Single-cell genomics-based analysis reveals a vital ecological role of Thiocapsa sp. LSW in the meromictic Lake Shunet, Siberia

Meromictic lakes usually harbour certain prevailing anoxygenic phototrophic bacteria in their anoxic zone, such as the purple sulfur bacterium (PSB) Thiocapsa sp. LSW (hereafter LSW) in Lake Shunet, Siberia. PSBs have been suggested to play a vital role in carbon, nitrogen and sulfur cycling at the oxic–anoxic interface of stratified lakes; however, the ecological significance of PSBs in the lake remains poorly understood. In this study, we explored the potential ecological role of LSW using a deep-sequencing analysis of single-cell genomics associated with flow cytometry. An approximately 2.7 Mb draft genome was obtained based on the co-assembly of five single-cell genomes. LSW might grow photolithoautotrophically and could play putative roles not only as a carbon fixer and diazotroph, but also as a sulfate reducer/oxidizer in the lake. This study provides insights into the potential ecological role of Thiocapsa sp. in meromictic lakes.

Permanent Thermal and Chemical Stratification in a Restored Urban Meromictic Lake

Meromictic lakes are unique aquatic ecosystems that occur extremely rarely. The phenomenon of meromixis can result from both natural and anthropogenic factors. The aim of this study was to analyse thermal and chemical stratification in a small, deep (6 ha, H max = 24.5 m) lake. The evaluated lake had a typical summer thermal profile with a shallow epilimnion, a sharp thermocline, and a distinct monimolimnion layer in the hypolimnion, which was also maintained during circulation. The lake had a clinograde oxygen profile, with an oxygen deficit in the metalimnion and permanent anoxic conditions in the deeper layers, including during circulation. A redox zone was identified during summer stagnation. The monimolimnion formed a thermally isolated layer at a depth of around 15 m, and the chemocline was situated above the monimolimnion. In the chemocline, the EC gradient ranged from 61 to 77 μS·cm−1 per meter of depth in the summer and from 90 to 130 μS·cm−1 per meter of depth during circulation. EC was significantly correlated with Ca2+ concentration (r2 = 0.549). Chemical stratification, particularly with regard to organic matter distribution, was observed in the chemocline. The monimolimnion severely limited nutrient internal loading.

Distribution of Dissolved Nitrogen Compounds in the Water Column of a Meromictic Subarctic Lake

In order to better understand the biogeochemical cycle of nitrogen in meromictic lakes, which can serve as a model for past aquatic environments, we measured dissolved concentrations of nitrate, nitrite, ammonium, and organic nitrogen in the deep (39 m maximal depth) subarctic Lake Svetloe (NW Russia). The lake is a rare type of freshwater meromictic water body with high concentrations of methane, ferrous iron, and manganese and low concentrations of sulfates and sulfides in the monimolimnion. In the oligotrophic mixolimnion, the concentration of mineral forms of nitrogen decreased in summer compared to winter, likely due to a phytoplankton bloom. The decomposition of the bulk of the organic matter occurs under microaerophilic/anaerobic conditions of the chemocline and is accompanied by the accumulation of nitrogen in the form of N-NH4 in the monimolimnion. We revealed a strong relationship between methane and nitrogen cycles in the chemocline and monimolimnion horizons. The nitrate concentrations in Lake Svetloe varied from 9 to 13 μM throughout the water column. This fact is rare for meromictic lakes, where nitrate concentrations up to 13 µM are found in the monimolimnion zone down to the bottom layers. We hypothesize, in accord with available data for other stratified lakes that under conditions of high concentrations of manganese and ammonium at the boundary of redox conditions and below, anaerobic nitrification with the formation of nitrate occurs. Overall, most of the organic matter in Lake Svetloe undergoes biodegradation essentially under microaerophilic/anaerobic conditions of the chemocline and the monimolimnion. Consequently, the manifestation of the biogeochemical nitrogen cycle is expressed in these horizons in the most vivid and complex relationship with other cycles of elements.

