Article
Evolutionary Biology
Jianing Wang, Xiaofang Wang, Keming Yang, Chunxia Lu, Bryden Fields, Yangchun Xu, Qirong Shen, Zhong Wei, Ville-Petri Friman
Summary: This study compared the evolution of phage resistance-virulence trade-offs in Ralstonia solanacearum bacterium at different temperature environments. The results showed that phages reduced the density of R. solanacearum, but did not affect the final level of phage resistance. Instead, small colony variants with increased growth rate and mutations in the quorum-sensing (QS) signaling receptor gene evolved in both temperature treatments. Interestingly, these variants were also phage-resistant and reached higher frequencies in the presence of phages. Evolution of phage resistance resulted in metabolic costs, leading to reduced biofilm formation and virulence in the bacteria.
Article
Plant Sciences
Helen M. Cockerton, Shiv S. Kaundun, Lieselot Nguyen, Sarah Jane Hutchings, Richard P. Dale, Anushka Howell, Paul Neve
Summary: The study reveals a positive correlation between glyphosate resistance level and EPSPS gene copy number, identifying gene amplification as the resistance mechanism. Glyphosate-resistant A. tuberculatus plants exhibit lower competitive responses and a growth trade-off associated with gene amplification mechanism under intra-phenotypic competition.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Abdelmonim Ali Ahmad, Hardian Susilo Addy, Qi Huang
Summary: A jumbo phage RsoM2USA isolated from a tomato field in Florida, U.S., has a long latent period and short infection cycle. With a genome size of 343,806 bp, it is the largest Ralstonia-infecting phage sequenced to date, belonging to the family Myoviridae. It infects multiple Ralstonia species and significantly reduces the virulence of susceptible strains in tomato plants.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rekha Gopalan-Nair, Marie-Francoise Jardinaud, Ludovic Legrand, David Landry, Xavier Barlet, Celine Lopez-Roques, Celine Vandecasteele, Olivier Bouchez, Stephane Genin, Alice Guidot
Summary: The study utilized experimental evolution to investigate the adaptive potential of Ralstonia solanacearum in overcoming the resistance of tomato cultivar Hawaii 7996. After over 300 generations of serial passaging, pathogen adaptation to the resistant cultivar's environment was observed without breakdown of plant resistance. Genomic and transcriptomic analyses revealed genetic alterations and convergent global rewiring of the virulence regulatory network in independently evolved clones.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Andre da Silva Xavier, Alessandra G. de Melo, Connor G. Hendrich, Denise M. Tremblay, Genevieve M. Rousseau, Pier-Luc Plante, Katrina T. Forest, Poliane Alfenas-Zerbini, Caitilyn Allen, Sylvain Moineau
Summary: Ralstonia solanacearum is a destructive plant pathogen that causes lethal bacterial wilt disease. Phages that kill R. solanacearum could offer effective and environmentally friendly wilt disease control, but only if the bacterium cannot easily evolve resistance. Research has shown that the resistance of Ralstonia solanacearum to phages is related to its Type II Secretion System (T2SS), and the phage also affects the pathogenicity of R. solanacearum.
Article
Biochemistry & Molecular Biology
Nao Matsukawa, Chiaki Tsumori, Kouhei Ohnishi, Kenji Kai
Summary: Strains of Ralstonia solanacearum species complex (RSSC) produce lipopeptides through the PKS-NRPS enzyme hybrid. Ralstonins have been found to be important in parasitism of RSSC to other hosts. This study discovered ralstopeptins A and B, cyclic lipopeptides with less amino acid residues than ralstonins, from strain MAFF 211519. The production of ralstopeptins was found to be dependent on the PKS-NRPS genes.
ACS CHEMICAL BIOLOGY
(2023)
Article
Virology
Keisuke Nakamura, Jumpei Fujiki, Tomohiro Nakamura, Takaaki Furusawa, Satoshi Gondaira, Masaru Usui, Hidetoshi Higuchi, Yutaka Tamura, Hidetomo Iwano
Summary: Pseudomonas aeruginosa exhibits rapid antimicrobial resistance due to large chromosomal fragment loss through evolutionary selection by MutL. The study reveals that the BigD region in the bacterial chromosome contains drug resistance genes which affect drug sensitivity and phage resistance, providing a potential strategy to control phage-resistant variants.
