed in intense heat and solar radiation. Salt-laden winds and scarce freshwater compound the problem, and in some cases irrigation depends on brackish water, making cultivation nearly impossible. Yet it is precisely in these frontline conditions of climate stress that evolution tends to produce its most resourceful survivors. When the researchers plated the soil sample on medium containing three percent sodium chloride, DTA1 emerged as a colony-forming, slime-producing survivor, its string-forming ability in a simple laboratory test immediately flagging it as a prolific exopolysaccharide producer.

Under the microscope, DTA1 presented as a rod-shaped, Gram-positive, endospore-forming bacterium two to three micrometers long, classic Bacillus morphology. But its physiological repertoire proved anything but ordinary. In tolerance assays, the strain grew in sodium chloride concentrations ranging from zero to 12.5 percent, and it tolerated magnesium sulfate up to ten percent, a level of halotolerance exceeding that reported for many related Bacillus species such as B. amyloliquefaciens, B. paramycoides and B. pumilus, whose tolerance typically spans two to ten percent. Only at 15 percent salt did growth cease entirely. More striking still was its heavy metal resilience: DTA1 withstood chromium and arsenic at concentrations up to 64 micrograms per milliliter, cadmium up to 32, and, at the far higher concentrations tested for the more benign metals, it endured up to 900 micrograms per milliliter of lead and zinc and 600 of iron.

The molecular basis for this toughness became clear when the team sequenced the bacterium’s entire genome. The assembled genome spans 3,898,926 base pairs with a GC content of 46.5 percent, closely matching the well-studied reference strain B. velezensis FZB42. Annotation revealed 3,784 protein-coding sequences, 62 transfer RNA genes and 11 ribosomal RNA genes, with a large share of the coding capacity devoted to amino acid, carbohydrate and secondary metabolism. Crucially, the genome harbors a dense arsenal of stress-response machinery: genes for osmoprotectant transporters such as the opu and gbs systems that import glycine and proline betaine, sodium export pumps including nha and mnh antiporters that expel salt from the cell, potassium import channels of the kht family that balance internal pressure, and metal resistance genes such as czcD, cadA, chrA, chrB and arsB that pump out or detoxify cadmium, zinc, cobalt, chromium and arsenic. Signaling genes like degU, degS, sodA and dnaK round out the toolkit, allowing the cell to sense and respond rapidly to environmental shocks.

But the genome’s most remarkable feature is its doubled-up exopolysaccharide production system. Most bacteria rely on a single pathway, yet DTA1 carries both the epsA–O operon, a 15.7-kilobase cluster of 15 genes driving the complex Wzx/Wzy-dependent pathway, and a separate 6.1-kilobase levan biosynthetic cluster built around the sacB gene encoding levansucrase. The epsA–O system operates like an intracellular factory: a membrane-bound priming glycosyltransferase called EpsE activates a lipid carrier, other glycosyltransferases including EpsL, EpsD, EpsH and EpsJ attach specific nucleotide sugars one by one, and modification enzymes such as EpsM and EpsN fine-tune each repeating unit. The Wzx flippase then shuttles completed units across the inner membrane, the Wzy polymerase EpsG stitches them into long chains, and the EpsA–EpsB tyrosine kinase pair regulates chain length and export. The levan pathway, by contrast, is elegantly simple: a single sucrase enzyme, SacB, assembles fructose units into a beta-2,6-linked homopolymer directly outside the cell, with the adjacent levB gene encoding a levanase that degrades the polymer when needed.

Feeding this dual machinery requires a sophisticated logistics network, and DTA1 has one. The genome encodes 22 phosphotransferase system transport proteins organized into 11 distinct sugar uptake systems, spanning glucose, fructose, sucrose, mannose, cellobiose, mannitol, trehalose, lactose, N-acetylglucosamine and more, plus permeases for arabinose and maltose and an ABC transporter for maltodextrin. Downstream, 29 genes encode enzymes that convert these various carbon sources into eight different nucleotide sugars, the activated building blocks from which complex polysaccharides are assembled. Laboratory testing confirmed the genomic predictions: of 49 carbohydrates offered, the strain could ferment 28, with glucose, fructose, mannose, esculin, cellobiose and sucrose among its favorites. Multiple gene copies for cellobiose, sucrose and arabinose transport appear to give the bacterium a particular edge in exploiting these sugars.

