Host Shaping Associated Microbiota in Hydrothermal Vent Snails from the Indian Ocean Ridge
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. 16S rRNA Gene Library Preparation, Sequencing and Analysis for 17 Samples from C. squamiferum (BC, WC) and G. aegis (G)
2.3. Metagenomic Sequencing, Assembly and Binning for Six Samples from C. squamiferum (BC, WC) and G. aegis (G)
2.4. Gene Annotation and Metabolic Analysis of MAGs and Metagenomes
2.5. Phylogenomic Analysis of MAGs
2.6. Data Availability
3. Results
3.1. Distributions of Snails on Indian Ocean Ridges and Ultrastructural Characterization of Scaly-Foot Snails by Scanning Electron Microscopy (SEM)
3.2. Characterization of Microbial Communities Associated with Hydrothermal Snails
3.2.1. Microbial Community Structure Revealed by High Throughput Sequencing
3.2.2. Metabolic Potential of the Microbial Community Based on Metagenomic Analysis
3.2.3. Phylogenomics and Predicted Metabolic Capabilities of Dominant Metagenome-Assembled Genomes (MAGs)
Chromatiales of Gammaproteobacteria
Thiotrichales of Gammaproteobacteria
Methylococcales of Gammaproteobacteria
Candidatus Endothiobacterales of Gammaproteobacteria
Campylobacterales of Campylobacterota
Flavobacteriales of Bacteroidetes
4. Discussion
4.1. Host-Specific Symbiont Type in Hydrothermal Snails
4.2. “Core” Microbial Community with Abundance Variation in the Hydrothermal Snail C. squamiferum
4.3. The Association of Hydrothermal Snails and Their Symbionts to Adapt to the Environment
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
KEGG | Kyoto Encyclopedia of Genes and Genomes |
ANI | Average Nucleotide Identity |
PCA | Principal Component Analysis |
MAG | Metagenome-Assembled Genome |
ASV | Amplicon Sequence Variant |
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Species | The Black Scaly Chrysomallon squamiferum (BC) | The White Scaly Chrysomallon squamiferum (WC) | Gigantopelta aegis (G) | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Samples | Scale Foot | Gland | Scale Foot | Gland | Foot | Gland | |||||||||||
ID | BC1F | BC2F | BC3F | BC1G | BC2G | BC3G | WC1F | WC2F | WC3F | WC1G | WC2G | WC3G | G1F | G2F | G3F | G1G | G2G |
Effective sequence tags | 83,413 | 41,705 | 48,417 | 102,478 | 86,262 | 77,152 | 72,329 | 15,542 | 71,883 | 72,329 | 58,503 | 65,641 | 95,143 | 89,073 | 84,091 | 101,179 | 100,557 |
ASV | 187 | 284 | 326 | 206 | 417 | 264 | 291 | 197 | 323 | 469 | 344 | 336 | 98 | 145 | 99 | 126 | 204 |
Shannon (H’) | 2.67 | 2.45 | 2.77 | 1.32 | 3.40 | 3.27 | 3.39 | 3.68 | 3.38 | 3.45 | 2.81 | 4.60 | 0.14 | 0.19 | 0.19 | 0.25 | 0.84 |
Simpson | 0.15 | 0.16 | 0.13 | 0.56 | 0.05 | 0.11 | 0.09 | 0.04 | 0.10 | 0.13 | 0.31 | 0.03 | 0.97 | 0.95 | 0.94 | 0.94 | 0.84 |
Chao1 | 202.79 | 387.46 | 475.24 | 226.04 | 458.17 | 277.00 | 340.40 | 230.91 | 395.55 | 508.00 | 378.50 | 493.50 | 152.09 | 224.69 | 147.46 | 140.25 | 246.86 |
Ace | 206.55 | 386.90 | 546.24 | 233.05 | 541.17 | 273.87 | 318.05 | 232.01 | 382.70 | 500.82 | 358.77 | 504.86 | 143.58 | 201.53 | 171.82 | 134.41 | 224.84 |
Taxonomy | Gammaproteobacteria | Campylobacterota | Bacteroidota | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Chromatiales | Thiotrichales | Methy- Lococcales | “Endothio- Bacterales” | Campylobacterales /Sulfurovum | Chitin- Ophagales | ||||||||