Paleolimnological evidence reveals climate-related preeminence of cyanobacteria in a temperate meromictic lake

Meromictic lakes provide a physically stable environment in which proxies for potentially harmful cyanobacteria are exceptionally well-preserved in the sediments. In Sunfish Lake, a meromictic lake that has recently become the focus of citizen concern due to the apparent rise in cyanobacteria blooms, we used a multi-proxy paleolimnological approach pairing novel spectral (i.e., VNIRS) and molecular (i.e., qPCR) assessment tools to explore long-term cyanobacteria trends. We hypothesized that climate change over the past 50 years altered the Sunfish Lake environment to favour cyanobacteria dominance, resulting in an increased incidence of bloom events. Spectral and genetic results aligned to reveal an unprecedented abundance of cyanobacteria in modern times and coincided with warmer and wetter climatic conditions in the region. Our findings offer evidence for climate-driven shifts in cyanobacteria abundance and suggest that a shift towards warmer and wetter conditions supports the rise of cyanobacteria in lakes.

Distribution of Dissolved Nitrogen Compounds in the Water Column of a Meromictic Subarctic Lake

In order to better understand the biogeochemical cycle of nitrogen in meromictic lakes, which can serve as a model for past aquatic environments, we measured dissolved concentrations of nitrate, nitrite, ammonium and organic nitrogen in deep (39 m maximal depth) subarctic Lake Svetloe (NW Russia). The lake is a rare type of freshwater meromictic water boy with high concentrations of methane, ferrous iron, manganese and low concentrations of sulfates and sulfides in the monimolimnion. In the oligotrophic mixolimnion, the concentration of mineral forms of nitrogen decreased in summer compared to winter, likely due to phytoplankton bloom. The decomposition of the bulk of organic matter occurs under microaerophilic/anaerobic conditions of the chemocline and accompanied by the accumulation of nitrogen in the form of N-NH4 in the monimonimlion. We revealed a strong relationship between methane and nitrogen cycles in the chemocline and monimolimnion horizons. The nitrate concentrations in Lake Svetloe varied in the range from 9 to 13 μM throughout the water column. This fact is rare for meromictic lakes, where nitrate concentrations up to 13 µM are found in the monimolimnion zone down to the bottom layers. We hypothesize, in accord with available data for other stratified lakes, that under conditions of high concentrations of manganese and ammonium at the boundary of redox conditions and below, anaerobic nitrification with the formation of nitrates occurs. Overall, most of organic matter in Lake Svetloe undergoes biodegradation essentially under microaerophilic/anaerobic conditions of the chemocline and the monimolimnion. Consequently, the manifestation of the biogeochemical nitrogen cycle is expressed in these horizons in the most vivid and complex relationship with other cycles of elements.

Discovery of Siderophore and Metallophore Production in the Aerobic Anoxygenic Phototrophs

Aerobic anoxygenic phototrophs have been isolated from a rich variety of environments including marine ecosystems, freshwater and meromictic lakes, hypersaline springs, and biological soil crusts, all in the hopes of understanding their ecological niche. Over 100 isolates were chosen for this study, representing 44 species from 27 genera. Interactions with Fe3+ and other metal(loid) cations such as Mg2+, V3+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Se4+ and Te2+ were tested using a chromeazurol S assay to detect siderophore or metallophore production, respectively. Representatives from 20 species in 14 genera of α-Proteobacteria, or 30% of strains, produced highly diffusible siderophores that could bind one or more metal(loid)s, with activity strength as follows: Fe > Zn > V > Te > Cu > Mn > Mg > Se > Ni > Co. In addition, γ-proteobacterial Chromocurvus halotolerans, strain EG19 excreted a brown compound into growth medium, which was purified and confirmed to act as a siderophore. It had an approximate size of ~341 Da and drew similarities to the siderophore rhodotorulic acid, a member of the hydroxamate group, previously found only among yeasts. This study is the first to discover siderophore production to be widespread among the aerobic anoxygenic phototrophs, which may be another key method of metal(loid) chelation and potential detoxification within their environments.