Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities

Abstract

Hydrothermally active submarine volcanoes are mineral-rich biological oases contributing significantly to chemical fluxes in the deep sea, yet little is known about the microbial communities inhabiting these systems. Here we investigate the diversity of microbial life in hydrothermal deposits and their metagenomics-inferred physiology in light of the geological history and resulting hydrothermal fluid paths in the subsurface of Brothers submarine volcano north of New Zealand on the southern Kermadec arc. From metagenome-assembled genomes we identified over 90 putative bacterial and archaeal genomic families and nearly 300 previously unknown genera, many potentially endemic to this submarine volcanic environment. While magmatically influenced hydrothermal systems on the volcanic resurgent cones of Brothers volcano harbor communities of thermoacidophiles and diverse members of the superphylum "DPANN," two distinct communities are associated with the caldera wall, likely shaped by two different types of hydrothermal circulation. The communities whose phylogenetic diversity primarily aligns with that of the cone sites and magmatically influenced hydrothermal systems elsewhere are characterized predominately by anaerobic metabolisms. These populations are probably maintained by fluids with greater magmatic inputs that have interacted with different (deeper) previously altered mineral assemblages. However, proximal (a few meters distant) communities with gene-inferred aerobic, microaerophilic, and anaerobic metabolisms are likely supported by shallower seawater-dominated circulation. Furthermore, mixing of fluids from these two distinct hydrothermal circulation systems may have an underlying imprint on the high microbial phylogenomic diversity. Collectively our results highlight the importance of considering geologic evolution and history of subsurface processes in studying microbial colonization and community dynamics in volcanic environments.

Keywords: Archaea; deep-sea hydrothermal; metagenomics; thermophiles; volcanics.

Fig. 1.

Location of hydrothermal vent sampling sites from Brothers volcano. (A) Overall bathymetric map of the volcano. (Inset) Location north of New Zealand. (B) Detail of NWC and UCW sites. (C) Detail of UC and LC sites. Total samples per area are indicated with n values.

Fig. 2.

Nonmetric multidimensional scaling (NDMS) plots of (A) Brothers volcano community composition, (B) functional gene diversity, (C) MAG phylogenetic diversity, and (D) Brothers volcano and ELSC-VFR deep-sea hydrothermal vent community diversity. Plots are based on Bray–Curtis matrices of (A) community composition of Brothers volcano samples constructed from amplicon sequence variants (ASVs) of 16S rRNA gene sequences at a depth of 3,000 sequences per sample; (B) relative abundance of select functional genes and gene categories described in the text (n = 123 genes/gene categories) and shown in Dataset S2B; (C) relative abundance of medium- to high-quality MAGs based on normalized read coverage of taxa assigned by GTDB-Tk (n = 251 taxonomic assignations). Relative abundance data are available in Dataset S3D; and (D) community composition of Brothers volcano and ELSC-VFR hydrothermal vent samples based on ASVs of 16S rRNA gene sequences at a depth of 3,000 sequences per sample. Points closer together on the ordination plot are more similar to each other. The number of samples at each area is indicated as an n value.

Fig. 3.

Relative normalized abundance of metabolic and functional genes involved in energy generation, oxygen tolerance, and biogeochemical cycling from Brothers volcano metagenome assemblies, including those discussed in the text. (A) Bubbles represent single genes or iron metabolism gene categories listed in Dataset S2B. Bubble size indicates normalized abundance, calculated by dividing the summed coverage for each gene/gene category in an assembly by the average summed coverage for 14 single-copy marker genes. Full gene names are shown in Dataset S2B. (B) Heat map shows the average normalized abundance of genes/gene categories discussed in the text. Normalized abundance was determined as described above and subsequently averaged across all assemblies at each particular area (UC, n = 3 assemblies; LC, n = 2 assemblies; NWC-A, n = 6 assemblies; NWC-B+UCW, n = 5 assemblies). Coloring is scaled relative to each row, with red indicating the highest average relative abundance of the four areas and yellow indicating the lowest average relative abundance. Normalized abundance of genes and gene categories and full gene names are shown in Dataset S2B.

