High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean

Abstract

Species within the genus Alcanivorax are well known hydrocarbon-degraders that propagate quickly in oil spills and natural oil seepage. They are also inhabitants of the deep-sea and have been found in several hydrothermal plumes. However, an in-depth analysis of deep-sea Alcanivorax is currently lacking. In this study, we used multiple culture-independent techniques to analyze the microbial community composition of hydrothermal plumes in the Northern Tonga arc and Northeastern Lau Basin focusing on the autecology of Alcanivorax. The hydrothermal vents feeding the plumes are hosted in an arc volcano (Niua), a rear-arc caldera (Niuatahi) and the Northeast Lau Spreading Centre (Maka). Fluorescence in situ hybridization revealed that Alcanivorax dominated the community at two sites (1210-1565 mbsl), reaching up to 48% relative abundance (3.5 × 10⁴ cells/ml). Through 16S rRNA gene and metagenome analyses, we identified that this pattern was driven by two Alcanivorax species in the plumes of Niuatahi and Maka. Despite no indication for hydrocarbon presence in the plumes of these areas, a high expression of genes involved in hydrocarbon-degradation was observed. We hypothesize that the high abundance and gene expression of Alcanivorax is likely due to yet undiscovered hydrocarbon seepage from the seafloor, potentially resulting from recent volcanic activity in the area. Chain-length and complexity of hydrocarbons, and water depth could be driving niche partitioning in Alcanivorax.

Fig. 1. Relative abundance of 16S rRNA gene amplicon sequence variants (ASVs).

The barchart depicts the taxonomic assignment of all ASVs annotated at the level of genera with 1% relative abundance threshold. Samples are grouped based on the properties of environment sampled, such as: background, plumes of different hydothermal sites such as: Niua North and South, Niuatahi and Maka and rising plume of Niuatahi and Maka. The ASVs were analyzed via a DADA2 pipeline [30].

Fig. 2. Phylogenetic analysis of the Alcanivorax genomes.

The phylogenetic tree is based on an alignment of 120 bacterial marker genes from Alcanivorax MAGs included in GTDB [59], fourteen MAGs from GROS [63] and six MAGs retrieved in this study. The tree was calculated using GTDB-Tk [59]. The isolation source of the cultivated species is given next to the accession numbers. Ca. Porisulfidus was used as an outgroup. The two subgroups exhibited a clear difference in GC content, <60% for Alcanivorax venustensis-related genomes (upper branch) and >63% for A. borkumensis-related genomes (lower branch).

Fig. 3. Expression level of genes in Alcanivorax MAGs.

Reads were recruited from each metatranscriptome, Nn-Site5-wp and Ns-Site6-bp, to the MAGs using BBmap with a 97% minimum identity threshold. Transcripts were normalized by gene length and the total number of reads in each metatranscriptome (TPM). Values shown represent the average TPM derived from two metatranscriptome technical replicates. Gray cells indicate that the gene is missing in the MAG. GH is an abbreviation for glycosyl hydrolases.

Fig. 4. Mapping of TARA Oceans and Malaspina metagenome datasets to Alcanivorax-MAGs.

A Mapping of Tara Oceans metagenomes. B Mapping of Malaspina metagenomes. The gray bar represents the threshold at which MAG presence in the metagenome was not reliable according to TAD80 [63].

Fig. 5. Features of the Niuatahi plume’s microbial community.

A Depiction of the microbial community composition in the rising plume and plume samples. Circles represent the most abundant taxa clarified on the legend on the left hand site. B Alcanivorax aggregates visualized in 3D by ALV461 probe in Nn-Site5-wp sample. C Alcanivorax single cells visualized by Alc461 probe in Ns-Site6-bp sample. Green - CARD-FISH signal; blue - DAPI signal. Imaging was done with a laser scanning microscope (LSM780) equipped with an Airyscan detector. Figure created with BioRender.com.