Mystique and Pristine Microbiome of Jeju Lava (Yongam) Seawater: Comparative Insights with Mineral Water and Adjacent Seawater

Abstract

Jeju lava (Yongam) seawater, naturally filtered through multi-layered basaltic strata, represents a distinctive marine water type that combines mineral enrichment with isolation from surface contaminants. This study aimed to evaluate its microbial purity and ecological transition during mineral water production. Using 16S rRNA-based metagenomic sequencing, the microbial communities of Yongam seawater, its derived mineral water, and adjacent natural seawater were analyzed and compared. The Yongam seawater microbiome was dominated by Neptuniibacter pectenicola (≈89%), indicating an extremely pristine and selective microbial environment. In contrast, the mineral water exhibited the emergence of Nocardioides marinus and Limnobacter alexandrii, species associated with oxidative metabolism and environmental adaptability, reflecting microbial adjustment to altered ionic and nutrient conditions. Adjacent seawater contained the highest taxonomic diversity, consistent with its dynamic environmental exposure. These results demonstrate the exceptional microbial purity of Jeju Yongam seawater and the ecological stability of its derived mineral water following processing. The pristine nature of Yongam seawater suggests its potential as a naturally uncontaminated marine resource, while the derived mineral water, maintaining a stable microbial profile, may be suitable for safe and functional utilization in marine-based cosmetic, nutraceutical, and biotechnology applications.

1. Introduction

Marine waters shaped by distinctive geologic settings have emerged as promising resources for both basic and applied research, spanning hydrogeology, microbiology, biomaterials, and skin science [1,2]. Jeju Island’s lava (Yongam) seawater (YSW)—seawater that percolates through multilayered basaltic strata—offers a rare natural system in which long residence times and rock–water interactions modulate ionic composition while attenuating organic contaminants and planktonic inputs [3,4]. Recent hydrogeologic observations on Jeju’s volcanic aquifers emphasize pronounced heterogeneity (e.g., hyaloclastite conduits vs. layered lavas) that governs fresh–saltwater mixing, tidal signal propagation, and step-like transition zones; such structural controls plausibly foster physicochemical stability in subsurface saline waters like YSW and set boundary conditions for their microbiomes [5]. Beyond geologic interest, the electrodialysis-derived mineral water (YMW) obtained from YSW has demonstrated multiple application-oriented bioactivities. In human keratinocyte models, desalinated mineral water derived from YSW enhanced wound closure via ERK activation and upregulation of MMP9 and pro-angiogenic factors, highlighting a mechanistic axis (ERK→MMP9) relevant to re-epithelialization and matrix remodeling [6]. In dermal fibroblasts, Jeju Yongam seawater itself (YSW) increased collagen production and activated antioxidant defenses through Nrf2 translocation with downstream induction of NQO1 and HO-1, suggesting potential against photoaging-associated oxidative stress [7]. From a biomaterials perspective, the controlled mineral hardness of electrodialyzed mineral water derived from YSW (YMW) modulates the ionotropic gelation of low-methoxyl pectin, tuning gel hardness, microstructure, syneresis, and thermal stability through mineral–carboxylate coordination and intrachain hydrogen bonding—properties exploitable for rheology control in food, nutraceutical, or topical delivery systems [8]. Microbiologically, Jeju’s saline volcanic aquifer has yielded novel bacterial taxa adapted to oligotrophic, mineral-rich subsurface conditions, including the recently described Constantimarinum furrinae gen. nov., sp. nov., isolated from lava seawater and phylogenomically differentiated from related Flavobacteriaceae lineages [9]. These findings collectively position Jeju Yongam seawater (YSW) and its electrodialysis-derived mineral water (YMW) as a uniquely clean, mineral-balanced matrix with demonstrated cellular bioactivities, tunable materials chemistry, and a specialized subsurface biosphere shaped by volcanic aquifer heterogeneity.

