For instance, albeit researchers are actively studying microbial samples from the hadal zone, the pathogenic and antibiotic resistant potentials of microbial populations therein have never been closely analyzed. Most previous studies described the taxonomic diversity of hadal microbial populations, while only limited studies investigated functional profiles of the communities. However, the biological features of microbial communities at hadal zones remain largely unknown. The ocean has been recently implicated as a global reservoir of clinically relevant antibiotic-resistant genes (ARGs). Likely because of its distinct biophysical and biochemical features, as well as geographical isolation, hadal zone harbors microbial communities that significantly differ from other oceanic microbial communities in compositions: common habitats in the hadal ocean include Proteobacteria, Chloroflexi, Thaumararchaea, Gemmatimonadetes, Planctomycetes, Actinobacteria, Patescibacteria, Acidobacteria, Firmicutes, and Bacterioidetes.

These studies together showed that the hadal microbial world is compositionally diverse, populationally abundant, and biologically flourishing. Due to the rapid technological advances in deep-sea exploration and high-throughput DNA sequencing, several hadal microbial communities in the Mariana, Puerto Rico, Japan, Yap, and Kermadec Trenches have been investigated over the past decade. Hadal zone (around 6000–11,000 m), which consists of almost exclusively plunging trenches, is the deepest part on the earth known to support microbial life. Our work unravels the contrasting and unique features of virulence genes, ARGs, and MGEs in the Mariana Trench bottom, providing new insights into the eco-environmental and biological processes underlying microbial pathogenicity, resistance, and adaptative evolution in the hadal environment. This study reports the landscape of virulence factors, antibiotic resistome, and mobilome in the sediment and seawater microbiota residing hadal environment of the deepest ocean bottom on earth. Notably, contig-level co-occurring and taxonomic analysis shows emerging evidence for substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria. Further analysis of mobilome (i.e., the collection of mobile genetic elements, MGEs) suggests horizontal gene transfer mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria. However, the shallower and more nearshore site sediment had a higher abundance and richer diversity of known antibiotic resistance genes (ARGs), especially for those clinically relevant ones (e.g., fosX, sul1, and TEM-family extended-spectrum beta-lactamases), revealing resistance selection under anthropogenic stresses. Virulence genes including several famous large translocating virulence genes (e.g., botulinum neurotoxins, tetanus neurotoxin, and Clostridium difficile toxins) were uniquely detected in the trench bottom.

The results indicate that the 10,898 m Challenger Deep bottom sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance, compared with the neighboring but shallower 6038 m steep wall site and the more nearshore 5856 m Pacific basin site. Here we used culture-independent metagenomic approaches to explore the virulence and antibiotic resistance in the hadal microbiota of the Mariana Trench. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level.

Challenger deep vs mariana trench