Publications by authors named "Dmitri Mavrodi"

55 Publications

Draft Genome Sequences of Six Strains Isolated from the Rhizosphere of Wheat Grown in Cadmium-Contaminated Soil.

Authors:
Vira Hovorukha Ankita Bhattacharyya Olga Iungin Hanna Tashyreva Victoria Romanovska Olesia Havryliuk Olena Bielikova Claire Blackwell Brian Burks Cara Cothern Jakia Elliott Jonathan Hoover Alexis Jones Christian Leise Linda Lowmiller Ahmed Mohamed Tiffany Mullen Ethan Nettleton Karshanda Polk Benny Tran Teresa Tran Manuel Vega Landon Ware Emily Welch Leandra Williams Madison Woodard Kaylin Young Olga Mavrodi Oleksandr Tashyrev Dmitri Mavrodi

Microbiol Resour Announc 2020 Aug 20;9(34). Epub 2020 Aug 20.

School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA

This study presents high-quality draft genome assemblies of six bacterial strains isolated from the roots of wheat grown in soil contaminated with cadmium. The results of this study will help to elucidate at the molecular level how heavy metals affect interactions between beneficial rhizobacteria and crop plants.
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http://dx.doi.org/10.1128/MRA.00676-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7441233PMC
August 2020

Draft Genome Sequences of Xylella fastidiosa subsp. Strains OK3, VB11, and NOB1, Isolated from Bunch and Muscadine Grapes Grown in Southern Mississippi.

Authors:
Olga V Mavrodi Dmitri V Mavrodi Eric T Stafne John J Adamczyk Ebrahiem M Babiker

Microbiol Resour Announc 2020 Jun 18;9(25). Epub 2020 Jun 18.

USDA-ARS Southern Horticultural Research Laboratory, Poplarville, Mississippi, USA

We report here high-quality draft whole-genome assemblies of subsp. strains OK3, VB11, and NOB1, which were isolated from symptomatic bunch and muscadine grape plants grown in southern Mississippi.
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http://dx.doi.org/10.1128/MRA.00562-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7303414PMC
June 2020

Comparative Analysis of Rhizosphere Microbiomes of Southern Highbush Blueberry ( L.), Darrow's Blueberry ( Camp), and Rabbiteye Blueberry ( Aiton).

Authors:
Jiangang Li Olga V Mavrodi Jinfeng Hou Chazden Blackmon Ebrahiem M Babiker Dmitri V Mavrodi

Front Microbiol 2020 12;11:370. Epub 2020 Mar 12.

Department of Cell and Molecular Biology, School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States.

Plants are inhabited by millions of parasitic, commensal, and mutualistic microorganisms that coexist in complex ecological communities, and profoundly affect the plant's productivity, health, and capacity to cope with environmental stress. Therefore, a better understanding of the rhizosphere microbiome may open a yet untapped avenue for the rational exploitation of beneficial plant-microbe interactions in modern agriculture. Blueberries encompass several wild and cultivated species of shrubs of the genus that are native to North America. They are grown commercially for the production of fruits, which are considered a health food due to the rich content of minerals, trace elements, and phenolic compounds with antioxidant, antitumor, and anti-inflammatory properties. Despite a long history of breeding and extensive commercial use, remarkably little is known about the composition and function of the blueberry root microbiome. To address this gap, we employed molecular approaches to characterize and compare microbial communities inhabiting the roots of rabbiteye blueberry (), Darrow's blueberry (), and southern highbush blueberry (SHB; an interspecific hybrid of and ). Our results revealed that these plant species share a common core rhizobiome, but at the same time differ significantly in the diversity, relative abundance, richness, and evenness of multiple groups of prokaryotic and eukaryotic microorganisms. Although the host signature effects were especially pronounced at the plant species level, we also observed genotype-level variations in the distribution of specific microbial taxa, which suggests that the assembly of the blueberry microbiome is shaped by the plant genotype and modifications associated with the domestication and breeding of members of the genus. We also demonstrated that the studied species differ in the abundance of beneficial rhizobacteria and ericoid mycorrhizal fungi, which play a vital role in their adaptation to soils with low pH and slow turnover of organic matter.
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http://dx.doi.org/10.3389/fmicb.2020.00370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081068PMC
March 2020

2-79 Transformed with Pyrrolnitrin Biosynthesis Genes Has Improved Biocontrol Activity Against Soilborne Pathogens of Wheat and Canola.

Authors:
Jibin Zhang Dmitri V Mavrodi Mingming Yang Linda S Thomashow Olga V Mavrodi Jason Kelton David M Weller

Phytopathology 2020 May 24;110(5):1010-1017. Epub 2020 Mar 24.

U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, U.S.A.

A four-gene operon () from Pf-5 encoding the biosynthesis of the antibiotic pyrronitrin was introduced into (formerly ) 2-79, an aggressive root colonizer of both dryland and irrigated wheat roots that naturally produces the antibiotic phenazine-1-carboxylic acid and suppresses both take-all and Rhizoctonia root rot of wheat. Recombinant strains ZHW15 and ZHW25 produced both antibiotics and maintained population sizes in the rhizosphere of wheat that were comparable to those of strain 2-79. The recombinant strains inhibited in vitro the wheat pathogens anastomosis group 8 (AG-8) and AG-2-1, var. , , , and significantly more than did strain 2-79. Both the wild-type and recombinant strains were equally inhibitory of . When applied as a seed treatment, the recombinant strains suppressed take-all, Rhizoctonia root rot of wheat, and Rhizoctonia root and stem rot of canola significantly better than did wild-type strain 2-79.
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http://dx.doi.org/10.1094/PHYTO-09-19-0367-RDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7238759PMC
May 2020

Exploring the Pathogenicity of Q8r1-96 and Other Strains of the Complex on Tomato.

Authors:
Mingming Yang Dmitri V Mavrodi Olga V Mavrodi Linda S Thomashow David M Weller

Plant Dis 2020 Apr 29;104(4):1026-1031. Epub 2020 Jan 29.

