Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms - the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the origin of mitochondria. However, most of our knowledge about the evolution and functions of eukaryotic symbioses comes from the study of animal hosts, which represent only a small subset of eukaryotic diversity. Here, we take a broad view of bacterial and archaeal symbioses with protist hosts, focusing on their evolution, ecology, and cell biology, and also explore what functions (if any) the symbionts provide to their hosts. With the immense diversity of protist symbioses starting to come into focus, we can now begin to see how these systems will impact symbiosis theory more broadly.
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http://dx.doi.org/10.1016/j.cub.2021.05.049 | DOI Listing |
Environ Microbiome
January 2025
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
Background: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored.
View Article and Find Full Text PDFGenome Res
January 2025
Centro de Astrobiología (CAB), CSIC-INTA, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza
Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short and long terms.
View Article and Find Full Text PDFCRISPR J
January 2025
Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA.
Bacteria and archaea acquire resistance to genetic parasites by preferentially integrating short fragments of foreign DNA at one end of a Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR). "Leader" DNA upstream of CRISPR loci regulates transcription and foreign DNA integration into the CRISPR. Here, we analyze 37,477 CRISPRs from 39,277 bacterial and 556 archaeal genomes to identify conserved sequence motifs in CRISPR leaders.
View Article and Find Full Text PDFSci Rep
January 2025
Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi'an, 710061, Shaanxi, China.
Bacteria, fungi, archaea, and viruses are reflective organisms that indicate soil health. Investigating the impact of crude oil pollution on the community structure and interactions among bacteria, fungi, archaea, and viruses in Calamagrostis epigejos soil can provide theoretical support for remediating crude oil pollution in Calamagrostis epigejos ecosystems. In this study, Calamagrostis epigejos was selected as the research subject and subjected to different levels of crude oil addition (0 kg/hm, 10 kg/hm, 40 kg/hm).
View Article and Find Full Text PDFNature
January 2025
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
Diversity-generating retroelements (DGRs) create massive protein sequence variation (up to 10) in ecologically diverse microorganisms. A recent survey identified around 31,000 DGRs from more than 1,500 bacterial and archaeal genera, constituting more than 90 environment types. DGRs are especially enriched in the human gut microbiome and nano-sized microorganisms that seem to comprise most microbial life and maintain DGRs despite reduced genomes.
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