New results of a palynological study of the Lake Doroninskoe sediments (Eastern Siberia, Transbaikalia)

This article presents the results of the study of the bottom sediments of the meromictic Lake Doroninskoe. For the study, the method of spore-pollen analysis was used. The record showed that during the accumulation of 65 cm of the sediment layer in the Chita-Ingodinskaya depression, pine and larch predominated along the ridges, with steppe and meadow associations in the lower parts of the depression. According to regional correlations, the distribution of light-coniferous-taiga vegetation in Transbaikalia occurred as early as the Middle Holocene, and it did not undergo cardinal changes until modern times. According to these data, sediments may have accumulated during this time period.

Bacterial, phytoplankton, and viral dynamics of meromictic Lake Cadagno offer insights into the Proterozoic ocean microbial loop

Meromictic Lake Cadagno, with its permanent stratification and persistent microbial bloom within the anoxic chemocline, serves as an ancient ocean analogue. Although the lake has been studied for over 25 years, the absence of simultaneous study of the bacteria, phytoplankton, and viruses, together with primary and secondary productivity, has hindered a comprehensive understanding of its microbial food web. This study evaluated the identities, abundances, and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified depths of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested high abundances of eukaryotic phytoplankton, primarily Chlorophyta, through the water column. Of these, a close relative of Ankyra judayi, a high-alpine adapted chlorophyte, peaked with oxygen in the mixolimnion, while Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. Chromatium, a genus of anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline, suggesting anoxygenic primary producers depended on heterotrophic nutrient remineralization. Virus-to-microbe ratios (VMR) peaked in the zone of high phytoplankton abundances, yet were at a minimum at the peak of Chromatium, dynamic trends that suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical dynamics of Lake Cadagno, this study provides a new perspective on the biological and geochemical connections that comprised the food webs of the Proterozoic ocean.

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.

Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach

Most of Earth’s bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning are usually highly fragmented genomes with heterogeneous sequence contamination. In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs—six novel bacterial orders, 20 families, 66 genera, and 154 species—from Lake Shunet, a secluded meromictic lake in Siberia. With our workflow, the average N50 of reconstructed MAGs greatly increased 10–40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia.

Complete and high-quality genomes of novel microbial species from a meromictic lake using a workflow combining long- and short-read sequencing platforms

Background: Most of Earth's bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning methods are usually highly fragmented genomes with heterogeneous sequence contamination, and this affects the accuracy and sensitivity of genomic analyses. Though the maturation of long-read sequencing technologies provides a good opportunity to fix the problem of highly fragmented MAGs as mentioned above, the method's error-prone nature causes severe problems of long-read-alone metagenomics. Hence, methods are urgently needed to retrieve MAGs by a combination of both long- and short-read technologies to advance genome-centric metagenomics. Results: In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs-six novel bacterial orders, 20 families, 66 genera, and 154 species-from Lake Shunet, a secluded meromictic lake in Siberia. Those new MAGs were underrepresented or undetectable in other MAGs studies using metagenomes from human or other common organisms or habitats. Using this newly developed workflow and strategy, the average N50 of reconstructed MAGs greatly increased 10-40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets, five of which belong to novel species. We used these as examples to demonstrate many novel and intriguing genomic characteristics discovered in these newly complete genomes and proved the importance of high-quality complete MAGs in microbial genomics and metagenomics studies. Conclusions: The results show that it is feasible to apply our workflow with a few additional long reads to recover numerous complete and high-quality MAGs from short-read metagenomes of high microbial diversity environment samples. The unique features we identified from five complete genomes highlight the robustness of this method in genome-centric metagenomic research. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia and broadens our knowledge by adding new genomic characteristics of bacteria. It demonstrates a strong need to recover MAGs from diverse unexplored habitats in the search for microbial dark matter.

