Ecology

Fennoscandian shield genomic database (FSGD)The Fennoscandian Shield bedrock contains an abundance of fracture zones with different groundwater characteristics that vary in water source, retention time, chemistry, and connectivity to surface-fed organic compounds (see Supplementary Data 1). The Äspö Hard Rock Laboratory (HRL) and Olkiluoto drillholes were sampled over time, covering a diversity of aquifers representing waters of differing ages and both planktonic and biofilm-associated communities. In order to provide a genome-resolved view of the Fennoscandian Shield bedrock Archaeal and bacterial communities, collected samples were used for an integrated analysis by combining metagenomes (n = 44), single-cell genomes (n = 564), and metatranscriptomes (n = 9) (see detailed statistics for the generated datasets in the Supplementary Data 1 and Supplementary Information). Assembly and binning of the 44 metagenomes (~1.3 TB sequenced data) resulted in the reconstruction of 1278 metagenome-assembled genomes (MAGs; ≥ 50% completeness and ≤ 5% contamination). By augmenting this dataset with 564 sequenced single-cell amplified genomes (SAGs; 114 of which were ≥ 50% complete with ≤ 5% contamination), we present a comprehensive genomic database for the archaeal and bacterial diversity of these oligotrophic deep groundwaters, hereafter referred to as the Fennoscandian Shield genomic database (FSGD; statistics in Fig. 1A & Supplementary Data 2). Phylogenomic reconstruction using reference genomes in the Genome Taxonomy Database (GTDB-TK; release 86) shows that the FSGD MAGs/SAGs span most branches on the prokaryotic tree of life (Fig. 2). Harboring representatives from 53 phyla (152 archaeal MAGs/SAGs in 7 phyla and 1240 bacterial MAGs/SAGs in 46 phyla), the FSGD highlights the remarkable diversity of these oligotrophic deep groundwaters. Apart from the exceptional case of a single-species ecosystem composed of ‘Candidatus Desulforudis audaxviator’ in the fracture fluids of an African gold mine17, other studies of deep groundwaters as well as aquifer sediments have also revealed a notable phylogenetic diversity of the Archaea and Bacteria10,11,18. For example, metagenomic and single-cell genomic analysis of the CO2-driven Crystal geyser (Colorado Plateau, Utah, USA) resulted in reconstructed genomes of 503 archaeal and bacterial species distributed across 104 different phylum-level lineages11.Fig. 1: Overview of the FSGD MAGs and SAGs.Statistics of the metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) of the Fennoscandian Shield Genomic Database (a). The number of genome clusters present in borehole samples (centerline, median; hinge limits, 25 and 75% quartiles; whiskers, 1.5x interquartile range; points, outliers). Numbers on top of each box plot represent the number of metagenomes generated for borehole samples (b). NMDS plot of unweighted binary Jaccard beta-diversities of presence/absence of all FSGD reconstructed MAGs/SAGs (c) and MAG and SAG clusters belonging to the common core microbiome present in both Äspö HRL and Olkiluoto (d). Numbers in the parenthesis show the number of overlapping points. The data used to generate these plots are available in Supplementary Data 4 and the Source Data.Full size imageFig. 2: Phylogenetic diversity of reconstructed MAGs and SAGs of the fennoscandian shield genomic database (FSGD).Genomes present in genome taxonomy database (GTDB) release 86 were used as reference. Archaea and Bacteria phylogenies are represented separately in the top and bottom panels, respectively. MAGs and SAGs of the FSGD are highlighted in red. Legend in front of each number at the bottom of the figure shows the list of taxa in the tree that are marked with the same number.Full size imageClustering reconstructed FSGD MAGs/SAGs into operationally defined prokaryotic species (≥ 95% average nucleotide identity (ANI) and ≥ 70% coverage) produced 598 genome clusters. Based on the GTDB-TK affiliated taxonomy, a single FSGD cluster may represent a novel phylum, whereas at the lower taxonomic levels, the FSGD harbors genome clusters representing seven novel taxa at class, 58 at order, 123 at family, and 345 at the genus levels. In addition, more than 94% of the reconstructed MAGs/SAGs clusters (n = 568) represent novel species with no existing representative in public databases (Supplementary Data 2). Mapping metagenomic reads against genome clusters represented exclusively by SAGs (n = 38, Fig. 1A) revealed that 14 genome clusters (20 SAGs) were not detectable in the metagenomes, suggesting they might represent rare species in the microbial community of the investigated deep groundwaters (Supplementary Data 3).To explore the community composition of different groundwaters and their temporal dynamics, presence/absence patterns were computed by competitively mapping the metagenomics reads against all reconstructed MAGs/SAGs of the FSGD. Contigs were discarded from the mapping results if More

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Thirty-five years after the explosion and meltdown at the Chernobyl Nuclear Power Plant in Ukraine, I study how amphibians in the region have changed, physically and genetically. In 2016, I joined an international research team to do this; since then, I have obtained various grants to continue the work. Chernobyl is a phenomenal place to study rapid evolution. I typically spend two to three weeks in the forests during the frogs’ spring breeding season.When I work in the ‘exclusion zone’, the 4,700 square kilometres around the reactor, I stay in a hostel in Chernobyl (20 kilometres from the reactor site), where we have a field laboratory inside an abandoned building. The radiation in the exclusion zone is roughly 1,000 times lower than at the time of the accident, and there are now two hostels, a bar, a couple of restaurants and a cash machine. In this image, I’m running a blood analysis on one of the tree frogs we have collected. The contamination maps on the wall behind me show that some hotspots of radiation persist.Around 8 p.m., we listen for male tree frogs calling in the field. Wearing chest waders and head lamps, we enter the ponds to gather frogs until 1 or 2 a.m.. Frogs in the exclusion zone are darker than those outside it, thanks to higher levels of melanin, which might be an adaptation that protects them from ionizing radiation. We analyse how much radiation their bodies contain, and tend to find damage to some, often to the liver.Once expected to become a wasteland, the Chernobyl area is now a nature reserve. New species have arrived, including European bison (Bison bonasus) and the wild Przewalski’s horse (Equus ferus przewalskii). We’re beginning to monitor these horses, originally from the Asian steppes: the effects on their health could be a proxy for what happens when humans return. The first 31 horses were released here in 1998, 12 years after the disaster, and it is one of the few places where they continue to live freely.

Nature 595, 464 (2021)
doi: https://doi.org/10.1038/d41586-021-01883-2

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