U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, U.S.A.

and related species of the complex have long been studied as biocontrol and growth-promoting rhizobacteria involved in suppression of soilborne pathogens. We report here that Q8r1-96 and other 2,4-diacetylphloroglucinol (DAPG)-producing fluorescent pseudomonads involved in take-all decline of wheat in the Pacific Northwest of the United States can also be pathogenic to other plant hosts. Strain Q8r1-96 caused necrosis when injected into tomato stems and immature tomato fruits, either attached or removed from the plant, but lesion development was dose dependent, with a minimum of 10 CFU ml required to cause visible tissue damage. We explored the relative contribution of several known plant-microbe interaction traits to the pathogenicity of strain Q8r1-96. Type III secretion system (T3SS) mutants of Q8r1-96, injected at a concentration of 10 CFU ml, were significantly less virulent, but not consistently, as compared with the wild-type strain. However, a DAPG-deficient mutant of Q8r1-96 was significantly and consistently less virulent as compared with the wild type. Strain Q8r1-96acc, engineered to over express ACC deaminase, caused a similar amount of necrosis as the wild type. Cell-free culture filtrates of strain Q8r1-96 and pure DAPG also cause necrosis in tomato fruits. Our results suggest that DAPG plays a significant role in the ability of Q8r1-96 to cause necrosis of tomato tissue, but other factors also contribute to the pathogenic properties of this organism.
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http://dx.doi.org/10.1094/PDIS-09-19-1989-REDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163159PMC
April 2020

Antimicrobial Activity of, and Cellular Pathways Targeted by, -Anisaldehyde and Epigallocatechin Gallate in the Opportunistic Human Pathogen Pseudomonas aeruginosa.

Authors:
Yetunde Adewunmi Sanchirmaa Namjilsuren William D Walker Dahlia N Amato Douglas V Amato Olga V Mavrodi Derek L Patton Dmitri V Mavrodi

Appl Environ Microbiol 2020 02 3;86(4). Epub 2020 Feb 3.

School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, Mississippi, USA

Plant-derived aldehydes are constituents of essential oils that possess broad-spectrum antimicrobial activity and kill microorganisms without promoting resistance. In our previous study, we incorporated -anisaldehyde from star anise into a polymer network called proantimicrobial networks via degradable acetals (PANDAs) and used it as a novel drug delivery platform. PANDAs released -anisaldehyde upon a change in pH and humidity and controlled the growth of the multidrug-resistant pathogen PAO1. In this study, we identified the cellular pathways targeted by -anisaldehyde by generating 10,000 transposon mutants of PAO1 and screened them for hypersensitivity to -anisaldehyde. To improve the antimicrobial efficacy of -anisaldehyde, we combined it with epigallocatechin gallate (EGCG), a polyphenol from green tea, and demonstrated that it acts synergistically with -anisaldehyde in killing We then used transcriptome sequencing to profile the responses of to -anisaldehyde, EGCG, and their combination. The exposure to -anisaldehyde altered the expression of genes involved in modification of the cell envelope, membrane transport, drug efflux, energy metabolism, molybdenum cofactor biosynthesis, and the stress response. We also demonstrate that the addition of EGCG reversed many -anisaldehyde-coping effects and induced oxidative stress. Our results provide insight into the antimicrobial activity of -anisaldehyde and its interactions with EGCG and may aid in the rational identification of new synergistically acting combinations of plant metabolites. Our study also confirms the utility of the thiol-ene polymer platform for the sustained and effective delivery of hydrophobic and volatile antimicrobial compounds. Essential oils (EOs) are plant-derived products that have long been exploited for their antimicrobial activities in medicine, agriculture, and food preservation. EOs represent a promising alternative to conventional antibiotics due to their broad-range antimicrobial activity, low toxicity to human commensal bacteria, and capacity to kill microorganisms without promoting resistance. Despite the progress in the understanding of the biological activity of EOs, our understanding of many aspects of their mode of action remains inconclusive. The overarching aim of this work was to address these gaps by studying the molecular interactions between an antimicrobial plant aldehyde and the opportunistic human pathogen The results of this study identify the microbial genes and associated pathways involved in the response to antimicrobial phytoaldehydes and provide insights into the molecular mechanisms governing the synergistic effects of individual constituents within essential oils.
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http://dx.doi.org/10.1128/AEM.02482-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6997733PMC
February 2020

Discovery and Characterization of Bacteriophage LuckyBarnes.

Authors:
Savannah L Underwood Amanda Foto Amanda F Ray Alexander E Nelms Keyshawn L Kennedy Shelby G Hartley Logan M Ryals Chandan Gurung William A D'Angelo Welkin H Pope Dmitri V Mavrodi

Microbiol Resour Announc 2019 Jun 20;8(25). Epub 2019 Jun 20.

Department of Cell and Molecular Biology, School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, Mississippi, USA

Here, we report the genome sequence of LuckyBarnes, a newly isolated singleton siphovirus that infects ATCC 15728 and has a 50,774-bp genome with 67 predicted genes.
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http://dx.doi.org/10.1128/MRA.00330-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588365PMC
June 2019

Rhizosphere Microbial Communities of and From Restored and Natural Tidal Marshes on Deer Island, Mississippi.

Authors:
Olga V Mavrodi Carina M Jung Jed O Eberly Samuel V Hendry Sanchirmaa Namjilsuren Patrick D Biber Karl J Indest Dmitri V Mavrodi

Front Microbiol 2018 11;9:3049. Epub 2018 Dec 11.

Department of Biological Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States.

The U. S. Gulf of Mexico is experiencing a dramatic increase in tidal marsh restoration actions, which involves planting coastal areas with smooth cordgrass () and black needlerush () for erosion control and to provide habitat for fish and wildlife. It can take decades for sedimentary cycles in restored marshes to approach reference conditions, and the contribution of the sediment microbial communities to these processes is poorly elucidated. In this study, we addressed this gap by comparing rhizosphere microbiomes of and from two restored marshes and a natural reference marsh located at Deer Island, MS. Our results revealed that plants from the restored and reference areas supported similar microbial diversity indicating the rapid colonization of planted grasses with indigenous soil microbiota. Although close in composition, the microbial communities from the three studied sites differed significantly in the relative abundance of specific taxa. The observed differences are likely driven by the host plant identity and properties of sediment material used for the creation of restored marshes. Some of the differentially distributed groups of bacteria include taxa involved in the cycling of carbon, nitrogen, and sulfur, and may influence the succession of vegetation at the restored sites to climax condition. We also demonstrated that plants from the restored and reference sites vary in the frequency of culturable rhizobacteria that exhibit traits commonly associated with the promotion of plant growth and suppression of phytopathogenic fungi. Our findings will contribute to the establishment of benchmarks for the assessment of the outcome of coastal restoration projects in the Gulf of Mexico and better define factors that affect the long-term resiliency of tidal marshes and their vulnerability to climate change.
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http://dx.doi.org/10.3389/fmicb.2018.03049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297177PMC
December 2018

Differential Response of Wheat Cultivars to Pseudomonas brassicacearum and Take-All Decline Soil.

