Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin

Abstract

Oceanic basalts host diverse microbial communities with various metabolisms involved in C, N, S, and Fe biogeochemical cycles which may contribute to mineral and glass alteration processes at, and below the seafloor. In order to study the microbial colonization on basaltic glasses and their potential biotic/abiotic weathering products, two colonization modules called AISICS ("Autonomous in situ Instrumented Colonization System") were deployed in hydrothermal deep-sea sediments at the Guaymas Basin for 8 days and 22 days. Each AISICS module contained 18 colonizers (including sterile controls) filled with basaltic glasses of contrasting composition. Chemical analyses of ambient fluids sampled through the colonizers showed a greater contribution of hydrothermal fluids (maximum temperature 57.6°C) for the module deployed during the longer time period. For each colonizer, the phylogenetic diversity and metabolic function of bacterial and archaeal communities were explored using a molecular approach by cloning and sequencing. Results showed large microbial diversity in all colonizers. The bacterial distribution was primarily linked to the deployment duration, as well as the depth for the short deployment time module. Some 16s rRNA sequences formed a new cluster of Epsilonproteobacteria. Within the Archaea the retrieved diversity could not be linked to either duration, depth or substrata. However, mcrA gene sequences belonging to the ANME-1 mcrA-guaymas cluster were found sometimes associated with their putative sulfate-reducers syntrophs depending on the colonizers. Although no specific glass alteration texture was identified, nano-crystals of barite and pyrite were observed in close association with organic matter, suggesting a possible biological mediation. This study gives new insights into the colonization steps of volcanic rock substrates and the capability of microbial communities to exploit new environmental conditions.

Keywords: Guaymas basin; basalt alteration; colonization module; hydrothermal systems; organic-rich sediment.

Figure 1

Schematic diagram illustrating the deployment of the in situ AISICS module at Mat Mound site. (1) Bathymetric map showing the location of Mat Mound site in the Southern Trough of the Guaymas Basin; (2) Mat Mound site exhibiting microbial mats and macro-fauna dominated by Riftia tub tube worms (Siboglinidae); (photo taken with the submersible Nautile during the BIG cruise, Dive 1745); (3) AISICS module covered by its lid before its deployment; (4) AISICS module without its lid before its deployment; (5) Diagram illustrating the internal structure of the incubator with biotic (α) and abiotic (β) mini-colonizers distributed per floor; the central titanium sheath containing the Micrel temperature sensor (γ) and the fluid sample probe (δ) hosted in a titanium sheath are placed in the middle of the incubator and are connected to the instrumented base; (6) The deployment site of AISICS1 and 2; (7) The deployed AISICS1 (photo was taken with the submersible Nautile during the BIG cruise, Dives 1745); (8) The deployed AISICS2 (photo was taken with the submersible Nautile during the BIG cruise, Dives 1763); (A) instrumented module; (B) cylindrical insulated chamber; (C) sampling pipes and temperature probe; (D) incubator; (E) sampling pouches, and (F) electronics.

Figure 2

Archaeal communities associated with the AISICS 1 and 2 mini-colonizers according the depth (i.e., position within the colonizer) and type of substratum for each colonization module. (A) Jackknife environment cluster tree (made using the weighted UniFrac metric, based 16S rRNA gene sequences determined by neighbor-joining tree) showing the phylogenetic relationships among the archaeal lineages detected in each AISICS 1 and 2 mini-colonizers according the depth and substrata. The jackknife statistical analysis was done with one hundred replicates; the jackknife value was tagged near their corresponding nodes (values higher 50%). The scale bar corresponds, in the Unifrac unit, to the distance between the different habitats. (B) Proportions of archaeal groups within the clone libraries obtained from each AISICS 1 and 2 mini-colonizers.

Figure 3

Bacterial communities associated with the AISICS 1 and 2 mini-colonizers according the depth (i.e., position within the colonizer) and type of substratum for each colonization module. (A) Jackknife environment cluster tree (made using the weighted UniFrac metric, based 16S rRNA gene sequences determined by neighbor-joining tree) showing the phylogenetic relationships among the bacterial lineages detected in each AISICS 1 and 2 mini-colonizers, according the depth and substrata. The jackknife statistical analysis was done with one hundred replicates; the jackknife value was tagged near their corresponding nodes (values higher 50%). The scale bar corresponds, in the Unifrac unit, to the distance between the different habitats. (B) Proportions of bacterial groups based on the frequency of 16S rRNA gene in clone libraries obtained from each AISICS 1 and 2 mini-colonizers.

Figure 4

Neighbor-joining phylogenetic tree of the Epsilonproteobacteria, based on the 16S rRNA gene sequences. Bootstrap values above 50% (from 1000 bootstrap samples) are indicated near their corresponding nodes. In Yellow, the cluster of Epsilonproteobacteria cluster Guaymas; Thermales were used as outgroup.

Figure 5

Neighbor-joining phylogenetic tree of mcrA gene sequences. Bootstrap values above 50% based on 1000 replicates are displayed.

Figure 6

Neighbor-joining phylogenetic tree of predicted amino acid translations of partial dsrAB gene. Bootstrap values above 50% based on 1000 replicates are reported.

Figure 7

Scanning electron microscopy photographs of basaltic glasses exposed to biotic conditions in AISICS1 module. (A) vesicle filled with nano-pyrite on natural basaltic glass; (B) vesicle containing cell like structures and pyrite grains on natural basaltic glass; (C) heap of organic matter and diatoms with barite nano-crystals encrusted in organic matter; (D) magnified of organic matter heaps with barite nano-crystals surrounded by salts.

Figure 8

Scanning electron microscopy photographs of natural basaltic glasses exposed to biotic condition in AISICS1 module showing in (A) cell-like structures and pyrite crystal inside a vesicle, in (B) cell-like structures, diatoms, and filaments at the glass surface and in (C) cell-like structure and pyrite crystal inside a vesicle.

Figure 9

Raman spectra on basaltic glasses exposed to biotic conditions. (A) Raman spectra (spect.1 and spect.2) at the surface of ⁵⁷Fe-doped synthetic basaltic glass showing the characteristic bands of disordered organic matter around 1360–1580 cm⁻¹, along with aliphatic stretching between 2800–3000 cm⁻¹, that could correspond to degraded microbial mat observed as aggregate at the surface. (B) Raman spectra (spect.1 and spect.2) inside a vesicle from natural basaltic glass showing similarly the presence of variably-degraded organic matter with typical bands around 1360–1580 cm⁻¹, and between 2800–3000 cm⁻¹ which could correspond to microbial mat, and two vibrational bands at 334 and 369 cm⁻¹ assigned to pyrite.

Figure 10

Schematic diagram showing the different pathways for pyrite formation in both biotic and abiotic mini-colonizers.