MAGs | WC1G. bin.1 | BC1G. bin.1 | G3F. bin1 | G1F. bin2 | WC3F. bin.10 | WC3F. bin.17 | G1F. bin.1 | WC1G. bin.2 | BC1F. bin.5 | WC3F. bin.9 | WC3F. bin.15 | WC3F. bin.11 | WC3F. bin.18 |
Completeness | 97.59 | 99.74 | 92.76 | 98.55 | 80.28 | 80.16 | 98.13 | 88.48 | 82.77 | 87.89 | 85.38 | 89.95 | 95.32 |
Genome size (bp) | 2,472,218 | 2,782,074 | 4,909,376 | 3,525,970 | 3,222,582 | 2,694,131 | 2,407,989 | 2,093,704 | 1,424,152 | 1,383,753 | 1,614,001 | 2,030,818 | 3,087,810 |
GC (%) | 65.54 | 64.89 | 61.05 | 40.24 | 53.60 | 42.37 | 45.43 | 57.7 | 44.77 | 46.10 | 38.91 | 31.71 | 29.11 |
No. protein coding gene | 2468 | 2668 | 4289 | 3256 | 3031 | 2369 | 2409 | 2187 | 1478 | 1438 | 1640 | 1906 | 2503 |
Coding density (%) | 89.50 | 89.66 | 76.25 | 85.74 | 77.26 | 76.37 | 88.36 | 86.88 | 79.77 | 88.01 | 83.29 | 77.03 | 76.98 |
Carbon Fixation | |||||||||||||
CBB (form I) | + | + | - | - | + | - | - | - | - | - | - | - | - |
CBB (form II) | + | + | + | + | - | + | - | + | - | - | - | - | - |
rTCA | - | - | - | - | - | - | - | - | + | + | + | + | - |
Sulfur oxidation | |||||||||||||
SoxBAZYX | + | + | + | + | + | + | - | + | - | - | - | + | - |
SoxCDYZ | - | - | - | - | - | - | - | - | + | + | + | + | - |
Sqr | + | + | + | + | + | + | - | + | + | + | + | + | + |
Fcc | - | + | + | + | + | + | - | + | - | - | - | - | - |
HdrABC | + | + | - | - | - | - | - | - | - | - | - | - | - |
DsrAB | + | + | + | + | + | + | - | + | - | - | - | - | - |
AprAB | + | + | + | - | + | + | - | + | - | - | - | - | - |
sat | + | + | + | + | + | + | + | + | + | + | + | + | + |
SoeABC | + | + | - | + | + | - | - | - | - | - | - | - | - |
Hydrogen oxidation | |||||||||||||
MBHL | + | + | + | - | - | + | - | - | - | - | - | - | - |
Hox | + | - | + | - | + | - | + | - | - | - | - | - | - |
Methano oxidation | |||||||||||||
pMMO | - | - | - | - | - | - | + | - | - | - | - | - | - |
CO oxidation | |||||||||||||
Coo | - | - | - | - | - | - | - | - | - | - | - | - | - |
Metal utilization and resistance | |||||||||||||
Iron oxidase Cyc2 | - | - | - | - | + | + | - | - | - | + | - | - | - |
Iron reduction genes | - | - | - | - | - | - | - | - | - | - | - | - | - |
Iron storage genes | - | - | - | - | - | - | + | + | + | - | + | - | + |
Arsenite oxidation genes | - | - | - | - | - | - | - | - | - | - | - | - | - |
ArsC | + | + | + | + | + | + | + | + | + | + | + | + | + |
MerA | + | + | + | + | + | - | - | - | - | - | - | - | - |
Copper resistance | + | + | + | + | + | + | + | + | + | + | + | + | + |
Oxygen respiration | |||||||||||||
Cox | + | + | + | + | - | - | + | + | - | - | - | - | + |
Cco | + | + | + | - | + | + | - | - | + | + | + | + | + |
Glc | + | + | + | - | + | + | - | - | - | - | - | - | - |
Nitrate and nitrite ammonification | |||||||||||||
NapAB | + | + | + | + | + | + | + | + | - | + | + | + | + |
NasA | + | + | + | + | + | - | + | + | + | - | + | - | + |
NirBD | + | + | + | + | + | - | + | + | + | - | + | - | + |
Electron transport chain | |||||||||||||
ATP synthase | F-type | F-type | F-type; V-type | F-type | F-type | F-type | F-type; V-type | F-type | F-type | F-type | F-type | F-type | F-type |