Authors:
Mingming Yang Dmitri V Mavrodi Linda S Thomashow David M Weller

Phytopathology 2018 Dec 17;108(12):1363-1372. Epub 2018 Oct 17.

First author: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, P.R. China; second author: Department of Cell and Molecular Biology, The University of Southern Mississippi, Hattiesburg 39406: and third and fourth authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430.

2,4-Diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. in the P. fluorescens complex are primarily responsible for a natural suppression of take-all of wheat known as take-all decline (TAD) in many fields in the United States. P. brassicacearum, the most common DAPG producer found in TAD soils in the Pacific Northwest (PNW) of the United States, has biological control, growth promoting and phytotoxic activities. In this study, we explored how the wheat cultivar affects the level of take-all suppression when grown in a TAD soil, and how cultivars respond to colonization by P. brassicacearum. Three cultivars (Tara, Finley, and Buchanan) supported similar rhizosphere population sizes of P. brassicacearum when grown in a TAD soil, however they developed significantly different amounts of take-all. Cultivars Tara and Buchanan developed the least and most take-all, respectively, and Finley showed an intermediate amount of disease. However, when grown in TAD soil that was pasteurized to eliminate both DAPG producers and take-all suppression, all three cultivars were equally susceptible to take-all. The three cultivars also responded differently to the colonization and phytotoxicity of P. brassicacearum strains Q8r1-96 and L5.1-96, which are characteristic of DAPG producers in PNW TAD soils. Compared with cultivar Tara, cultivar Buchanan showed significantly reduced seedling emergence and root growth when colonized by P. brassicacearum, and the response of Finley was intermediate. However, all cultivars emerged equally when treated with a DAPG-deficient mutant of Q8r1-96. Our results indicate that wheat cultivars grown in a TAD soil modulate both the robustness of take-all suppression and the potential phytotoxicity of the antibiotic DAPG.
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http://dx.doi.org/10.1094/PHYTO-01-18-0024-RDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483097PMC
December 2018

Phenazine-1-carboxylic acid and soil moisture influence biofilm development and turnover of rhizobacterial biomass on wheat root surfaces.

Authors:
Melissa K LeTourneau Matthew J Marshall John B Cliff Robert F Bonsall Alice C Dohnalkova Dmitri V Mavrodi S Indira Devi Olga V Mavrodi James B Harsh David M Weller Linda S Thomashow

Environ Microbiol 2018 06 26;20(6):2178-2194. Epub 2018 Jul 26.

United States Department of Agriculture - Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, USA.

Phenazine-1-carboxylic acid (PCA) is produced by rhizobacteria in dryland but not in irrigated wheat fields of the Pacific Northwest, USA. PCA promotes biofilm development in bacterial cultures and bacterial colonization of wheat rhizospheres. However, its impact upon biofilm development has not been demonstrated in the rhizosphere, where biofilms influence terrestrial carbon and nitrogen cycles with ramifications for crop and soil health. Furthermore, the relationships between soil moisture and the rates of PCA biosynthesis and degradation have not been established. In this study, expression of PCA biosynthesis genes was upregulated relative to background transcription, and persistence of PCA was slightly decreased in dryland relative to irrigated wheat rhizospheres. Biofilms in dryland rhizospheres inoculated with the PCA-producing (PCA ) strain Pseudomonas synxantha 2-79RN were more robust than those in rhizospheres inoculated with an isogenic PCA-deficient (PCA ) mutant strain. This trend was reversed in irrigated rhizospheres. In dryland PCA rhizospheres, the turnover of N-labelled rhizobacterial biomass was slower than in the PCA and irrigated PCA treatments, and incorporation of bacterial N into root cell walls was observed in multiple treatments. These results indicate that PCA promotes biofilm development in dryland rhizospheres, and likely influences crop nutrition and soil health in dryland wheat fields.
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http://dx.doi.org/10.1111/1462-2920.14244DOI Listing
June 2018

Long-Term Irrigation Affects the Dynamics and Activity of the Wheat Rhizosphere Microbiome.

Authors:
Dmitri V Mavrodi Olga V Mavrodi Liam D H Elbourne Sasha Tetu Robert F Bonsall James Parejko Mingming Yang Ian T Paulsen David M Weller Linda S Thomashow

Front Plant Sci 2018 21;9:345. Epub 2018 Mar 21.

Wheat Health, Genetics and Quality Research Unit, USDA Agricultural Research Service, Pullman, WA, United States.

The Inland Pacific Northwest (IPNW) encompasses 1. 6 million cropland hectares and is a major wheat-producing area in the western United States. The climate throughout the region is semi-arid, making the availability of water a significant challenge for IPNW agriculture. Much attention has been given to uncovering the effects of water stress on the physiology of wheat and the dynamics of its soilborne diseases. In contrast, the impact of soil moisture on the establishment and activity of microbial communities in the rhizosphere of dryland wheat remains poorly understood. We addressed this gap by conducting a three-year field study involving wheat grown in adjacent irrigated and dryland (rainfed) plots established in Lind, Washington State. We used deep amplicon sequencing of the V4 region of the 16S rRNA to characterize the responses of the wheat rhizosphere microbiome to overhead irrigation. We also characterized the population dynamics and activity of indigenous Phz rhizobacteria that produce the antibiotic phenazine-1-carboxylic acid (PCA) and contribute to the natural suppression of soilborne pathogens of wheat. Results of the study revealed that irrigation affected the Phz rhizobacteria adversely, which was evident from the significantly reduced plant colonization frequency, population size and levels of PCA in the field. The observed differences between irrigated and dryland plots were reproducible and amplified over the course of the study, thus identifying soil moisture as a critical abiotic factor that influences the dynamics, and activity of indigenous Phz communities. The three seasons of irrigation had a slight effect on the overall diversity within the rhizosphere microbiome but led to significant differences in the relative abundances of specific OTUs. In particular, irrigation differentially affected multiple groups of and , including taxa with known plant growth-promoting activity. Analysis of environmental variables revealed that the separation between irrigated and dryland treatments was due to changes in the water potential (Ψ) and pH. In contrast, the temporal changes in the composition of the rhizosphere microbiome correlated with temperature and precipitation. In summary, our long-term study provides insights into how the availability of water in a semi-arid agroecosystem shapes the belowground wheat microbiome.
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http://dx.doi.org/10.3389/fpls.2018.00345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5871930PMC
March 2018

A bio-based pro-antimicrobial polymer network via degradable acetal linkages.