Despite this momentum, systematic community-level comparisons of YSW, its derived YMW, and nearby surface seawater (NSW) remain scarce [10,11,12]. Questions central to resource safety and functional deployment—including the degree of microbial “pristineness,” indicator taxa that define YSW’s selectivity, and the ecological transitions that accompany desalination—have not been thoroughly addressed with high-resolution 16S rRNA profiling. In this study, we apply amplicon sequence variant (ASV)-level metagenomics to verify the microbial purity and taxonomic distinctiveness of YSW, assess the ecological stability and adaptation of YMW, and benchmark both against the more variable microbiome of adjacent natural seawater. By integrating community composition, diversity metrics, and indicator species analysis—with attention to taxa such as Neptuniibacter pectenicola—we provide a reproducible baseline that links Jeju’s volcanic aquifer hydrogeology to microbiome structure while contextualizing downstream opportunities in marine-based cosmetics, nutraceuticals, biomaterials, and biotechnology that are already suggested by mechanistic cell studies and ionotropic gelation chemistry [2,3,4].

2. Materials and Methods

2.1. Sample Collection and DNA Extractions

Water samples were collected from three distinct sources on Jeju Island, Republic of Korea, including natural YSW obtained from the Yongam Seawater Center of Jeju Technopark (Gujwa-eup, Jeju-si; GPS 33.5423512, 126.8123823), YMW produced through electrodialysis desalination of the same lava seawater source, and adjacent NSW collected near the Haemajihaean-ro coast (Gujwa-eup, Jeju-si; GPS 33.5557515, 126.7992036). The NSW sampling site was intentionally selected from the coastal area directly influenced by tidal mixing, where seawater regularly permeates the subsurface lava bed before returning to the ocean. This location provides an ecologically relevant reference point for comparing the microbial transition between pristine lava-filtered seawater and naturally circulating coastal seawater. The Yongam seawater sampling well (Well No. 1) was drilled to a depth of approximately 130 m into basaltic strata, operated under a maximum pressure of 60 bar, and driven by a motor with a rated output of 18.5 kW. Electrodialysis desalination was performed using ion-exchange membranes (NEOSEPTA AMX-SB anion and NEOSEPTA CIMS cation; Astom Corporation, Tokyo, Japan) under the following operational conditions: direct current voltage and current up to 100 V × 150 A (two-series configuration), anolyte and catholyte flow rates of 4 m³ h⁻¹ each, and pH adjusted to 3–4 at the concentrate outlet and 2–2.4 at the catholyte outlet by controlled HCl supply. The resulting Yongam mineral water exhibited an electrical conductivity of approximately 50,000 µS cm⁻¹ and a hardness of 7000 mg L⁻¹ as CaCO₃. For microbiome analysis, triplicate samples (50 mL each) were collected from each site in sterile polypropylene bottles, kept on ice during transport, and directly delivered to Macrogen Inc. (Seoul, Republic of Korea) for immediate use in DNA extraction and sequencing. Microbial biomass was recovered by filtration through 0.22 μm pore-size polyethersulfone membrane filters (Merck Millipore, Burlington, MA, USA) under aseptic conditions, and the filters were immediately stored at −80 °C until DNA extraction. Metagenomic DNA was extracted using a standardized microbial DNA isolation protocol optimized for marine and mineral-rich water matrices. (NanoDrop 2000, Thermo Fisher Scientific, Waltham, MA, USA) and agarose gel electrophoresis. Only samples meeting the minimum quality threshold (A260/A280 ≈ 1.8–2.0) were used for downstream library construction.

2.2. Library Preparation and Illumina Sequencing

The V3–V4 hypervariable regions of the bacterial 16S rRNA gene were amplified using universal primers 341F (5′-CCTACGGGNGGCWGCAG-3′) and 805R (5′-GACTACHVGGGTATCTAATCC-3′). Amplicons were purified, quantified, and pooled in equimolar concentrations for library preparation according to the Illumina MiSeq workflow. Sequencing was performed on an Illumina MiSeq platform (Illumina Inc., San Diego, CA, USA) using paired-end reads (2 × 300 bp).

