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ENIGMA

Ecosystems and Networks Integrated with Genes and Molecular Assemblies

Whole genome sequence reveals molecular mechanisms underlying adaptation of Rhodanobacter strains to multiple stressors

The Genomic Features Underlying Adaptation of Rhodanobacter Strains to Stressful Conditions (denitrification processes, heavy metal resistance, and restriction-modification systems) present at ENIGMA Field Site ORR. 

Restriction-modification system genes (A, FW107-2APBS1 was used as the reference) and methylation motifs of 5mC (B) and 6mA (C) in four Rhodanobacter genomes. The methylation motifs vary in four R. denitrificans genomes (from the top to the bottom: DSM24678, FW104-10F02, FW104-R3, and FW104-R5). Image courtesy of Mu Peng et al. Microbiology Spectrum 2022

Rhodanobacter species have been found dominant in the subsurface of Oak Ridge Reservation (ORR) site contaminated with acid, nitrate, metal radionuclides, and other heavy metals. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples. However, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. We used Illumina, PacBio, and Oxford Nanopore sequencing platforms to obtain the whole genome sequences of eight Rhodanobacter strains. Comparison of the whole genomes demonstrated the genetic diversity, and analysis of the long nanopore reads revealed the unique methylation patterns in four strains.

Whole genome sequences are required to uncover the genomics features underlying the adaptation of Rhodanobacter strains to multiple stressors present at ORR, such as genes involved in denitrification process, heavy metal resistance, restriction-modification systems. We obtained the whole genome sequences of eight Rhodanobacter strains using both Illumina sequencing platform which generates short reads, PacBio and Oxford Nanopore sequencing platform which generate long reads. Nanopore long reads are critical for whole genome sequence assembly, analysis of the Nanopore reads also reveals genomic DNA methylation patterns that contribute to survival in the environment but may be hostile to future lab genetic manipulation.

With comparative genomic analysis tools, the genomic features related to adaptation were revealed, for instance, high pan-genome rates, abundant genomic islands which contains many heavy metal resistance genes. The results demonstrated the important roles of horizontal gene transfer and negative selection in adaptation. Although all strains contained a complete set of denitrifying genes including nitrate reductase (nar), nitrite reductase (nir), nitric-oxide reductase (nor) and nitrous oxide reductase (nos), the predicted tertiary structures of NosZ differed. In addition, the complex restriction-modification systems and unique 5mC methylation patterns suggested the potential recalcitrance to genetic manipulation.

Mu Peng, University of Oklahoma

Peng,M.; D. Wang, L. M. Lui, T. Nielsen, R. Tian, M. L. Kempher, X. Tao, C. Pan, R. Chakraborty, A. M. Deutschbauer, M. P. Thorgersen, M. W. W. Adams, M. W. Fields, T. C. Hazen, A. P. Arkin, A. Zhou, J. Zhou (2022) Genomic features and pervasive negative selection in Rhodanobacter strains isolated from nitrate and heavy metal contaminated aquifer. Microbiology Spectrum, 10(1), e02591-21

[DOI]: 10.1128/spectrum.02591-21 PMID: 35107332

Aifen Zhou <Aifen.Zhou-1@ou.edu>
University of Oklahoma

Jizhong Zhou <jzhou@ou.edu>
University of Oklahoma