Evaluation of micro-biodiversity in three Spratly Islands by metagenomics

Pham Kien Cuong; Tran Thi Huyen Nga; Nguyen Thi Tam Thu; Bui Thi Thu Ha; Nguyen Thu Hoai; Le Thi Nhi Cong; Nguyen Viet Linh

doi:10.15625/2525-2518/21728

Author affiliations

Authors

Pham Kien Cuong \(^1\) Institute of Materials, Biology and Environment, Academy of Military Science and Technology, 17 Hoang Sam Street, Nghia Do Ward, Ha Noi, Viet Nam
Tran Thi Huyen Nga \(^2\) VNU University of Science, 334 Nguyen Trai Street, Thanh Xuan Ward, Ha Noi, Viet Nam
Nguyen Thi Tam Thu \(^1\) Institute of Materials, Biology and Environment, Academy of Military Science and Technology, 17 Hoang Sam Street, Nghia Do Ward, Ha Noi, Viet Nam https://orcid.org/0000-0002-6821-8407
Bui Thi Thu Ha \(^1\) Institute of Materials, Biology and Environment, Academy of Military Science and Technology, 17 Hoang Sam Street, Nghia Do Ward, Ha Noi, Viet Nam
Nguyen Thu Hoai \(^3\) Joint Vietnam - Russia Tropical Science and Technology Research Center, 63 Nguyen Van Huyen Street, Nghia Do Ward, Ha Noi, Viet Nam
Le Thi Nhi Cong \(^4\) Institute of Biology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Nghia Do, Ha Noi, Viet Nam
\(^5\) Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Nghia Do, Ha Noi, Viet Nam https://orcid.org/0000-0002-9849-2300
Nguyen Viet Linh \(^4\) Institute of Biology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Nghia Do, Ha Noi, Viet Nam
\(^5\) Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Nghia Do, Ha Noi, Viet Nam

DOI:

https://doi.org/10.15625/2525-2518/21728

Keywords:

Metagenomic, microbe, micro-biodiversity, Spratly Islands, sea

Abstract

The biodiversity of microbial communities of the soil on three islands of the Spratly Islands, Viet Nam has been analyzed by metagenomic approaches. A total of 77,689 reads were obtained from the sample of Spratly Island (Truong Sa Lon - TSL), while only 62,447 reads were collected from the sample of Sand Cay Island (Son Ca - SC), and 70,150 reads from that of Southwest Cay Island (Song Tu Tay - STT). The validated reads of these islands were 35,253, 10,279, and 10,380, respectively. The reads from TSL were divided into 31 phyla, 80 classes, 185 orders, 291 families, 458 genera, and 397 species. Those from SC included 24 phyla, 45 classes, 98 orders, 133 families, 176 genera, and 100 species. STT had 20 phyla, 39 classes, 95 orders, 129 families, 169 genera, and 110 species. Although the composition and proportions of each taxonomic level are unique and different from each other and from those collected in other island research, the results have shown the diversity and characteristics of microbiomes of TSL, SC, and STT islands. These characteristics reflect the natural and human-induced conditions and determine the dominance of bacteria populations on each island.

Downloads

Download data is not yet available.

References

Mol. Biol. Rev., 68 (2004) 669–685. https://doi.org/10.1128/mmbr.68.4.669-685.2004.

2. Hong S. W., Lee J. S., Chung K. S. – Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of bacterial community structure in the food, intestines, and feces of earthworms. J. Microbiol., 49 (2011) 544–550. https://doi.org/10.1007/s12275-011-0423-8.

3. Islam E., Sar P. – Culture-dependent and -independent molecular analysis of the bacterial community within uraniumore. J. Basic Microbiol., 51 (2011) 372–384. https://doi.org/10.1002/jobm.201000327.

4. Shokralla S., Spall J. L., Gibson J. F., Hajibabaei M. – Next-generation sequencing technologies for environmental DNA research. Mol. Ecol., 21 (2012) 1794–1805. https://doi.org/10.1111/j.1365-294x.2012.05538.x.

5. Streit W. R., Schmitz R. A. – Metagenomics—the key to the uncultured microbes. Curr. Opin. Microbiol., 7 (2004) 492–498. https://doi.org/10.1016/j.mib.2004.08.002.

6. Zhalnina K., de Quadros P. D., Camargo F. A., Triplett E. W. – Drivers of archaeal ammonia-oxidizing communities in soil. Front. Microbiol., 3 (2012) 210. https://doi.org/10.3389/fmicb.2012.00210.

7. Gilles A., Meglécz E., Pech N., Ferreira S., Malausa T., Martin J. F. – Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 12 (2011) 245. https://doi.org/10.1186/1471-2164-12-245.

8. Li A., Chu Y., Wang X., Ren L., Yu J., Liu X., Yan J., Zhang L., Wu S., Li S. – A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol. Biofuels, 6 (2013) 3. https://doi.org/10.1186/1754-6834-6-3.

9. Abraham B. S., Caglayan D., Carrillo N. V., Chapman M. C., Hagan C. T., Hansen S. T., Jeanty R. O., Klimczak A. A., Klingler M. J., Kutcher T. P., et al. – Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades. Environ. Microbiome, 15 (2020) 2. https://doi.org/10.1186/s40793-019-0352-4.

10. Mohd-Yusof N. S., Abdul-Latix M. A., Mohd-Ridwan A. R., Badrulisham A. S., Yaakop S., Md-Nor S., Md-Zain B. M. – First report on metagenomic analysis of gut microbiome in Island Flying Fox (Pteropus hypomelanus) revealing latitudinal correlation as opposed to host phylogeny in island populations of Malaysia. Mol. Ecol. (2020). https://doi.org/10.22541/au.159121433.35769721.

11. Hidalgo K. J., Sierra-Garcia I. N., Dellagnezze B. M., de Oliveira V. M. – Metagenomic insights into the mechanisms for biodegradation of polycyclic aromatic hydrocarbons in the oil supply chain. Front. Microbiol., 11 (2020) 561506. https://doi.org/10.3390/fmicb.2020.561506.

12. Eze M. O. – Metagenome analysis of hydrocarbon-degrading bacterial consortium reveals the specific roles of BTEX biodegraders. Genes, 12 (2021) 98. https://doi.org/10.3390/genes12010098.

13. Kim Y. E., Yoon H., Kim M., Nam Y. J., Kim H., Seo Y., Lee G. M., Kim Y. J., Kong W. S., Kim J. G., et al. – Metagenomic analysis of bacterial communities on Dokdo Island. J. Gen. Appl. Microbiol., 60 (2014) 65–74. https://doi.org/10.2323/jgam.60.65.