2.3. Sequence Processing and Amplicon Sequence Variant (ASV) Generation

Raw sequence data were processed using Cutadapt v3.2 [13], DADA2 v1.18.0 [14], and QIIME2 v2024.2 [15]. Adapter and primer sequences were trimmed with Cutadapt, and the forward and reverse reads were truncated to 250 bp and 200 bp, respectively. Low-quality reads with expected errors ≥ 2 were excluded. Denoising, error correction, and merging of paired-end reads were performed using the DADA2 plugin within QIIME2, followed by chimera removal with the consensus method (removeBimeraDenovo function). ASVs shorter than 350 bp, corresponding to incomplete 16S V3–V4 regions, were discarded prior to downstream analysis. To minimize bias across samples, the datasets were rarefied to the sequencing depth of the sample with the lowest read count. The final ASV feature table was then used for all subsequent analyses.

2.4. Taxonomic Assignment

Each ASV was taxonomically classified using the Naïve Bayesian Classifier [16] implemented in DADA2 against the NCBI 16S rRNA Reference Database with a confidence threshold of 50%. The taxonomic profiles were summarized from phylum to species levels, and relative abundance data were calculated for comparative microbiome analyses. Representative sequences were aligned using MAFFT (v7.475) [17], and a phylogenetic tree was constructed with FastTreeMP (v2.1.10) [18] to support diversity analysis and phylogenetic inference.

2.5. Diversity Analyses

Microbial community diversity was analyzed using QIIME (v1.9.0) [15]. Alpha diversity metrics, including Shannon, Gini–Simpson, PD_whole_tree, and observed ASVs, were calculated to evaluate the richness and evenness of microbial communities within each sample. Beta diversity was estimated using Bray–Curtis, Weighted UniFrac, and Unweighted UniFrac distance matrices to determine dissimilarities among samples. The resulting distance matrices were further subjected to Principal Coordinates Analysis (PCoA) and hierarchical clustering based on the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), allowing visualization of overall compositional differences among the lava seawater, mineral water, and adjacent seawater microbiomes.

2.6. Statistical and Comparative Analyses

Statistical analyses of taxonomic composition and microbial diversity were conducted using R software (v4.0.3), with all bioinformatics workflows executed under a consistent computational environment to ensure reproducibility. Quality control metrics, ASV counts, and diversity indices were summarized and visualized using R and Microsoft Excel. Differences in microbial community composition among YSW, YMW, and adjacent NSW were evaluated by one-way ANOVA and permutational multivariate analysis of variance (PERMANOVA) based on Bray–Curtis dissimilarity matrices. Principal coordinate analysis (PCoA) was applied to visualize overall community separation patterns, and relative abundance plots at the phylum, genus, and species levels were generated to identify key taxa contributing to compositional variation. The top 20 taxa at each taxonomic level were visualized using customized R scripts, and particularly abundant or indicator species—such as Neptuniibacter pectenicola, Nocardioides marinus, and Limnobacter alexandrii—were highlighted to interpret microbial purity and ecological adaptation across different water types.

3. Results

3.1. Sequencing Output and Data Quality

A total of nine metagenomic libraries were successfully generated from the lava seawater (YSW), electrodialyzed mineral water (YMW), and adjacent natural seawater (NSW) samples, each analyzed in triplicate. Paired-end sequencing (2 × 301 bp) using the Illumina MiSeq platform yielded high-quality amplicon reads targeting the 16S rRNA V3–V4 region. Across all samples, Q20 and Q30 exceeded 99% and 98%, respectively, confirming the reliability of the dataset. The total read counts ranged from 130 k to 395 k per sample, with GC contents of 52.8–53.5% (YSW), 55.5–56.4% (YMW), and 53.6–53.8% (NSW) (

Table 1. Summary of raw sequencing data obtained from Yongam seawater (YSW), mineral water (YMW), and nearby seawater (MSW) samples.

Water Samples	Total Bases (bp)	Total Reads	GC (%)	AT (%)	Q20 (%)	Q30 (%)
YSW 1	47,879,468	159,068	53.3	46.7	99.7	98.6
YSW 2	78,448,426	260,626	52.8	47.2	99.6	98.5
YSW 3	39,237,758	130,358	53.5	46.5	99.6	98.5
YMW 1	119,115,934	395,734	55.7	44.3	99.6	98.4
YMW 2	118,143,102	392,502	56.4	43.6	99.5	98.3
YMW 3	56,205,128	186,728	55.5	44.5	99.6	98.3
NSW 1	66,512,572	220,972	53.7	46.3	99.6	98.5
NSW 2	60,112,108	199,708	53.6	46.4	99.6	98.4
NSW 3	50,712,480	168,480	53.8	46.2	99.6	98.5

). These results confirm that all libraries were of excellent quality for downstream microbiome analysis.

