Preliminary Insights into Summer Archaeal Communities in Eutrophic Jinhae Bay, Korea

Abstract

Marine archaea play crucial roles in global biogeochemical cycles and climate regulation, yet their ecological functions in many coastal environments remain poorly understood. Jinhae Bay (JB), a eutrophic and environmentally stressed coastal system in Korea, has attracted growing attention; however, its archaeal community composition has not been characterized. In this preliminary study, we investigated the summer archaeal community structure in JB water columns based on a survey conducted in July 2018. We identified 5 archaeal phyla—primarily Euryarchaeota and Thaumarchaeota—along with 11 classes and 18 orders, with Nitrosopumilales and Methanobacteriales as dominant orders. Several ammonia-oxidizing archaea (AOA), including Candidatus Nitrosopumilus adriaticus, Candidatus Nitrosopumilus salaria, Candidatus Nitrosopumilus sediminis, and unclassified Nitrosopumilus spp., were detected. Additionally, the presence of methane-oxidizing archaea (MOA) such as Candidatus Methanoperedens nitroreducens, although at low relative abundance, suggests potential roles in nitrogen and methane cycling. These findings provide initial insights into the archaeal contributions to biogeochemical processes in JB, highlighting the need for further seasonal and functional investigations.

1. Introduction

Archaea constitute one of the three domains of life, alongside bacteria and eukarya [1]. Initially, archaeal species were discovered in extreme environments such as hot springs, high-salinity habitats, and anaerobic conditions, leading to the early belief that they were restricted to such niches [2]. However, the development of advanced molecular biological techniques has revealed that archaea are widespread across diverse environments, including oceans, lakes, and soils [3,4].

In recent years, extensive studies have focused on the ecological roles of archaea in marine ecosystems. For instance, ammonia-oxidizing archaea (AOA) have been identified as key players in the marine nitrogen cycle, particularly in the nitrification process [5,6]. Additionally, archaea have been implicated in climate regulation through the production of potent greenhouse gases, such as nitrous oxide (N₂O) and methane (CH₄) [3,6]. Nevertheless, our understanding of archaeal functions across different marine environments remains limited [3,7].

Jinhae Bay (JB), located on the southeastern coast of South Korea, is a semi-enclosed coastal system with shallow depths (<50 m), and exchanges water with offshore regions via the Gadeok Channel [8,9]. Over the past decades, this region has been affected by anthropogenic pressures such as aquaculture, domestic sewage, and industrial activities, which may influence microbial community structures. Due to this semi-enclosed geography, water residence time in JB is relatively long, resulting in limited circulation [10,11]. Over the past five decades, intensified anthropogenic pressures—including rapid industrialization and aquaculture development—have led to excessive nutrient inputs into JB, causing severe eutrophication [12]. Consequently, frequent harmful algal blooms and recurring summer hypoxia (dissolved oxygen < 2 mg L⁻¹) have been reported, particularly in the bottom waters [2,13].

Numerous studies have investigated planktonic and benthic communities in JB in response to these environmental disturbances [14,15], and recent work has also examined bacterial community structures in the water column [8]. However, despite the growing interest in archaea, their community composition in the eutrophic and seasonally hypoxic waters of JB remains largely unknown.

In this preliminary study, we (1) provide the first report on archaeal community composition in JB’s summer water columns and (2) infer their potential ecological and biogeochemical functions based on taxonomic identities.

2. Methods

2.1. Seawater Sampling

Given the frequent and persistent hypoxic conditions in the bottom waters of Jinhae Bay (JB) during summer [12,16], a field survey was conducted in July 2018. To assess the potential differences in archaeal community composition under oxic and hypoxic conditions, seawater samples were collected from two stations, selected to represent typical environmental extremes within the bay: Station 1 (St. 1; 34.98° N, 128.49° E), a hypoxic site, and Station 2 (St. 2; 35.07° N, 128.70° E), an oxic site (Figure 1 and

Table 1. Seawater properties of JB water columns during the sampling period (July 2018).

