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Tokmakova AD, Tarakanov RI, Lukianova AA, Evseev PV, Dorofeeva LV, Ignatov AN, Dzhalilov FSU, Subbotin SA, Miroshnikov KA. Phytopathogenic Curtobacterium flaccumfaciens Strains Circulating on Leguminous Plants, Alternative Hosts and Weeds in Russia. PLANTS (BASEL, SWITZERLAND) 2024; 13:667. [PMID: 38475514 DOI: 10.3390/plants13050667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
Many bacterial plant pathogens have a broad host range important for their life cycle. Alternate hosts from plant families other than the main (primary) host support the survival and dissemination of the pathogen population even in absence of main host plants. Metabolic peculiarities of main and alternative host plants can affect genetic diversity within and between the pathogen populations isolated from those plants. Strains of Gram-positive bacterium Curtobacterium flaccumfaciens were identified as being causal agents of bacterial spot and wilt diseases on leguminous plants, and other crop and weed plants, collected in different regions of Russia. Their biochemical properties and susceptibility to copper compounds have been found to be relatively uniform. According to conventional PCR assays, all of the isolates studied were categorised as pathovar Curtobacterim flaccumfaciens pv. flaccumfaciens, a pathogen of legumes. However, the strains demonstrated a substantial diversity in terms of virulence on several tested host plants and different phylogenetic relationships were revealed by BOX-PCR and alanine synthase gene (alaS) sequencing.
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Affiliation(s)
- Anna D Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
| | - Rashit I Tarakanov
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, Moscow 127434, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
| | - Lyubov V Dorofeeva
- All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Prosp. Nauki 5, Pushchino 142290, Russia
| | - Alexander N Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, Moscow 117198, Russia
| | - Fevzi S-U Dzhalilov
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, Moscow 127434, Russia
| | - Sergei A Subbotin
- Center of Parasitology, Severtsov Institute of Ecology and Evolution, Leninsky Prosp., 33, Moscow 119071, Russia
- California Department of Food and Agriculture, 1220 N. Str., Sacramento, CA 95832, USA
| | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
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Banaszkiewicz S, Tabiś A, Wałecki B, Łyżwińska K, Bystroń J, Bania J. spa Types and Staphylococcal Enterotoxin Production of Staphylococcus aureus Isolated from Wild Boar. MICROBIAL ECOLOGY 2023; 86:2184-2191. [PMID: 37156959 PMCID: PMC10497643 DOI: 10.1007/s00248-023-02236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
Little is known about the structure of S. aureus population and the enterotoxin gene content in wild boar. In 1025 nasal swabs from wild boars, 121 S. aureus isolates were identified. Staphylococcal enterotoxin (SE) genes were identified in 18 isolates (14.9%). The seb gene was found in 2 S. aureus isolates, sec in 2 isolates, the see and seh genes were found in 4 and 11 isolates, respectively. The production of SEs was evaluated in bacteria grown in microbial broth. Concentration of SEB reached 2.70 µg/ml after 24 h and 4.46 µg/ml at 48 h. SEC was produced at 952.6 ng/ml after 24 h and 7.2 µg/ml at 48 h. SEE reached 124.1 ng/ml after 24 h and 191.6 ng/ml at 48 h of culture. SEH production reached 4.36 µg/ml at 24 h and 5.42 µg/ml at 48 h of culture. Thirty-nine spa types were identified among S. aureus isolates. The most prevalent spa types were t091 and t1181, followed by t4735 and t742, t3380 and t127. Twelve new spa types, i.e., t20572‒t20583 were identified. The wild boar S. aureus population was shown to contain previously identified animal/human-associated spa types and spa types not identified in humans or animals. We also indicate that wildlife animals can be a significant reservoir of see-positive S. aureus.
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Affiliation(s)
- Sylwia Banaszkiewicz
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Aleksandra Tabiś
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Bartosz Wałecki
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Karolina Łyżwińska
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jarosław Bystroń
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland.
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Pei Y, Ma L, Zheng X, Yao K, Fu X, Chen H, Chang X, Zhang M, Gong G. Identification and Genetic Characterization of Pseudomonas syringae pv. actinidiae from Kiwifruit in Sichuan, China. PLANT DISEASE 2023; 107:3248-3258. [PMID: 37005505 DOI: 10.1094/pdis-01-23-0005-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Pseudomonas syringae pv. actinidiae causes kiwifruit bacterial canker and poses a major threat to the kiwifruit industry. This study aimed to investigate the genetic characteristics of the P. syringae pv. actinidiae population from kiwifruit in Sichuan, China. Sixty-seven isolates obtained from diseased plants were characterized using morphological features, multiplex-PCR, and multilocus sequence analysis (MLSA). The isolates exhibited the typical colony morphology of P. syringae pv. actinidiae. Multiplex PCR amplification identified every isolate as P. syringae pv. actinidiae biovar 3. MLSA of the three housekeeping genes gapA, gyrB, and pfk, revealed that the reference strains of the five described biovars were clearly distinguished by a combined phylogenetic tree, and all of the tested isolates clustered with the reference strains of P. syringae pv. actinidiae biovar 3. Through a phylogenetic tree constructed from a single gene, it was found that pkf gene alone could distinguish biovar 3 from the other biovars. Furthermore, all P. syringae pv. actinidiae isolates analyzed by BOX-A1R-based repetitive extragenic palindromic (BOX)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR clustered into four groups. The clustering results of BOX- and ERIC-PCR indicated that group III had the largest number of isolates, accounting for 56.72 and 61.19% of all 67 isolates, respectively, and the two characterization methods were similar and complementary. The results of this study revealed that the genomes of P. syringae pv. actinidiae isolates from Sichuan had rich genetic diversity but no obvious correlation was found between clustering and geographical region. This research provides novel methodologies for rapidly detecting kiwifruit bacterial canker pathogen and a molecular differentiation at genetic level of P. syringae pv. actinidiae biovar diversity in China.
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Affiliation(s)
- Yangang Pei
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Li Ma
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
- Plant Protection Station, Sichuan Provincial Department of Agriculture and Rural Affairs, Chengdu 610041, P.R. China
| | - Xiaojuan Zheng
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Kaikai Yao
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Xiangru Fu
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Huabao Chen
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Xiaoli Chang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Ming Zhang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Guoshu Gong
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
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Agarwal V, Stubits R, Nassrullah Z, Dillon MM. Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks. Front Microbiol 2023; 14:1213261. [PMID: 37476668 PMCID: PMC10356107 DOI: 10.3389/fmicb.2023.1213261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.
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Affiliation(s)
- Viplav Agarwal
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Rachel Stubits
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Zain Nassrullah
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Marcus M. Dillon
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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El-Fatah BESA, Imran M, Abo-Elyousr KAM, Mahmoud AF. Isolation of Pseudomonas syringae pv. Tomato strains causing bacterial speck disease of tomato and marker-based monitoring for their virulence. Mol Biol Rep 2023; 50:4917-4930. [PMID: 37076705 DOI: 10.1007/s11033-023-08302-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/23/2023] [Indexed: 04/21/2023]
Abstract
BACKGROUND The bacterial speck disease of tomato caused by a bacterial pathogen Pseudomonas syringae pv. tomato is a most important disease causing severe crop losses. METHODS AND RESULTS Present study was conducted to investigate and characterize the population diversity of P. syringae pv. tomato pathogen isolated from infected tomato plants from various regions of Egypt. Significant variation among the isolates was observed which demonstrated considerable virulence. All isolates were pathogenic and the CFU population recovered from inoculate tomato leaves by isolate Pst-2 was higher than other isolates. Genetic disparity among the isolates was investigated by PCR analysis by amplifying hrpZ gene using random amplified polymorphic DNA (RAPD), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeats (ISSR) markers. The amplified products for ITS1 were found to have 810 bp length whereas 536 bp length was observed for hrpZ gene using primer pairs (1406-f/23S-r) and (MM5-F, MM5-R) respectively. The restriction analysis of amplified regions "ITS" and hrpZ by using 5 and 4 endonucleases respectively demonstrated slight variation among the bacterial isolates. The results of RAPD, ISSR and SRAP showed higher polymorphism (60.52%) within the isolates which may assist for successful characterization by unique and specific markers based on geographical distribution, origin and virulence intensity. CONCLUSION The results of present study suggested that the use of molecular approach may provide successful and valuable information to differentiate and classify P. syringae pv. tomato strains in future for the detection and confirmation of pathogenicity.