3.2. Taxonomic Composition of Microbial Communities

The genus-level microbial composition differed greatly among the three water types (Figure 1). In YSW, the community was overwhelmingly dominated by the genus Neptuniibacter, which accounted for nearly the entire bacterial assemblage, with only trace levels of minor genera such as Nocardioides, Limnobacter, and Glaciecola. This highly skewed pattern reflects the strong selective pressure imposed by the pristine lava-filtered seawater environment.

In YMW, produced by electrodialysis desalination, the dominance of Neptuniibacter was markedly reduced, and a broader set of low-abundance genera emerged in detectable proportions, including Parasynechococcus, Hydrogenophaga, and Polaribacter. This diversification suggests that desalination relaxes ionic and osmotic stress, enabling taxa that were previously suppressed or undetectable to proliferate.

In NSW, the microbial community exhibited the highest genus-level diversity, with co-occurring contributions from Glaciecola, Roseobacteraceae-affiliated genera, Parasynechococcus, and several notable marine heterotrophic genera such as Vibrio, Alteromonas, and Pseudoalteromonas. The strong presence of the phototrophic genus Parasynechococcus is characteristic of natural open-seawater systems and reflects typical marine primary-production dynamics (Figure 1).

3.3. Species-Level Diversity in Each Water Type

At the species level, distinct microbial signatures characterized each environment (

Table 2. Relative abundance of dominant species identified in the Yongam lava seawater (YSW) microbiome.

No.	Species	YSW 1	YSW 2	YSW 3	Mean ± SD (%)
1	Neptuniibacter pectenicola	98.97	77.38	91.10	89.15 ± 10.92
2	Unclassified (NA)	0.68	15.23	2.49	6.13 ± 7.93
3	Polaribacter pectinis	0.00	1.59	0.00	0.53 ± 0.92
4	Alcanivorax borkumensis	0.00	0.00	1.10	0.37 ± 0.64
5	Ketobacter alkanivorans	0.00	0.00	0.93	0.31 ± 0.54
6	Bosea thiooxidans	0.00	0.00	0.92	0.31 ± 0.53
7	Acinetobacter tjernbergiae	0.00	0.10	0.67	0.26 ± 0.36
8	Acuticoccus yangtzensis	0.00	0.61	0.00	0.20 ± 0.35
9	Francisella halioticida	0.00	0.61	0.00	0.20 ± 0.35
10	Lactobacillus gasseri	0.00	0.00	0.59	0.20 ± 0.34
11	Lacticaseibacillus paracasei	0.00	0.51	0.00	0.17 ± 0.29
12	Tepidisphaera mucosa	0.00	0.00	0.48	0.16 ± 0.28
13	Lawsonella clevelandensis	0.00	0.00	0.45	0.15 ± 0.26
14	Olsenella intestinalis	0.00	0.00	0.42	0.14 ± 0.24
15	Rhodopila globiformis	0.00	0.00	0.39	0.13 ± 0.23

Notes: Species-level composition of the YSW microbiome based on normalized relative abundance of 16S rRNA gene reads. YSW exhibited extreme single-species dominance, with N. pectenicola comprising nearly 89% of the total community. This pattern reflects a highly selective and oligotrophic environment shaped by lava-bed natural filtration. Only a few minor taxa (<1%) were sporadically observed across replicates.

,

Table 3. Relative abundance of dominant species identified in the electrodialyzed mineral water (YMW) microbiome.