Station	Depth (m)	T (°C)	S	DO (mg L−1)	Oxygen Conditions
1	0	28.2	30.7	7.82	Oxic
	10	22.3	32.1	7.61	Oxic
	21	17.7	33.3	1.55	Hypoxic
2	0	24.7	32.3	8.64	Oxic
	11	22.9	32.3	8.31	Oxic
	23	19.2	32.8	10.27	Oxic

). The bottom depths at St. 1 and St. 2 were 23 m and 24 m, respectively. Seawater was sampled at three depths at each station: surface (0 m), middle (~10 m), and bottom (~1 m above the seafloor). Physical parameters—including temperature (T), salinity (S), and dissolved oxygen (DO)—were measured using a conductivity–temperature–depth (CTD) profiler (RBR Ltd., Ottawa, ON, Canada). For archaeal community analysis, approximately 1 L of seawater per depth was collected using Niskin bottles and filtered through 0.2 μm polycarbonate membrane filters (Whatman, 47 mm, Maidstone, UK). The filters were immediately frozen and stored at −80 °C until DNA extraction.

2.2. DNA Analysis

Microbial DNA libraries were prepared using the TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions. Genomic DNA was sheared using a Covaris LE220 Focused-ultrasonicator (Woburn, MA, USA) to obtain ~350 bp fragments, which were then end-repaired and adenylated. Indexing adapters were ligated, and DNA libraries were enriched by PCR. Library quality and fragment size distribution were evaluated using the Agilent D1000 ScreenTape system on an Agilent 2200 TapeStation (Santa Clara, CA, USA). Final library quantification was performed using the PicoGreen dsDNA assay (Thermo Fisher Scientific, Waltham, MA, USA) and a Victor3 plate reader (PerkinElmer, Waltham, MA, USA). Libraries were sequenced on an Illumina HiSeq X-10 platform using paired-end 150 bp reads. For each sample, 3–4 Gb of sequencing data were generated. Raw sequencing reads were quality-filtered using Trimmomatic [17]. Taxanomic classification of archaeal sequences was conducted using Centrifuge [18], and community composition was visualized through Krona plots [19].

2.3. Data Visualization and Availability

Figure visualizations were generated using Ocean Data View (https://odv.awi.de) and R software (v4.2.2) with associated packages for microbial community analysis. Raw sequence data have been deposited in the National Center for Biotechnology Information (NCBI) with Sequence Read Archive (SRA) accession number SRR8842383-SRR8842388.

3. Results and Discussion

3.1. Physical Features of Water Columns

Vertical profiles of temperature (T), salinity (S), and dissolved oxygen (DO) were measured at both stations in Jinhae Bay during July 2018 (Figure 1 and Table 1). Surface temperature was higher at Station 1 (26.1 °C) than at Station 2 (25.4 °C), while the bottom temperature was lower at St. 1 (16.2 °C) than at St. 2 (17.5 °C). A sharp temperature gradient between the surface and bottom layers (ΔT = 10.5 °C) was observed at St. 1, compared to a smaller gradient (ΔT = 5.5 °C) at St. 2. Similarly, a strong salinity gradient (ΔS = 2.6) was evident at St. 1, whereas only a slight difference (ΔS = 0.5) was recorded at St. 2. These results indicate that water-column stratification was more strongly developed at St. 1, likely restricting vertical mixing. Dissolved oxygen concentrations were markedly lower at St. 1 across all depths, with hypoxic conditions (DO < 2 mg L⁻¹) detected only at the bottom layer of St. 1. In contrast, all water layers at St. 2 remained oxic. In summary, St. 1 exhibited strong thermal and haline stratification, which likely contributed to bottom water hypoxia. In contrast, St. 2 exhibited relatively weaker stratification and was characterized by fully oxic conditions throughout the water column.

