Microbiomes of marine fish gut and sediments : biodiversity and ARGs

Abstract

Marine ecosystems, covering over 70% of Earth’s surface, support various organisms, play crucial roles in the global biogeochemical cycle and provide a wide variety of resources. Marine fish digestive tract and sediment respectively represents host-associated and free-living microbial community, which harbor plentiful species involving in marine biochemical activities. Marine ecosystems and marine organisms are closely associated with the human health through provision of resources, climatic regulation and recreational services. Notably, antibiotic resistant genes (ARGs) as emerging contaminants have been increasingly detected in marine coastal environments that may pose threats to human and animal health. At present, biodiversity and antibiotic resistome in marine sediments as well as diversity of microorganisms in the gut of a wide range of fish species have not been fully uncovered. Thus, this thesis aims at comprehensively investigating microbiomes in fish gut, biodiversity and ARGs in marine sediment, and microbial flow among different environmental compartments.

Gut microbiomes of marine fishes and their relationships with host-associated factors were investigated based on 115 fish individuals of 20 species by 16S rRNA gene amplicon sequencing. The fish gut microbiome was a remarkably simple community with low diversity and has high proportion of unknown species. The gut microbial community structure was significantly shaped by host-associated factors, including the fish taxon, feeding habit and trophic level. The data and observations reported herein pave the way for further investigations on the physiological functions of gut microorganisms, and the development of probiotics for improving the health of aquaculture fish species.

Biodiversity of animals, plants, fungi, bacteria and archaea in marine sediments collected from four coastal areas in Hong Kong were comprehensively characterized using environmental DNA (eDNA) metabarcoding (COI, rbcL, ITS2 and 16S rRNA gene) and metagenomics. Metagenomics detected a broader range of lineages at the higher taxa level, while metabarcoding obtained more lineages from order to species level. The results contributed to the DNA barcoding databases and local biodiversity catalogue of marine species and benefited the application of eDNA for monitoring marine biodiversity in Hong Kong and beyond.

The geographical ARG profile of 288 global marine sediment metagenomic datasets were quantified, and associations among ARGs, mobile genetic elements (MGEs) and antibiotic-resistant bacteria (ARB) were examined. A wide range of ARGs, MGEs and ARB were detected in marine sediments worldwide. The antibiotic resistome was significantly correlated with certain bacterial species. Some pathogens containing both ARGs and MGEs were identified as the riskiest bacteria. The results unraveled the influence of anthropogenic pressure on ARGs dissemination and evaluated the potential risk of marine sediments as a global reservoir of ARGs.

To track the microbial source across diverse environments, I used the machine-learning tool (SourceTracker) to develop a community-based quantitative machine-learning classifier for 15 environmental types of sources through training and analysis of microbial community profiles of 3654 16S rRNA gene datasets. The results demonstrated the superiority of this community-based microbial source tracking method for advancing the capability in chasing the source of microorganisms in a complex environment and enabling the identification of potential sources of microbial contamination.