RT Journal Article
SR Electronic
T1 Improving the visualization of viruses in soil
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2024.09.30.615710
DO 10.1101/2024.09.30.615710
A1 Parvate, Amar D.
A1 Alfaro, Trinidad
A1 McDearis, Regan
A1 Zimmerman, Amy
A1 Hofmockel, Kirsten
A1 Nelson, William C.
A1 Evans, James E.
YR 2024
UL http://biorxiv.org/content/early/2024/09/30/2024.09.30.615710.abstract
AB Viruses are numerically the most abundant forms on Earth, and most are present in soil. Scientific study is usually restricted to viruses or phages which are known to either positively or negatively impact human activities, livestock or crops. Visualizing the diverse morphotypes within native soil virus populations has been challenging even though viruses are highly abundant in soil and critical to rhizosphere function; primarily due to a lack of an established and reliable method of performing high-resolution structural studies on viruses natively isolated from soil. Suspensions of viruses natively isolated from soil contain nanometer to micron scale debris which renders protein crystallography for structural studies unfeasible and makes sample prep for cryo-TEM extremely challenging. Conventional TEM provides only low-resolution structural information. Here we employed and compared a simple spin filtration method to cleanup solutions of extracted viruses for direct observation with cryo-electron microscopy. The method is agnostic to isolation approaches as it is a physical biochemical separation to remove large and small debris that hinders high-resolution imaging. In addition to improving image quality and preservation of structural features, the method visualizes morphotypes not typically seen with conventional TEM imaging and enables capturing a particle library with both 2D and 3D information. In addition to tailed and non-tailed polyhedral phages, our study reports several other under reported or novel morphotypes of soil viruses.Competing Interest StatementThe authors have declared no competing interest.