Authors:
Douglas V Amato Dahlia N Amato Logan T Blancett Olga V Mavrodi William B Martin Sarah N Swilley Michael J Sandoz Glenmore Shearer Dmitri V Mavrodi Derek L Patton

Acta Biomater 2018 02 18;67:196-205. Epub 2017 Dec 18.

School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, MS 39406, United States. Electronic address:

The synthesis of a fully degradable, bio-based, sustained release, pro-antimicrobial polymer network comprised of degradable acetals (PANDA) is reported. The active antimicrobial agent - p-anisaldehyde (pA) (an extract from star anise) - was converted into a UV curable acetal containing pro-antimicrobial monomer and subsequently photopolymerized into a homogenous thiol-ene network. Under neutral to acidic conditions (pH < 8), the PANDAs undergo surface erosion and exhibit sustained release of pA over 38 days. The release of pA from PANDAs was shown to be effective against both bacterial and fungal pathogens. From a combination of confocal microscopy and transmission electron microscopy, we observed that the released pA disrupts the cell membrane. Additionally, we demonstrated that PANDAs have minimal cytotoxicity towards both epithelial cells and macrophages. Although a model platform, these results point to promising pathways for the design of fully degradable sustained-release antimicrobial systems with potential applications in agriculture, pharmaceuticals, cosmetics, household/personal care, and food industries.

Statement Of Significance: With the increasing number of patients prescribed immunosuppressants coupled with the rise in antibiotic resistance - life-threatening microbial infections are a looming global threat. With limited success within the antibiotic pipeline, nature-based essential oils (EOs) are being investigated for their multimodal effectiveness against microbes. Despite the promising potential of EOs, difficulties in their encapsulation, limited water solubility, and high volatility limit their use. Various studies have shown that covalent attachment of these EO derivatives to polymers can mitigate these limitations. The current study presents the synthesis of a fully-degradable, sustained release, cytocompatible, pro-antimicrobial acetal network derived from p-anisaldehyde. This polymer network design provides a pathway toward application-specific EO releasing materials with quantitative encapsulation efficiencies, sustained release, and broad-spectrum antimicrobial activity.
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http://dx.doi.org/10.1016/j.actbio.2017.12.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6064185PMC
February 2018

Genome Sequences of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, DarthP, Hammy, Krueger, LastHope, Peanam, PhelpsODU, Phrank, SirPhilip, Slimphazie, and Unicorn.

Authors:
Kirk R Anders Nazir Barekzi Aaron A Best Gregory D Frederick Dmitri V Mavrodi Edwin Vazquez Nana Yaa A Amoh Frederick N Baliraine William J Buchser Thomas P Cast Carmen E Chamberlain Hui-Min Chung William A D'Angelo Christian T Farris Mariceli Fernandez-Martinez Haley D Fischman Mark H Forsyth Anna G Fortier Kara F Gallo Greta J Held Miguel A Lomas Natalia Y Maldonado-Vazquez Claudia H Moonsammy Peace Namboote Sudip Paudel Sarah-Elizabeth M Polley Gabriella M Reyes Michael R Rubin Margaret S Saha Joseph Stukey Tristan D Tobias Rebecca A Garlena Ty H Stoner Steven G Cresawn Deborah Jacobs-Sera Welkin H Pope Daniel A Russell Graham F Hatfull

Genome Announc 2017 Dec 7;5(49). Epub 2017 Dec 7.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

We report the genome sequences of 14 cluster K mycobacteriophages isolated using mc²155 as host. Four are closely related to subcluster K1 phages, and 10 are members of subcluster K6. The phage genomes span considerable sequence diversity, including multiple types of integrases and integration sites.
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http://dx.doi.org/10.1128/genomeA.01202-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5721135PMC
December 2017

Draft genome sequences of strains SMB35, sp. MH3R3-1 and sp. SMB17 from the Verkhnekamsk potash mining region of Russia.

Authors:
Björn E Olsson Ekaterina S Korsakova Lyudmila N Anan'ina Anna A Pyankova Olga V Mavrodi Elena G Plotnikova Dmitri V Mavrodi

Stand Genomic Sci 2017 19;12:39. Epub 2017 Jul 19.

Department of Biological Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406 USA.

Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of SMB35, sp. MH3R3-1 and sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the capacity of halomonads to tolerate osmotic stress and adapt to hypersaline environments. The study also revealed that and share 75-90% of the predicted proteome, but also harbor a set of genus-specific genes, which in amounted to approximately 0.5 Mbp. These genus-specific genome segments may contribute to the phenotypic diversity of the and the ability of these organisms to adapt to changing environmental conditions and colonize new ecological niches.
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http://dx.doi.org/10.1186/s40793-017-0251-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5518125PMC
July 2017

Relationships between Root Pathogen Resistance, Abundance and Expression of Antimicrobial Genes, and Soil Properties in Representative Swiss Agricultural Soils.

Authors:
Nicola Imperiali Francesca Dennert Jana Schneider Titouan Laessle Christelle Velatta Marie Fesselet Michele Wyler Fabio Mascher Olga Mavrodi Dmitri Mavrodi Monika Maurhofer Christoph Keel

Front Plant Sci 2017 29;8:427. Epub 2017 Mar 29.

Department of Fundamental Microbiology, University of LausanneLausanne, Switzerland.