Article
Microbiology
Keming Yang, Xiaofang Wang, Rujiao Hou, Chunxia Lu, Zhe Fan, Jingxuan Li, Shuo Wang, Yangchun Xu, Qirong Shen, Ville-Petri Friman, Zhong Wei
Summary: This study investigates the influence of rhizosphere phage communities on soil suppressiveness and bacterial wilt disease. It shows that healthy plants are associated with phage communities that have stronger control over the pathogen R. solanacearum. Additionally, phages that target pathogen-inhibiting bacteria are more abundant in diseased plant microbiomes. These findings suggest that rhizosphere phage communities play a crucial role in determining bacterial wilt disease outcomes and soil suppressiveness.
Article
Virology
Jing Zheng, Wenyuan Chen, Hao Xiao, Fan Yang, Xiaowu Li, Jingdong Song, Lingpeng Cheng, Hongrong Liu
Summary: In this study, the structure of the GP4 head of Ralstonia solanacearum phage was resolved to near-atomic resolution using cryo-electron microscopy. The head was found to contain 540 copies of major capsid protein (MCP) gp2 and 540 copies of cement protein (CP) gp1, arranged in an icosahedral shell. The assembly pattern of the GP4 head provides insights into the interaction between Ralstonia solanacearum and phages.
Article
Virology
Belen alvarez, Laura Gadea-Pallas, Alejandro Rodriguez, Begonya Vicedo, Angela Figas-Segura, Elena G. Biosca
Summary: This study confirms the feasibility of lyophilization as a preservation method for lytic bacteriophages. The lyophilized bacteriophages maintained high viability and stability throughout the experimental period and exhibited effective biocontrol capability against bacterial wilt.
Article
Virology
Elena G. Biosca, Jose Francisco Catala-Senent, Angela Figas-Segura, Edson Bertolini, Maria M. Lopez, Belen alvarez
Summary: The genomic sequences of three lytic bacteriophages against Ralstonia solanacearum were analyzed, revealing that they belong to the same novel species within the Gyeongsanvirus family. These phages have the potential for biological control of R. solanacearum.
Article
Microbiology
Ying Liu, Xi Tan, Yanxin Pan, Jiamin Yu, Yiran Du, Xiaojiao Liu, Wei Ding
Summary: This study used experimental evolution to evaluate the adaptability and mechanism of Ralstonia solanacearum in a long-term acidic environment. The results showed that R. solanacearum can adapt to acidic conditions and significantly increase its growth rate, which is associated with the loss of function in the phcA gene.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Man Qi, Niv DeMalach, Yueping Dong, Hailin Zhang, Tao Sun
Summary: Resource competition theory predicts coexistence and exclusion patterns, but in reality, systems often exhibit preemption exploitation. This study found that under preemption conditions, an R*-preemption trade-off is necessary for species coexistence, and under total preemption, the trade-off alone is sufficient. However, under partial preemption, additional conditions are required for coexistence.
AMERICAN NATURALIST
(2022)
Article
Biochemical Research Methods
Sylvain Blois, Benjamin M. Goetz, James J. Bull, Christopher S. Sullivan
Summary: The concept of nucleic acid barcodes in pathogen genomes is easy to understand, but implementing it may be challenging due to potential issues like fitness alteration, mutation accumulation, and unintended barcode generation. In this study, approximately 5000 randomized barcodes were generated in the genome of a small DNA virus, and a post-sequencing method was developed to interpret the barcode sequences. These findings may have implications for the use of randomized barcodes in other microbial systems and provide a useful approach for future studies involving nucleic acid barcoded pathogens.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Kaitlyn E. Kortright, Simon Doss-Gollin, Benjamin K. Chan, Paul E. Turner
Summary: This study found that selection for Escherichia coli to resist phage T6, phage U115, or albicidin often results in cross-resistance evolution, but these mutants did not exhibit measurable growth deficiencies. This suggests that when considering new antibacterial therapies, thorough investigation into the evolutionary consequences of the treatment should be conducted to avoid potential evolved trade-ups.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Bryden Fields, Emma K. Moffat, Ellie Harrison, Stig U. Andersen, J. Peter W. Young, Ville-Petri Friman
Summary: Genetic diversity influences facilitative and competitive interactions between different genospecies in the Rhizobium leguminosarum species complex, which can impact bacterial community composition, diversity, and functioning.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Xiaoxuan Zheng, Martin T. Jahn, Mingming Sun, Ville-Petri Friman, Jose Luis Balcazar, Jinfeng Wang, Yu Shi, Xin Gong, Feng Hu, Yong-Guan Zhu
Summary: This study found that in organochlorine pesticide-contaminated soils, the relative abundance of bacteria was lower, but the diversity of viruses was higher, and these viruses contained genes related to pesticide degradation and metabolism. The diversity and abundance of these genes increased with the severity of pesticide contamination. Functional experiments demonstrated that virus-encoded genes were able to degrade pesticide precursors, promoting bacterial growth at sub-inhibitory pesticide concentrations.
