Microbial community structure and function in deep-sea polymetallic nodules and surrounding sediments

doi:10.3969/j.issn.1001-909X.2025.01.004

Abstract

Abstract:

Deep-sea sediments and polymetallic nodules are rich habitats for microorganisms. Exploring their community structure and functionality is crucial for understanding microbial genetic resources and their role in mineral formation. Current research on the bacterial diversity and structure within the nodules and surrounding sediments is limited, especially regarding microbial contributions to nodule formation. Using full-length 16S rRNA sequencing, we analyzed the bacterial composition of various nodule types and surrounding sediments in the Pacific Ocean. Scanning electron microscopy and energy dispersive spectroscopy revealed bacterial-like microsphere structures and metal element distribution on their surfaces. The bacterial community composition varied among different nodules and sediments, with Proteobacteria and Bacteroidetes dominating. Functional groups like Shewanella and Colwellia, known for metal oxidation-reduction and biofilm formation, may contribute to nodule formation. These microsphere structures promoted metal aggregation, potentially serving as mineral precipitation sites. This study enhanced our understanding of microbial functions and mineral interactions, crucial for insights into deep-sea biogeochemical cycles and microbial mineralization.

Key words: polymetallic nodules, deep-sea sediments, 16S rRNA sequencing, scanning electron microscopy, bacterial diversity, community structure, functional bacteria, Pacific Ocean

CLC Number:

X172
P744.3

HE Xinyi, LIU Qian, LI Xiaohu, LI Zhenggang, WANG Hao, ZHU Zhimin, LI Huaiming. Microbial community structure and function in deep-sea polymetallic nodules and surrounding sediments[J]. Journal of Marine Sciences, 2025, 43(1): 34-46.

Figures/Tables 9

Fig.1 Locations of sampling sites in the western and eastern Pacific Ocean

Fig.2 Main morphologies of nodule samples and the appearance of corresponding thin sections (a-d: Morphologies and corresponding thin sections of nodule samples collected at M2-BC78 site from the western Pacific; e-h: Morphologies and corresponding thin sections of nodule samples collected at KW1-BC05 site from the eastern Pacific.)

Tab.1 Bacterial sequence information and diversity index

项目	西太平洋M2-MC02站		东太平洋KW1-MC04站
项目	结核 (WNAt)	沉积物 (WSA)	结核 (ENBt)	沉积物 (ESB)
序列数/条	10 319	9 535	11 553	6 862
OTU数/个	960	1 169	893	1 065
ACE	1 024	1 490	1 201	1 512
Shannon指数	8.38	8.45	6.26	7.45
覆盖率/%	99	99	99	99

Fig.3 Distribution of bacterial OTUs in nodules and sediments

Fig.4 Sample rarefaction curves

Fig.5 Bacterial community composition in nodules and sediments of the eastern and western Pacific Ocean (“unassigned” represents a collection of sequences that cannot be definitively classified into known genera, “uncultured” represents a collection of genera that cannot be cultivated from the environment using traditional cultivation methods.)

Fig.6 Relative abundance average clustering heatmap at the genus level (top 30) (The color in the figure signifies the degree of enrichment of the genus within the sample, with deeper red hues indicating a higher level of enrichment. “unassigned” represents a collection of sequences that cannot be definitively classified into known genera, “uncultured” represents a collection of genera that cannot be cultivated from the environment using traditional cultivation methods.)

Fig.7 Internal structures of nodules (BSE mode)

Fig.8 Microsphere structures in the nodules and corresponding energy dispersive spectroscopy results (a-b: Microsphere structures and corresponding EDS results in the western Pacific nodules; c-d: Microsphere structures and corresponding EDS results in the eastern Pacific nodules.)

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