No.	Species	YMW 1	YMW 2	YMW 3	Mean ± SD (%)
1	Nocardioides marinus	45.26	58.43	39.53	47.74 ± 9.70
2	Limnobacter alexandrii	29.31	19.41	35.90	28.21 ± 8.30
3	Hydrogenophaga flava	8.71	7.46	8.82	8.33 ± 0.76
4	Unclassified (NA)	4.00	4.77	3.46	4.08 ± 0.66
5	Minwuia thermotolerans	3.07	3.83	3.98	3.63 ± 0.49
6	Polycyclovorans algicola	5.08	1.20	2.23	2.84 ± 2.01
7	Novosphingobium decolorationis	0.93	0.88	1.53	1.11 ± 0.36
8	Nocardioides ginkgobilobae	0.42	0.88	0.89	0.73 ± 0.27
9	Brevundimonas subvibrioides	0.58	0.86	0.40	0.61 ± 0.24
10	Paraperlucidibaca wandonensis	0.67	0.48	0.52	0.56 ± 0.10
11	Parvibaculum lavamentivorans	0.28	0.37	0.39	0.34 ± 0.06
12	Thalassobaculum fulvum	0.15	0.04	0.31	0.17 ± 0.13
13	Marinoscillum luteum	0.06	0.23	0.19	0.16 ± 0.09
14	Bosea thiooxidans	0.25	0.01	0.21	0.16 ± 0.13
15	Sphingomonas echinoides	0.00	0.15	0.18	0.11 ± 0.10

Notes: Species-level composition of the electrodialyzed YMW microbiome based on normalized relative abundance of 16S rRNA gene reads. Electrodialysis resulted in a distinct ecological transition, reducing the extreme dominance seen in YSW and allowing multiple previously undetected low-abundance taxa to emerge consistently across replicates. This indicates the early formation of a more diversified microbial assemblage following desalination.

and

Table 4. Relative abundance of dominant species identified in the adjacent natural seawater (NSW) microbiome.

No.	Species	NSW 1	NSW 2	NSW 3	Mean ± SD (%)
1	Unclassified (NA)	41.72	52.78	40.79	45.10 ± 6.67
2	Glaciecola amylolytica	31.63	21.37	28.42	27.14 ± 5.25
3	Parasynechococcus marenigrum	8.05	8.74	6.63	7.81 ± 1.08
4	Polaribacter marinivivus	4.82	5.72	3.60	4.71 ± 1.06
5	Vibrio chagasii	0.09	0.13	9.39	3.20 ± 5.36
6	Pseudoalteromonas marina	3.39	1.06	1.65	2.03 ± 1.21
7	Litorivicinus marinus	2.16	1.65	1.87	1.89 ± 0.25
8	Opacimonas viscosa	1.46	1.16	1.12	1.25 ± 0.18
9	Luminiphilus syltensis	0.78	0.71	0.85	0.78 ± 0.07
10	Candidatus Pelagibacter communis	0.79	0.89	0.58	0.75 ± 0.16
11	Marinobacterium marisflavi	0.55	0.51	0.56	0.54 ± 0.03
12	Phaeobacter italicus	0.40	0.49	0.40	0.43 ± 0.05
13	Alteromonas abrolhosensis	0.18	0.42	0.19	0.26 ± 0.14
14	Halioglobus pacificus	0.28	0.23	0.17	0.23 ± 0.05
15	Mameliella alba	0.22	0.21	0.24	0.22 ± 0.01

Notes: Species-level composition of the adjacent NSW microbiome based on normalized relative abundance of 16S rRNA gene reads. NSW showed the highest taxonomic complexity, characterized by multiple co-dominant phototrophic, heterotrophic, and symbiotic taxa. Unlike the simplified profiles of YSW and YMW, NSW represents a fully established natural marine microbial network with balanced ecological functions.

). YSW (Table 2) was almost entirely dominated by Neptuniibacter pectenicola (mean ≈ 89.15%), with all other species—such as Polaribacter pectinis, Alcanivorax borkumensis, and Ketobacter alkanivorans—contributing < 1%. This pattern confirms a highly selective, oligotrophic environment limited to a few halotolerant chemoheterotrophs. Table 2. Species-level composition of the YSW microbiome based on normalized relative abundance of 16S rRNA gene reads. The community was dominated by Neptuniibacter pectenicola (mean ≈ 89%), whereas minor taxa (<1%) appeared sporadically among replicates. In YMW (Table 3), Neptuniibacter disappeared and was replaced by Nocardioides marinus (47.74%), Limnobacter alexandrii (28.21%), and Hydrogenophaga flava (8.33%). These taxa, belonging to Actinomycetota and Betaproteobacteria, are typical of moderate-salinity and nutrient-rich environments, indicating that electrodialysis strongly restructured the microbial community. Table 3. Species-level composition of the electrodialyzed YMW microbiome based on normalized relative abundance of 16S rRNA gene reads. The YMW community shows a marked shift from the original YSW, with several new taxa emerging across replicates. In NSW (Table 4), the microbial community exhibited the greatest diversity. Dominant taxa included Glaciecola amylolytica (27.14%), Parasynechococcus marenigrum (7.81%), Polaribacter marinivivus (4.71%), and Vibrio chagasii (3.20%), together with ~45% unclassified bacteria. This composition reflects a natural coastal ecosystem balancing phototrophic, heterotrophic, and symbiotic interactions. Table 4. Species-level composition of the adjacent NSW microbiome based on normalized relative abundance of 16S rRNA gene reads. Unlike YSW and YMW, the NSW microbiome displayed a diverse and multi-trophic structure with several co-dominant taxa.

