The chemosynthetic biofilm microbiome of deep-sea hydrothermal vents across space and time

Abstract

Microbial biofilms colonize mineral and biological substrates exposed to fluid circulation at deep-sea hydrothermal vents, providing a biologically active interface along redox boundaries. Since many biofilms at deep-sea vents are associated with invertebrates, microbial distribution and abundance are not only constrained by local fluid geochemistry, but also through host-microbe interactions. This study examined the spatial distribution and diversity of established microbial biofilm communities collected from three distinct biological regimes characteristic of the East Pacific Rise (9°50 N, 104°17 W) vent system, as well as newly established biofilms on experimental microbial colonization devices. Transcripts from 16S rRNA-based amplicon sequencing revealed that Campylobacterota of the Sulfurimonas and Sulfurovum genera dominated newly-formed biofilms across all biological regimes. Statistical analyses using environmental chemistry data from each sampling site suggest that community composition is significantly impacted by biofilm age, temperature and sulfide concentration ranges, and to a lesser extent, locality. Further, metatranscriptomic analyses were used to investigate changes in community gene expression between seafloor and subseafloor biofilms. Our findings revealed differences in the type and abundance of transcripts related to respiratory pathways, carbon fixation and reactive oxygen species (ROS) detoxification. Overall, this study provides a novel conceptual framework for evaluating biofilm structure and function at deep-sea vents by showing a transition from a niche-specific pioneer microbial community in newly-formed biofilms, to a complex population of increased diversity in established biofilms and by identifying key changes in gene expression in taxonomically similar biofilms during the transition from the shallow subseafloor to the seafloor.

Keywords: Sulfurimonas; Sulfurovum; Biofilms; Campylobacterota; Chemosynthesis; Deep-sea hydrothermal vents; Metatranscriptome; Succession.

Fig. 1

Multivariate polygons plots (https://github.com/giovannellilab/polygonPlot) showing the environmental temperature, pH, and H₂S concentration boundaries observed for the six bioregimes (polygons) (A) and boxplots of Shannon–Wiener alpha diversity index of deep-sea hydrothermal vent-associated microbial communities, sorted from lowest to highest, and colored by the bioregime (B)

Fig. 2

UPGMA (unweighted pair group method with arithmetic mean) cluster analysis of hydrothermal vent-associated microbial communities (using the Euclidean algorithm) based on weighted Unifrac distances between samples shows clustering by substrate-type, and bioregime. Relative abundances of dominant taxa based on the 16S rRNA gene sequences (ASVs > 1%) of microbial communities from deep-sea hydrothermal vent bioregimes displayed from left to right phylum-level, (middle) class-level, and genus-level of reads, respectively

Fig. 3

Principal Coordinate Analysis (PCoA) ordination of the hydrothermal vent-associated microbial communities based on the weighted Jaccard dissimilarity index. Ordisurf models for temperature (left) and sulfide concentration (right) were overlapped on the PCoA where samples are colored by bioregime and shaped by substrate (A); PCoA showing the two foundation taxa Campylobacteria (orange) and Gammaproteobacteria (blue) displayed along with the vector fitting for temperature and sulfide concentration; each dot represents an ASV related to the Campylobacteria (orange) and to the Gammaproteobacteria (blue) (B)

Fig. 4

Venn diagrams showing the abundance of ASVs shared among—and unique to—the biofilms associated with the Riftia, Alvinella and mussel bioregimes (A). Age-related (established and newly-formed), within-bioregime abundance of ASVs (B). Taxonomic affiliations of the most abundant (> 1%) ASVs specific to the established biofilms in each bioregime (C)

Fig. 5

Metatranscriptome analysis of seafloor and subseafloor microbial biofilms from the Crab Spa vent site. Taxonomic affiliation of transcripts (relative abundance of taxa per transcript) from the seafloor (1) and subseafloor (4) biofilms. Bubble plots of transcripts (italics) scaled according to transcripts per million (TPM) for the seafloor (2) and subsurface (3) biofilms; For clarity, the respective transcript-encoded enzymes are also shown