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Affiliation(s)
- Bahaa E S Abd El-Fatah
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526, Assiut, Egypt.
| | - Muhammad Imran
- Department of Arid Land Agriculture, King Abdulaziz University, 80208, Jeddah, Saudi Arabia
| | - Kamal A M Abo-Elyousr
- Department of Arid Land Agriculture, King Abdulaziz University, 80208, Jeddah, Saudi Arabia
- Department of Plant pathology, Faculty of Agriculture, Assiut University, 71526, Assiut, Egypt
| | - Amer F Mahmoud
- Department of Plant pathology, Faculty of Agriculture, Assiut University, 71526, Assiut, Egypt
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Ivanović M, Prokić A, Gašić K, Menković J, Kuzmanović N, Zlatković N, Obradović A. Characterization of Pseudomonas syringae Strains Associated with Shoot Blight of Raspberry and Blackberry in Serbia. PLANT DISEASE 2023; 107:826-833. [PMID: 35952382 DOI: 10.1094/pdis-06-22-1425-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
During May 2016, severe blight symptoms were observed in several raspberry and blackberry fields in Serbia. In total, 22 strains were isolated: 16 from symptomatic raspberry shoots, 2 from asymptomatic raspberry leaves, and 4 from symptomatic blackberry shoots. Additionally, eight raspberry strains, isolated earlier from two similar outbreaks, were included in the study. Pathogenicity of the strains was confirmed on detached raspberry and blackberry shoots by reproducing the symptoms of natural infection. The strains were Gram-negative, fluorescent on King's medium B, ice nucleation positive, and utilized glucose oxidatively. All strains were levan positive, oxidase negative, nonpectolytic, arginine dihydrolase negative, and induced hypersensitivity in tobacco leaves (LOPAT + - - - +, Pseudomonas group Ia). Furthermore, all strains liquefied gelatin and hydrolyzed aesculin but did not show tyrosinase activity or utilize tartrate (GATTa + + - -). Tentative identification using morphology, LOPAT, GATTa, and ice-nucleating ability tests suggested that isolated strains belong to Pseudomonas syringae. The syrB gene associated with syringomycin production was detected in all strains. DNA fingerprints with REP, ERIC, and BOX primers generated identical profiles for 29 strains, except for strain KBI 222, which showed a unique genomic fingerprint. In all, 9 of 10 selected strains exhibited identical sequences of four housekeeping genes: gyrB, rpoD, gapA, and gltA. Five nucleotide polymorphisms were found in strain KBI 222 at the rpoD gene locus only. In the phylogenetic tree based on a concatenated sequence of all four housekeeping genes, strains clustered within phylogroup 2 (i.e., genomospecies 1) of the P. syringae species complex, with pathotype strains of P. syringae pv. aceris and P. syringae pv. solidagae as their closest relatives. There was no correlation between genotype and geographic origin, particular outbreak, host, or cultivar.
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Affiliation(s)
- Milan Ivanović
- University of Belgrade-Faculty of Agriculture, 11080 Belgrade-Zemun, Serbia
| | - Anđelka Prokić
- University of Belgrade-Faculty of Agriculture, 11080 Belgrade-Zemun, Serbia
| | - Katarina Gašić
- Institute for Plant Protection and Environment, 11040 Belgrade, Serbia
| | - Jelena Menković
- University of Belgrade-Faculty of Agriculture, 11080 Belgrade-Zemun, Serbia
| | - Nemanja Kuzmanović
- Institute for Plant Protection in Horticulture and Forests, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, 38104 Braunschweig, Germany
| | - Nevena Zlatković
- Institute for Plant Protection and Environment, 11040 Belgrade, Serbia
| | - Aleksa Obradović
- University of Belgrade-Faculty of Agriculture, 11080 Belgrade-Zemun, Serbia
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Jelušić A, Mitrović P, Marković S, Iličić R, Milovanović P, Stanković S, Popović Milovanović T. Diversity of Bacterial Soft Rot-Causing Pectobacterium Species Affecting Cabbage in Serbia. Microorganisms 2023; 11:microorganisms11020335. [PMID: 36838301 PMCID: PMC9962274 DOI: 10.3390/microorganisms11020335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
The aim of this work was to identify and characterize the pectolytic bacteria responsible for the emergence of bacterial soft rot on two summer cabbage hybrids (Cheers F1 and Hippo F1) grown in the Futog locality (Bačka, Vojvodina), known for the five-century-long tradition of cabbage cultivation in Serbia. Symptoms manifesting as soft lesions on outer head leaves were observed during August 2021, while the inner tissues were macerated, featuring cream to black discoloration. As the affected tissue decomposed, it exuded a specific odor. Disease incidence ranged from 15% to 25%. A total of 67 isolates producing pits on crystal violet pectate (CVP) medium were characterized for their phenotypic and genotypic features. The pathogenicity was confirmed on cabbage heads. Findings yielded by the repetitive element palindromic-polymerase chain reaction (rep-PCR) technique confirmed interspecies diversity between cabbage isolates, as well as intraspecies genetic diversity within the P. carotovorum group of isolates. Based on multilocus sequence typing (MLST) using genes dnaX, mdh, icdA, and proA, five representative isolates were identified as Pectobacterium carotovorum (Cheers F1 and Hippo F1), while two were identified as Pectobacterium versatile (Hippo F1) and Pectobacterium odoriferum (Hippo F1), respectively, indicating the presence of diverse Pectobacterium species even in combined infection in the same field. Among the obtained isolates, P. carotovorum was the most prevalent species (62.69%), while P. versatile and P. odoriferum were less represented (contributing by 19.40% and 17.91%, respectively). Multilocus sequence analysis (MLSA) performed with concatenated sequences of four housekeeping genes (proA, dnaX, icdA, and mdh) and constructed a neighbor-joining phylogenetic tree enabled insight into the phylogenetic position of the Serbian cabbage Pectobacterium isolates. Bacterium P. odoriferum was found to be the most virulent species for cabbage, followed by P. versatile, while all three species had comparable virulence with respect to potato. The results obtained in this work provide a better understanding of the spreading routes and abundance of different Pectobacterium spp. in Serbia.
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Affiliation(s)
- Aleksandra Jelušić
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia
- Correspondence: (A.J.); (T.P.M.)
| | - Petar Mitrović
- Institute for Field and Vegetable Crops, National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, Serbia
| | - Sanja Marković
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia
| | - Renata Iličić
- Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000 Novi Sad, Serbia
| | | | - Slaviša Stanković
- Faculty of Biology, University of Belgrade, Studentski Trg 16, 11000 Belgrade, Serbia
| | - Tatjana Popović Milovanović
- Institute for Plant Protection and Environment, Teodora Drajzer 9, 11040 Belgrade, Serbia
- Correspondence: (A.J.); (T.P.M.)
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Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition. Int J Mol Sci 2022; 23:ijms232315248. [PMID: 36499572 PMCID: PMC9740669 DOI: 10.3390/ijms232315248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.
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Effects of Phenotypic Variation on Biological Properties of Endophytic Bacteria Bacillus mojavensis PS17. BIOLOGY 2022; 11:biology11091305. [PMID: 36138785 PMCID: PMC9495571 DOI: 10.3390/biology11091305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022]
Abstract
Simple Summary Microorganisms play an important role in agriculture by protecting and stimulating the growth of plants. The phenotypic activities of microbial biological agents (MBA) can change under different environmental conditions. However, to adapt to these harsh conditions, genetic mutations take place in bacteria that are seen phenotypically, which might not be beneficial or less beneficial to the plants. Some adaptative mechanisms used by microorganisms, especially bacteria, to face these environmental factors lead to the appearance of subpopulations with different morphotypes that may be more adapted to survive in stressful conditions. Moreover, in favorable conditions, these subpopulations may become dominant among the overall bacterial population. In this study, Bacillus mojavensis undergoes phase variation when grown in a minimal medium, in which two colonies, opaque (morphotype I) and translucent (morphotype II), were generated. The characteristics of the generated morphotypes were determined and compared with those of their original strain. Overall, the results obtained showed that the phenotypic characteristics of morphotype I statistically differed from morphotype II. This phenomenon may be one of the factors behind the dissimilarities in the results between the laboratory and field data on the application of MBA. Abstract The use of microorganism-based products in agricultural practices is gaining more interest as an alternative to chemical methods due to their non-toxic bactericidal and fungicidal properties. Various factors influence the efficacy of the microorganisms used as biological control agents in infield conditions as compared to laboratory conditions due to ecological and physiological aspects. Abiotic factors have been shown to trigger phase variations in bacterial microorganisms as a mechanism for adapting to hostile environments. In this study, we investigated the stability of the morphotype and the effects of phenotypic variation on the biological properties of Bacillus mojavensis strain PS17. B. mojavensis PS17 generated two variants (opaque and translucent) that were given the names morphotype I and II, respectively. The partial sequence of the 16S rRNA gene revealed that both morphotypes belonged to B. mojavensis. BOX and ERIC fingerprinting PCR also showed the same DNA profiles in both morphotypes. The characteristics of morphotype I did not differ from the original strain, while morphotype II showed a lower hydrolytic enzyme activity, phytohormone production, and antagonistic ability against phytopathogenic fungi. Both morphotypes demonstrated endophytic ability in tomato plants. A low growth rate of the strain PS17(II) in a minimal medium was observed in comparison to the PS17(I) strain. Furthermore, the capacity for biocontrol of B. mojavensis PS17(II) was not effective in the suppression of root rot disease in the tomato plants caused by Fusarium oxysporum f. sp. radices-lycopersici stain ZUM2407, compared to B. mojavensis PS17(I), whose inhibition was almost 47.9 ± 1.03% effective.