3.2. Community Structures of Archaea in Jinhae Bay and Comparison with Other Hypoxia Regions

In the summer water columns of Jinhae Bay (JB), bacterial reads accounted for 99.05% of the total metagenomic sequences across the three domains (bacteria, archaea, and viruses), while archaea and viruses represented 0.66% and 0.29%, respectively (Figure 2). The proportion of archaeal reads varied by depth: 0.52% (surface), 0.16% (middle), and 1.60% (bottom) at Station 1; and 0.40% (surface), 0.36% (middle), and 0.91% (bottom) at Station 2 (Table S1). In comparison, the northern Gulf of Mexico (nGOM)—a well-studied hypoxic and eutrophic coastal system—has shown archaeal relative abundances of up to ~20% [5]. Basic dissimilarity metrics (e.g., Bray–Curtis) were used to explore compositional differences among depths. This suggests that the role or abundance of archaea in JB may be lower than in nGOM; however, a direct comparison is difficult due to limited data on archaeal communities in JB.

To compare archaeal community structures between stations and depths, we normalized the taxonomic abundance data by considering archaeal reads as 100% (Figure 3). Five archaeal phyla were detected across all samples, with considerable variation in relative abundance by depth. Euryarchaeota dominated the surface and middle layers (68.87–87.20%), whereas Thaumarchaeota were predominant in the bottom layers (57.89–62.16%). Crenarchaeota were consistently present at low abundance (2.64–6.23%). Candidatus Micrarchaeota and Candidatus Korarchaeota were also detected but at very low levels (<0.09%). At the class level (Figure 3b), 11 archaeal classes were identified. The dominant groups included Halobacteria, unclassified Thaumarchaeota, Methanobacteria, and Methanomicrobia, comprising over 80% of the archaeal communities in most samples. Depth-specific dominance patterns were evident: Halobacteria were more abundant in surface and middle waters (e.g., 34.51% at the surface of St. 1 and 33.24% at the middle layer of St. 2), whereas unclassified Thaumarchaeota dominated the bottom layers (>50%).

Next, to examine the difference in the archaeal community composition between two stations, we determined the relative abundance in the data of archaeal reads, which was considered as 100% (

Table 2. Archaeal species (top 35) found in Jinhae Bay water columns.