Strains of that produce antimicrobial metabolites and control soilborne plant diseases have often been isolated from soils defined as disease-suppressive, i.e., soils, in which specific plant pathogens are present, but plants show no or reduced disease symptoms. Moreover, it is assumed that pseudomonads producing antimicrobial compounds such as 2,4-diacetylphloroglucinol (DAPG) or phenazines (PHZ) contribute to the specific disease resistance of suppressive soils. However, pseudomonads producing antimicrobial metabolites are also present in soils that are conducive to disease. Currently, it is still unknown whether and to which extent the abundance of antimicrobials-producing pseudomonads is related to the general disease resistance of common agricultural soils. Moreover, virtually nothing is known about the conditions under which pseudomonads express antimicrobial genes in agricultural field soils. We present here results of the first side-by-side comparison of 10 representative Swiss agricultural soils with a cereal-oriented cropping history for (i) the resistance against two soilborne pathogens, (ii) the abundance of bacteria harboring genes involved in the biosynthesis of the antimicrobials DAPG, PHZ, and pyrrolnitrin on roots of wheat, and (iii) the ability to support the expression of these genes on the roots. Our study revealed that the level of soil disease resistance strongly depends on the type of pathogen, e.g., soils that are highly resistant to often are highly susceptible to and vice versa. There was no significant correlation between the disease resistance of the soils, the abundance of bacteria carrying DAPG, PHZ, and pyrrolnitrin biosynthetic genes, and the ability of the soils to support the expression of the antimicrobial genes. Correlation analyses indicated that certain soil factors such as silt, clay, and some macro- and micronutrients influence both the abundance and the expression of the antimicrobial genes. Taken together, the results of this study suggests that pseudomonads producing DAPG, PHZ, or pyrrolnitrin are present and abundant in Swiss agricultural soils and that the soils support the expression of the respective biosynthetic genes in these bacteria to various degrees. The precise role that these pseudomonads play in the general disease resistance of the investigated agricultural soils remains elusive.
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http://dx.doi.org/10.3389/fpls.2017.00427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372754PMC
March 2017

Genome Sequence of Mycobacterium Phage Waterfoul.

Authors:
Paige N Jackson Ella K Embry Christa O Johnson Tiara L Watson Sayre K Weast Caroline J DeGraw Jessica R Douglas J Michael Sellers William A D'Angelo Dmitri V Mavrodi

Genome Announc 2016 Nov 17;4(6). Epub 2016 Nov 17.

Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA

Waterfoul is a newly isolated temperate siphovirus of Mycobacterium smegmatis mc155. It was identified as a member of the K5 cluster of Mycobacterium phages and has a 61,248-bp genome with 95 predicted genes.
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http://dx.doi.org/10.1128/genomeA.01281-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114377PMC
November 2016

Destruction of Opportunistic Pathogens via Polymer Nanoparticle-Mediated Release of Plant-Based Antimicrobial Payloads.

Authors:
Dahlia N Amato Douglas V Amato Olga V Mavrodi Dwaine A Braasch Susan E Walley Jessica R Douglas Dmitri V Mavrodi Derek L Patton

Adv Healthc Mater 2016 05 4;5(9):1094-103. Epub 2016 Mar 4.

School of Polymers and High Performance Materials, University of Southern Mississippi, Hattiesburg, MS, 39406, USA.

The synthesis of antimicrobial thymol/carvacrol-loaded polythioether nanoparticles (NPs) via a one-pot, solvent-free miniemulsion thiol-ene photopolymerization process is reported. The active antimicrobial agents, thymol and carvacrol, are employed as "solvents" for the thiol-ene monomer phase in the miniemulsion to enable facile high capacity loading (≈50% w/w), excellent encapsulation efficiencies (>95%), and elimination of all postpolymerization purification processes. The NPs serve as high capacity reservoirs for slow-release and delivery of thymol/carvacrol-combination payloads that exhibit inhibitory and bactericidal activity (>99.9% kill efficiency at 24 h) against gram-positive and gram-negative bacteria, including both saprophytic (Bacillus subtilis ATCC 6633 and Escherichia coli ATCC 25922) and pathogenic species (E. coli ATCC 43895, Staphylococcus aureus RN6390, and Burkholderia cenocepacia K56-2). This report is among the first to demonstrate antimicrobial efficacy of essential oil-loaded nanoparticles against B. cenocepacia - an innately resistant opportunistic pathogen commonly associated with debilitating respiratory infections in cystic fibrosis. Although a model platform, these results point to promising pathways to particle-based delivery of plant-derived extracts for a range of antimicrobial applications, including active packaging materials, topical antiseptics, and innovative therapeutics.
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http://dx.doi.org/10.1002/adhm.201500974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474087PMC
May 2016

Draft Genome Sequence of the Phenazine-Producing Pseudomonas fluorescens Strain 2-79.

Authors:
Kai Nesemann Susanna A Braus-Stromeyer Andrea Thuermer Rolf Daniel Dmitri V Mavrodi Linda S Thomashow David M Weller Gerhard H Braus

Genome Announc 2015 Mar 26;3(2). Epub 2015 Mar 26.

Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August Universität, Göttingen, Germany

Pseudomonas fluorescens strain 2-79, a natural isolate of the rhizosphere of wheat (Triticum aestivum L.), possesses antagonistic potential toward several fungal pathogens. We report the draft genome sequence of strain 2-79, which comprises 5,674 protein-coding sequences.
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http://dx.doi.org/10.1128/genomeA.00130-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384134PMC
March 2015

Biocontrol and plant growth-promoting activity of rhizobacteria from Chinese fields with contaminated soils.

Authors:
Xuefei Wang Dmitri V Mavrodi Linfeng Ke Olga V Mavrodi Mingming Yang Linda S Thomashow Na Zheng David M Weller Jibin Zhang

Microb Biotechnol 2015 May 15;8(3):404-18. Epub 2014 Sep 15.

State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA.

The aim of this study was to inventory the types of plant growth-promoting rhizobacteria (PGPR) present in the rhizosphere of plants grown in soils contaminated with heavy metals, recalcitrant organics, petroleum sewage or salinity in China. We screened 1223 isolates for antifungal activity and about 24% inhibited Rhizoctonia solani or Sclerotinia sclerotiorum. Twenty-four strains inhibitory to R. solani, Gaeumannomyces graminis var. tritici and/or S. sclerotiorum and representing the dominant morphotypes were assayed for PGPR activity. Seven strains contained phlD, prnD, pltC or phzF genes and produced the antibiotics 2,4-diacetylphloroglucinol, pyrrolnitrin, pyoluteorin and phenazines respectively. Six strains contained acdS, which encodes 1-aminocyclopropane-1-carboxylic acid deaminase. Phylogenetic analysis of 16S rDNA and phlD, phzF and acdS genes demonstrated that some strains identified as Pseudomonas were similar to model PGPR strains Pseudomonas protegens Pf-5, Pseudomonas chlororaphis subsp. aureofaciens 30-84 and P. brassicacearum Q8r1-96. Pseudomonas protegens- and P. chlororaphis-like strains had the greatest biocontrol activity against Rhizoctonia root rot and take-all of wheat. Pseudomonas protegens and P. brassicacearum-like strains showed the greatest promotion of canola growth. Our results indicate that strains from contaminated soils are similar to well-described PGPR found in agricultural soils worldwide.
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http://dx.doi.org/10.1111/1751-7915.12158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408174PMC
May 2015

Pseudomonas protegens Pf-5 causes discoloration and pitting of mushroom caps due to the production of antifungal metabolites.