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Afordoanyi DM, Diabankana RGC, Akosah YA, Validov SZ. Are formae speciales pathogens really host specific? A broadened host specificity in Fusarium oxysporum f.sp. radicis-cucumerinum. Braz J Microbiol 2022; 53:1745-1759. [PMID: 35841534 PMCID: PMC9679123 DOI: 10.1007/s42770-022-00793-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023] Open
Abstract
Phytopathogenic strains of Fusarium oxysporum Schlecht exhibit clear host specificity, which appears to be a persistent characteristic and a dependable base for the forma specialis system of these pathogens. Here, we report an altered host specificity of the F. oxysporum f.sp. radicis-cucumerinum strain V03-2 g (Forc V03-2 g) - a causative agent of cucumber root-rot, the clonal derivates of which acquired the ability to infect tomato plants. Since the clonal derivates of Forc V03-2 g with transformed host specificity preserved their ability to parasitize on cucumber plants, the changes that occurred can be classified as broadening of host specificity. To our knowledge, this is the first observation of pathogenicity changes in formae speciales of F. oxysporum. The clonal derivates acquired could be used to trace genetic determinants of the host specificity of phytopathogenic strains of F. oxysporum.
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Affiliation(s)
- Daniel Mawuena Afordoanyi
- Laboratory of Molecular Genetics and Microbiological Methods, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia ,Department of Animal Husbandry and Veterinary Medicine, Tatar Scientific Research Institute of Agrochemistry and Soil Science, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | | | - Yaw Abayie Akosah
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York City, USA
| | - Shamil Zavdatovich Validov
- Laboratory of Molecular Genetics and Microbiological Methods, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
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11
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Kozieł M, Kalita M, Janczarek M. Genetic diversity of microsymbionts nodulating Trifolium pratense in subpolar and temperate climate regions. Sci Rep 2022; 12:12144. [PMID: 35840628 PMCID: PMC9287440 DOI: 10.1038/s41598-022-16410-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Rhizobia are soil-borne bacteria forming symbiotic associations with legumes and fixing atmospheric dinitrogen. The nitrogen-fixation potential depends on the type of host plants and microsymbionts as well as environmental factors that affect the distribution of rhizobia. In this study, we compared genetic diversity of bacteria isolated from root nodules of Trifolium pratense grown in two geographical regions (Tromsø, Norway and Lublin, Poland) located in distinct climatic (subpolar and temperate) zones. To characterize these isolates genetically, three PCR-based techniques (ERIC, BOX, and RFLP of the 16S-23S rRNA intergenic spacer), 16S rRNA sequencing, and multi-locus sequence analysis of chromosomal house-keeping genes (atpD, recA, rpoB, gyrB, and glnII) were done. Our results indicate that a great majority of the isolates are T. pratense microsymbionts belonging to Rhizobium leguminosarum sv. trifolii. A high diversity among these strains was detected. However, a lower diversity within the population derived from the subpolar region in comparison to that of the temperate region was found. Multi-locus sequence analysis showed that a majority of the strains formed distinct clusters characteristic for the individual climatic regions. The subpolar strains belonged to two (A and B) and the temperate strains to three R. leguminosarum genospecies (B, E, and K), respectively.
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Affiliation(s)
- Marta Kozieł
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland
| | - Monika Janczarek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 19 Akademicka, 20-033, Lublin, Poland.
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12
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Hossain MM, Masud MM, Hossain MI, Haque MM, Uddin MS, Alam MZ, Islam MR. Rep-PCR Analyses Reveal Genetic Variation of Ralstonia solanacearum Causing Wilt of Solanaceaous Vegetables in Bangladesh. Curr Microbiol 2022; 79:234. [PMID: 35767115 DOI: 10.1007/s00284-022-02932-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
Ralstonia solanacearum, a soil-borne and seed-borne plant pathogenic bacterium, causes bacterial wilt to several important crop plants causing substantial economic losses. To provide population information on this pathogen for developing effective control strategies, Rep-PCR was used to analyze the genetic variation of 18 representative isolates of R. solanacearum collected in Bangladesh. Phenotypic analyses revealed that all eighteen isolates belong to biotype 3 with wide diversity in aggressiveness on eggplant, tomato, and chili. Rep-PCR studies utilizing the REP, ERIC, and BOXIR primers showed a wide variation at the genetic level among the R. solanacearum isolates used in this study. Dendrogram constructed using REP, ERIC, and BOXIR primers based on banding patterns implied that R. solanacearum isolates were genetically diversified and distributed in four clusters at 83%, 80%, and 63% similarity index, respectively. The genetic relationship assayed by rep-PCR highlighted a wide range of genetic variation but no relation among geographical origin, aggressiveness, and phylogenetic groups of R. solanacearum isolates. These results conceded that other molecular markers related to virulence gene(s) might reveal the complex relationship among geographical origin, aggressiveness, and phylogenetic groups.
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Affiliation(s)
- Md Mosharraf Hossain
- Agricultural Research Station (ARS), Bangladesh Agricultural Research Institute (BARI), Satkhira, 9403, Bangladesh
| | - Md Mostafa Masud
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Muhammad Iqbal Hossain
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Mohammad Mahbubul Haque
- Plant Pathology Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, 2202, Bangladesh
| | - Mohammad Sharif Uddin
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Zahangir Alam
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Rashidul Islam
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
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13
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Oksel C, Avin FA, Mirik M, Baysal-Gurel F. Identification and Genetic Characterization of Pseudomonas syringae pv. syringae from Sweet Cherry in Turkey. PLANT DISEASE 2022; 106:1253-1261. [PMID: 34818912 DOI: 10.1094/pdis-10-21-2241-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pseudomonas syringae pv. syringae, which causes bacterial canker, is the most polyphagous bacterium in the P. syringae complex because of its broad host range. This pathogen is considered the major bacterial disease in cherry orchards. In this study, several samples were collected from infected sweet cherry (Prunus avium L.) trees in different locations of the Marmara region in Turkey between 2016 and 2018. Sixty-three isolates were identified as P. syringae pv. syringae by pathogenicity, LOPAT, GATTa, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry tests. Total genomic DNA was extracted to confirm identity, followed by PCR amplification of syrB and cfl genes. Out of 63 isolates, 12 were randomly selected for repetitive element sequence-based PCR and multilocus sequence typing analyses to gain insight into the relationships of those isolates. The cluster analysis of enterobacterial repetitive intergenic consensus-, repetitive extragenic palindromic-, and BOX-A1R-based repetitive extragenic-palindromic-PCR techniques could classify the isolates into two distinct clusters. Phylogenetic analysis was carried out to obtain the relation between isolates and the location. The multilocus sequencing typing analysis of gyrB, rpoDp, rpoDs, and gltA genes allowed a clear allocation of the isolates into two separate main clusters. The relationships among the isolates were also evaluated by constructing a genealogical median-joining network (MJN). The isolates from six locations produced 11 haplotypes that were illustrated in the MJN. The results of this study proved that location could not be an indicator for showing the genetic diversity of P. syringae pv. syringae from cherry orchards. As the genetic variability of Pseudomonads has been demonstrated, this study also showed high diversity among different isolates even within the populations. While more research is recommended, the results of this study contributed to a better understanding of the evolutionary progress of P. syringae pv. syringae and the genetic diversity of sweet cherry isolates.
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Affiliation(s)
- Cansu Oksel
- Department of Plant Protection, Tekirdag Namık Kemal University, Tekirdag 59100, Turkey
| | - Farhat A Avin
- Department of Agricultural and Environmental Sciences, Otis L. Floyd Nursery Research Center, Tennessee State University, McMinnville, TN 37110, U.S.A
| | - Mustafa Mirik
- Department of Plant Protection, Tekirdag Namık Kemal University, Tekirdag 59100, Turkey
| | - Fulya Baysal-Gurel
- Department of Agricultural and Environmental Sciences, Otis L. Floyd Nursery Research Center, Tennessee State University, McMinnville, TN 37110, U.S.A
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Bernal E, Rotondo F, Roman-Reyna V, Klass T, Timilsina S, Minsavage GV, Iruegas-Bocardo F, Goss EM, Jones JB, Jacobs JM, Miller SA, Francis DM. Migration Drives the Replacement of Xanthomonas perforans Races in the Absence of Widely Deployed Resistance. Front Microbiol 2022; 13:826386. [PMID: 35369455 PMCID: PMC8971904 DOI: 10.3389/fmicb.2022.826386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Changes in Xanthomonas race and species composition causing bacterial spot of tomato have occurred throughout the world and are often associated with epidemics. Knowledge of bacterial population structure is key for resistance discovery and deployment. We surveyed Xanthomonas spp. composition from processing tomato fields in the Midwestern United States over a 4-year period between 2017 and 2020, compared these to strains collected previously, and found that X. perforans is currently the most prevalent species. We characterized 564 X. perforans isolates for sequence variation in avrXv3 to distinguish between race T3 and T4 and validated race designation using hypersensitive response (HR) assays for 106 isolates. Race T4 accounted for over 95% of X. perforans isolates collected in the Midwest between 2017 and 2020. Whole genome sequencing, Average Nucleotide Identity (ANI) analysis, core genome alignment and single nucleotide polymorphism (SNP) detection relative to a reference strain, and phylogenomic analysis suggest that the majority of Midwestern X. perforans strains collected between 2017 and 2020 were nearly identical, with greater than 99.99% ANI to X. perforans isolates collected from Collier County, Florida in 2012. These isolates shared a common SNP variant resulting an a premature stop codon in avrXv3. One sequenced isolate was identified with a deletion of avrXv3 and shared 99.99% ANI with a strain collected in Collier Co., Florida in 2006. A population shift to X. perforans T4 occurred in the absence of widely deployed resistance, with only 7% of tomato varieties tested having the resistant allele at the Xv3/Rx-4 locus. The persistence of nearly identical strains over multiple years suggests that migration led to the establishment of an endemic population. Our findings validate a genomics-based framework to track shifts in X. perforans populations due to migration, mutation, drift, or selection based on comparisons to 146 genomes.