Genus	Species	St. 1			St. 2			Functions
		Surface (%)	Middle (%)	Bottom (%)	Surface (%)	Middle (%)	Bottom (%)
Candidatus Nitrosomarinus	catalina	1.27	16.86	42.50	10.36	7.25	46.55
Nitrosopumilus	sp. Nsub	0.45	4.17	8.22	2.27	1.63	8.72
Methanosarcina	Unclassified. Methanosarcina	1.96	2.21	1.04	1.89	2.00	0.83
Methanobrevibacter	arboriphilus	1.79	1.47	0.73	1.91	1.83	0.81
Methanococcus	maripaludis	1.94	1.35	0.80	1.82	1.69	0.74
Methanobrevibacter	smithii	1.78	1.37	0.81	1.66	1.55	0.82
Methanobrevibacter	oralis	1.45	1.65	0.61	1.21	1.22	0.62
Methanosarcina	barkeri	1.46	0.89	0.64	1.25	1.25	0.54
Candidatus Nitrosopelagicus	brevis	0.44	0.28	1.84	0.88	0.78	1.66
Methanobrevibacter	Unclassified. Methanobrevibacter	1.31	0.83	0.59	1.24	1.03	0.60
Nitrosopumilus	Unclassified. Nitrosopumilus	0.56	0.89	1.28	0.80	0.67	1.36	AOA
Methanobacterium	Unclassified. Methanobacterium	1.07	0.84	0.64	1.13	1.28	0.55
Halorubrum	Unclassified. Halorubrum	1.44	0.76	0.56	0.91	1.18	0.49
Methanosarcina	mazei	1.03	1.13	0.52	0.90	0.90	0.45
Methanobrevibacter	olleyae	0.91	0.80	0.47	0.79	0.85	0.40
Haloferax	Unclassified. Haloferax	0.87	0.76	0.40	0.71	0.79	0.35
Sulfolobus	islandicus	0.86	0.80	0.34	0.80	0.59	0.37
Nitrosopumilus	Candidatus Nitrosopumilus adriaticus	0.59	0.57	0.64	0.60	0.54	0.69	AOA
Methanocaldococcus	villosus	0.88	0.59	0.37	0.76	0.65	0.36
Methanobrevibacter	curvatus	0.67	0.56	0.38	0.71	0.80	0.36
	Unclassified. Natrialbaceae	0.90	0.60	0.36	0.62	0.66	0.28
Methanobacterium	formicicum	0.71	0.59	0.32	0.77	0.59	0.29
Methanobrevibacter	cuticularis	0.75	0.61	0.28	0.71	0.54	0.31
Methanobrevibacter	sp. 87.7	0.58	0.85	0.24	0.56	0.59	0.35
Methanobacterium	paludis	0.51	1.28	0.16	0.41	0.57	0.19
Methanobrevibacter	filiformis	0.71	0.43	0.34	0.60	0.57	0.34
Nitrosopumilus	Candidatus Nitrosopumilus salaria	0.37	0.55	0.56	0.49	0.44	0.52	AOA
Candidatus Nitrosoarchaeum	limnia	0.64	0.54	0.39	0.50	0.39	0.41
Candidatus Nitrosoarchaeum	koreensis	0.48	0.54	0.40	0.50	0.47	0.40
Methanobrevibacter	millerae	0.60	0.49	0.37	0.60	0.48	0.23
Methanobrevibacter	wolinii	0.49	0.46	0.28	0.54	0.60	0.27
Methanosphaera	sp. WGK6	0.68	0.40	0.27	0.54	0.45	0.25
Methanocaldococcus	bathoardescens	0.42	0.61	0.20	0.54	0.42	0.20
Methanocaldococcus	fervens	0.43	0.69	0.20	0.37	0.46	0.21
Candidatus Methanoperedens	nitroreducens	0.43	0.50	0.25	0.43	0.40	0.21	MOA

AOA: ammonia-oxidizing archaea; MOA: methane-oxidizing archaea.

and Figure 3). Five archaeal phyla were found in all six samples, but their compositions were considerably different; the detailed relative abundances are shown in Figure 3a. Euryarchaeota was the dominant phylum in the surface and middle samples of the two stations with a relative abundance of 68.87–87.20%, whereas their relative abundance was not more than ~40% in the bottom samples. Thaumarchaeota, which were found in the northern Gulf of Mexico (nGOM) hypoxic zone [6], dominated the bottom samples (57.89–62.16%). In the nGOM, Thaumarchaeota were also highly dominant, accounting for approximately 60–80% of the archaeal community [6]. This suggests a broadly similar dominance pattern between JB and nGOM bottom waters, despite geographic and environmental differences. Crenarchaeota, which were found in the open North Pacific [3], were one of the common archaea in the surface, middle, and bottom samples but with a low relative abundance of 2.64–6.23%. Candidatus Micrarchaeota and Candidatus Korarchaeota were also found in all the samples, but the proportion of relative abundance was very low (<~0.09%).

The distribution characteristics of the archaeal class level are shown in Figure 3b. Eleven archaeal classes were found in the six samples, and one archaeal class showing an extremely low relative abundance was classified as “Other”. Halobacteria, unclassified Thaumarchaeota, Methanobacteria, and Methanomicrobia were the dominant classes in the surface, middle, and bottom samples with relative abundances >~80%. However, the most dominant class differed with depth. In particular, Halobacteria were abundant at the surface and in the middle, accounting for 34.51% and 27.19% in the surface samples from St. 1 and St. 2, respectively, and 23.01% and 33.24% in the middle samples from St. 1 and St. 2, respectively. However, unclassified Thaumarchaeota showed the highest relative abundance (>50%) in the bottom samples.