Authors:
Marcella D Henkels Teresa A Kidarsa Brenda T Shaffer Neal C Goebel Peter Burlinson Dmitri V Mavrodi Michael A Bentley Lorena I Rangel Edward W Davis Linda S Thomashow T Mark Zabriskie Gail M Preston Joyce E Loper

Mol Plant Microbe Interact 2014 Jul;27(7):733-46

Bacteria in the diverse Pseudomonas fluorescens group include rhizosphere inhabitants known for their antifungal metabolite production and biological control of plant disease, such as Pseudomonas protegens Pf-5, and mushroom pathogens, such as Pseudomonas tolaasii. Here, we report that strain Pf-5 causes brown, sunken lesions on peeled caps of the button mushroom (Agaricus bisporus) that resemble brown blotch symptoms caused by P. tolaasii. Strain Pf-5 produces six known antifungal metabolites under the control of the GacS/GacA signal transduction system. A gacA mutant produces none of these metabolites and did not cause lesions on mushroom caps. Mutants deficient in the biosynthesis of the antifungal metabolites 2,4-diacetylphloroglucinol and pyoluteorin caused less-severe symptoms than wild-type Pf-5 on peeled mushroom caps, whereas mutants deficient in the production of lipopeptide orfamide A caused similar symptoms to wild-type Pf-5. Purified pyoluteorin and 2,4-diacetylphloroglucinol mimicked the symptoms caused by Pf-5. Both compounds were isolated from mushroom tissue inoculated with Pf-5, providing direct evidence for their in situ production by the bacterium. Although the lipopeptide tolaasin is responsible for brown blotch of mushroom caused by P. tolaasii, P. protegens Pf-5 caused brown blotch-like symptoms on peeled mushroom caps through a lipopeptide-independent mechanism involving the production of 2,4-diacetylphloroglucinol and pyoluteorin.
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http://dx.doi.org/10.1094/MPMI-10-13-0311-RDOI Listing
July 2014

Biological control of wheat root diseases by the CLP-producing strain Pseudomonas fluorescens HC1-07.

Authors:
Ming-Ming Yang Shan-Shan Wen Dmitri V Mavrodi Olga V Mavrodi Diter von Wettstein Linda S Thomashow Jian-Hua Guo David M Weller

Phytopathology 2014 Mar;104(3):248-56

Pseudomonas fluorescens HC1-07, previously isolated from the phyllosphere of wheat grown in Hebei province, China, suppresses the soilborne disease of wheat take-all, caused by Gaeumannomyces graminis var. tritici. We report here that strain HC1-07 also suppresses Rhizoctonia root rot of wheat caused by Rhizoctonia solani AG-8. Strain HC1-07 produced a cyclic lipopeptide (CLP) with a molecular weight of 1,126.42 based on analysis by electrospray ionization mass spectrometry. Extracted CLP inhibited the growth of G. graminis var. tritici and R. solani in vitro. To determine the role of this CLP in biological control, plasposon mutagenesis was used to generate two nonproducing mutants, HC1-07viscB and HC1-07prtR2. Analysis of regions flanking plasposon insertions in HC1-07prtR2 and HC1-07viscB revealed that the inactivated genes were similar to prtR and viscB, respectively, of the well-described biocontrol strain P. fluorescens SBW25 that produces the CLP viscosin. Both genes in HC1-07 were required for the production of the viscosin-like CLP. The two mutants were less inhibitory to G. graminis var. tritici and R. solani in vitro and reduced in ability to suppress take-all. HC1-07viscB but not HC-07prtR2 was reduced in ability to suppress Rhizoctonia root rot. In addition to CLP production, prtR also played a role in protease production.
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http://dx.doi.org/10.1094/PHYTO-05-13-0142-RDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5523110PMC
March 2014

Role of bacterial communities in the natural suppression of Rhizoctonia solani bare patch disease of wheat (Triticum aestivum L.).

Authors:
Chuntao Yin Scot H Hulbert Kurtis L Schroeder Olga Mavrodi Dmitri Mavrodi Amit Dhingra William F Schillinger Timothy C Paulitz

Appl Environ Microbiol 2013 Dec 20;79(23):7428-38. Epub 2013 Sep 20.

Department of Plant Pathology, Washington State University, Pullman, Washington, USA.

Rhizoctonia bare patch and root rot disease of wheat, caused by Rhizoctonia solani AG-8, develops as distinct patches of stunted plants and limits the yield of direct-seeded (no-till) wheat in the Pacific Northwest of the United States. At the site of a long-term cropping systems study near Ritzville, WA, a decline in Rhizoctonia patch disease was observed over an 11-year period. Bacterial communities from bulk and rhizosphere soil of plants from inside the patches, outside the patches, and recovered patches were analyzed by using pyrosequencing with primers designed for 16S rRNA. Taxa in the class Acidobacteria and the genus Gemmatimonas were found at higher frequencies in the rhizosphere of healthy plants outside the patches than in that of diseased plants from inside the patches. Dyella and Acidobacteria subgroup Gp7 were found at higher frequencies in recovered patches. Chitinophaga, Pedobacter, Oxalobacteriaceae (Duganella and Massilia), and Chyseobacterium were found at higher frequencies in the rhizosphere of diseased plants from inside the patches. For selected taxa, trends were validated by quantitative PCR (qPCR), and observed shifts of frequencies in the rhizosphere over time were duplicated in cycling experiments in the greenhouse that involved successive plantings of wheat in Rhizoctonia-inoculated soil. Chryseobacterium soldanellicola was isolated from the rhizosphere inside the patches and exhibited significant antagonism against R. solani AG-8 in vitro and in greenhouse tests. In conclusion, we identified novel bacterial taxa that respond to conditions affecting bare patch disease symptoms and that may be involved in suppression of Rhizoctonia root rot and bare batch disease.
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http://dx.doi.org/10.1128/AEM.01610-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837727PMC
December 2013

Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis.

Authors:
Ningna Xu Ekta Gayanji Ahuja Petra Janning Dmitri Valeryevich Mavrodi Linda S Thomashow Wulf Blankenfeldt

Acta Crystallogr D Biol Crystallogr 2013 Aug 13;69(Pt 8):1403-13. Epub 2013 Jul 13.

Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany.