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Affiliation(s)
- Eduardo Bernal
- Department of Horticulture and Crop Science, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - Francesca Rotondo
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - Veronica Roman-Reyna
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Taylor Klass
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Sujan Timilsina
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Gerald V. Minsavage
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Fernanda Iruegas-Bocardo
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Erica M. Goss
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Jeffrey B. Jones
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jonathan M. Jacobs
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Sally A. Miller
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - David M. Francis
- Department of Horticulture and Crop Science, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH, United States
- *Correspondence: David M. Francis,
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15
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Longhi RD, Correia SDS, Bruzaroski SR, Poli-Frederico RC, Fagnani R, Santana EHWD. Pseudomonas fluorescens and Pseudomonas putida from refrigerated raw milk: genetic diversity and lipoproteolytic activity. J DAIRY RES 2022; 89:1-4. [PMID: 35144712 DOI: 10.1017/s0022029922000048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this research communication the genetic diversity of Pseudomonas fluorescens (n = 67) and Pseudomonas putida (n = 44) isolated from refrigerated raw milk from bulk tank trucks were verified. The relationship between the genetic profile of the isolates and their lipoproteolytic potential was evaluated using skim milk agar and tributyrin agar (21°C/72 h). The lipoproteolytic potential (low or high), evaluated by the diameter of the halos (cm), was correlated with the number of milk producing properties that contributed to each sample (one sample = one bulk tank truck; 8-80 producers/sample) and the distance between the dairy properties and the processing plant (21-370 km). P. fluorescens was confirmed in all samples, while P. putida in 60% samples. For both species, two clusters (I and II) were observed, and the first one showed lower genotypic diversity and the presence of isolates with 100% similarity. P. fluorescens isolates presenting at least 70% similarity were 83.9% in Cluster I (n = 31) and 44.4% in Cluster II. In both clusters (I and II) observed in the P. fluorescens dendrogram, the occurrence of high proteolytic and lipolytic potential were equivalent. The higher the number of farms per milk sample, the greater the lipoproteolytic intensity of P. fluorescens isolates. In relation to P. putida isolates, 74% presented at least 50% similarity in Cluster I (n = 27) and only 35% in Cluster II (n = 17). The occurrence of high proteolysis linked to P. putida was proportional between both Clusters, but the occurrence of high lipolysis was greater in Cluster II. No significant association was detected between P. putida isolates and the variables studied. The results indicate the circulation of P. putida and P. fluorescens with 100% similarity in different milk producing regions. The level of genetic diversity was related only to the lipolytic capacity of P. putida.
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Affiliation(s)
- Rosana De Longhi
- Universidade Pitágoras Unopar (UNOPAR), Mestrado em Ciência e Tecnologia de Leite e Derivados, Londrina, Paraná, Brazil
| | | | - Samera Rafaela Bruzaroski
- Universidade Pitágoras Unopar (UNOPAR), Mestrado em Ciência e Tecnologia de Leite e Derivados, Londrina, Paraná, Brazil
| | | | - Rafael Fagnani
- Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Elsa Helena Walter de Santana
- Universidade Pitágoras Unopar (UNOPAR), Mestrado em Ciência e Tecnologia de Leite e Derivados, Londrina, Paraná, Brazil
- UNOPAR, Mestrado em Saúde e Produção Animal, Arapongas, Paraná, Brazil
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16
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Chen G, Kong C, Yang L, Zhuang M, Zhang Y, Wang Y, Ji J, Fang Z, Lv H. Genetic Diversity and Population Structure of the Xanthomonas campestris pv. campestris Strains Affecting Cabbages in China Revealed by MLST and Rep-PCR Based Genotyping. THE PLANT PATHOLOGY JOURNAL 2021; 37:476-488. [PMID: 34847634 PMCID: PMC8632610 DOI: 10.5423/ppj.oa.06.2021.0088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/15/2021] [Indexed: 05/09/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot for cruciferous vegetables worldwide, especially for the cole crops such as cabbage and cauliflower. Due to the lack of resistant cabbage cultivars, black rot has brought about considerable yield losses in recent years in China. Understanding of the pathogen features is a key step for disease prevention, however, the pathogen diversity, population structure, and virulence are largely unknown. In this study, we studied 50 Xcc strains including 39 Xcc isolates collected from cabbage in 20 regions across China, using multilocus sequence genotyping (MLST), repetitive DNA sequence-based PCR (rep-PCR), and pathogenicity tests. For MLST analysis, a total of 12 allelic profiles (AP) were generated, among which the largest AP was AP1 containing 32 strains. Further cluster analysis of rep-PCR divided all strains into 14 DNA groups, with the largest group DNA I comprising of 34 strains, most of which also belonged to AP1. Inoculation tests showed that the representative Xcc strains collected from diverse regions performed differential virulence against three brassica hosts compared with races 1 and 4. Interestingly, these results indicated that AP1/DNA I was not only the main pathotype in China, but also a novel group that differed from the previously reported type races in both genotype and virulence. To our knowledge, this is the first extensive genetic diversity survey for Xcc strains in China, which provides evidence for cabbage resistance breeding and opens the gate for further cabbage-Xcc interaction studies.
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Affiliation(s)
- Guo Chen
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Congcong Kong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialei Ji
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Fang
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Co-corresponding authors: Z. Fang, Phone, FAX) +86-01082105972, E-mail) . H. Lv, Phone, FAX) +86-01062135629, E-mail)
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Co-corresponding authors: Z. Fang, Phone, FAX) +86-01082105972, E-mail) . H. Lv, Phone, FAX) +86-01062135629, E-mail)
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17
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Husni AAA, Ismail SI, Jaafar NM, Zulperi D. Current Classification of the Bacillus pumilus Group Species, the Rubber-Pathogenic Bacteria Causing Trunk Bulges Disease in Malaysia as Assessed by MLSA and Multi rep-PCR Approaches. THE PLANT PATHOLOGY JOURNAL 2021; 37:243-257. [PMID: 34111914 PMCID: PMC8200583 DOI: 10.5423/ppj.oa.02.2021.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Bacillus pumilus is the causal agent of trunk bulges disease affecting rubber and rubberwood quality and yield production. In this study, B. pumilus and other closely related species were included in B. pumilus group, as they shared over 99.5% similarity from 16S rRNA analysis. Multilocus sequence analysis (MLSA) of five housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using REP, ERIC, and BOX primers conducted to analyze the diversity and systematic relationships of 20 isolates of B. pumilus group from four rubber tree plantations in Peninsular Malaysia (Serdang, Tanah Merah, Baling, and Rawang). Multi rep-PCR results revealed the genetic profiling among the B. pumilus group isolates, while MLSA results showed 98-100% similarity across the 20 isolates of B. pumilus group species. These 20 isolates, formerly established as B. pumilus, were found not to be grouped with B. pumilus. However, being distributed within distinctive groups of the B. pumilus group comprising of two clusters, A and B. Cluster A contained of 17 isolates close to B. altitudinis, whereas Cluster B consisted of three isolates attributed to B. safensis. This is the first MLSA and rep-PCR study on B. pumilus group, which provides an in-depth understanding of the diversity of these rubber-pathogenic isolates in Malaysia.
