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Background: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies. Results: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla. Conclusions: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. 62j11owDS1FAqTqkQkf7rC Video Abstract [ABSTRACT FROM AUTHOR]

The origin of the eukaryotic cell and its shared evolutionary history with Archaea are among the hottest topics in modern biology. Recent improvements in cultureindependent genomics and phylogenomic analyses provided compelling evidence in support of the emergence of eukaryotes from within the Archaea. An important step towards revealing the identity and nature of the archaeal ancestor was made following metagenomics-based discovery of the Asgardarchaeota superphylum, a group of uncultivated archaea consisting of Loki-, Thor-, Heimdall- and Odinarchaeia. Their recognition as the closest extant relatives of the eukaryotes has reignited a decades-old debate regarding the topology of the Tree of Life. Moreover, genomic investigations of Asgardarchaeota revealed a plethora of "Eukaryote Signature Proteins" (ESPs), previously thought to be unique to eukaryotes, which may help shed light on the molecular events in early eukaryogenesis. In this work, we briefly review current knowledge about the geographical distribution, phylogeny, ESP content and metabolic capabilities of the highly diverse Asgardarchaeota in an attempt to picture the lifestyle and early evolution of eukaryotes. [ABSTRACT FROM AUTHOR]

In recent years, RNA-sequencing (RNA-Seq) transcriptomics emerged as the standard approach for measuring and comparing gene expression patterns across varying experimental conditions. Although the molecular and biochemical mechanisms underlying metal resistance in prokaryotes have been intensively studied, the RNA-Seq-based assessment of the metal-induced cellular responses could provide broader insights into the engagement of versatile microorganisms possessing rare metabolic capacities (i.e. metal and hypersalinity resistance) in the bioremediation of heavy metal-polluted industrial wastewaters with salinity fluctuation. The transcriptional landscape of the extremely halophilic archaeon Haloferax alexandrinus DSM 27206 cultivated in the presence of increasing AgNO3 concentrations was analyzed by RNA-Seq. Total RNA was extracted using the Zymo Research Direct-zol MiniPrep Kit, followed by cDNA library preparation and sequencing on Illumina Hiseq 2500 PE150 platform (performed by a commercial provider). RNA transcript quantification was performed by the pseudoalignmentbased Salmon software using the Hfx. alexandrinus genome as reference, followed by transcript abundance normalization using the edgeR software package. Preliminary data suggested that exposure to silver influenced transcription patterns of a large set of genes involved in basic metabolic pathways, environment-specific microbial metabolism, and biosynthesis of secondary metabolites. Genes participating in ATP synthesis, cysteine biosynthesis, as well as metallic ions transporters were overexpressed proportionally with increasing AgNO3 concentrations. Cells exposed to highest silver concentrations showed abundant transcripts putatively involved in oxidative stress management, as well as in DNA replication and repair processes. RNA-Seq profiling was employed to compare transcriptomes of silver-stressed Hfx. alexandrinus. We demonstrated that the investigated strain was able to elicit a tailored response to the presence of increasing concentrations of silver salts based on the differential expression of genes mainly associated with energy metabolism, oxidative stress, DNA replication and membrane transport processes. [ABSTRACT FROM AUTHOR]

In this work, we explored the structure of prokaryotic communities inhabiting the sediments of nine lakes with different salinities (from 84 to 344 g L-1) located in Central and South-Eastern Romania. The 16S amplicon sequencing approach combined with geochemical measurements were employed to i) assess local molecular diversity of prokaryotic communities, ii) evaluate the geographical and environmental factors affecting the community composition among sediments of distinct geochemical conditions, and iii) infer key microbial players in the biogeochemical cycling of C, S, and Fe. High relative abundances of 16S rRNA gene reads were assigned to Actinobacteria, Alphaproteobacteria, Bacteroidia, Clostridia, Deltaproteobacteria, Gammaproteobacteria, Mollicutes, and Rhodothermia bacterial classes and to Halobacteria, Thermoplasmata, and Woesearchaeia among the Archaea. Highest richness and diversity were found in sediments containing 96 g L-1 and 300 g L-1 NaCl. Additionally, the analyzed saline sediments appeared to be inhabited by uncultured Bacteria (Gracilibacteria, Marinimicrobia, Omnitrophicaeota, Patescibacteria) and Archaea (Altiarchaeota, Asgardarchaeota, Diapherotrites, Hadesarchaeota) with possible crucial roles in C and S cycling. A microbially-driven Fe cycle could be speculated from the presence of Zetaproteobacteria-affiliated reads in five sediments with different salinities. In conclusion, we provided clues about the microbial diversity and its putative functional capabilities in poorly investigated, saline aquatic habitats. [ABSTRACT FROM AUTHOR]

Toxic levels of heavy metals pose a significant threat on living cells, triggering metabolic strategies that help in adaptation to heavy metal-induced stress. We explored the mechanisms assisting the silver resistance in the extremely halophilic archaeon Halomicrobium mukohataei DSM 12286. The modulatory effects of AgNO3 on the cellular antioxidant systems were assessed by evaluating the malondialdehyde levels, the catalase activity, and the total antioxidant, non-enzymatic capacity. Biosynthesized silver nanoparticles were characterized using UV-VIS spectroscopy, bright-field microscopy, transmission and scanning electron microscopy, energy-dispersive X-ray spectroscopy, dynamic light scattering, and the zeta potential measurement. Additionally, bioinformatic approaches were used to infer putative Cu/Ag-transporters that might mediate the evidenced intracellular accumulation of silver nanoparticles. H. mukohataei was seemingly able to mitigate Ag-induced oxidative stress mainly by using non-enzymatic cellular antioxidants. Additionally, we noted the synthesis of spherical and electrically stable intracellular nanoparticles, with sizes ranging from 20 to 100 nm. It was further speculated that active Ag-resistance in H. mukohataei could be achieved through Ag+ uptake by PIB type ATPases followed by accumulation of silver in its colloidal form. To the best of our knowledge, the present work is the first documentation of intracellular silver accumulation in halophilic Archaea, thus broadening current knowledge on heavy-metal resistance in salt-loving microbes, with implications for their potential uses in biomining or bioremediation strategies. [ABSTRACT FROM AUTHOR]

Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, there are currently very few cultured NOB or representative NOB genome sequences from marine environments. In this study, we employed enrichment culturing and genomic approaches in order to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 (0.1 mM nitrite as optimum) and 30.0 µM (0.3 mM nitrite) nitrite per day, respectively. Each enrichment culture exhibited different tolerance to varying nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserve metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and thus may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla, and suggests that these NOB may play important biogeochemical roles in marine habitats. [ABSTRACT FROM AUTHOR]

Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus , genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K 2 , cbb 3 -type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus , with two new species named " A. lacustris " and " A. fluvialis ". Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota , which is a free-living, slow-growing scavenger in freshwater environments., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)