3.4. Alpha and Beta Diversity

Alpha-diversity indices showed clear quantitative differences among the three water types. YSW exhibited the lowest diversity (Shannon = 2.26, Simpson = 0.29), reflecting its extreme dominance by N. pectenicola. YMW displayed intermediate diversity (Shannon = 2.56, Simpson = 0.31), consistent with community restructuring after electrodialysis. NSW demonstrated the highest richness and evenness (Shannon = 4.69, Simpson = 0.12), corresponding to its broader environmental heterogeneity. These metrics provide a quantitative baseline for interpreting the distinct microbial community profiles of each water type.

Beta-diversity analyses based on Bray–Curtis, unweighted UniFrac, and weighted UniFrac distances further revealed clear separation among YSW, YMW, and NSW microbiomes in ordination space. YSW samples clustered tightly due to the dominance of N. pectenicola, whereas YMW formed an intermediate but distinct cluster, reflecting ecological restructuring after electrodialysis. NSW samples showed the greatest dispersion, consistent with their higher environmental heterogeneity. PERMANOVA confirmed significant differences among the three water types (Bray–Curtis: pseudo-F = 8.87, R² = 0.747, p = 0.002). The high R² indicates that 74.7% of the variation in community composition is explained by group differences, demonstrating robust divergence even without graphical visualization.

3.5. Comparative Ecological Shifts Among YSW, YMW, and NSW

A comparative species-level analysis (

Table 5. Comparative shifts in dominant bacterial species among YSW, YMW, and NSW samples.

Representative Species	YSW (%)	YMW (%)	NSW (%)	Ecological Interpretation
Neptuniibacter pectenicola	89.15	0	0	Extreme oligotrophic specialist dominant only in confined lava seawater
Nocardioides marinus	0	47.74	0	Emerges after desalination; indicator of moderate-salinity adaptive community
Limnobacter alexandrii	0	28.21	0	Desalination-associated taxon with oxidative flexibility
Hydrogenophaga flava	0	8.33	0	Early colonizer in oxygen-exposed, reduced-salinity environments
Glaciecola amylolytica	0	0	27.14	Coastal heterotroph typical of natural seawater
Parasynechococcus marenigrum	0	0	07.81	Phototrophic cyanobacterium; absent in YSW/YMW due to light isolation
Vibrio chagasii	0	0	3.20	Opportunistic marine bacterium reflecting open-sea variability

Notes: Species-level composition of the adjacent NSW microbiome based on normalized relative abundance of 16S rRNA gene reads. Unlike the highly selective YSW and the transitional YMW communities, the NSW microbiome exhibited the greatest taxonomic diversity, characterized by multiple co-dominant taxa typical of natural coastal seawater.

) revealed a clear ecological progression across environments. YSW showed extreme dominance of N. pectenicola (89.15%), whereas YMW exhibited a diversified assemblage dominated by N. marinus and L. alexandrii. NSW presented the most balanced structure with coexisting phototrophic (Parasynechococcus), heterotrophic (Glaciecola, Vibrio), and symbiotic taxa. The sequential transition from YSW → YMW → NSW demonstrates that desalination via electrodialysis induces a major ecological shift—from extremophile dominance to a complex, stable microbial network resembling natural seawater.

