Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench

Abstract

Background The Kuril–Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment. Results As for the bacterial communities, we found that Proteobacteria (56.1–74.5%), Bacteroidetes (6.5–19.1%), and Actinobacteria (0.9–16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9–91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril–Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench. Conclusions This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril–Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.

Uncovering the Prokaryotic Diversity of the Bathyal Waters above the Kuril–Kamchatka Trench

“…It should be noted that the only study that has examined the bathyal prokaryotic communities in the Kuril-Kamchatka Trench area is that carried out by Li et al [33]; however, the authors did not provide a taxonomic profiling of the communities at the genus level. The only comparison that can be made is with the abyssalhadal communities of the KKT that we have recently described [38]. Nevertheless, it is important to highlight that the samples analyzed in our previous study differ significantly from those of the current one.…”

“…The archaeal community analysis was carried out targeting the V3 hypervariable region of the 16S rDNA by the Arch349F and Arch571R primers [41,42]. The amplicon libraries were prepared by a dual PCR approach, as previously reported by Gorrasi et al [38]. The sequencing was performed at an external service (Nuova Genetica Italiana SRL, Monza-Brianza, Italy) by Illumina MiSeq (Illumina, San Diego, CA, USA) using a 2 × 250 bp paired-end protocol.…”

“…Its absence in these remote trench regions might reflect an adaptation or distribution specificity, which highlights the need for additional investigation in order to identify the factors affecting Pseudofrancisiella distribution. A list of the bacterial genera found in the bathyal zone (current work) and/or in the abyssal-hadal zone (previous work; [38]) of the KKT was supplied to provide a more detailed comparison of their occurrence among the two trench regions (Table S2).…”

“…Our investigations aimed at profiling the prokaryotic diversity of the KKT ecosystem, which is practically unknown. In a very recent study [38], we provided the first description of the prokaryotic communities found in the abyssal-hadal zone of the trench. The investigation was carried out on samples of the benthic-boundary layer (water layer that is directly adjacent to the ocean bottom and can contain particles derived from the resuspension of surface sediments) that were collected at various locations within the trench and in the neighboring abyssal plain (depth range 5146-9540 m).…”

Rambellisea gigliensis and Rambellisea halocynthiae, gen. et spp. nov. (Lulworthiaceae) from the Marine Tunicate Halocynthia papillosa

“…The sea represents a limitless resource of unexploited substrata and new microorganisms [5][6][7][8]. Over the last decades, researchers have paid close attention to marine microbiology, investigating new environments and/or substrata [6,9,10]. In particular, scientists have spent much effort to expand our understanding of fungal biodiversity and highlight fungi's importance in several ecosystem services [6,[11][12][13][14].…”