A new microbial discovery in the mangroves: meet Neptunitalea lumnitzerae

In the lush, biodiverse mangrove forests of Iriomote Island, Okinawa-Japan, researchers have uncovered a new bacterial species that could deepen our understanding of marine and plant-associated microbiomes. This novel microorganism was isolated from the leaves of a mangrove plant species.
A new microbial discovery in the mangroves: meet Neptunitalea lumnitzerae
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Neptunitalea lumnitzerae sp. nov. isolated from the phyllosphere of the mangrove Lumnitzera racemosa Willd. - Antonie van Leeuwenhoek

A Gram-stain-negative, rod-shaped, non-motile, aerobic, light-yellow-pigmented bacterium, designated as strain Y10T, was isolated from Lumnitzera racemosa leaf in Iriomote island mangrove forests in Japan. The 16S rRNA gene sequence analysis revealed that the isolate Y10T was affiliated with the family Flavobacteriaceae, and the sequence showed the highest sequence identity to that of Neptunitalea chrysea NBRC 110019T (97.2%) and others with below 96% sequence identity. The draft genome analysis revealed that its genomic size is 3.85 Mbp with G + C content 34.1%. The average nucleotide identity, average amino acid identity, and digital DNA–DNA hybridization values between strain Y10T and Neptunitalea chrysea NBRC 110019T was 79.07%, 76.35% and 19.6%, respectively, which were below the thresholds for prokaryotic species delineation (95–96%, 85%, and 70%, respectively). MK-6 was the only menaquinone, and the major cellular fatty acids (> 10% of the total fatty acids) were iso-C15:0, iso-C17:0 3-OH, and summed feature 3 (comprised of C16:1ω7c-iso and C15:0 2-OH). Based on its distinct phylogenetic position and genotypic and phenotypic characteristics, the strain represents a novel species of the genus Neptunitalea, for which the name Neptunitalea lumnitzerae sp. nov. is proposed. The type strain is Y10T (= DSM 110280T = NBRC 115783T).

Mangrove forests are known for their unique and challenging environments, characterized by high salinity, fluctuating water levels, and rich organic matter. These conditions create a niche for specialized microorganisms that play crucial roles in nutrient cycling and ecosystem stability.

During our research trip to Okinawa in July 2018, we collected various samples from the mangrove forests of Iriomote Island, including samples from Lumnitzera racemosa (white-flowered black mangrove) leaves. This research trip was an integral part of our broader research efforts to explore and document microbial diversity in unique ecosystems. For fieldwork in mangroves, we took advantage of the research facilities of the University of the Ryukyus, Tropical Biosphere Research Center (TBRC), Iriomote Station. The station has been playing a central role as a research base or station for the study of mangrove ecosystems.

A view from the mangrove forests where field studies were conducted

A New Member of Flavobacteriaceae

The Flavobacteriaceae family is known for its widespread presence in various ecosystems, including freshwater, soil, and marine environments. Many of its members play essential roles in nutrient cycling, particularly in the breakdown of complex carbohydrates. The genus Neptunitalea was first established in 2015 with the identification of Neptunitalea chrysea, a species isolated from seawater in Japan. Until now, it remained the only known species of the genus. The discovery of Neptunitalea lumnitzerae represents a major step in expanding our knowledge of this group and its interactions with plant hosts. Beyond genetic and biochemical differences from its close relatives,  the bacterium was also found to be resistant to several antibiotics, including nalidixic acid, neomycin, and streptomycin. This resistance is likely due to the presence of multidrug efflux pump genes rather than exposure to clinical antibiotics, reinforcing the idea that natural environments, especially pristine habitats like mangrove forests, harbor bacteria with intrinsic resistance mechanisms. Moreover, pigment analysis revealed that the yellow coloration of Neptunitalea lumnitzerae is linked to the production of zeaxanthin, a carotenoid with known antioxidant properties. Carotenoids have significant commercial value, being widely used in food, cosmetics, and pharmaceuticals. Future research could explore whether Neptunitalea lumnitzerae serves as a viable source for natural pigment production.

The discovery of Neptunitalea lumnitzerae not only expands our understanding of microbial diversity in mangrove ecosystems but also underscores the importance of preserving these unique habitats. The metabolic capabilities of this bacterium have potential applications in biotechnology and environmental management. Our study revealed several unique characteristics of Neptunitalea lumnitzerae. Genome analysis revealed the presence of unique genes, confirming its distinct metabolic capabilities. The bacterium exhibits unique adaptations to the high-salinity and fluctuating conditions of the mangrove environment, highlighting its ecological significance.

Why This Discovery Matters

The discovery of Neptunitalea lumnitzerae is more than just an addition to bacterial taxonomy; it highlights the intricate relationships between microorganisms and their plant hosts. Mangroves, which are vital coastal ecosystems, depend on microbial communities to maintain their health and productivity. Understanding the role of bacteria like Neptunitalea lumnitzerae could provide insights into plant-microbe interactions, bioremediation potential, and ecosystem resilience. Additionally, this research underscores the importance of preserving biodiversity-rich habitats like mangrove forests. These environments are not only crucial for carbon sequestration and coastal protection but also serve as reservoirs of untapped microbial diversity with potential applications in biotechnology, medicine, and environmental sustainability. Moving forward, we aim to explore the interactions between Neptunitalea lumnitzerae and other microbial communities in the mangroves, as well as its potential roles in biogeochemical cycles. Further studies will also investigate the bacterium's potential for industrial applications, given its robust metabolic capabilities.

We are deeply grateful for the hard work and contributions of my co-authors and collaborators at the Institute of Plant Science and Resources (IPSR), Plant Environmental Microbiology Group and University of the Ryukyus, Tropical Biosphere Research Center (TBRC), without whom this achievement would not have been possible. We also extend our thanks to the Ohara Agricultural Scholarship Association for their support.

 We invite the scientific community to read our full article and engage in discussions that can further advance our understanding of microbial diversity and ecosystem functioning.

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Microbiology
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