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Archaeal Diversity and CO2 Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems 时间:2017-07-04 09:20 来源:未知作者:admin 点击: 次 Abstract:Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of 13CO2 stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO2, while archaeal autotrophy seems to be limited in the groundwater.
1. Introduction
Groundwater ecosystems are known to harbor a large range of prokaryotic diversity [1]. In the subsurface in the absence of light, lithoautotrophic prokaryotes can use inorganic compounds as energy sources, thus producing organic compounds available for heterotrophic prokaryotes. Another strategy for prokaryotes to scavenge for carbon and nutrient sources is to attach to aquifer rock surfaces or particles. However, little is known about the microbial diversity attached to percolated solid surfaces (fractures, pores) or within aquifer rock matrices compared to groundwater [2, 3]. In this study, we assessed archaeal diversity in aquifer and aquitard rocks of a mixed carbonate-/siliciclastic-rock aquifer system, as well as in surface soils, along a transect of monitoring wells in the Hainich Critical Zone Exploratory (CZE) in central Germany. Protists (flagellates, ciliates, and amoeba), fungi, bacteria, and Archaea were previously detected via diversity analyses of Hainich CZE groundwater [4]. Quantitative PCR using 16S rRNA genes indicated that on average, Archaea represented 0.03 to 8.2% of the total microbial population across all sites in the Hainich CZE transect [4]. Archaea typically compose the minority fraction of the microbial community in aquifer habitats. Nonetheless, Archaea have been shown to play an important role in key biogeochemical cycles in marine sediments [5] and terrestrial habitats [6]. Since most of the archaeal community diversity in these habitats has been identified using culture-independent 16S rRNA gene surveys, numerous clades of uncultured Archaea have been described, which are diverse and widespread [7]. Until the recent development of metagenomics, little was known about the metabolism of these uncultured Archaea. New archaeal candidate phyla are being described on a regular basis [7–10]; therefore, our knowledge on the physiology and participation of these uncultured Archaea in their environments is constantly growing. A large majority of the Archaea described in terrestrial aquifers are related to either anaerobic methane oxidizers or methanogenic Archaea [11, 12]. However, other studies have reported the presence of a high number of uncultured archaeal clades [13–18]. Hence, broader archaeal diversity and metabolisms are expected in aquifer ecosystems.
The hill slope well transect of the Hainich CZE passes through a variety of surface land use types, extending from forest (site H1) or unmanaged woodland (national park, site H2) in the Hainich low-mountain ridge area to grassland/cropland (site H3) and cropland agricultural (sites H4 and H5) areas [4] (Figure 1). In the dipping Upper Muschelkalk strata (Middle Triassic), two aquifer assemblages are distinguished in alternating sequence of limestones and marlstones, whose recharge areas are located mainly on the Hainich hill slope. Both superimposed and partially disjointed aquifer assemblages are separated by aquitards, sealing marlstones, leading to substantial differences in their groundwater chemistry. The lower aquifer assemblage (HTL) shows intensive karstification and widened fractures in its single aquifer that allow for faster flow and transport and present variable-dissolved oxygen concentrations [4]. The upper aquifer assemblage, in turn, contains several minor aquifer storeys that are characterized by very low to no dissolved oxygen content (HTU). Moreover, nitrate concentrations are on average lower and ammonium concentrations higher in the upper aquifer assemblage compared to the lower aquifer. Their differences in oxygen availability are probably linked to their respective surface recharge zones and aquifer permeability. Indeed, the aquifers within the upper assemblage receive recharge through the thicker soil cover [4], while the lower aquifer receives quick recharge from the Hainich ridge area characterized by thinner soil cover and forest and woodland land use. Dissolved oxygen was also shown to decrease along the transect following the major flow direction (from sites H1 to H5) [4]. In the downhill direction, the Upper Muschelkalk formations are overlain by younger mixed carbonate/siliciclastic rocks from Lower Keuper and Quarternary age.