Fig. 4.

Maximum-likelihood phylogenetic reconstruction of bacterial metagenome-assembled genomes from Brothers volcano using GTDB-Tk. The tree was constructed using 120 bacterial marker genes. Branch support was determined with the SH test, and support values from 0.8 to 1.0 are indicated with filled circles. Collapsed taxonomic clades are shown as triangles, with blue triangles indicating clades containing Brothers volcano MAGs with the number of MAGs shown in parentheses. Clades with Brothers MAG are labeled using NCBI taxonomy followed by GTDB-Tk taxonomy in brackets, while gray clades without Brothers MAGs are shown with GTDB-Tk taxonomy only. Due to the extensive reordering of the Tree of Life within GTDB-Tk taxonomy, the NCBI taxonomy is approximate and represents large-scale taxa equivalencies. The scale bar indicates expected amino acid substitutions per site. The uncollapsed phylogenetic tree used to create this figure is available online (28) at https://itol.embl.de/shared/alrlab and on FigShare in phyloXML format (21) at https://doi.org/10.6084/m9.figshare.c.5099348.

Fig. 5.

Maximum-likelihood phylogenetic tree of archaeal MAGs from Brother volcano, constructed in GTDB-Tk using 122 archaeal marker genes. SH branch support (0.8 to 1.0) is shown with dark circles. Major clades are collapsed into triangles, and triangle coloring is based on GTDB-Tk phylum-level taxonomic classifications. Individual clades are labeled using NCBI taxonomy with GTDB-Tk nomenclature shown in brackets, and novel clades are named using GTDB-Tk taxonomy. Taxonomic groups containing Brothers volcano MAGs are indicated by blue text, with the number of MAGs shown in parentheses. The scale bar shows expected substitutions per amino acid. The uncollapsed tree used to create this figure is available as SI Appendix, Fig. S4 and at iTOL (29) (https://itol.embl.de/shared/alrlab).

Fig. 6.

The proposed influence of subsurface hydrogeological processes on the microbial phylogenetic and functional diversity associated with Brothers volcano and its hydrothermal systems. Schematic cross-section adapted from de Ronde et al. (9) from southeast to northwest. Overall, the shallow subsurface is influenced by seawater-dominated hydrothermal circulation (blue arrows = recharge; red arrows = discharge). Recharge of seawater occurs both at a volcano scale through the caldera floor and faults along the caldera wall and more locally at the 100- to 200-m scale at the vent sites [see Caratori Tontini et al. (35)]. Red arrows denote heated (modified) seawater after reaction with the rocks; purple arrows represent hot, magmatically influenced fluids; red-brown arrows represent magmatic volatiles. Cross-hatching represents zones of inferred magmatic salt [see de Ronde et al. (9)]. (A) Bubble plots of the average relative abundance of key taxa (NCBI taxonomy) amplicons discussed in the text from each area are shown, with bubble size corresponding to percent average relative abundance (Dataset S1C; UC, n = 3 samples; LC, n = 2 samples; NWC-A, n = 6 samples; NWC-B, n = 3 samples; UCW, n = 2 samples). The average relative abundance of Archaea was calculated separately using only archaeal taxa, and bubble size represents the percent average relative abundance of Archaea (UC, n = 2 samples; LC, n = 2 samples; NWC-A, n = 6 samples; NWC-B, n = 3 samples; UCW, n = 2 samples). (B) Associated enrichment of key functional genes where bubble size corresponds to relative abundances as described for Fig. 3A (Dataset S2B), averaged across samples at each area. Enrichment of carbon dioxide (CO₂), sulfate (SO₄²⁻), magnesium (Mg), hydrogen sulfide (H₂S), iron (Fe) and hydrogen (H₂) and pH shifts are shown for each site (Dataset S1B). The combination of different geochemical environments intersected by the circulating hydrothermal fluids, and different scales of recharge, may explain some of the shifts in diversity of the microbial communities observed at Brothers volcano.