The archaeal community composition at the order level is shown in Figure 3c. Eighteen archaeal orders were identified in the six samples, and one archaeal order showing extremely low relative abundance was classified as “Other”. The relative abundances of different orders were considerably different. Nitrosopumilales was the most dominant order in the bottom samples, with their relative abundances being 57.67% (bottom layer of St. 1) and 62.09% (bottom layer of St. 2), whereas Methanobacteriales dominated the surface and middle samples, with relative abundances of 21.17% (surface layer of St. 1), 19.53 (surface layer of St. 2), 17.50% (middle layer of St. 1), and 18.59% (middle layer of St. 2).

Owing to the large amount of data, the dominant species and the relative abundances of only the top 35 species are listed in Table 2. In surface waters, Candidatus Nitrosomarinus catalina (Thaumarchaeota) (St. 1: 1.27% and St. 2: 10.36%), Methanosarcina (Euryarchaeota) (St. 1: 1.96% and St. 2: 1.89%), and Methanococcus maripaludis (Euryarchaeota) (St. 1: 1.94% and St. 2: 1.82%) were detected. Candidatus Nitrosomarinus catalina (Thaumarchaeota) (St. 1: 16.86% and St. 2: 7.25%), Nitrosopumilus sp. Nsub (Thaumarchaeota) (St. 1: 4.17% and St. 2: 1.63%), and Methanosarcina (Euryarchaeota) (St. 1: 2.21% and St. 2: 2.00%) were found in middle waters. In bottom waters, Candidatus Nitrosomarinus catalina (Thaumarchaeota) (St. 1: 42.50% and St. 2: 46.55%), Nitrosopumilus sp. Nsub (Thaumarchaeota) (St. 1: 8.22% and St. 2: 8.72%), and Candidatus Nitrosopelagicus brevis (Thaumarchaeota) (St. 1: 1.84% and St. 2: 1.66%) were found. In summary, Candidatus Nitrosomarinus catalina (Thaumarchaeota) exclusively occupied the JB water columns (>60%), except in the surface layer of St. 1 (showing strong stratification). In particular, they were mainly distributed in the deeper layers of the water (>40%).

Overall, the summer archaeal composition of the two stations appeared very similar, although they showed different seawater physical features. We could not determine whether the archaeal compositions were homogeneous over the JB water columns in different seasons. Furthermore, we could not determine whether the JB archaeal composition has changed in response to anthropogenic activities, as no studies have reported the archaeal community compositions in the JB water columns yet. Therefore, these aspects need to be investigated in future to better understand the JB archaeal compositions.

Meanwhile, to gain more information about the characteristics of the JB archaeal composition, we compared it with the summer microbial community composition observed in bottom waters of the northern Gulf of Mexico (nGOM) that hypoxia formed [6]. The nGOM study showed high relative abundances of the archaeal phylum groups Thaumarchaeota and Euryarchaeota. The result was comparable with this study (Figure 3a). However, there is still a lack of available information to compare archaeal community compositions between various marine environments. Thus, there is a need to create a marine archaeal database for such comparisons in the near future.

3.3. Inferring Potential Biogeochemical Functions

Functional inferences were based on previously published knowledge regarding the metabolic capacities of the identified archaeal taxa, rather than direct gene function annotation. Archaeal reads accounted for approximately 0.66% of the total microbial community. In contrast to this low archaeal abundance, bacteria dominated the JB water columns and are expected to play major roles in nitrogen and carbon cycling, including processes such as denitrification and organic matter degradation.

Although archaea occupied a tiny fraction among the three domains in the JB summer water columns, the degree of their contribution to biogeochemical cycles remains unknown. Therefore, we attempted to infer the biogeochemical functions of archaea in the JB summer water columns on the basis of the known biogeochemical functions of the identified species (Table 2).

