Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth’s microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies. 

While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems. 

Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake Mälaren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake Mälaren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes.

While genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity, the link between ubiquity, relative abundance and genome size in freshwater prokaryotes has not been investigated comprehensively beyond specific case studies. Here, we provide the first systematic evaluation at a global scale of the ecological implications of genome size variability in the abundance, prevalence, co-occurrence and biosynthesis of essential metabolites in freshwater Archaea and Bacteria. In this work, we leveraged 80,561 medium-to-high quality genomes (>50% completeness and <5% contamination) to investigate the ecological implications of genome size variability across freshwater prokaryotes. This dataset of genomes was de-replicated into 24,050 species-level clusters (ANI >95%), and mapped against a manually curated dataset 636 freshwater metagenomes distributed across the globe to estimate their relative abundance and prevalence. Our results show the presence of 9,028 species-clusters on at least one metagenomic sample. Their estimated genome size correlated negatively with their prevalence and relative abundance, indicating that reduced genomes are found in a larger number of freshwater metagenomes and at larger relative abundances than prokaryotic genomes of bigger size. By inferring a co-occurrence network, we also observed that prokaryotes with reduced genomes and high prevalence tend to co-occur in cohorts. Metabolic annotation shows that these co-occurrence cohorts might be supported by the exchange of essential metabolites (either passive or active), as observed the vitamin B12. Lastly, we hypothesize that prokaryotes with reduced genomes could follow two different strategies, either by increasing their coding density and compacting their genomes, or by losing a large number of the functions involved in catabolism and structure.

Genome size variability reflects ecological patterns in aquatic bacterial phyla, but the interplay at the genus level between the environment and different genomic features such as genomic islands and metabolic potential, is still to be explored. In this work, we selected 340 publicly available high-quality genomes (>90% completeness and <5% contamination, including MAGs and genomes from isolates) from genus Rhodoferax (family Burkholderaceae) to better understand the implications of intragenus genome size variability. To explore the importance of genomic islands, we complemented this dataset with high-quality genomes from other six bacterial genera present in freshwaters. We found that not only bacterial genera with larger average estimated genome sizes (such as Mycobacterium, Rhodoferax and Flavypsychrobacter) are more variable in genome size, but they also contain more genomic islands and they span for larger segments of the genome than genera with more reduced genomes. Moreover, we observed that genus Rhodoferax hosts 96 different species-level clusters (ANI >95% similarity) with average estimated genome sizes ranging from 2.41 Mbp to 6.92 Mbp, distributed mainly in freshwater environments, but also across terrestrial and host-associated. The metabolic potential and completeness of biosynthetic pathways for essential metabolites of these genomes are linked with their estimated genome sizes, indicating that Rhodoferax species-clusters with larger genomes contain less auxotrophies and more metabolic capabilities, such as for nitrogen cycling. Lastly, we observed that Rhodoferax species-clusters are present across global freshwater lakes, with the only exception of the African continent, and are abundant at different depths in freshwater lakes, reaching relative abundances of up to 20.4% in lake Lomtjärnan (Sweden). Overall, the genus Rhodoferax is a highly diverse and prevalent freshwater genus and offers valuable insights to understand the importance of genome size variability in freshwater Bacteria.