Archaeal and Bacterial Communities Respond Differently to Environmental Gradients in Anoxic Sediments of a California Hypersaline Lake,the Salton Sea

Sulfidic, anoxic sediments of the moderately hypersaline Salton Sea contain gradients in salinity and carbon that potentially structure the sedimentary microbial community. We investigated the abundance, community structure, and diversity of Bacteria and Archaea along these gradients to further distinguish the ecologies of these domains outside their established physiological range. Quantitative PCR was used to enumerate 16S rRNA gene abundances of Bacteria, Archaea, and Crenarchaeota. Community structure and diversity were evaluated by terminal restriction fragment length polymorphism (T-RFLP), quantitative analysis of gene (16S rRNA) frequencies of dominant microorganisms, and cloning and sequencing of 16S rRNA. Archaea were numerically dominant at all depths and exhibited a lesser response to environmental gradients than that of Bacteria. The relative abundance of Crenarchaeota was low (0.4 to 22%) at all depths but increased with decreased carbon content and increased salinity. Salinity structured the bacterial community but exerted no significant control on archaeal community structure, which was weakly correlated with total carbon. Partial sequencing of archaeal 16S rRNA genes retrieved from three sediment depths revealed diverse communities of Euryarchaeota and Crenarchaeota, many of which were affiliated with groups previously described from marine sediments. The abundance of these groups across all depths suggests that many putative marine archaeal groups can tolerate elevated salinity (5.0 to 11.8% wt/vol]) and persist under the anaerobic conditions present in Salton Sea sediments. The differential response of archaeal and bacterial communities to salinity and carbon patterns is consistent with the hypothesis that adaptations to energy stress and availability distinguish the ecologies of these domains.The vast majority of cultured Archaea isolates are characterized as extremophiles, which thrive under environmental extremes of temperature, pH, salinity, and oxygen availability. Unlike Bacteria, these organisms are well defined by select physiologies or catabolic activities. Cultivated halophilic archaea are obligate aerobes, and with a few exceptions (58), most 16S rRNA gene sequences affiliated with this physiological group have been recovered primarily from environments with oxygen present. Thermophilic archaea, many of which utilize hydrogen-based metabolisms, have temperature requirements that preclude their survival and growth in more moderate environments. Other archaeal physiological groups include acidophiles, which thrive in acidic and mostly high-temperature environments, the obligate anaerobic methanogens, which are capable of competing with Bacteria when more energetically favorable electron acceptors are not available (i.e., sulfate), and methane-oxidizing archaea, which require methane for energy production. Recent work on several Crenarchaeota isolates points to nitrification as their primary energy metabolism, but these organisms have been detected in cold, predominantly aerobic environments, such as open ocean waters and soil (47), and in hyperthermophilic environments (24).Several archaeal groups identified using only 16S rRNA genes, for which no current isolates exist, have been detected in anaerobic sediments of the marine subsurface (6), estuaries (42), freshwater (46), and salt lakes (29). While their physiology and catabolism remain a source of speculation, the environmental distribution patterns of these mesophilic, presumably anaerobic, groups seemingly exclude the physiological and catabolic types outlined above. That is, the persistence of diverse archaeal populations in anoxic sediments at moderate temperature and salinity and at circumneutral pH with only trace levels of methane strongly suggests that alternative metabolic or physiological activities must characterize these populations.Saline lakes are ubiquitous and can be found on all continents. Although many saline lakes are labeled “extreme” environments, microbial diversity within their sediments is often equivalent to that reported for studies of freshwater and marine systems (28). Most studies of the microbial ecology within saline lakes have focused on gradients within the water column, with very few studies on patterns within the sediments. Specifically, these studies have examined how changes in water column salinity lead to shifts in microbial productivity and diversity (8). However, particle-associated microbial communities are known to differ fundamentally from water column or free-living populations (1, 18). These observed differences could be explained by the type and strength of environmental gradients that microbial communities in sediments experience, as opposed to those encountered by pelagic communities.Sediments contain strong environmental gradients, such as time (e.g., sediment age at depth), nutrient and carbon availability, and the dominant terminal electron-accepting process (TEAP) resulting from the sequential use of available oxidants by the microbial community (41). These gradients can lead to changes in the dominant microbial groups (i.e., a shift from sulfate reducers to methanogens with depth and age). Many saline lakes are highly productive and shallow and experience large fluctuations in water level due to climatic changes or to changes in inflows due to urban and agricultural activities. Changes in lake level can lead to dramatic shifts in mixing regimens, nutrient cycling, and water chemistry. Historic fluctuations in water column salinity are often recorded within the sediments in the form of evaporite deposits, which may act as additional sources of ionic loading of the water column (62). These sedimentary salinity gradients may modulate the metabolic activity of some microbial groups. For example, Oren (44) proposed bioenergetic constraints as a possible explanation for the reduced activity or absence of some microbial groups within high-salinity environments. Thus, saline lake sediments are excellent natural laboratories in which to study changes and adaptations of microbial communities due to large-scale changes in environmental gradients.The Salton Sea is a large (980 km²), eutrophic, moderately hypersaline (48 to 50 g liter⁻¹), terminal lake located 69 m below sea level in the Salton Basin, CA. Several large lakes have formed in the Salton Basin over geologic history, the most recent of which was Lake Cahuilla ca. 300 years ago (7). The current lake was unintentionally created in 1905-1907, when the Colorado River flooded the Salton Basin for a period of 16 months. Profundal sediments are highly sulfidic, and sulfate reduction is suspected to be the dominant TEAP within these sediments (54). Based on elemental analysis (51) and ¹³⁷Cs activity (37) of sediment layers, a depth of ∼22 cm marks the point when flooding of the Salton Basin occurred. Sediment above this depth represents the ca. 102 years of historical change within the Salton Sea, including a shift from a water column salinity of 35 g liter⁻¹ to the hypersaline conditions that currently exist. Sediments below this depth consist of low-carbon, gypsum-rich evaporite deposits that were present on the older dry lake bed prior to the formation of the current lake. A previous study reported several strong geochemical gradients within pore water across this relatively small depth range (62).In this work, a suite of cultivation-independent techniques and geochemical analyses was utilized to correlate shifts in abundance, community structure, and diversity of Archaea and Bacteria in Salton Sea sediments with changes in environmental gradients. Large differences in abundance and community structure patterns of Archaea and Bacteria were found along the gradients. In addition, the majority of archaeal sequences retrieved were affiliated with previously described but as yet uncultivated groups identified from various marine sedimentary environments. This indicates that these groups are able to tolerate the higher salinity and anaerobic conditions characteristic of Salton Sea sediments. Fundamental differences between the metabolic capacities and ecologies of Archaea and Bacteria are discussed to explain these patterns.