At present, AOA are widely known to be involved in ammonium oxidation, the first step of nitrification (i.e., NH₄⁺ → NO₂⁻) [20,21,22]. This step is essential to provide nitrate, the nitrogen form required during primary production [23,24]. In addition, AOA act as N₂O producers, along with ammonia-oxidizing bacteria (AOB) [25]. In the JB summer water columns, we found the AOA species of unclassified Nitrosopumilus, Candidatus Nitrosopumilus adriaticus, Candidatus Nitrosopumilus salaria [26], and Candidatus Nitrosopumilus sediminis [27] (Table 2), which are known to play an important role in the nitrogen cycle [28]. However, Candidatus Nitrosopumilus maritimus, which is known as a representative of AOA species and is commonly found in diverse marine and terrestrial environments [29,30], was not detected in the JB waters investigated in this study. This absence may reflect environmental distinctions in JB, such as eutrophic nutrient conditions, lower salinity, or seasonal shifts, which may not favor the dominance of this otherwise cosmopolitan species.

Archaea are known to be involved not only in the nitrogen cycle but also in other biogeochemical cycles [31]. In particular, it was reported that methanogenic archaea, belonging to the phylum Euryarchaeota, contribute to the production of CH₄, which is one of the strong greenhouse gases [32]. We also found methanogenic archaea such as Methanosarcina and Methanococcus maripaludis in the summer JB water columns via this study with a relative abundance of <~2.3% (Table 2). Conversely, we also found methane-oxidizing archaea (MOA) such as Candidatus Methanoperedens nitroreducens in the water columns; these are involved in a microbial process to oxidize CH₄ with electron acceptors which is considered to be important for reducing marine CH₄ production [33,34], even though their relative abundance was very small (<~0.5%) (Table 2). In the present study, we found AOA and MOA species, albeit at a very low relative abundance, so this finding may provide insights into the role of archaea in CH₄ dynamics in the JB water columns.

As a result, it is important to investigate the quantitative contribution of archaea to nitrogen and CH₄ cycles in the eutrophic waters of Jinhae Bay in future studies. However, we acknowledge that inferring the functional roles of archaeal taxa based solely on their taxonomic identity can be limiting, as actual metabolic activity may vary depending on environmental context or strain-level differences. Therefore, our interpretations of the biogeochemical roles of archaeal groups in Jinhae Bay should be considered tentative. Moreover, while the observed community patterns appear to correspond to environmental gradients such as depth stratification and nutrient availability, it is also possible that stochastic processes—such as ecological drift, random colonization, or dispersal limitation—may have contributed to the current community structure. Future studies incorporating functional gene profiling (e.g., metatranscriptomics) and null model approaches are needed to clarify the actual ecological roles and underlying drivers of archaeal community assembly.

4. Summary and Conclusions

Although this study is based on a snapshot and brief analysis, we present, for the first time, the archaeal community composition at the phylum, class, order, and species levels in the eutrophic waters of Jinhae Bay (JB) during July 2018. The identified archaeal sequences belonged to 5 phyla (dominant: Euryarchaeota and Thaumarchaeota), 11 classes (dominant: Halobacteria, unclassified Thaumarchaeota, Methanobacteria, and Methanomicrobia), and 18 orders (dominant: Nitrosopumilales and Methanobacteriales). At the species level, we identified several archaeal taxa involved in key biogeochemical processes, including ammonia-oxidizing archaea (AOA) such as unclassified Nitrosopumilus, Candidatus Nitrosopumilus adriaticus, Candidatus Nitrosopumilus salaria, and Candidatus Nitrosopumilus sediminis, and a methane-oxidizing archaeon (MOA), Candidatus Methanoperedens nitroreducens. Although these AOA and MOA species were present in low relative abundances, their presence suggests potential functional roles in the biogeochemical processes of eutrophic JB waters. Therefore, further research is warranted to better understand the extent of archaeal contributions to biogeochemical cycling in Jinhae Bay.