Niche differentiation among sulfur-oxidizing bacterial populations in cave waters

Abstract

The sulfidic Frasassi cave system affords a unique opportunity to investigate niche relationships among sulfur-oxidizing bacteria, including epsilonproteobacterial clades with no cultivated representatives. Oxygen and sulfide concentrations in the cave waters range over more than two orders of magnitude as a result of seasonally and spatially variable dilution of the sulfidic groundwater. A full-cycle rRNA approach was used to quantify dominant populations in biofilms collected in both diluted and undiluted zones. Sulfide concentration profiles within biofilms were obtained in situ using microelectrode voltammetry. Populations in rock-attached streamers depended on the sulfide/oxygen supply ratio of bulk water (r ¼ 0.97; Po0.0001). Filamentous epsilonproteobacteria dominated at high sulfide to oxygen ratios (4150), whereas Thiothrix dominated at low ratios (o75). In contrast, Beggiatoa was the dominant group in biofilms at the sediment-water interface regardless of sulfide and oxygen concentrations or supply ratio. Our results highlight the versatility and ecological success of Beggiatoa in diffusion-controlled niches, and demonstrate that high sulfide/oxygen ratios in turbulent water are important for the growth of filamentous epsilonproteobacteria.

A novel symbiosis between chemoautotrophic bacteria and a freshwater cave amphipod

“…N. ictus appears to confer a similar benefit to its epibiotic bacteria. In Frasassi waters, free-living Thiothrix are numerically dominant microbial populations only in turbulent, high oxygen, low sulfide niches (Macalady et al, 2008). In contrast, the N. ictus epibionts flourish along with their hosts in streams and lakes with a much broader range of sulfide and oxygen concentrations and water flow characteristics.…”

“…Amphipods throughout the large cave system are colonized by a single phylotype of Thiothrix that is extremely rare or absent in stream biofilms (Table 1). Several types of filamentous sulfur-oxidizing bacteria abundant in the Frasassi ecosystem are adapted to life in flowing water and attach themselves to surfaces using structures called 'holdfasts' (Campbell et al, 2006;Macalady et al, 2008). These clades include Thiothrix and filamentous e-proteobacteria, both of which form thick mats in N. ictus habitats.…”

“…For a detailed description of the geochemistry and microbial communities within the cave system, please refer to Macalady et al (2008) and Macalady et al (2006) Supplementary Figure 2 for map of the Frasassi cave system and location of collection sites). Samples for FISH and clone library construction were collected into sterile tubes, stored on ice, and transferred to four parts RNAlater (Ambion/ Applied Biosystems, Foster City, CA, USA) to one part sample (v/v) within 4-6 h after collection, and stored at À20 1C until further analysis.…”

“…N. ictus individuals used for scanning electron microscopy were transferred to a 2.5% glutaraldehyde solution made in phosphate buffer saline (PBS), and stored at 4 1C until analysis. Dissolved sulfide and oxygen concentrations of cave waters at the various study sites were determined as described earlier (Macalady et al, 2008).…”

“…Detailed studies conducted earlier by our group revealed that the biofilms are predominantly composed of sulfurcycling bacteria within the b-, d-, g-, and e-proteobacterial clades (Macalady et al, 2006). Specifically, filamentous Thiothrix, Beggiatoa, and e-proteobacteria dominate the biomass of microbial biofilms, inhabiting separate niches defined by water chemistry and stream flow characteristics (Macalady et al, 2008).…”