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Affiliation(s)
- Ainur Ainiah Azman Husni
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Noraini Md. Jaafar
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Dzarifah Zulperi
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Laboratory of Sustainable Resources Management, Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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Choi O, Kim S, Kang B, Lee Y, Bae J, Kim J. Genetic Diversity and Distribution of Korean Isolates of Burkholderia glumae. PLANT DISEASE 2021; 105:1398-1407. [PMID: 33325743 DOI: 10.1094/pdis-08-20-1795-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Burkholderia glumae causes panicle blight of rice (grain rot in Japan and Korea), and the severity of damage is increasing worldwide. During 2017 and 2018, 137 isolates of B. glumae were isolated from symptomatic grain rot of rice cultivated in paddy fields throughout South Korea. Genetic diversity of the isolates was determined using transposase-based PCR (Tnp-PCR) genomic fingerprinting. All 138 isolates, including the B. glumae BGR1 strain, produced toxoflavin in various amounts, and 17 isolates produced an unidentified purple or orange pigment on Luria-Bertani medium and casamino acid-peptone-glucose medium, respectively, at 28°C. Transposase-based PCR genomic fingerprinting was performed using a novel primer designed based on transposase (tnp) gene sequences located at the ends of the toxoflavin efflux transporter operon; this method provided reliable and reproducible results. Through Tnp-PCR genomic fingerprinting, the genetic groups of Korean B. glumae isolates were divided into 11 clusters and three divisions. The Korean B. glumae isolates were mainly grouped in division I (73%). Interestingly, most of the pigment-producing isolates were grouped in divisions II and III; of these, 10 were grouped in cluster VIII, which comprised 67% of this cluster. Results of a phylogenetic analysis based on tofI and hrpB gene sequences were consistent with classification by Tnp-PCR genomic fingerprinting. The BGR1 strain did not belong to any of the clusters, indicating that this strain does not exhibit the typical genetic representation of B. glumae. B. glumae isolates showed diversity in the use of carbon and nitrogen sources, but no correlation with genetic classification by PCR fingerprinting was found. This is the first study to analyze the geographical distribution and genetic diversity of Korean B. glumae isolates.
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Affiliation(s)
- Okhee Choi
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Seunghoe Kim
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Byeongsam Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Yeyeong Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Juyoung Bae
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jinwoo Kim
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
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Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
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Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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Getahun A, Kiros S, Muleta D, Assefa F. Genetic and metabolic diversities of rhizobacteria isolated from degraded soil of Ethiopia. Heliyon 2020; 6:e05697. [PMID: 33367126 PMCID: PMC7749386 DOI: 10.1016/j.heliyon.2020.e05697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/03/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022] Open
Abstract
Genetic and metabolic diversities of rhizobacteria are the fundamental sources for their adaptation to cope with abiotic and biotic stresses in order to enhance growth and health of plants in the soil. Thus, this study was initiated to assess the genetic and metabolic diversities of rhizobacteria isolated from plants grown in degraded soil through BOX-PCR and partial sequencing of 16S rRNA genes. A total of eighty isolates were recovered and subjected to phenotypic profiling of carbohydrate and amino acid utilization, BOX PCR and 16S rRNA profiling. The phenotypic profiling showed remarkable metabolic versatility with Ochrobactrum spp, Pseudomonas spp and Klebsiella spp, and BOX-PCR showed greater discriminatory power for fingerprinting of rhizobacterial isolates with high degree of polymorphism. Bacillus spp showed the highest Simpson's diversity Index. The 16S rRNA genes sequence assigned the rhizobacteria to phyla Proteobacteria with Gammaproteobacteria and Alphaproteobacteria classes and Firmicutes with Bacilli class. The data also showed that the most dominant species were Pseudomonas and Ochrobactrum. Genetic and metabolic diversities of the rhizobacterial isolates reveal the potential of these microbes for plant growth improvement under water deficient soil after testing other inoculant traits.
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Affiliation(s)
| | - Solomon Kiros
- AddisAbaba Institute of Technology, Addis Ababa University, Ethiopia
| | - Diriba Muleta
- College of Natural Sciences, Addis Ababa University, Ethiopia
- Corresponding author.
| | - Fassil Assefa
- College of Natural Sciences, Addis Ababa University, Ethiopia
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Rotondo F, Testen AL, Horvat MM, Roman-Reyna V, Klass TL, Jacobs JM, Miller SA. First report of Xanthomonas hortorum causing bacterial leaf spot of lavender ( Lavandula × intermedia) in Ohio. PLANT DISEASE 2020; 105:484-484. [PMID: 32945738 DOI: 10.1094/pdis-08-20-1684-pdn] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In July 2018, a sample of lavender var. Grosso (Lavandula × intermedia 'Grosso') from Miami County, OH was received by The Ohio State University Vegetable Pathology Laboratory in Wooster. Lavender plants were field-grown in sandy clay soil with plastic mulch under drip irrigation. Disease incidence ranged from 0 to 32% depending on variety. Leaves and stems showed dark necrotic lesions that varied from roughly circular (ca. 0.3 to 0.5 mm diameter) to large coalesced necrotic areas surrounded by a water-soaked halo. Bacterial streaming from lesions was observed microscopically. Leaf tissue pieces (~0.5 cm2) were surface sterilized in 70% ethanol for 30 seconds and rinsed in sterile deionized water. The tissue was sliced aseptically into smaller sections in 100 μl sterile water and the bacterial suspension was streaked on yeast dextrose calcium carbonate agar medium. Ten yellow Xanthomonas-like colonies were selected after 72 hours of incubation at 28ºC in the dark. Strains were gram negative, oxidase negative and caused hypersensitive reactions on Nicotiana benthamiana (L.). All strains were genotyped after whole-cell DNA extraction by BOX-PCR (Louws et al. 1999) and had the same banding profile. Four 8-wk-old lavender plants (Lavandula dentata and Lavandula × ginginsii 'Goodwin Creek Gray') were spray-inoculated with a 106 CFU/ml suspension of strain SM175-2018 in sterile water. Control plants were sprayed with sterile water. Plants were kept in plastic bags for the first 48 h at 28°C with a 14-h photoperiod. Water-soaked necrotic lesions appeared 14 days after inoculation with SM175-2018, whereas mock-inoculated plants did not show symptoms. Bacterial isolation from symptomatic leaf tissue was carried out as described above. The BOX-PCR profile of the re-isolated strain was identical to that of SM175-2018. Multilocus sequence analysis of the housekeeping genes fuyA, gyrB, and rpoD was performed (Accession numbers: MT764834 - MT764836). The resulting concatenated data set was used to perform a phylogenetic analysis using maximum likelihood criteria to evaluate relationships with closely related Xanthomonas spp. using published reference sequences (Young et al. 2008). SM175-2018 was assigned to the X. hortorum clade (Moriniere et al. 2020) with strong bootstrap support. The strain was subjected to whole genome analysis. Genomic DNA was extracted using a QIAGEN Genomic DNA buffer set with genomic-tip 100/G following manufacturer's protocol and sequenced using the iSeq-100 Illumina platform with the Nextera DNA Flex Library Prep protocol kit and Nextera DNA CD indexes. Average nucleotide identity (ANI) analysis was performed with the ANI-Matrix software Enveomics tool (Rodriguez-R and Konstantinidis 2016) using the sequenced genome (NCBI GenBank Biosample no. SAMN11831455) and those of other X. hortorum (Vauterin et al. 1995) bacteria (pvs. hederae, carotae, vitians). SM175-2018 shared a 96% ANI with other X. hortorum strains. X. hortorum is associated with bacterial leaf spot of carrot (Scott and Dung, 2020) and also reported on ornamental plants (Mirik et al. 2010, Oliver et al. 2012, Roberts and Parkinson 2014, Klass et al. 2019), however additional research is needed to establish the host specificity of lavender strains. To our knowledge this is the first report of X. hortorum causing bacterial leaf spot of lavender in Ohio. The disease may negatively impact the yield and quality of flowers used in production of lavender oils and essences.
