Microbial Hydrocarbon Degradation in Guaymas Basin-Exploring the Roles and Potential Interactions of Fungi and Sulfate-Reducing Bacteria

Abstract

Hydrocarbons are degraded by specialized types of bacteria, archaea, and fungi. Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions, using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system. This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments, and thus selects for diverse hydrocarbon-degrading communities of which methane, alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied. Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments, and draw attention to possible fungal-bacterial interactions. In this Hypothesis and Theory article, we report on background, recent results and outcomes, and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021, and that we will revisit during our ongoing investigations of bacterial, archaeal, and fungal communities in the deep sedimentary subsurface of Guaymas Basin.

Keywords: Guaymas Basin; fungi; hydrocarbon; microbial interaction; sulfate-reducing bacteria.

FIGURE 1

Hydrocarbon-rich hydrothermal sites in Guaymas Basin. (A) Hydrocarbon-soaked concretions at the base of the “Rebecca’s Roost” hydrothermal edifice (27°N00.70′/111°W24.23′). Nearby hydrocarbon-rich sediments were sampled by Deep-sea submersible Alvin in December 2016, and analyzed for geochemical properties and microbial community composition (Alvin core 4870-16, temperatures 31–52°C; Song et al., 2021 and Teske et al., 2021a). (B) Oil-soaked hydrothermal concretions, informally called “Ace chimney” (27°N00.671′/111°W24.262′), sampled in November 2018 during Alvin dives 4994 and 5000, yielding predominately Desulfobacterales in sulfate-reducing enrichments on mixed aromatic hydrocarbons (Supplementary Figure 1 and Supplementary Table 1). (C) Oil-soaked concretions on the eastern approach to Rebecca’s Roost (27°N00.686′/111°W24.379′), sampled in December 2016 during Alvin dive 4872, amended with mixed n-alkanes (C₆–C₁₂) and crude oil, and yielding enrichments of alkane-oxidizing sulfate-reducing bacteria (Desulfobacterales) at 30 and 55°C (Renxing et al., 2021). Photos by Alvin group, Woods Hole Oceanographic Institution.

FIGURE 2

16S rRNA gene distance phylogeny of frequently occurring deltaproteobacterial ASV sequences according to Escherichia coli nucleotide positions 515–926 using forward primer 515F-Y and reverse primer 926R (Ramírez et al., 2021) in hydrothermal sediments of Guaymas Basin, southern axial valley. The branching pattern was checked by 1000 NJ Bootstrap iterations. The tree was rooted with the Desulfofervidales as outgroup. Modified by inferred substrate usage from Ramírez et al. (2021) (Supplements).

FIGURE 3

16S rRNA gene distance phylogeny of frequently occurring deltaproteobacterial ASV sequences according to Escherichia coli nucleotide positions 518–926 using forward primer 518F, and three versions of reverse primer 926R (Teske et al., 2019) in cold shallow subsurface sediments of Guaymas Basin, northwest of the axial valley. The taxon labels refer to number of sequences recovered from piston core 10 and 11 sediment subsections (10-2 = 1.24–1.29 mbsf; 10-4 = 3.73–3.78 mbsf; 11-2 = 1.15–1.20 mbsf). The branching pattern was checked by 1000 NJ Bootstrap iterations. Modified by inferred substrate usage, from Teske et al. (2019) (supplements).

FIGURE 4

Microphotographs of Guaymas Basin fungal strains imaged under fluorescence after calcofluor staining, which highlights the chitin cell walls of fungi. Strains were isolated from Guaymas Basin sediments (Table 1), and images were taken after 40 days of incubation with the polyaromatic substrate naphthalene (5 μg/ml) in co-culture with Desulfobacterales-dominated sulfate-reducing bacteria. Panel (A) shows growth of the filamentous ascomycete fungus Cadophora malorum, and panel (B) shows filamentous arrangement of cells of the yeast-like ascomycete fungus Aureobasidium pullulans.

FIGURE 5

Concept sketch for potential interactions of hydrocarbon-degrading fungi and sulfate-reducing bacteria in Guaymas Basin sediments. (A) Spatially separated, redox-stratified niches for aerobic hydrocarbon-degrading fungi and sulfate-reducing anaerobic bacteria, implying compartmentalized hydrocarbon degradation in distinct steps. (B) Co-occurrence and potential syntrophic associations of hydrocarbon-degrading fungi and sulfate-reducing bacteria in sediments with fluctuating redox gradients, or fully sulfidic conditions, visualized by superimposition of both microphotographs. The fungal isolate used for this sketch is Cladosporium_GB1 (Table 1) grown on naphthalene as sole carbon source; the bacterial image shows Desulfothermus naphthae strain TD3, a thermophilic hexadecane-degrading sulfate reducer from Guaymas Basin sediments (Rüter et al., 1994).