Article
Ecology
Michael J. Bottery, Jessica L. Matthews, A. Jamie Wood, Helle Krogh Johansen, Jon W. Pitchford, Ville-Petri Friman
Summary: The study found that multidrug-resistant Stenotrophomonas maltophilia can provide high levels of antibiotic protection to Pseudomonas aeruginosa, but is ineffective against another antibiotic. The level of exposure protection against different carbapenems is determined by differences in antibiotic efficacy and inactivation rate.
Article
Biology
Meaghan Castledine, Daniel Padfield, Pawel Sierocinski, Jesica Soria Pascual, Adam Hughes, Lotta Makinen, Ville-Petri Friman, Jean-Paul Pirnay, Maya Merabishvili, Daniel de Vos, Angus Buckling, Gisela Storz
Summary: With rising antibiotic resistance, there is increasing interest in using bacteriophages to treat pathogenic bacteria. However, one limitation is that bacteria can quickly evolve resistance to phage therapy. This study investigates the parallels between in vitro and in vivo evolutionary dynamics and suggests that in vitro experiments can provide useful insights for predicting clinical outcomes.
Article
Microbiology
Chen Zhu, Ville-Petri Friman, Ling Li, Qicheng Xu, Junjie Guo, Shiwei Guo, Qirong Shen, Ning Ling
Summary: The composition, diversity, and distribution of soil diazotrophs vary across different soil ecosystems, with environmental factors playing a significant role in their abundance and distribution. Cyanobacteria are the most abundant taxa in crust ecosystems, while Proteobacteria dominate other terrestrial ecosystems. Azospirillum zeae, Skermanella aerolata, and four Bradyrhizobium species are identified as key indicator species of potential diazotroph activity.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Jianing Wang, Waseem Raza, Gaofei Jiang, Zhang Yi, Bryden Fields, Samuel Greenrod, Ville-Petri Friman, Alexandre Jousset, Qirong Shen, Zhong Wei
Summary: Volatile organic compounds (VOCs) produced by soil bacteria have been found to influence the biocontrol potential of plant pathogens due to their antimicrobial activity. This study investigated the adaptation of Ralstonia solanacearum bacteria to VOCs produced by a biocontrol bacterium and how these adaptations affect its virulence. The findings showed that VOC selection led to increased VOC-tolerance and cross-tolerance to antibiotics, resulting in a loss of pathogenicity in plants. The genetic analysis revealed mutations in genes associated with antimicrobial permeability and virulence. Overall, microbial VOCs are important drivers of bacterial evolution and can be utilized in biocontrol to select for less virulent pathogens.
Article
Microbiology
Keming Yang, Xiaofang Wang, Rujiao Hou, Chunxia Lu, Zhe Fan, Jingxuan Li, Shuo Wang, Yangchun Xu, Qirong Shen, Ville-Petri Friman, Zhong Wei
Summary: This study investigates the influence of rhizosphere phage communities on soil suppressiveness and bacterial wilt disease. It shows that healthy plants are associated with phage communities that have stronger control over the pathogen R. solanacearum. Additionally, phages that target pathogen-inhibiting bacteria are more abundant in diseased plant microbiomes. These findings suggest that rhizosphere phage communities play a crucial role in determining bacterial wilt disease outcomes and soil suppressiveness.