Phenazines are redox-active secondary metabolites that many bacteria produce and secrete into the environment. They are broad-specificity antibiotics, but also act as virulence and survival factors in infectious diseases. Phenazines are derived from chorismic acid, but important details of their biosynthesis are still unclear. For example, three two-electron oxidations seem to be necessary in the final steps of the pathway, while only one oxidase, the FMN-dependent PhzG, is conserved in the phenazine-biosynthesis phz operon. Here, crystal structures of PhzG from Pseudomonas fluorescens 2-79 and from Burkholderia lata 383 in complex with excess FMN and with the phenazine-biosynthesis intermediates hexahydrophenazine-1,6-dicarboxylate and tetrahydrophenazine-1-carboxylate generated in situ are reported. Corroborated with biochemical data, these complexes demonstrate that PhzG is the terminal enzyme in phenazine biosynthesis and that its relaxed substrate specificity lets it participate in the generation of both phenazine-1,6-dicarboxylic acid (PDC) and phenazine-1-carboxylic acid (PCA). This suggests that competition between flavin-dependent oxidations through PhzG and spontaneous oxidative decarboxylations determines the ratio of PDC, PCA and unsubstituted phenazine as the products of phenazine biosynthesis. Further, the results indicate that PhzG synthesizes phenazines in their reduced form. These reduced molecules, and not the fully aromatized derivatives, are the likely end products in vivo, explaining why only one oxidase is required in the phenazine-biosynthesis pathway.
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http://dx.doi.org/10.1107/S0907444913008354DOI Listing
August 2013

pA506, a conjugative plasmid of the plant epiphyte Pseudomonas fluorescens A506.

Authors:
Virginia O Stockwell Edward W Davis Alyssa Carey Brenda T Shaffer Dmitri V Mavrodi Karl A Hassan Kevin Hockett Linda S Thomashow Ian T Paulsen Joyce E Loper

Appl Environ Microbiol 2013 Sep 28;79(17):5272-82. Epub 2013 Jun 28.

Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA.

Conjugative plasmids are known to facilitate the acquisition and dispersal of genes contributing to the fitness of Pseudomonas spp. Here, we report the characterization of pA506, the 57-kb conjugative plasmid of Pseudomonas fluorescens A506, a plant epiphyte used in the United States for the biological control of fire blight disease of pear and apple. Twenty-nine of the 67 open reading frames (ORFs) of pA506 have putative functions in conjugation, including a type IV secretion system related to that of MOBP6 family plasmids and a gene cluster for type IV pili. We demonstrate that pA506 is self-transmissible via conjugation between A506 and strains of Pseudomonas spp. or the Enterobacteriaceae. The origin of vegetative replication (oriV) of pA506 is typical of those in pPT23A family plasmids, which are present in many pathovars of Pseudomonas syringae, but pA506 lacks repA, a defining locus for pPT23A plasmids, and has a novel partitioning region. We selected a plasmid-cured derivative of A506 and compared it to the wild type to identify plasmid-encoded phenotypes. pA506 conferred UV resistance, presumably due to the plasmid-borne rulAB genes, but did not influence epiphytic fitness of A506 on pear or apple blossoms in the field. pA506 does not appear to confer resistance to antibiotics or other toxic elements. Based on the conjugative nature of pA506 and the large number of its genes that are shared with plasmids from diverse groups of environmental bacteria, the plasmid is likely to serve as a vehicle for genetic exchange between A506 and its coinhabitants on plant surfaces.
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http://dx.doi.org/10.1128/AEM.01354-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753976PMC
September 2013

Taxonomy and distribution of phenazine-producing Pseudomonas spp. in the dryland agroecosystem of the Inland Pacific Northwest, United States.

Authors:
James A Parejko Dmitri V Mavrodi Olga V Mavrodi David M Weller Linda S Thomashow

Appl Environ Microbiol 2013 Jun 12;79(12):3887-91. Epub 2013 Apr 12.

School of Molecular Biosciences, Washington State University, Pullman, WA, USA.

We investigated the taxonomic placement of phenazine-producing fluorescent Pseudomonas spp. in the Inland Pacific Northwest region of the United States. Five distinct species were identified, two of which were provisionally considered to be new. Agroclimatic zone and soil silt content affected the species diversity across the region.
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http://dx.doi.org/10.1128/AEM.03945-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675913PMC
June 2013

Recent insights into the diversity, frequency and ecological roles of phenazines in fluorescent Pseudomonas spp.

Authors:
Dmitri V Mavrodi James A Parejko Olga V Mavrodi Youn-Sig Kwak David M Weller Wulf Blankenfeldt Linda S Thomashow

Environ Microbiol 2013 Mar 13;15(3):675-86. Epub 2012 Aug 13.

Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA.

Phenazine compounds represent a large class of bacterial metabolites that are produced by some fluorescent Pseudomonas spp. and a few other bacterial genera. Phenazines were first noted in the scientific literature over 100 years ago, but for a long time were considered to be pigments of uncertain function. Following evidence that phenazines act as virulence factors in the opportunistic human and animal pathogen Pseudomonas aeruginosa and are actively involved in the suppression of plant pathogens, interest in these compounds has broadened to include investigations of their genetics, biosynthesis, activity as electron shuttles, and contribution to the ecology and physiology of the cells that produce them. This minireview highlights some recent and exciting insights into the diversity, frequency and ecological roles of phenazines produced by fluorescent Pseudomonas spp.
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http://dx.doi.org/10.1111/j.1462-2920.2012.02846.xDOI Listing
March 2013

Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions.

Authors:
Joyce E Loper Karl A Hassan Dmitri V Mavrodi Edward W Davis Chee Kent Lim Brenda T Shaffer Liam D H Elbourne Virginia O Stockwell Sierra L Hartney Katy Breakwell Marcella D Henkels Sasha G Tetu Lorena I Rangel Teresa A Kidarsa Neil L Wilson Judith E van de Mortel Chunxu Song Rachel Blumhagen Diana Radune Jessica B Hostetler Lauren M Brinkac A Scott Durkin Daniel A Kluepfel W Patrick Wechter Anne J Anderson Young Cheol Kim Leland S Pierson Elizabeth A Pierson Steven E Lindow Donald Y Kobayashi Jos M Raaijmakers David M Weller Linda S Thomashow Andrew E Allen Ian T Paulsen

PLoS Genet 2012 Jul 5;8(7):e1002784. Epub 2012 Jul 5.

Agricultural Research Service, US Department of Agriculture, Corvallis, Oregon, United States of America.

