Taxonomy and functional interactions in upper and bottom waters of an oligotrophic high-mountain deep lake (Redon, Pyrenees) unveiled by microbial metagenomics

Highlights

• High mountain lakes are sensitive systems to external forcing and good sentinels of global changes.

• Unexpected and mostly unseen energy and biomass pathways were found in high mountain Lake Redon.

• Carbon monoxide oxidation and phosphonates processing were important unseen processes.

• A general biogeochemical framework that may operate in sentinel Lake Redon is provided.

Abstract

High mountain lakes are, in general, highly sensitive systems to external forcing and good sentinels of global environmental changes. For a better understanding of internal lake processes, we examined microbial biodiversity and potential biogeochemical interactions in the oligotrophic deep high-mountain Lake Redon (Pyrenees, 2240 m altitude) using shotgun metagenomics. We analyzed the two ends of the range of environmental conditions found in Lake Redon, at 2 and 60 m depths. Bacteria were the most abundant component of the metagenomic reads (>90%) and the diversity indices of both taxonomic (16S and 18S rRNA) and functional (carbon-, nitrogen-, sulfur-, and phosphorous-cycling) related genes were higher in the bottom dark layer than in the upper compartment. A marked segregation was observed both in biodiversity and in the dominant energy and biomass generating pathways between the extremes. The aerobic respiration was mainly dominated by heterotrophic Burkholderiales at the top and Actinobacteria and Burkholderiales at the lake bottom. The potential for an active nitrogen cycle (nitrogen fixation, nitrification, nitrite oxidation, and nitrate reduction) was mainly found at 60 m, and potential for methanogenesis, anaerobic ammonia oxidation and dissimilatory sulfur pathways were only observed there. Some unexpected and mostly unseen energy and biomass pathways were found relevant for the biogeochemical cycling in lake Redon, i.e., those related to carbon monoxide oxidation and phosphonates processing. We provide a general scheme of the main biogeochemical processes that may operate in the sentinel deep Lake Redon. This framework may help for a better understanding of the whole lake metabolism.

Introduction

High mountain lakes are, in general, highly sensitive systems to external forcing and, in some cases, atmospheric depositions closely connected to large-scale environmental changes can be easily detected (Grimalt et al., 2001; Camarero and Catalan, 2012; Triadó-Margarit et al., 2019). Because of its isolation level and highly diluted nature of high mountain waters, the status of some lake indicators such as water temperature, dissolved geochemical compounds, or plankton composition are very good sensors on the remote effects of human-induced perturbations at the ecosystem scale, making these lakes particularly suitable as long-term ecological research field sites and model systems to unveil diffuse impacts of global change (Adrian et al., 2009). Overall, mountain lakes are considered very appropriate sentinels and recorders of past and present environmental changes (Catalan et al., 2006; Williamson et al., 2009). However, the value of lakes as proper sentinels of climate change is closely related to the level of accurate understanding of internal lake processes (Adrian et al., 2009).

Most mountain lakes are relatively shallow, and water is highly transparent (Catalan et al., 2009). Consequently, the trophogenic zone, where primary production is higher than respiration, extends from the top to the bottom of the water column. Only during winter, when snow accumulates on top of the ice cover and light cannot penetrate, the water column becomes tropholithic and heterotrophic processes dominate over autotrophic. The extent and temporal duration of these tropholithic zones are particularly relevant for the in-lake alkalinity generation by processes that constitute a net consumption of anions (Psenner, 1988). The high-mountain Lake Redon (2240 m a.s.l., Pyrenees, Spain) is an extensively studied freshwater system and a good model for deep glacial dimictic lakes (Catalan et al., 2006). In a deep lake, such as Redon, trophogenic and tropholithic zones coexist during summer stratification, because near the bottom light levels are extremely low. Near the surface and near the bottom, Lake Redon holds two of the extremes of the range of conditions that can be found in high-mountain ecosystems. Lake Redon also has a long water renewal time for a high-mountain lake. The average time is four years, and deep layers are estimated to renew every 15 years (Catalan, 1988). Consequently, the water column dynamics is largely influenced by the internal load of nutrients. During the summer and winter (ice cover) stratifications, there is a progressive accumulation of compounds in the deep layers, coming from sinking material and in situ mineralization or diffusion from the highly organic sediments (Catalan et al., 1992). During autumn and spring mixing periods, the accumulated nutrients are brought to the photic zone and used by aerobic phototrophs producing the peaks of primary production in the lake. In contrast, the top layer has low inputs from the small streams flowing into the lake, which usually dries out at the end of summer, and remains isolated by a thick metalimnion from the more productive bottom layers in these lakes, located between 30 and 45 m depths. Therefore, the deep layers are naturally richer in all kind of organic and inorganic compounds involved in the C, N, P and S cycles (Catalan et al., 1992). Conversely, the high UVR in the top layer (Catalan et al., 2006) may enhance the concentration of some unusual compounds that result from photoreactions (Valentine and Zepp, 1993). In essence, all these conditions provide an excellent case to investigate the main features of an integrated view of the carbon, nitrogen, sulfur and phosphorus cycles and on the biogeochemical interactions with the bacterial and archaeal populations inhabiting the lake.

Metagenomics and in-silico metabolic pathway reconstruction is a way to unveil the complexity of the biogeochemical networks (e.g., Tyson et al. (2004)) and to provide solid foundations for the understanding of the microbiological processes in the environment (e.g., Llorens-Mares et al., 2015; Simon et al., 2009). We applied this approach in Lake Redon for a better understanding of the internal lake processes using two composite samples collected from the near surface and from the near bottom, respectively. We aimed to establish a current framework for some of the microbial biogeochemical processes that may help to support the identification of potential future climate and global change signals in the lake. We analyzed the two ends of the range of conditions found in Lake Redon. We hypothesized a limited dissimilatory sulfur cycle, and an important presence and diversity of nitrogen- and phosphorus-cycling genes in order to overcome the nutrient limitation inherent to these oligotrophic systems. We also expected to find unseen metabolic processes in the lake in both of the studied extremes that the particular conditions of high mountain lakes may favor but have been understudied to date.