Article
Biotechnology & Applied Microbiology
Shujian Yuan, Ville-Petri Friman, Jose Luis Balcazar, Xiaoxuan Zheng, Mao Ye, Mingming Sun, Feng Hu
Summary: This study investigated the assembly processes of bacterial and viral communities in clean and OCP-contaminated soils in China. The results showed that assembly of bacterial taxa and genes was dominated by a deterministic process, while assembly of viral taxa and AMGs was driven by a stochastic process. Additionally, viruses showed promise for the dissemination of functional genes among bacterial communities in OCP-contaminated soil.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Yian Gu, Zhidan Li, Peng Lei, Rui Wang, Hong Xu, Ville-Petri Friman
Summary: Through sampling in Hongze Lake during both Autumn and Spring, it was found that bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers, while distance-decay relationships were relatively stable with both sampling time points for both bacterial and microeukaryotic communities. This suggests that abiotic environmental factors play an important role in explaining mainly bacterial community assembly in the sediment, but other potential drivers, such as spatial heterogeneity and biotic species interactions, also need to be considered.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Ecology
Hanpeng Liao, Chen Liu, Chaofan Ai, Tian Gao, Qiu-E Yang, Zhen Yu, Shaoming Gao, Shungui Zhou, Ville-Petri Friman
Summary: By studying mesophilic and thermophilic bacteria and their viruses during industrial-scale hyperthermophilic composting (HTC), it was found that the dynamics and activity of virus-bacteria are closely related and play an important role in nutrient cycling. The viruses specific to mesophilic bacteria encode and express several auxiliary metabolic genes (AMGs) linked to carbon cycling and impact nutrient turnover alongside bacteria. The positive correlation between nutrient turnover and virus-host ratio suggests a positive relationship between ecosystem functioning, viral abundances, and viral activity. DNA viruses were found to be the main drivers of nutrient cycling during HTC. These findings suggest that viruses could be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.
Article
Biochemistry & Molecular Biology
Bryden Fields, Sara Moeskjaer, William J. Deakin, Emma K. Moffat, Niels Roulund, Stig U. Andersen, J. Peter W. Young, Ville-Petri Friman
Summary: This study compared the impact of different clover varieties and genotypes on the structure of Rhizobium populations in root nodules. The results showed that different clover varieties and genotypes selected for different Rhizobium communities, and the strength of host filtering was positively correlated with symbiotic efficiency.
Article
Microbiology
Samuel T. E. Greenrod, Martina Stoycheva, John Elphinstone, Ville-Petri Friman
Summary: Ralstonia solanacearum species complex (RSSC) is a destructive group of plant pathogenic bacteria and the causative agent of bacterial wilt disease. Experimental studies have attributed RSSC virulence to insertion sequences (IS), transposable genetic elements which can both disrupt and activate host genes. Yet, the global diversity and distribution of RSSC IS are unknown.
Article
Biochemistry & Molecular Biology
Karoline Rehm, Vera Vollenweider, Shaohua Gu, Ville-Petri Friman, Rolf Kuemmerli, Zhong Wei, Laurent Bigler
Summary: In this study, a novel citrate-based siderophore called chryseochelin A was identified and found to promote the health and growth of plants. The structure of this siderophore, along with its unstable isomer chryseochelin B and fatty acid derivative chryseochelin C, was elucidated using NMR spectroscopy and mass spectrometry. It was demonstrated that chryseochelin A can reduce the access to iron of the plant pathogenic bacterium Ralstonia solanacearum, indicating its potential in plant protection.
Article
Evolutionary Biology
Jianing Wang, Xiaofang Wang, Keming Yang, Chunxia Lu, Bryden Fields, Yangchun Xu, Qirong Shen, Zhong Wei, Ville-Petri Friman
Summary: This study compared the evolution of phage resistance-virulence trade-offs in Ralstonia solanacearum bacterium at different temperature environments. The results showed that phages reduced the density of R. solanacearum, but did not affect the final level of phage resistance. Instead, small colony variants with increased growth rate and mutations in the quorum-sensing (QS) signaling receptor gene evolved in both temperature treatments. Interestingly, these variants were also phage-resistant and reached higher frequencies in the presence of phages. Evolution of phage resistance resulted in metabolic costs, leading to reduced biofilm formation and virulence in the bacteria.