4. Discussion

The present metagenomic analysis provides the first ecological insight into the microbial architecture of Jeju’s lava (Yongam) seawater and its derived mineral water, revealing a distinctive pattern of microbial selectivity, ecological succession, and biotechnological relevance. The overwhelming dominance of Neptuniibacter pectenicola in the Yongam seawater (YSW) indicates an extremely selective microbial environment, in which a single chemoheterotrophic, halophilic lineage has adapted to persist under oligotrophic and geochemically stable conditions. Members of the genus Neptuniibacter are known for their strict aerobic metabolism, oxidative flexibility, and preference for saline yet nutrient-poor habitats, which explains their prevalence within the basalt-filtered subsurface aquifer of Jeju Island [19,20]. The filtration through volcanic strata, combined with a lack of sunlight and minimal organic influx, creates a physically and chemically isolated ecosystem that effectively excludes opportunistic or fast-growing copiotrophs [21,22,23]. Consequently, the YSW can be regarded as a natural microbial filter that allows only taxa optimized for ionic and osmotic homeostasis to survive, reflecting an equilibrium state between geochemical stability and microbial minimalism.

Following electrodialysis desalination, the microbial community of the resulting mineral water (YMW) underwent a clear ecological transition in which the previously monodominant Neptuniibacter population was replaced by a more diverse assemblage of actinobacterial and betaproteobacterial taxa, including Nocardioides marinus and Limnobacter alexandrii. Both genera are characterized by metabolic versatility—particularly aerobic carbon utilization, oxidative metabolism, and facultative denitrification—which enables their persistence in low-nutrient, moderately low-salinity, and oxygen-variable environments [24,25]. These traits suggest that the electrodialysis process not only reduced ionic strength but also created physicochemical conditions that selectively favored oligotrophic, metabolically flexible taxa rather than introducing foreign microorganisms. Consistently, no exogenous or pathogenic bacteria were detected in YMW, indicating that the observed restructuring reflects natural ecological succession rather than contamination.

The enrichment of N. marinus and L. alexandrii in YMW is highly consistent with previous studies showing that desalination processes—such as electrodialysis, reverse osmosis, and low-salinity polishing steps—often promote communities dominated by adaptable, oligotrophic bacteria capable of rapid adjustment to shifts in salinity and nutrient availability. Nocardioides species are frequently reported in brackish waters, drinking-water distribution systems, and post-desalination environments, where their broad substrate utilization and tolerance to low ionic strength offer a competitive advantage. Likewise, Limnobacter species are well documented in treated freshwater, membrane-filtration systems, and low-salinity biofilms, and have been described as pioneer taxa during microbial succession following salinity reduction [26,27,28,29].

Together, these ecological patterns support the interpretation that the transition from Neptuniibacter-dominated YSW to a Nocardioides–Limnobacter consortium in YMW represents a predictable microbial succession driven by reduced salinity, ion-selective electrodialysis, and subtle nutrient redistribution during mineral-water production. This shift results in a stable yet microbiologically clean community structure appropriate for applications where both safety and compositional consistency are critica.

In contrast, the adjacent natural seawater (NSW) exhibited the highest species richness, including Glaciecola amylolytica, Polaribacter marinivivus, Vibrio chagasii, and Parasynechococcus marenigrum, reflecting the open and dynamic nature of the coastal marine ecosystem. The coexistence of heterotrophic and phototrophic lineages indicates an ecologically mature, multi-trophic network supported by fluctuating nutrient and light conditions. The appearance of Cyanobacteria exclusively in NSW but not in YSW or YMW highlights the strong physical isolation of the subsurface lava seawater system from the surface marine environment, further emphasizing that the Yongam aquifer represents a closed, geochemically conservative, and microbially pure ecosystem. The progressive increase in taxonomic complexity from YSW to YMW and finally to NSW demonstrates that physicochemical modulation—particularly the reduction in salinity and the introduction of oxygen during desalination—can trigger predictable microbial successions from extremophile dominance to a balanced, naturally structured microbial network [30,31,32].