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.
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http://dx.doi.org/10.1371/journal.pgen.1002784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390384PMC
July 2012

Induced systemic resistance in Arabidopsis thaliana against Pseudomonas syringae pv. tomato by 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens.

Authors:
David M Weller Dmitri V Mavrodi Johan A van Pelt Corné M J Pieterse Leendert C van Loon Peter A H M Bakker

Phytopathology 2012 Apr;102(4):403-12

United States Department of Agriculture–Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA 99164-6430, USA.

Pseudomonas fluorescens strains that produce the polyketide antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG) are among the most effective rhizobacteria that suppress root and crown rots, wilts, and damping-off diseases of a variety of crops, and they play a key role in the natural suppressiveness of some soils to certain soilborne pathogens. Root colonization by 2,4-DAPG-producing P. fluorescens strains Pf-5 (genotype A), Q2-87 (genotype B), Q8r1-96 (genotype D), and HT5-1 (genotype N) produced induced systemic resistance (ISR) in Arabidopsis thaliana accession Col-0 against bacterial speck caused by P. syringae pv. tomato. The ISR-eliciting activity of the four bacterial genotypes was similar, and all genotypes were equivalent in activity to the well-characterized strain P. fluorescens WCS417r. The 2,4-DAPG biosynthetic locus consists of the genes phlHGF and phlACBDE. phlD or phlBC mutants of Q2-87 (2,4-DAPG minus) were significantly reduced in ISR activity, and genetic complementation of the mutants restored ISR activity back to wild-type levels. A phlF regulatory mutant (overproducer of 2,4-DAPG) had ISR activity equivalent to the wild-type Q2-87. Introduction of DAPG into soil at concentrations of 10 to 250 μM 4 days before challenge inoculation induced resistance equivalent to or better than the bacteria. Strain Q2-87 induced resistance on transgenic NahG plants but not on npr1-1, jar1, and etr1 Arabidopsis mutants. These results indicate that the antibiotic 2,4-DAPG is a major determinant of ISR in 2,4-DAPG-producing P. fluorescens, that the genotype of the strain does not affect its ISR activity, and that the activity induced by these bacteria operates through the ethylene- and jasmonic acid-dependent signal transduction pathway.
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http://dx.doi.org/10.1094/PHYTO-08-11-0222DOI Listing
April 2012

Irrigation differentially impacts populations of indigenous antibiotic-producing pseudomonas spp. in the rhizosphere of wheat.

Authors:
Olga V Mavrodi Dmitri V Mavrodi James A Parejko Linda S Thomashow David M Weller

Appl Environ Microbiol 2012 May 2;78(9):3214-20. Epub 2012 Mar 2.

Department of Plant Pathology, Washington State University, Pullman, Washington, USA.

This work determined the impact of irrigation on the seasonal dynamics of populations of Pseudomonas spp. producing the antibiotics phenazine-1-carboxylic acid (Phz(+)) and 2,4-diacetylphloroglucinol (Phl(+)) in the rhizosphere of wheat grown in the low-precipitation zone (150 to 300 mm annually) of the Columbia Plateau of the Inland Pacific Northwest. Population sizes and plant colonization frequencies of Phz(+) and Phl(+) Pseudomonas spp. were determined in winter and spring wheat collected during the growing seasons from 2008 to 2009 from selected commercial dryland and irrigated fields in central Washington State. Only Phz(+) bacteria were detected on dryland winter wheat, with populations ranging from 4.8 to 6.3 log CFU g(-1) of root and rhizosphere colonization frequencies of 67 to 100%. The ranges of population densities of Phl(+) and Phz(+) Pseudomonas spp. recovered from wheat grown under irrigation were similar, but 58 to 100% of root systems were colonized by Phl(+) bacteria whereas only 8 to 50% of plants harbored Phz(+) bacteria. In addition, Phz(+) Pseudomonas spp. were abundant in the rhizosphere of native plant species growing in nonirrigated areas adjacent to the sampled dryland wheat fields. This is the first report that documents the impact of irrigation on indigenous populations of two closely related groups of antibiotic-producing pseudomonads that coinhabit the rhizosphere of an economically important cereal crop. These results demonstrate how crop management practices can influence indigenous populations of antibiotic-producing pseudomonads with the capacity to suppress soilborne diseases of wheat.
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http://dx.doi.org/10.1128/AEM.07968-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346461PMC
May 2012

Population structure and diversity of phenazine-1-carboxylic acid producing fluorescent Pseudomonas spp. from dryland cereal fields of central Washington State (USA).

Authors:
James A Parejko Dmitri V Mavrodi Olga V Mavrodi David M Weller Linda S Thomashow

Microb Ecol 2012 Jul 2;64(1):226-41. Epub 2012 Mar 2.

School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4234, USA.

Certain strains of the rhizosphere bacterium Pseudomonas fluorescens contain the phenazine biosynthesis operon (phzABCDEFG) and produce redox-active phenazine antibiotics that suppress a wide variety of soilborne plant pathogens. In 2007 and 2008, we isolated 412 phenazine-producing (Phz(+)) fluorescent Pseudomonas strains from roots of dryland wheat and barley grown in the low-precipitation region (<350 mm annual precipitation) of central Washington State. Based on results of BOX-PCR genomic fingerprinting analysis, these isolates, as well as the model biocontrol Phz(+) strain P. fluorescens 2-79, were assigned to 31 distinct genotypes separated into four clusters. All of the isolates exhibited high 16S rDNA sequence similarity to members of the P. fluorescens species complex including Pseudomonas orientalis, Pseudomonas gessardii, Pseudomonas libanensis, and Pseudomonas synxantha. Further recA-based sequence analyses revealed that the majority of new Phz(+) isolates (386 of 413) form a clade distinctly separated from P. fluorescens 2-79. Analysis of phzF alleles, however, revealed that the majority of those isolates (280 of 386) carried phenazine biosynthesis genes similar to those of P. fluorescens 2-79. phzF-based analyses also revealed that phenazine genes were under purifying selection and showed evidence of intracluster recombination. Phenotypic analyses using Biolog substrate utilization and observations of phenazine-1-carboxylic acid production showed considerable variability amongst members of all four clusters. Biodiversity indices indicated significant differences in diversity and evenness between the sampled sites. In summary, this study revealed a genotypically and phenotypically diverse group of phenazine producers with a population structure not seen before in indigenous rhizosphere-inhabiting Phz(+) Pseudomonas spp.
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http://dx.doi.org/10.1007/s00248-012-0015-0DOI Listing
July 2012