The paper identifies and characterizes diverse extrachromosomal elements in Methanoperedens archaea, including mini-Borgs and viruses, and shows their genetic exchange and potential impact on archaeal activity.

bioRxiv · Aug 2, 2023 · PreprintMicrobiology

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

M. C. Schoelmerich, L. Ly, J. West-Roberts, L.-D. Shi, C. Shen, N. Malvankar, N. Taib, S. Gribaldo, B. J. Woodcroft, B. Al-Shayeb, X. Dai, C. Mozsary, S. Hickey, C. He, J. A. Beaulaurier, , J. Banfield

The paper identifies conserved genetic repertoires in Borg extrachromosomal elements of methane-oxidizing archaea and shows their higher expression than host genes.

bioRxiv · Aug 1, 2023Microbiology

Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

Y. Peng, Z. Lu, D. Pan, L.-D. Shi, Z. Zhao, Q. Liu, C. Zhang, K. Jia, J. Li, C. R. J. Hubert, X. Dong

The paper examines viral genetic features and evolutionary patterns in deep-sea cold seep sediments, identifying diverse survival strategies and genetic conservation within species.

bioRxiv · Mar 12, 2023Microbiology

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

C. Zhang, X. Liu, L.-D. Shi, J. Li, X. Xiao, Z. Shao, X. Dong

The paper analyzes metagenomic and metatranscriptomic data from cold seeps to identify As-cycling genes and microbes, revealing unexpected diversity and functional roles in arsenic transformation.

bioRxiv · Nov 20, 2022 · PreprintMicrobiology

A mixed blessing of viruses in wastewater treatment plants

L.-D. Shi, X. Dong, Z. Liu, Y. Yang, J.-G. Lin, M. Li, J.-D. Gu, L.-Z. Zhu, H.-P. Zhao

This study investigates the role of viruses in wastewater treatment plants, finding they can enhance contaminant degradation but also spread antibiotic resistance.

bioRxiv · Nov 8, 2021Microbiology