AUTHOR=Rodríguez-Gijón Alejandro , Nuy Julia K. , Mehrshad Maliheh , Buck Moritz , Schulz Frederik , Woyke Tanja , Garcia Sarahi L. 

TITLE=A Genomic Perspective Across Earth’s Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 12 - 2021

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.761869

DOI=10.3389/fmicb.2021.761869

ISSN=1664-302X

ABSTRACT=Our view of genome size in Archaea and Bacteria has remained skewed with data dominated by genomes of microorganisms cultivated under laboratory settings. However, the continuous effort to catalog Earth’s microbiome 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 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 Mbp 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 3Mbp. 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 using 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. In summary, despite biases, the estimated genome size of MAGs offers valuable insights. Finally, to better understand the ecological drivers of genome size, we discuss the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.