Experiments revealed that the environment profoundly shapes what the bacterium builds. Although DTA1 grew best under benign conditions, its exopolysaccharide output rose significantly under salt or heavy metal stress, with total sugar and protein content in the polymer roughly doubling. Elemental analysis showed the polymer acting as a molecular sponge: sodium and chlorine, barely detectable in EPS from salt-free cultures at 0.73 and 0.52 percent, surged to 9.03 and 2.04 percent under salt stress, and cations including cobalt, cadmium, manganese, iron, copper, zinc and silver appeared in the EPS only when those metals were present in the medium. The negatively charged functional groups in the polymer, including amine, thiol, carboxyl, hydroxyl and phosphate groups, bind cations through complexation, ion exchange and precipitation, effectively locking toxic ions away from the cell.

Sugar supply proved equally decisive for both yield and architecture. Adding sucrose or glucose boosted EPS production well above the control level of 16.35 grams per liter, and sucrose outperformed glucose at every dose, reaching 30.39 grams per liter at 50 grams per liter sucrose, a yield exceeding those reported for several other B. velezensis strains. The polymer’s monosaccharide composition shifted dramatically with the feedstock: glucose-fed cultures produced EPS dominated by mannose, rising to 99.37 percent at the higher glucose concentration, while sucrose-fed cultures yielded a five-sugar blend of glucose, rhamnose, fructose, mannose and N-acetylglucosamine, with fructose appearing only in sucrose-rich media, exactly as the levan pathway would predict. This is the first clear demonstration in B. velezensis of how glucose and sucrose concentrations jointly govern both the quantity and the monosaccharide makeup of EPS, and the first report of both the epsA–O operon and levan synthesis coexisting in this species.

The practical implications reach far beyond the laboratory bench. Saline soils are spreading rapidly worldwide and are projected to affect up to half of all cultivated land by 2050, while Vietnam, with its long coastline and scattered islands, sits squarely in the path of climate-driven salinization. Exopolysaccharide-producing bacteria can attack this problem on several fronts: their polymers adsorb and immobilize sodium and heavy metals, reducing bioavailability; their high molecular weight and hydrophilic groups promote soil aggregation and water retention; and the biofilms they form protect both microbes and plant roots under stress. Because B. velezensis is regarded as a safe organism already used in microbial fertilizers, and because DTA1 is a native strain pre-adapted to the very conditions that need fixing, the researchers argue it is an ideal candidate for rehabilitating arid, saline coral sand and coastal soils. As salt creeps across the world’s farmland, the answer may lie in the genome of a bacterium that learned to thrive where almost nothing else can.

Subject of Research: Genomic and biochemical characterization of the salt-tolerant, exopolysaccharide-producing bacterium Bacillus velezensis DTA1 isolated from Vietnamese coral island soil for soil remediation

Article Title: Genomic insights into salt-tolerant, exopolysaccharide-producing Bacillus velezensis DTA1 isolated from coral island soil in Vietnam: Implications for soil remediation

Article References: Le, H., Tran, T., Nguyen, S., La, D., Vu, N., Le, M. H., & Nguyen, H. (2025). Genomic insights into salt-tolerant, exopolysaccharide-producing Bacillus velezensis DTA1 isolated from coral island soil in Vietnam: Implications for soil remediation. One Ecosystem, 10, Article e158806. https://doi.org/10.3897/oneeco.10.e158806

Image Credits: AI Generated

DOI: 10.3897/oneeco.10.e158806

Keywords: Bacillus velezensis, exopolysaccharides, salt tolerance, soil remediation, whole genome sequencing, heavy metal resistance, coral island soil, Vietnam, levan, epsA-O operon, halophilic bacteria, saline soils