Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes

Abstract

The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.

Figure 1. Nilemah transect showing position of microbial mats and metabolic rates measured.

Top panel: schematic showing transect with tide and mat position of the microbial mats investigated in the present study. (A) and (B) In situ depth profiles of oxygen and sulfide concentrations in Shark Bay microbial mats ((A), smooth mats; (B), pustular mats) measured with needle electrodes. Oxygen and sulfide concentrations were measured during peak photosynthesis between noon and 2:00 pm (green symbols and lines) and the end of the night, between 4:00 and 5:00 am (purple symbols and lines). Squares represent oxygen concentrations, triangles represent sulfide concentrations. (C) and (E) Depth profiles of oxygen production and consumption in Shark Bay microbial mats ((C), smooth mats; (E), pustular mats). Oxygen production and consumption were measured ex situ using the light-dark shift technique. Blue bars = oxygen production, orange bars = oxygen consumption. (D) and (F): Two-dimensional distribution of sulfate reduction in Shark Bay mats visualized using the silver foil technique ((D), smooth mats; (F) pustular mats). Trace near the top of the panels indicates the surface of the mats. Pixels indicate locations of sulfate reduction activity; darker pixels represent higher rates. (G) and (H): Time series of methane production in unamended Shark Bay microbial mat slurries ((G), smooth mats; (H) pustular mats), expressed as methane produced per cm mat used for the slurry preparation. Symbols represent average of three replicate bottles. Error bars represent ± one standard deviation.

Figure 2. Archaeal community composition in Shark Bay microbial mats with depth.

(A) Archaeal distribution (class level) in pustular mats at 2 mm depth intervals. (B) PCA biplot of Shark Bay pustular mats microbial community profiles from different depths. Blue lines indicate the direction of increased taxon abundance at class or order level, and the length indicates the degree of correlation of the taxa with community data (C) Archaeal distribution (class level) in smooth mats at 2 mm depth intervals. (D) PCA biplot of Shark Bay smooth mat microbial community profiles from different depths. Blue lines indicate the direction of increased taxon abundance at class or order level, and the length indicates the degree of correlation of the taxa with community data. MBGB - Marine Benthic Group B; DSEG - Deep Sea Euryarchaeotal Group; MCG - Miscellaneous Crenarchaeotal Group; MHVG - Marine Hydrothermal Vent Group.

Figure 3. Methane production in slurries prepared from the surface layer (oxic part) of Shark Bay microbial mats.

(A) Pustular mat. (B) Smooth mat. Symbols used in both panels: squares = control (no additions); diamonds = molybdate; circles = headspace replaced with air daily; triangles = H₂/CO₂ headspace; methane production is expressed per cm mat used for the preparation of the slurries. Symbols represent average of three replicate bottles. Error bars represent ± one standard deviation.

Figure 4. Schematic illustrating some of the key putative microbial interactions occurring in Shark Bay microbial mats inferred from the present study.

Putative interactions are based on archaeal distribution determined by 16S rDNA sequencing and methanogenesis measurements, as well as previous work on bacterial distribution with depth in these microbial mat systems (Wong et al., 2015). (A) Putative key interactions in smooth mats (B) putative key interactions in pustular mats.