Identification of Free-Living and Particle-Associated Microbial Communities Present in Hadal Regions of the Mariana Trench

Abstract

Relatively few studies have described the microbial populations present in ultra-deep hadal environments, largely as a result of difficulties associated with sampling. Here we report Illumina-tag V6 16S rRNA sequence-based analyses of the free-living and particle-associated microbial communities recovered from locations within two of the deepest hadal sites on Earth, the Challenger Deep (10,918 meters below surface-mbs) and the Sirena Deep (10,667 mbs) within the Mariana Trench, as well as one control site (Ulithi Atoll, 761 mbs). Seawater samples were collected using an autonomous lander positioned ~1 m above the seafloor. The bacterial populations within the Mariana Trench bottom water samples were dissimilar to other deep-sea microbial communities, though with overlap with those of diffuse flow hydrothermal vents and deep-subsurface locations. Distinct particle-associated and free-living bacterial communities were found to exist. The hadal bacterial populations were also markedly different from one another, indicating the likelihood of different chemical conditions at the two sites. In contrast to the bacteria, the hadal archaeal communities were more similar to other less deep datasets and to each other due to an abundance of cosmopolitan deep-sea taxa. The hadal communities were enriched in 34 bacterial and 4 archaeal operational taxonomic units (OTUs) including members of the Gammaproteobacteria, Epsilonproteobacteria, Marinimicrobia, Cyanobacteria, Deltaproteobacteria, Gemmatimonadetes, Atribacteria, Spirochaetes, and Euryarchaeota. Sequences matching cultivated piezophiles were notably enriched in the Challenger Deep, especially within the particle-associated fraction, and were found in higher abundances than in other hadal studies, where they were either far less prevalent or missing. Our results indicate the importance of heterotrophy, sulfur-cycling, and methane and hydrogen utilization within the bottom waters of the deeper regions of the Mariana Trench, and highlight novel community features of these extreme habitats.

Diversity of culturable heterotrophic bacteria from the Mariana Trench and their ability to degrade macromolecules

“…Due to the rapid progress of deep-sea sampling techniques in recent years, the microbial community structures at different water depths of the Mariana Trench have been extensively studied by either 16S rRNA gene high-throughput sequencing (Nunoura et al 2015;Peoples et al 2018;Tarn et al 2016;Tian et al 2018) or metagenomic sequencing (Liu et al 2019c;Wang et al 2019). There have also Edited by Chengchao Chen.…”

In situ meta‐omic insights into the community compositions and ecological roles of hadal microbes in the Mariana Trench

“…Critical for life, sulfur metabolism has also drawn a great deal of attention. The sulfur oxidizing bacteria (SOB) of SUP05 clade have been proposed to be a prominent group in hadal samples (Tarn et al, 2016). A Gammaproteobacteria MAG P9 that was closely related to SUP05 has also been retrieved from Fig.…”

“…The following work exhibited a vertical profile of planktonic microbial communities from surface water to the deepest region of the Mariana Trench, in which heterotrophic microbial lineages were more abundant in the hadal waters compared to the upper abyssal oceans and potentially represented distinct microbial ecosystem driven by endogenous recycling of organic matter (Nunoura et al ., ). Dominant species in hadal free‐living and particle‐associated microbial communities were then uncovered, which highlighted the potential importance of heterotrophy, sulfur‐cycling, and methane and hydrogen utilization within the hadal bottom waters of the Mariana Trench (Tarn et al ., ). The most recent comparative analysis of microbial communities in different trenches further indicated the occurrence of distinctive hadal biospheres in global trench environments (Nunoura et al ., ; Liu et al ., ; Peoples et al ., ).…”

“…Since then, hundreds of new microbial strains were isolated from hadal trenches and the composition of hadal microbial communities was also casually determined using culturing and/or conventional 16S rRNA gene cloning methods (Bartlett, 2009;Cao et al, 2014). Only recently, nextgeneration sequencing techniques facilitated the studies on hadal microbial communities and provided in-depth insight on them (Eloe et al, 2011a;Nunoura et al, 2015Nunoura et al, , 2016Tarn et al, 2016;Liu et al, 2018;Peoples et al, 2018;Wang et al, 2019a). Compositions of microbial assemblages in the Puerto Rico Trench (PRT) from 6000 m depth were the first hadal microbial communities reported using the improved sequencing techniques (Eloe et al, 2011a).…”

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1)

“…It is located in the western Pacific Ocean, extending to a depth of approximately 10 920 m (Nakanishi and Hashimoto, 2011), corresponding to about 110 megapascals (MPa) of hydrostatic pressure. This environment has been shown to have high microbial activity in surface sediments based on oxygen utilization (Glud et al, 2013) but little is known about the diversity of its microbial community (Kato et al, 1998;Pathom-Aree et al, 2006;Yoshida et al, 2013;Tarn et al, 2016). During the Deepsea Challenge (DSC) Expedition a sediment core was obtained by the manned submersible Deepsea Challenger, and from it single cell-derived genomes were obtained, including a number derived from members of the candidate Parcubacteria (OD1) superphylum.…”