Antibiotic Resistance Genes from Mat and Planktonic Microbiomes of Antarctic Lake Fryxell and Lake Bonney, and a Mat-forming Culture of Rhodoferax antarcticus

The Antarctic Taylor Valley Lakes Fryxell and Bonney harbor oligotrophic microbial communities that are separated geographically from other aquatic systems. Their microbiomes include planktonic as well as lift-off mat communities that float to the underside of the perennial ice cover and eventually emerge at the surface. We investigated the antibiotic resistance genes (ARGs) from metagenomes of lift-off mats emerging from ice, from filtered water samples of Lake Fryxell, and from filtered water samples of Lake Bonney. ARG sequence markers were designed by ShortBRED-Identify using the Comprehensive Antibiotic Resistance Database (CARD). The overall proportion of ARG hits in the metagenomes was found to be similar to that found in temperate-zone rural water bodies with moderate human inputs (0.0002-0.0007%). The specific ARGs found showed distinct distributions for the two lakes, and for mat versus planktonic sources. An enrichment culture of Rhodoferax antarcticus from a Lake Fryxell mat sample showed a mat-forming phenotype not previously reported for this species. Its genome showed no ARGs associated with Betaproteobacteria, but had ARGs consistent with a Pseudomonas minor component. The Antarctic lake mats and water showed specific ARGs distinctive to the mat and water sources, but overall ARG levels were similar to those of temperate water bodies.

Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure

This study characterized a unique cultivated representative of the genus Legionella isolated from an Antarctic lake. This psychrotolerant strain had some common properties of known Legionella species but also displayed other characteristics, such as plasticity in fatty acid composition and an enrichment of mobile genes in the genome.

Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial “dark matter” taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.

Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake

Organic Lake in Antarctica is a marine-derived, cold (−13∘C), stratified (oxic-anoxic), hypersaline (>200 gl–1) system with unusual chemistry (very high levels of dimethylsulfide) that supports the growth of phylogenetically and metabolically diverse microorganisms. Symbionts are not well characterized in Antarctica. However, unicellular eukaryotes are often present in Antarctic lakes and theoretically could harbor endosymbionts. Here, we describe Candidatus Organicella extenuata, a member of the Verrucomicrobia with a highly reduced genome, recovered as a metagenome-assembled genome with genetic code 4 (UGA-to-Trp recoding) from Organic Lake. It is closely related to Candidatus Pinguicocccus supinus (163,218 bp, 205 genes), a newly described cytoplasmic endosymbiont of the freshwater ciliate Euplotes vanleeuwenhoeki (Serra et al., 2020). At 158,228 bp (encoding 194 genes), the genome of Ca. Organicella extenuata is among the smallest known bacterial genomes and similar to the genome of Ca. Pinguicoccus supinus (163,218 bp, 205 genes). Ca. Organicella extenuata retains a capacity for replication, transcription, translation, and protein-folding while lacking any capacity for the biosynthesis of amino acids or vitamins. Notably, the endosymbiont retains a capacity for fatty acid synthesis (type II) and iron–sulfur (Fe-S) cluster assembly. Metagenomic analysis of 150 new metagenomes from Organic Lake and more than 70 other Antarctic aquatic locations revealed a strong correlation in abundance between Ca. Organicella extenuata and a novel ciliate of the genus Euplotes. Like Ca. Pinguicoccus supinus, we infer that Ca. Organicella extenuata is an endosymbiont of Euplotes and hypothesize that both Ca. Organicella extenuata and Ca. Pinguicocccus supinus provide fatty acids and Fe-S clusters to their Euplotes host as the foundation of a mutualistic symbiosis. The discovery of Ca. Organicella extenuata as possessing genetic code 4 illustrates that in addition to identifying endosymbionts by sequencing known symbiotic communities and searching metagenome data using reference endosymbiont genomes, the potential exists to identify novel endosymbionts by searching for unusual coding parameters.

Former bay of the desiccating Aral Sea as the newly formed world’s largest heliothermal lake

<p>The Aral Sea desiccation is the worst aquatic ecological disaster of the last century, important for understanding the worldwide trends to degradation of arid lakes under water use and climate change. Formerly the fourth largest lake worldwide, the Aral Sea has lost ~90% of its water since the early 1960s due to irrigation in its drainage basin. Basing on field observations and numerical simulations, we show that the former bay of the Aral Sea — Chernyshev — turned to a meromictic heliothermal water body with extreme temperature, light and chemical regimes. The heliothermal regime of Chernyshev keeps the deep monimolimnion warm (about 15-16°C) throughout cold winter. Among less than 30 heliothermal waters worldwide, Chernyshev with its area of ~80-90 km<sup>2</sup> is the largest heliothermal lake, the second one being permanently ice-covered Antarctic lake Vanda. Chernyshev is also the youngest heliothermal lake, emerged within the last half-century. Seasonal themal cycle of the basin, scenarios of its formation and possible consequences for the ecosystem are discussed.</p><p>The study is funded by the Russian Foundation for Basic Research (RFBR project № 20-55-12007) and German Research Foundation (DFG KI 853-16/1).</p>

Diverse Biotransformation of Sulfur in Antarctic Lake Sediments

Microbial communities, sulfur isotope of sulfides (δ34SAVS and δ34SCRS) and sulfur and oxygen isotopes of sulfate (δ34SSO4 and δ18OSO4) in sediments were analyzed to study the biotransformation of sulfur in a penguin-affected lake Y2 and a pristine YO from Fildes Peninsula, Antarctic Peninsula. The microbial communities in Y2 were mainly associated with penguin activities, while those in YO were limited by nutrients. The much enriched δ34SSO4 recorded at depth of 30, 41 and 52 cm in Y2 indicates very strong sulfate reduction therein. The sulfur-degrading bacteria Pseudomonas in 0–23 cm of Y2 was 3.5 times as abundant as that of sulfur oxidizing bacteria (SOB), indicating remarkable remineralization of organic sulfur. While abundant SOB and 34S-depleted sulfate indicate considerable sulfur oxidation in 34–56 cm layer in Y2. In YO sediments, the highest abundance of Desulfotalea and the most enriched δ34SSO4 (35.2‰) and δ34SCRS (2.5‰) indicate strongest sulfate reduction in 28 cm layer. High abundance of Pseudomonas indicates active remineralization of organic sulfur in 3–5 cm layer in YO. While the medium δ34SSO4 and considerable abundance of SOB and SRB indicate concurrence of sulfur oxidation and sulfate reduction in other layers in YO. Our results show that high level of organic matter inputs from penguin populations support the diverse microbial community and biotransformation of sulfur in freshwater ecosystems in Antarctica.