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Affiliation(s)
- Francesca Rotondo
- The Ohio State University, Plant Pathology, 1680 Madison Ave, Wooster, Ohio, United States, 44691;
| | - Anna Louise Testen
- USDA Agricultural Research Service, 17123, Plant Introduction Research Unity, G212 Agronomy Hall, Iowa State University, Ames, Iowa, United States, 50011
- United States;
| | - Madeline M Horvat
- The Ohio State University, Plant Pathology, Wooster, Ohio, United States;
| | - Veronica Roman-Reyna
- Ohio State University, 2647, Department of Plant Pathology, 201 Kottman Hall, 2021 Coffey Rd, Columbus, Ohio, United States, 43210;
| | - Taylor L Klass
- The Ohio State University, Plant Pathology, 201 Kottman Hall, 2021 Coffey Road, Columbus, Ohio, United States, 43210
- The Ohio State University, Ohio, United States;
| | - Jonathan Michael Jacobs
- Ohio State University, 2647, Department of Plant Pathology, 2021 Coffey Road, 201C Kottman Hall, Columbus, Ohio, United States, 43210-1132
- United States;
| | - Sally Ann Miller
- The Ohio State University, Plant Pathology, 1680 Madison Ave., Wooster, Ohio, United States, 44691;
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Endophytes from Gnetum gnemon L. can protect seedlings against the infection of phytopathogenic bacterium Ralstonia solanacearum as well as promote plant growth in tomato. Microbiol Res 2020; 238:126503. [DOI: 10.1016/j.micres.2020.126503] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/19/2020] [Accepted: 04/25/2020] [Indexed: 02/01/2023]
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Figueira D, Garcia E, Ares A, Tiago I, Veríssimo A, Costa J. Genetic Diversity of Pseudomonas syringae pv. actinidiae: Seasonal and Spatial Population Dynamics. Microorganisms 2020; 8:microorganisms8060931. [PMID: 32575724 PMCID: PMC7357126 DOI: 10.3390/microorganisms8060931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Pseudomonassyringae pv. actinidiae (Psa) is a gram-negative bacterium responsible for the bacterial canker in Actinidia chinensis var. deliciosa and A. chinensis var. chinensis, a quarantine organism threatening the kiwifruit industry sustainability. The present study aimed to determine the genetic structure of the endophytic and epiphytic populations of Psa isolated from four different Portuguese orchards with distinct abiotic conditions in two consecutive seasons. The results identified several coexisting and highly heterogeneous Psa populations. Moreover, evident changes in population structure occurred between the epiphytic and endophytic populations, and between seasons with a notable decrease in Psa diversity in autumn. This work provided solid evidence that the initial clonal expansion of Psa in Europe was followed by a wide genomic diversification. This perspective is important for the understanding of kiwifruit bacterial canker disease occurrence and Psa evolution, namely when adopting strategies for management of epidemics.
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Affiliation(s)
- Daniela Figueira
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Eva Garcia
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Aitana Ares
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Igor Tiago
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
| | - António Veríssimo
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
| | - Joana Costa
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (D.F.); (E.G.); (A.A.); (I.T.); (A.V.)
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
- Correspondence: ; Tel.: +351-239-700-920
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Fourier Transform Infrared Spectroscopy Is a New Option for Outbreak Investigation: a Retrospective Analysis of an Extended-Spectrum-Beta-Lactamase-Producing Klebsiella pneumoniae Outbreak in a Neonatal Intensive Care Unit. J Clin Microbiol 2020; 58:JCM.00098-20. [PMID: 32161093 DOI: 10.1128/jcm.00098-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/28/2020] [Indexed: 12/13/2022] Open
Abstract
The IR Biotyper is a new automated typing system based on Fourier-transform infrared (FT-IR) spectroscopy that gives results within 4 h. We aimed (i) to use the IR Biotyper to retrospectively analyze an outbreak of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP) in a neonatal intensive care unit and to compare results to BOX-PCR and whole-genome sequencing (WGS) results as the gold standard and (ii) to assess how the cutoff values used to define clusters affect the discriminatory power of the IR Biotyper. The sample consisted of 18 isolates from 14 patients. Specimens were analyzed in the IR Biotyper using the default analysis settings, and spectra were analyzed using OPUS 7.5 software. The software contains a feature that automatically proposes a cutoff value to define clusters; the cutoff value defines up to which distance the spectra are considered to be in the same cluster. Based on FT-IR, the outbreak represented 1 dominant clone, 1 secondary clone, and several unrelated clones. FT-IR results, using the cutoff value generated by the accompanying software after 4 replicates, were concordant with WGS for all but 1 isolate. BOX-PCR was underdiscriminatory compared to the other two methods. Using the cutoff value generated after 12 replicates, the results of FT-IR and WGS were completely concordant. The IR Biotyper can achieve the same typeability and discriminatory power as genome-based methods. However, to attain this high performance requires either previous, strain-dependent knowledge about the optimal technical parameters to be used or validation by a second method.
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Santiago TR, Lopes CA, Caetano-Anollés G, Mizubuti ESG. Genetic Structure of Ralstonia solanacearum and Ralstonia pseudosolanacearum in Brazil. PLANT DISEASE 2020; 104:1019-1025. [PMID: 31994983 DOI: 10.1094/pdis-09-19-1929-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial wilt-causing Ralstonia threaten numerous crops throughout the world. We studied the population structure of 196 isolates of Ralstonia solanacearum and 39 isolates of Ralstonia pseudosolanacearum, which were collected from potato- and tomato-growing areas in 19 states of Brazil. Regardless of the species, three groups of isolates were identified. One group encompassed R. pseudosolanacearum isolates. The other two groups comprise isolates of R. solanacearum (phylotype II) split according to geographic regions, one made of isolates from the North and Northeast and the other made of isolates from the Central, Southeast, and South regions (CSS). Among the isolates collected in CSS, those from tomato were genetically distinct from the potato isolates. The genetic variability in the population of R. pseudosolanacearum was lower than that of R. solanacearum, suggesting that the former was introduced in Brazil. Conversely, the high genetic variability of R. solanacearum in all regions, hosts, and times supports the hypothesis that this species is autochthonous in South America, more precisely in Brazil and Peru. For R. solanacearum, higher variability and lower migration rates were observed when tomato isolates were analyzed, indicating that the variability is caused mainly by the differences of the local, native soil population. The North subpopulation was distinct from all others, possibly because of differences in environmental features of this region. The proximity of some geographic regions and the movement of potato tubers could have facilitated migration and therefore low genetic differentiation between geographic regions. Finally, geography, which also influences host distribution, affects the structure of the population of R. solanacearum in Brazil. Despite quarantine procedures in Brazil, increasing levels of trade are a threat to biosecurity, and these results emphasize the need for improving our regional efforts to prevent the dispersal of pathogens.
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Affiliation(s)
- Thaís Ribeiro Santiago
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36.570-900, Brazil
| | | | | | - Eduardo S G Mizubuti
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36.570-900, Brazil
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Bophela KN, Petersen Y, Bull CT, Coutinho TA. Identification of Pseudomonas Isolates Associated With Bacterial Canker of Stone Fruit Trees in the Western Cape, South Africa. PLANT DISEASE 2020; 104:882-892. [PMID: 31935341 DOI: 10.1094/pdis-05-19-1102-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial canker is a common bacterial disease of stone fruit trees. The causal agents responsible for the disease include several pathovars in Pseudomonas syringae sensu lato and newly described Pseudomonas species. Pseudomonad strains were isolated from symptomatic stone fruit trees, namely apricot, peach, and plum trees cultivated in spatially separated orchards in the Western Cape. A polyphasic approach was used to identify and characterize these strains. Using a multilocus sequence typing approach of four housekeeping loci, namely cts, gapA, gyrB, and rpoD, the pseudomonad strains were delineated into two phylogenetic groups within P. syringae sensu lato: P. syringae sensu stricto and Pseudomonas viridiflava. These results were further supported by LOPAT diagnostic assays and analysis of clades in the rep-PCR dendrogram. The pseudomonad strains were pathogenic on both apricot and plum seedlings, indicative of a lack of host specificity between Pseudomonas strains infecting Prunus spp. This is a first report of P. viridiflava isolated from plum trees showing symptoms of bacterial canker. P. viridiflava is considered to be an opportunistic pathogen that causes foliar diseases of vegetable crops, fruit trees, and aromatic herbs, and thus the isolation of pathogenic P. viridiflava from twigs of plum trees showing symptoms of bacterial canker suggests that this bacterial species is a potentially emerging stem canker pathogen of stone fruit trees in South Africa.
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Affiliation(s)
- Khumbuzile N Bophela
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield 0028, Pretoria, South Africa
| | - Yolanda Petersen
- Crop Development Division, Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA 16801, U.S.A
| | - Teresa A Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield 0028, Pretoria, South Africa
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Identification and Characterization of Novel Thermophilic Bacteria from Hot Springs, Erzurum, Turkey. Curr Microbiol 2020; 77:979-987. [DOI: 10.1007/s00284-020-01880-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/09/2020] [Indexed: 12/13/2022]
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28
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Popović T, Jelušić A, Dimkić I, Stanković S, Poštić D, Aleksić G, Veljović Jovanović S. Molecular Characterization of Pseudomonas syringae pv. coriandricola and Biochemical Changes Attributable to the Pathological Response on Its Hosts Carrot, Parsley, and Parsnip. PLANT DISEASE 2019; 103:3072-3082. [PMID: 31596690 DOI: 10.1094/pdis-03-19-0674-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf spot caused by the plant pathogenic bacterium Pseudomonas syringae pv. coriandricola (Psc) was observed on carrot, parsnip, and parsley grown on a vegetable farm in the Vojvodina Province of Serbia. Nonfluorescent bacterial colonies were isolated from diseased leaves and characterized using different molecular techniques. Repetitive element PCR fingerprinting with five oligonucleotide primers (BOX, ERIC, GTG5, REP, and SERE) and the randomly amplified polymorphic DNA-PCR with the M13 primer revealed identical fingerprint patterns for all tested strains. Multilocus sequence analysis of four housekeeping genes (gapA, gltA, gyrB, and rpoD) showed a high degree (99.8 to 100%) of homology with sequences of Psc strains deposited in the Plant-Associated Microbes Database and NCBI database. The tested strains caused bacterial leaf spot symptoms on all three host plants. Host-strain specificity was not found in cross-pathogenicity tests, but the plant response (peroxidase induction and chlorophyll bleaching) was more pronounced in carrot and parsley than in parsnip.