Nuo | + | + | + | + | + | + | - | + | + | + | + | + | + |
Fdh | + | + | + | - | - | - | + | - | - | - | - | - | - |
Sdh | + | + | + | + | + | + | + | + | + | + | + | + | + |
Nqr | - | - | - | - | - | - | + | - | - | - | - | - | - |
Rnf | + | + | + | + | - | + | + | + | - | - | - | - | - |
Motility | |||||||||||||
Flagellum | + | + | - | + | + | - | + | - | - | - | - | - | - |
Pili | + | + | + | + | + | + | + | + | - | - | - | - | - |
Gliding | - | - | - | - | - | - | - | - | - | - | - | - | + |
Vitamin and cofactor | |||||||||||||
Thiamine (Vitamin B1) | + | + | + | + | - | + | + | + | + | + | + | + | - |
Riboflavin (Vitamin B2) | + | + | + | - | - | + | - | + | + | + | + | + | + |
pyridoxine (Vitamin B6) | + | + | - | + | - | + | + | - | + | + | - | + | - |
Biotin (Vitamin B7) | + | + | + | + | + | - | + | + | + | - | - | + | - |
Folic acid (Vitamin B9) | + | + | + | + | + | - | + | + | + | + | + | + | + |
Cobalamin (vitamin B12) | - | - | - | + | + | - | + | + | - | - | - | - | - |
Host | Habitat | Symbiont Location | Symbiont Type | Main Symbiont Community | Refs |
---|---|---|---|---|---|
Alviniconcha spp. /Provannidae | SWIR, CR, Indian Ocean; Western Pacific Ocean | Intracellular; Gill; | SOB; HOB; | Sulfurimonas/Sulfurovum, Helicobacteraceae, Campylobacterales, Campylobacterota | [7,71] |
SOB; HOB; | Ectothiorhodospiraceae, Chromatiales, Gammaproteobacteria Chromatiaceae, Chromatiales, Gammaproteobacteria | ||||
Gigantopelta spp. /Peltospiridae | SWIR, Indian Ocean; Southern Ocean | Intracellular; Gland; | SOB; MOB | Ectothiorhodospiraceae, Chromatiales, Gammaproteobacteria Methylococcaceae, Methylococcales, Gammaproteobacteria | [13] This study |
Chrysomallon squamiferum /Peltospiridae | SWIR, CIR, CR, Indian Ocean | Scale; | SOB; HOB; HB | Sulfurovum, Helicobacteraceae, Campylobacterales, Campylobacterota Thiotrichaceae, Thiotrichales, Gammaproteobacteria Flavobacteriales, Bacteroidota | [16,36] This study |
Intracellular; Gland; | SOB; HOB; | Chromatiaceae, Chromatiales, Gammaproteobacteria Thiotrichaceae, Thiotrichales, Gammaproteobacteria “Endothiobacterales”, Gammaproteobacteria |
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Share and Cite
Zeng, X.; Chen, J.; Liu, G.; Zhou, Y.; Wang, L.; Zhang, Y.; Liu, S.; Shao, Z. Host Shaping Associated Microbiota in Hydrothermal Vent Snails from the Indian Ocean Ridge. Biology 2025, 14, 954. https://doi.org/10.3390/biology14080954
Zeng X, Chen J, Liu G, Zhou Y, Wang L, Zhang Y, Liu S, Shao Z. Host Shaping Associated Microbiota in Hydrothermal Vent Snails from the Indian Ocean Ridge. Biology. 2025; 14(8):954. https://doi.org/10.3390/biology14080954
Chicago/Turabian StyleZeng, Xiang, Jianwei Chen, Guilin Liu, Yadong Zhou, Liping Wang, Yaolei Zhang, Shanshan Liu, and Zongze Shao. 2025. "Host Shaping Associated Microbiota in Hydrothermal Vent Snails from the Indian Ocean Ridge" Biology 14, no. 8: 954. https://doi.org/10.3390/biology14080954
APA StyleZeng, X., Chen, J., Liu, G., Zhou, Y., Wang, L., Zhang, Y., Liu, S., & Shao, Z. (2025). Host Shaping Associated Microbiota in Hydrothermal Vent Snails from the Indian Ocean Ridge. Biology, 14(8), 954. https://doi.org/10.3390/biology14080954