Metagenomic Insights Into the Structure and Function of Intestinal Microbiota of the Hadal Amphipods

Jiulin Chan; Daoqiang Geng; Binbin Pan; Qiming Zhang; Qianghua Xu

doi:10.3389/fmicb.2021.668989

Metagenomic Insights Into the Structure and Function of Intestinal Microbiota of the Hadal Amphipods

Front Microbiol. 2021 Jun 7:12:668989. doi: 10.3389/fmicb.2021.668989. eCollection 2021.

Authors

Jiulin Chan¹, Daoqiang Geng¹, Binbin Pan^{1

2}, Qiming Zhang³, Qianghua Xu^{1

2

4}

Affiliations

¹ Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
² Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
³ Shanghai Rainbowfish Ocean Technology Co., Ltd, Shanghai, China.
⁴ National Distant-water Fisheries Engineering Research Center, Shanghai Ocean University, Shanghai, China.

Abstract

Hadal trenches are the deepest known areas of the ocean. Amphipods are considered to be the dominant scavengers in the hadal food webs. The studies on the structure and function of the hadal intestinal microbiotas are largely lacking. Here, the intestinal microbiotas of three hadal amphipods, Hirondellea gigas, Scopelocheirus schellenbergi, and Alicella gigantea, from Mariana Trench, Marceau Trench, and New Britain Trench, respectively, were investigated. The taxonomic analysis identified 358 microbial genera commonly shared within the three amphipods. Different amphipod species possessed their own characteristic dominant microbial component, Psychromonas in H. gigas and Candidatus Hepatoplasma in A. gigantea and S. schellenbergi. Functional composition analysis showed that "Carbohydrate Metabolism," "Lipid Metabolism," "Cell Motility," "Replication and Repair," and "Membrane Transport" were among the most represented Gene Ontology (GO) Categories in the gut microbiotas. To test the possible functions of "Bacterial Chemotaxis" within the "Cell Motility" category, the methyl-accepting chemotaxis protein (MCP) gene involved in the "Bacterial Chemotaxis" pathway was obtained and used for swarming motility assays. Results showed that bacteria transformed with the gut bacterial MCP gene showed significantly faster growths compared with the control group, suggesting MCP promoted the bacterial swimming capability and nutrient utilization ability. This result suggested that hadal gut microbes could promote their survival in poor nutrient conditions by enhancing chemotaxis and motility. In addition, large quantities of probiotic genera were detected in the hadal amphipod gut microbiotas, which indicated that those probiotics would be possible contributors for promoting the host's growth and development, which could facilitate adaptation of hadal amphipods to the extreme environment.

Keywords: adaptation; amphipod; gut microbiota; hadal trench; metagenomics.