Long Term Sediment Modification Effects after Applications of P Inactivation Method in Meromictic Lake (Starodworskie Lake, Olsztyn Lakeland, Poland)

Lake restoration is a part of geoengineering, which is a useful tool for landscape management. The phosphorus inactivation method is one of the most popular lake restoration methods. Using chemical compounds for P binding is leading to the creation of sediment “active layer”, which should show higher P adsorption abilities, compared to non-modified sediment. Howewer, it provides rather little information, how long the modified sediment remains active, and whether it is effective in continuous P binding. Lake meromixis is not commonly observed phenomenon, and sediment located in monimolimnion area is subjected long term anoxia. Therefore, observation of “active layer” in a meromictic lake can give very important data about durability of restoration effects. The object of our study was meromictic Starodworskie Lake (5.57 ha, max. depth 24.5 m), located in Olsztyn Lakeland, Poland. In the past the analyzed lake was subjected to various restoration methods, and phosphorus inactivation method by alum use (1994–1995) was the last used treatment type. The mixing regime of this lake had changed from bradimictic (before and during restoration time) into durable meromictic (post-restoration period). The research made two decades after implementing of P inactivation showed the presence of “active” sediment layer 10–15 cm below sediment surface. This sediment layer showed much higher content of P bound to aluminum, compared to surficial sediment layer. P binding molar ratio was assessed and amounted to 16.1 straightly after restoration and 6.1 after 21 years. This fraction amounts were higher that the values noted before restoration (ca. 358% higher than in 1994 and during restoration (ca. 86% higher than in 1995), which was probably the effect of continuous phosphorus adsorption by “active layer” in post-restoration period.

Holocene phototrophic community and anoxia dynamics in meromictic Lake Jaczno (NE Poland) using high-resolution hyperspectral imaging and HPLC data

Global spread of hypoxia and less frequent mixing in lakes is a major growing environmental concern. Climate change and human impact are expected to increasingly deteriorate aquatic ecosystems. The study of processes and drivers of such changes in the past provides a great asset for prevention and remediation in the future. We used a multiproxy approach combining high-resolution bulk pigment data measured by hyperspectral imaging (HSI) with lower-resolution specific chlorophyll types and carotenoids measured by HPLC to examine Holocene trophic state changes and anoxia evolution in the meromictic Lake Jaczno, NE Poland. A redundancy analysis (RDA) including pollen-inferred vegetation cover, temperature and human impacts provides insight into specific conditions and drivers of changing trophic and redox states in the lake. Anoxic and sulfidic conditions were established in Lake Jaczno after initial basin infilling 9500 years ago. Until 6700 cal BP, lake trophy was relatively low, water turbidity was high and green sulfur bacteria (GSB) were abundant within the phototrophic community, suggesting a deep oxic–anoxic boundary and weak stratification. The period between 6700–500 cal BP is characterized by constantly increasing lake production and a gradual shift from GSB to purple sulfur bacteria (PSB), suggesting a shallower oxic–anoxic boundary and pronounced stratification. Yet, the presence of spheroidene and speroidenone in the sediments indicates intermittent anoxia. After 500 cal BP, increasing human impact, deforestation and intensive agriculture promoted lake eutrophication, with a shift to PSB dominance and establishment of permanent anoxia and meromixis. Our study unambiguously documents the legacy of human impact on processes determining eutrophication and anoxia.

Anoxygenic photo- and chemosynthesis of phototrophic sulfur bacteria from an alpine meromictic lake

Meromictic lakes are interesting ecosystems to study anaerobic microorganisms due their permanent stratification allowing the formation of a stable anoxic environment. The crenogenic meromictic Lake Cadagno harbors an important community of anoxygenic phototrophic sulfur bacteria responsible for almost half of its total productivity. Besides their ability to fix CO2 through photosynthesis, these microorganisms also showed high rates of dark carbon fixation via chemosyntesis. Here, we grew in pure cultures three populations of anoxygenic phototrophic sulfur bacteria previously isolated from the lake, accounting for 72.8% of the total microbial community, and exibiting different phenotypes: 1) the motile, large-celled purple sulfur bacterium (PSB) Chromatium okenii, 2) the small-celled PSB Thiodictyon syntrophicum, and 3) the green sulfur bacterium (GSB) Chlorobium phaeobacteroides. We measured their ability to fix CO2 through photo- and chemo-synthesis, both in situ in the lake and in laboratory under different incubation conditions. We also evaluated the efficiency and velocity of H2S photo-oxidation, an important reaction in the anoxygenic photosynthesis process. Our results confirm that phototrophic sulfur bacteria strongly fix CO2 in the presence of light and that oxygen increases chemosynthesis at night, in laboratory conditions. Moreover, substancial differences were displayed between the three selected populations in terms of activity and abundance.