Although the extreme dominance of N. pectenicola in YSW might raise the possibility of methodological artifacts, several lines of evidence suggest that this pattern primarily reflects the in situ community structure rather than technical bias. First, all water types (YSW, YMW, and NSW) were processed in parallel using the same DNA extraction protocol, filtration procedure, and Illumina library preparation workflow, together with the broadly used universal 341F/805R primer set for 16S rRNA V3–V4 amplification. Under these identical conditions, only YSW showed near-mono-dominance by N. pectenicola, whereas YMW and NSW exhibited taxonomically diverse and multi-trophic communities without enrichment of this genus. Second, the dominance of N. pectenicola was reproducible among three independent YSW replicates, indicating that it is not an isolated outlier effect. Taken together, these observations support the interpretation that the Yongam lava seawater aquifer is populated by a highly selective, oligotrophic microbial assemblage in which N. pectenicola is the key specialist taxon. Nonetheless, we acknowledge that 16S rRNA amplicon sequencing cannot completely rule out primer- or extraction-related biases, and future work using shotgun metagenomics, multiple primer sets, or complementary cell-counting approaches will be important to further validate the dominance of Neptuniibacter in this system.

From a hydrogeologic perspective, the findings confirm that the Yongam seawater originates from a confined basaltic aquifer with minimal hydrological mixing, where the high degree of microbial purity corresponds to the integrity of the geologic barrier. Such microbial simplicity serves as a biological indicator of aquifer isolation and provides a scientific foundation for its utilization as a safe and renewable industrial resource. The absence of contaminant-associated or opportunistic species underscores its suitability for applications requiring sterilized or biocompatible water matrices.

From an industrial and biotechnological viewpoint, the ecological characteristics of YSW and YMW align with prior evidence that Yongam mineral water exerts wound-healing, antioxidant, and anti-photoaging effects through ERK–MMP9 and Nrf2–HO-1 signaling pathways [6,7]. The metagenomic findings presented here extend these biochemical observations by demonstrating that such functional benefits originate from a microbiologically stable and pristine source environment. In YSW, the extreme monodominance of N. pectenicola reflects a highly selective and ecologically stable habitat, minimizing external microbial interference and supporting physicochemical consistency—conditions that contribute to the reproducibility of the previously reported bioactivities. Following electrodialysis, YMW undergoes a predictable ecological transition toward low-nutrient–adapted taxa such as N. marinus and L. alexandrii. Importantly, these shifts do not introduce pathogenic or metabolically disruptive organisms, indicating that the functional properties of the water are preserved despite community restructuring. Collectively, these results establish a direct link between microbiome stability and the functional integrity of Yongam seawater–derived products, thereby reinforcing its value as a reliable source for therapeutic and cosmetic application.

In summary, the YSW system represents an exceptional example of a geochemically and biologically self-purifying marine aquifer, where selective microbial survival yields a near-monoculture of N. pectenicola. The electrodialyzed YMW derived from it maintains ecological integrity while accommodating moderate microbial diversity, and the natural seawater, in turn, provides an external ecological benchmark characterized by higher complexity. This continuum from purity to diversity elucidates how geological isolation and engineered desalination shape microbial community dynamics. Furthermore, it implies that lava-filtered seawater and its derivatives constitute promising sources for safe, stable, and functionally active biomaterials applicable to the fields of cosmeceuticals, nutraceuticals, and therapeutic mineral research. The present study therefore establishes not only the ecological uniqueness of Jeju YSW but also its broader potential as a model system for understanding microbial adaptation, aquifer ecology, and sustainable bioresource utilization.

5. Conclusions

This study demonstrates that Jeju’s Yongam lava seawater (YSW) harbors an exceptionally pristine, highly selective, and microbiologically stable community dominated by Neptuniibacter pectenicola, reflecting the geochemical stability and isolation of the basaltic aquifer. Electrodialysis desalination transformed this mono-dominant community into a metabolically diverse yet biologically safe consortium led by Nocardioides marinus and Limnobacter alexandrii in the mineral water (YMW). In contrast, the adjacent natural seawater (NSW) exhibited the highest diversity, representing an open and dynamic marine ecosystem. These findings reveal a clear ecological continuum from geologically confined to environmentally exposed systems.

Rather than being “naturally sterilized,” YSW represents a uniquely purified and ecologically isolated water source, offering reliable microbial stability and biotechnological value for safe and functional applications in marine-derived cosmetic, nutraceutical, and therapeutic materials.