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Affiliation(s)
- Tatjana Popović
- Institute for Plant Protection and Environment, Belgrade, Serbia
| | - Aleksandra Jelušić
- Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Ivica Dimkić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | - Dobrivoj Poštić
- Institute for Plant Protection and Environment, Belgrade, Serbia
| | - Goran Aleksić
- Institute for Plant Protection and Environment, Belgrade, Serbia
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29
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Gazdag O, Kovács R, Parádi I, Füzy A, Ködöböcz L, Mucsi M, Szili-Kovács T, Inubushi K, Takács T. Density and Diversity of Microbial Symbionts under Organic and Conventional Agricultural Management. Microbes Environ 2019; 34:234-243. [PMID: 31189767 PMCID: PMC6759338 DOI: 10.1264/jsme2.me18138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/01/2019] [Indexed: 12/23/2022] Open
Abstract
The influence of organic and conventional farming and agroecology on the diversity and functioning of indigenous soil microbial communities was examined using a multifactorial analysis based on an extended minimum data set of classical status and functional tests. Main soil physicochemical properties and selected microbiological indicators, the quantity of heterotrophic or aerobic spore-forming bacteria, basal and substrate-induced respiration, catabolic activity with MicroResp™, and fluorescein diacetate enzyme activity were characterized. A pot experiment applying the most probable number method was designed with soil dilution series using Pisum sativum L. and Triticum spelta L. to assess the symbiotic infectivity and genetic diversity of key indicator groups of the plant microbiome, e.g. nitrogen-fixing bacteria (rhizobia) and arbuscular mycorrhizal fungi. Soil pH, humus content, CFU, enzyme activity, and soil respiration were significantly higher in organic soils. The activity of soil microorganisms was mainly related to clay, humus, calcium, and magnesium parameters. A redundancy analysis test of catabolic activities showed that samples were grouped according to different substrate utilization patterns and land uses were also clearly separated from each other. Farming practice influenced the abundance and diversity of microbial populations. Dark septate endophytic fungi were only found in conventional soils. In addition to confirming soil health improvements by organic management, our results highlight the importance of a complex evaluation including both classical status and functional parameters of soil microbiota, which may more reliably indicate a shift in the quality status of soils.
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Affiliation(s)
- Orsolya Gazdag
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - Ramóna Kovács
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - István Parádi
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
- Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd UniversityH 1117, Pázmány Péter sétány 1/C., BudapestHungary
| | - Anna Füzy
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - László Ködöböcz
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - Márton Mucsi
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - Tibor Szili-Kovács
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
| | - Kazuyuki Inubushi
- Graduate School of Horticulture, Chiba UniversityMatsudo, ChibaJapan
| | - Tünde Takács
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of SciencesHerman Ottó u. 15, BudapestHungary
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Borah A, Das R, Mazumdar R, Thakur D. Culturable endophytic bacteria of Camellia species endowed with plant growth promoting characteristics. J Appl Microbiol 2019; 127:825-844. [PMID: 31216598 DOI: 10.1111/jam.14356] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 05/29/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022]
Abstract
AIM Tea (Camellia sinensis (L.) O. Kuntze) is an economically important caffeine-containing beverage crop with massive plantation in the Northeast corner of the agroclimatic belt of India. The main aim of the work was to isolate, identify and characterize the native plant growth promoting endophytes associated with tea for future microbe based bioformulation. METHODS AND RESULTS A total of 129 endophytic bacteria were isolated and characterized for plant growth promoting traits such as indole-3-acetic acid (IAA), phosphate solubilization, ammonia production, biocontrol traits like siderophore and extracellular enzyme production. BOX-PCR fingerprinting was used to differentiate the various bacterial isolates obtained from six different tea species. 16S rRNA sequencing and blast analysis showed that these isolates belonged to different genera, that is, Bacillus, Brevibacterium, Paenibacillus and Lysinibacillus. Lysinibacillus sp. S24 showed the highest phosphate solubilization and IAA acid production efficiency of 268·4 ± 14·3 and 13·5 ± 0·5 µg ml-1 , respectively. Brevibacterium sp. S91 showed the highest ammonia production of 6·2 ± 0·5 µmol ml-1 . Chitinase, cellulase, protease and pectinase activities were shown by 4·6, 34·1, 27·13 and 13·14% of the total isolates, respectively. Similarly, 41% of the total isolates were positive for 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. Further, the potent PGP isolates, S24 and S91 were able to enhance the vegetative parameters such as dry/fresh weight of root and shoot of tea plants in nursery conditions. CONCLUSION Our findings corroborate that tea endophytic bacteria possess the potential to demonstrate multiple PGP traits both, in vivo and in vitro and have the potential for further large-scale trials. SIGNIFICANCE AND IMPACT OF THE STUDY The exploration of tea endophytic bacterial community is suitable for the development of bioformulations for an integrated nutrient management and thus sustainable crop production and decreasing the hazardous effects of chemical fertilizers on the environment and human health.
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Affiliation(s)
- A Borah
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
| | - R Das
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
| | - R Mazumdar
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
| | - D Thakur
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
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Genomic and pathogenic properties of Pseudomonas syringae pv. syringae strains isolated from apricot in East Azerbaijan province, Iran. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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32
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Yin Y, Ni P, Liu D, Yang S, Almeida A, Guo Q, Zhang Z, Deng L, Wang D. Bacteriophage potential against Vibrio parahaemolyticus biofilms. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.11.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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33
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Rasul M, Yasmin S, Suleman M, Zaheer A, Reitz T, Tarkka MT, Islam E, Mirza MS. Glucose dehydrogenase gene containing phosphobacteria for biofortification of Phosphorus with growth promotion of rice. Microbiol Res 2019; 223-225:1-12. [PMID: 31178042 DOI: 10.1016/j.micres.2019.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/07/2019] [Accepted: 03/07/2019] [Indexed: 12/17/2022]
Abstract
Phosphorus (P) is an essential plant nutrient, but often limited in soils for plant uptake. A major economic constraint in the rice production is excessive use of chemical fertilizers to meet the P requirement. Bioaugmentation of phosphate solubilizing rhizobacteria (PSB) can be used as promising alternative. In the present study 11 mineral PSB were isolated from Basmati rice growing areas of Pakistan. In broth medium, PSB solubilized tricalcium phosphate (27-354 μg mL-1) with concomitant decrease in pH up to 3.6 due to the production of different organic acids, predominantly gluconic acid. Of these, 4 strains also have ability to mineralize phytate (245-412 μg mL-1). Principle component analysis showed that the gluconic acid producing PSB strains (Acinetobacter sp. MR5 and Pseudomonas sp. MR7) have pronounced effect on grain yield (up to 55%), plant P (up to 67%) and soil available P (up to 67%), with 20% reduced fertilization. For simultaneous validation of gluconic acid production by MR5 and MR7 through PCR, new specific primers were designed to amplify gcd, pqqE, pqqC genes responsible for glucose dehydrogenase (gcd) mediated phosphate solubilization. These findings for the first time demonstrated Acinetobacter soli as potent P solubilizer for rice and expands our knowledge about genus specific pqq and gcd primers. These two gcd containing PSB Acinetobacter sp. MR5 (DSM 106631) and Pseudomonas sp. MR7 (DSM 106634) submitted to German culture collection (DSMZ), serve as global valuable pool to significantly increase the P uptake, growth and yield of Basmati rice with decreased dependence on chemical fertilizer in P deficit agricultural soils.
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Affiliation(s)
- Maria Rasul
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Sumera Yasmin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
| | - M Suleman
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Institute of Microbiology, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Ahmad Zaheer
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defence Road, Lahore, Pakistan
| | - Thomas Reitz
- UFZ - Helmholtz-Centre for Environmental Research, Soil Ecology Department, Theodor-Lieser-Straße 4, 06120 Halle, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Mika T Tarkka
- UFZ - Helmholtz-Centre for Environmental Research, Soil Ecology Department, Theodor-Lieser-Straße 4, 06120 Halle, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ejazul Islam
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
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Damnjanovic D, Harvey M, Bridge WJ. Application of colony BOXA2R-PCR for the differentiation and identification of lactic acid COCCI. Food Microbiol 2019; 82:277-286. [PMID: 31027784 DOI: 10.1016/j.fm.2019.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/12/2019] [Accepted: 02/22/2019] [Indexed: 11/15/2022]
Abstract
Repetitive-PCR (rep-PCR) is a well-established genetic method for bacterial strain fingerprinting that is used mostly with REP, ERIC, (GTG)5, BOXA1R and occasionally BOXA2R repetitive primers. In this study, it was demonstrated that BOXA2R-PCR could effectively discriminate between Lactococcus lactis, Leuconostoc mesenteroides and Streptococcus thermophilus; differentiate Lactococcus lactis strains and subspeciate them into lactis and cremoris in a single reaction; generate unique strain fingerprints of various lactic acid bacteria (LAB species) commonly isolated from fermented dairy products, including occasional spoilage bacteria and yeasts. Furthermore, using direct colony PCR a reproducible and rapid method was developed for the differentiation and identification of lactic acid cocci. The simplicity and speed of this microbial identification method has potential practical value for dairy microbiologists, which was demonstrated through a microbiota investigation of select Australian retail dairy products.
