Rodriguez-Gijon, Alejandro and Nuy, Julia K. and Mehrshad, Maliheh and Buck, Moritz and Schulz, Frederik and Woyke, Tanja and Garcia, Sarahi L.
(2022).
A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.
Frontiers in Microbiology. 12
, 761869
[Article Review/Survey]
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Abstract
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.
Authors/Creators: | Rodriguez-Gijon, Alejandro and Nuy, Julia K. and Mehrshad, Maliheh and Buck, Moritz and Schulz, Frederik and Woyke, Tanja and Garcia, Sarahi L. | ||||||
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Title: | A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy | ||||||
Series Name/Journal: | Frontiers in Microbiology | ||||||
Year of publishing : | 2022 | ||||||
Volume: | 12 | ||||||
Article number: | 761869 | ||||||
Number of Pages: | 9 | ||||||
Publisher: | FRONTIERS MEDIA SA | ||||||
ISSN: | 1664-302X | ||||||
Language: | English | ||||||
Publication Type: | Article Review/Survey | ||||||
Article category: | Scientific peer reviewed | ||||||
Version: | Published version | ||||||
Copyright: | Creative Commons: Attribution 4.0 | ||||||
Full Text Status: | Public | ||||||
Subjects: | (A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109) | ||||||
Keywords: | microbial ecology, genome size, bacteria, archaea, genomics | ||||||
URN:NBN: | urn:nbn:se:slu:epsilon-p-115860 | ||||||
Permanent URL: | http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-115860 | ||||||
Additional ID: |
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ID Code: | 27193 | ||||||
Faculty: | NJ - Fakulteten för naturresurser och jordbruksvetenskap | ||||||
Department: | (NL, NJ) > Dept. of Aquatic Sciences and Assessment | ||||||
Deposited By: | SLUpub Connector | ||||||
Deposited On: | 23 Feb 2022 14:29 | ||||||
Metadata Last Modified: | 23 Feb 2022 14:31 |
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