the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 02 Jul 2026
Proteobacteria Dominance and Neutral Assembly Processes of Bacterial Communities in the Chukchi Sea, Arctic
Abstract. Bacteria play a vital role in maintaining ecosystem functioning under rapidly changing environmental conditions, however, the characteristics and assembly mechanisms of bacterial communities at regional scales in the marine ecosystem of the Arctic Chukchi Sea remain poorly understood. Using 16S rRNA gene amplicon sequencing, we investigated the composition, diversity, and assembly processes of bacterial communities across three distinct water layers (Surface, Middle, and Bottom) in the Chukchi Sea. The results revealed a significant increase in community richness in the Middle and Bottom layers compared to the Surface layer, with Alphaproteobacteria, Cyanobacteriia, and Bacteroidia as the predominant classes. The bacterial community structures differed significantly across the water layers, and their β-diversity was primarily driven by species turnover. Environmental variables explained approximately 48.2 % of the variation in community structure, with water depth, dissolved oxygen (DO) and silicate were identified as driving factors (p<0.05). Furthermore, network analysis indicated that the bacterial co-occurrence network in the middle layer exhibited greater complexity and stability. The Neutral community model (which explained 61.9 % of community variation) and null model analyses collectively demonstrated that while both deterministic and stochastic processes govern bacterial community assembly in the Chukchi Sea, stochasticity is the dominant force. These findings advance our understanding of depth-stratified bacterial ecology in the Chukchi Sea and provide a crucial foundation for future studies on ecosystem responses to ongoing environmental changes in the Arctic.
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Status: open (until 20 Aug 2026)
- RC1: 'Comment on egusphere-2026-3709', Anonymous Referee #1, 20 Jul 2026 reply
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This manuscript reports bacterial community composition based on 16S rRNA gene amplicon sequencing in and around the Chukchi Sea. A total of 24 samples were collected from 8 stations at 3 depth categories: Surface (S), Middle (M), and Bottom (B). The authors found a high relative abundance of Alphaproteobacteria, Cyanobacteria, and Bacteroidia throughout the water column, particularly in the surface layer. Alpha diversity was higher in the M and B layers than in the S. They describe depth-dependent bacterial community structures. Furthermore, they sought to determine whether the bacterial communities are influenced primarily by deterministic or stochastic processes and concluded that stochastic processes are the dominant driver.
Although this manuscript has the potential to provide valuable bacterial taxonomic data from the Arctic Ocean and addresses interesting ecological questions, I am not fully convinced that the main claims are supported by the data as currently presented. First, the classification into the three depth categories (S, M, and B) is not sufficiently clear or oceanographically justified. These categories appear to represent relative sampling depths at each station. For example, at station R13, the M and B samples were collected at 150 and 164 m, respectively, and have similar environmental parameters (Table S1), yet are treated as different categories. Conversely, the M category ranges 100-500 m, whereas the B category ranges 162-1175 m. This leads to samples with very similar depths being assigned to different categories, whereas samples with very different depths are grouped together. Because most subsequent analyses rely heavily on these depth categories, the results are difficult to interpret ecologically in their current form. In addition, because water masses are generally identified using temperature, salinity, and depth, and are central to the interpretation of this study, temperature and salinity should also be presented.
The analysis of “deterministic and stochastic processes” is interesting. However, given this limited sample set (8 stations with 3 depths each), I am not fully convinced that the stochastic process is identified as the dominant process. Unexplained variation may arise from unmeasured environmental variables, measurement error, or other sources of variation, and therefore cannot by itself be interpreted as evidence of stochasticity.
Previous studies have already well documented prokaryotic community structure and water mass-related patterns in this region, e.g., Pan et al. (2025, Microbiol Spectr), as cited by the authors, and Han et al. (2015, Deep-Sea Res). Therefore, the novelty of this work could be better presented in relation to previous work.
Finally, several statements in the Results and Discussion are not fully supported by the data presented and should be revised more carefully (see below).
Specific comments:
L77-81: Please clarify how these stations are classified as shelf and slope stations. Also, P2_08 appears close to the Northwind Ridge or the basin margin in Fig. 1, rather than clearly within the Canada Basin. Please provide station coordinates, bottom depths, bathymetric information, and the criteria used for the geographical classification. Overall, both the depth categories and the geographical classification of the stations require clarification.
L82: S, M, and B are sampling depth categories, not water masses.
L96: The primer pair used is expected to amplify both bacterial and archaeal 16S rRNA genes. Please explain why archaeal sequences were not included in the analysis.
L108: Please provide more detail on how turnover and nestedness were calculated and explain their ecological meaning.
L122: I cannot clearly identify strong taxonomic stratification in Fig. 2 because the M and B communities appear relatively similar and the major taxonomic groups remain broadly consistent.
L129: It is unclear what is meant by “dramatic shifts” in Alphaproteobacteria. Based on Fig. 2, the relative abundance change does not appear substantially greater than that of Cyanobacteria. In addition, because Alphaproteobacteria is a broad taxonomic class, this statement should either be quantified or supported by analyses at a lower taxonomic level.
L151: The statement that “M and B partially overlapped” may reflect the strong overlap and heterogeneity in the underlying depth categories.
L159: A broader calculated niche breadth does not by itself demonstrate expanded resource use.
L185: “L” is not shown in Fig. 5a
L187-188: The network analysis is based on only 8 samples per depth category. This limitation needs to be explained more explicitly.
L191: The M layer network appears to contain more highly connected nodes than the S and B networks. However, this comparison is difficult to interpret because the depth categories are broad and environmentally heterogeneous. In addition, Fig. 6a does not indicate which panels correspond to S, M, and B.
L216: The authors should briefly explain the ecological meanings of dispersal limitation and drift. More importantly, I am not convinced that the relative contributions of these processes can be robustly estimated from the present dataset and sampling design.
L234-237: I am not sure what evidence from the present dataset supports the statement that Alphaproteobacteria are associated with primary production or chlorophyll a. According to Table S1, only two samples showed relatively elevated chlorophyll a, while most values were low. It is therefore unclear whether the present dataset supports this association. Similarly, I cannot see how the increase in Gammaproteobacteria was linked specifically to organic matter input from sea-ice melting. Was sea-ice melt or melt-derived organic matter directly measured?
L238-244: Neither the present dataset nor the cited references demonstrate that members of the SAR406 clade are barophilic. The suggested role in refractory DOM degradation and carbon sequestration should also be presented more cautiously because no functional measurements were made.
L250-252: What data support the statement that M and B layer communities are associated specifically with nutrient cycling and that the observed pattern demonstrates habitat filtering?
L253-254: The higher alpha diversity in deeper samples does not by itself demonstrate that deeper water is a microbial “diversity reservoir.” The term may be appropriate in some contexts, but this interpretation is not established by the present dataset.
L485: The DOI link is incorrect
Table S1: Units are missing for all environmental variables. The reported numerical precision is also inconsistent.