Isolation, 16S rRNA-based Taxonomic Profiling and Potential Roles of Endophytic Bacteria Colonizing Dalbergia reniformis (Koroch)

Deep within the tissues of plants, hidden from the naked eye, lives a bustling community of microscopic partners. These are endophytes, bacteria that reside inside roots, stems, and leaves without causing harm. For decades, scientists have known that these invisible neighbors are not merely passengers; they are active participants in a plant's life. They can help their hosts gather nutrients from the soil, produce hormones that spur growth, and even defend against disease. This relationship is a cornerstone of sustainable agriculture, offering a natural alternative to chemical fertilizers and pesticides. The question that drives researchers today is not just whether these helpers exist, but which specific ones are the most effective, and where they can be found in nature's most challenging environments.

In the heart of Bangladesh lies a unique and fragile ecosystem known as Ratargul Swamp Forest, the country's only freshwater swamp. Here, the water levels rise and fall dramatically with the seasons, submerging the landscape for months at a time. Dominating this watery world is the Koroch tree, a resilient species that thrives even when its roots are underwater for half the year. Despite its ecological importance and its ability to survive such harsh conditions, the microscopic world living inside the Koroch tree had never been explored. A team of researchers from Shahjalal University of Science and Technology and Daffodil International University set out to uncover this hidden diversity, hoping to find bacteria that could one day help other plants grow in difficult soils.

The team began by carefully collecting samples of roots, stems, and leaves from healthy Koroch trees. To ensure they were studying only the bacteria living inside the plant, and not those clinging to the surface, they subjected the samples to a rigorous cleaning process. They washed the plant parts in a series of solutions, including alcohol and bleach, to sterilize the outside. They then placed small pieces of the sterilized tissue onto nutrient-rich plates in a laboratory. If bacteria grew from these pieces, it confirmed they had originated from within the plant. From the initial harvest, the researchers isolated thirty-four distinct bacterial colonies. They selected eighteen of these, each looking different under a microscope, to study in detail.

Using a technique that reads the genetic code of the bacteria, specifically a segment of DNA known as the 16S rRNA gene, the scientists identified who these microbes were. The results revealed a diverse community spanning ten different genera, or families, of bacteria. The most common group they found was Pantoea, which appeared in five of the eighteen samples. Other families included well-known names like Bacillus, Pseudomonas, and Klebsiella. These bacteria were not limited to one part of the tree; they were found in the roots, stems, and leaves alike, suggesting that the Koroch tree hosts a rich and varied internal ecosystem.

The researchers then put these eighteen bacterial isolates through a series of tests to see what useful skills they possessed. They were looking for traits that help plants grow, such as the ability to produce ammonia, which is a form of nitrogen that plants can use, or to create siderophores, which are molecules that grab iron from the environment and make it available to the plant. The results were striking: every single one of the eighteen bacteria produced ammonia and siderophores. This means that the entire community they studied has the built-in capacity to help a plant access essential nutrients.

Beyond these universal traits, the bacteria showed a wide range of other abilities. Nearly all of them could produce organic acids and an enzyme called phytase, which helps break down complex phosphorus in the soil. A large majority could dissolve zinc, a vital micronutrient, making it easier for plants to absorb. About half of the bacteria could produce hydrogen cyanide, a compound that can suppress harmful pathogens, while others produced enzymes that break down proteins, fats, or plant fibers like cellulose. Perhaps most notably, every single isolate produced gibberellic acid, a powerful plant hormone that stimulates growth and cell division.

When the scientists measured the strength of these abilities, they found that some bacteria were particularly potent. One isolate, labeled EB_12, stood out as a powerhouse. It showed the highest ability to dissolve both phosphate and zinc among all the samples, while also producing high levels of growth hormones and other beneficial compounds. Another isolate, EB_13, produced the highest amount of gibberellic acid. The researchers noted that these top performers, along with a few others, demonstrated a combination of skills that could make them excellent candidates for use as bioinoculants. These are natural preparations applied to seeds or soil to boost plant health without the need for synthetic chemicals.

The study highlights that the Koroch tree, thriving in the fluctuating waters of the Ratargul Swamp, harbors a community of bacteria that is not only diverse but functionally rich. The fact that these microbes can dissolve nutrients and produce growth hormones suggests they are well-adapted to the challenging, waterlogged conditions of the swamp. While the researchers caution that these findings are based on bacteria they could grow in a lab—a fraction of the total community—the results are promising. They suggest that the endophytes of the Koroch tree hold significant potential for developing new, natural tools to support agriculture, particularly in environments where soil nutrients are scarce or difficult for plants to reach. The work opens a door to understanding how nature's own microscopic allies can be harnessed to help crops flourish.