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Affiliation(s)
- Dragica Damnjanovic
- School of Biotechnology and Biomolecular Sciences (BABS), Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Melissa Harvey
- School of Biotechnology and Biomolecular Sciences (BABS), Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Wallace John Bridge
- School of Biotechnology and Biomolecular Sciences (BABS), Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia.
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Abstract
In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial "species" and "clones." Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series. *This article is part of a curated collection.
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Li H, Cai X, Gong J, Xu T, Ding GC, Li J. Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight ( Phytophthora capsici). Front Microbiol 2019; 10:342. [PMID: 30873141 PMCID: PMC6401385 DOI: 10.3389/fmicb.2019.00342] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Soil-borne diseases are often less severe in organic farms, possibly because of the recruitment of beneficial microorganisms by crops. Here, the suppressiveness of organic, integrated, and conventionally managed soils to pepper blight (Phytophthora capsici) was studied in growth chamber experiments. Disease incidence was 41.3 and 34.1% lower in the soil from an organic farming system than in either the soil from the integrated or from the conventional farming systems, respectively. Beta-diversity of rhizospheric microbial communities differed among treatments, with enrichment of Bacillus, Sporosarcina, Acidobacteria Gp5, Gp6, Gp22, and Ignavibacterium by the organic soil. Cultivation-dependent analysis indicated that 50.3% of in vitro antagonists of P. capsici isolated from the rhizosphere of healthy peppers were affiliated to Bacillus. An integration of in vitro antagonists and bacterial diversity analyses indicated that Bacillus antagonists were higher in the rhizosphere of pepper treated by the organic soil. A microbial consortium of 18 in vitro Bacillus antagonists significantly increased the suppressiveness of soil from the integrated farming system against pepper blight. Overall, the soil microbiome under the long-term organic farming system was more suppressive to pepper blight, possibly owing to Bacillus antagonism in the rhizosphere. This study provided insights into microbiome management for disease suppression under greenhouse conditions.
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Affiliation(s)
- Huixiu Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Xiaoxu Cai
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Jingyang Gong
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Ting Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guo-chun Ding
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, China
| | - Ji Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, China
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Kumar AS, Aiyanathan KEA, Nakkeeran S, Manickam S. Documentation of virulence and races of Xanthomonas citri pv. malvacearum in India and its correlation with genetic diversity revealed by repetitive elements (REP, ERIC, and BOX) and ISSR markers. 3 Biotech 2018; 8:479. [PMID: 30456013 PMCID: PMC6232235 DOI: 10.1007/s13205-018-1503-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/01/2018] [Indexed: 11/28/2022] Open
Abstract
Thirty-four Xanthomonas citri pv. malvacearum (Xcm) isolates collected from three cotton-growing zones of India were subjected for virulence and race documentation and further correlated with genetic diversity as revealed by repetitive elements [repetitive extragenic palindromic (REP), enterobacterial repetitive intergenic consensus (ERIC) and BOX elements] and intersimple sequence repeat (ISSR)-PCR analyses. Among the 34 isolates tested for virulence on susceptible cultivar LRA 5166, 7 were recorded as highly virulent (HV), 16 were moderately virulent (MV) and 11 were less virulent (LV). Eight different races were recorded by using ten cotton host differentials. Twenty-two isolates (65%) belonged to race 18. Twelve isolates (35%) pertained to races 3, 5, 6, 7, 8, 11 and 13. REP, ERIC, BOX, combined repetitive elements, and ISSR analyses revealed the presence of 7, 10, 9, 11, and 8 clusters, respectively, at similarity coefficient of 0.70 in dendrograms. Principal coordinate analysis (PCoA) exhibited 76.4% and 77.5% cumulative variability for combined repetitive elements and ISSR analyses. ERIC produced the highest polymorphic information content (PIC) value (0.928). A lot of intra-pathovar variability was observed in virulence and genomic fingerprinting among Xcm isolates. Many of the isolates grouped based on geographical origin irrespective of virulence or race. The spread of the pathogen races in India might be due to the transport of germplasm lines and seed materials from one place to others.
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Affiliation(s)
- A. Sampath Kumar
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | | | - S. Nakkeeran
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - S. Manickam
- ICAR-Central Institute for Cotton Research Regional Station, Maruthamalai Road, Coimbatore, 641003 India
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da Gama MAS, Mariano RDLR, da Silva Júnior WJ, de Farias ARG, Barbosa MAG, Ferreira MÁDSV, Costa Júnior CRL, Santos LA, de Souza EB. Taxonomic Repositioning of Xanthomonas campestris pv. viticola (Nayudu 1972) Dye 1978 as Xanthomonas citri pv. viticola (Nayudu 1972) Dye 1978 comb. nov. and Emendation of the Description of Xanthomonas citri pv. anacardii to Include Pigmented Isolates Pathogenic to Cashew Plant. PHYTOPATHOLOGY 2018; 108:1143-1153. [PMID: 29688131 DOI: 10.1094/phyto-02-18-0037-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Grapevine bacterial canker, which is caused by Xanthomonas campestris pv. viticola, is one of the most important grapevine diseases in the northeastern region of Brazil. This disease causes severe damage and represents a high potential risk to the development of Brazilian viticulture. In turn, pigmented isolates pathogenic to cashew plant, making cashew fruit unfit for sale, also have been detected in Northeastern Brazil. Given that the taxonomic position of these bacteria is unclear, the multilocus sequence analysis (MLSA) technique, average nucleotide identity (ANI) values and tetranucleotide frequency correlation coefficients (TETRA) were used to analyze their phylogenetic relationship in relation to other Xanthomonas species. X. campestris pv. viticola was closely related to X. citri pv. mangiferaeindicae (repetitive-polymerase chain reaction [rep-PCR], MLSA, and ANI) and X. citri subsp. citri (MLSA and ANI). Pigmented isolates pathogenic to cashew plant were closely related to X. citri pv. anacardii (rep-PCR, MLSA, ANI, and TETRA). The results obtained in this study support the emendation of the description of X. citri pv. anacardii to include pigmented isolates of Xanthomonas pathogenic to cashew plant. In addition, the reclassification of X. campestris pv. viticola as X. citri pv. viticola comb. nov. is suggested.
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Affiliation(s)
- Marco Aurélio Siqueira da Gama
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Rosa de Lima Ramos Mariano
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Wilson José da Silva Júnior
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Antônio Roberto Gomes de Farias
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Maria Angélica Guimarães Barbosa
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Marisa Álvares da Silva Velloso Ferreira
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - César Raimundo Lima Costa Júnior
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Liliana Andréa Santos
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Elineide Barbosa de Souza
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
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Environmental and Clinical Pseudomonas aeruginosa Isolates with Pooled Presence of exo S, exo U, exo T and exo Y genes. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.3.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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40
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Suleman M, Yasmin S, Rasul M, Yahya M, Atta BM, Mirza MS. Phosphate solubilizing bacteria with glucose dehydrogenase gene for phosphorus uptake and beneficial effects on wheat. PLoS One 2018; 13:e0204408. [PMID: 30240432 PMCID: PMC6150522 DOI: 10.1371/journal.pone.0204408] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/04/2018] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to isolate, characterize and use phosphate solubilizing bacteria to enhance the bioavailability of insoluble Ca-phosphate for wheat plants. For this purpose, 15 phosphorus solubilizing bacteria (PSB) were isolated from wheat rhizospheric soils of Peshawar and southern Punjab region, Pakistan. These isolates were identified using light microscopy and 16S rRNA gene. Among the isolated bacteria, two strains (Pseudomonas sp. MS16 and Enterobacter sp. MS32) were the efficient P solubilizers based on their P solubilization activity determined qualitatively (solubilization index 3.2-5.8) as well as quantitatively (136-280 μg mL-1). These two strains produced indole-3-acetic acid (25.6-28.1 μg mL-1), gibberellic acid (2.5-11.8), solubilized zinc compounds (SI 2.8-3.3) and showed nitrogenase and 1-Aminocyclopropane-1-carboxylic acid deaminase activity in vitro. Phosphate solubilization activity of Pseudomonas sp. MS16 was further validated by amplification, sequencing and phylogenetic analysis of glucose dehydrogenase (gcd) gene (LT908484) responsible for P solubilization. Response Surface Methodology for large-scale production was used to find optimal conditions (Temperature 22.5°C, pH 7) for P solubilization. Glucose was found to support higher P solubilization in vitro. In an in vitro experiment, PSB treated wheat seedlings improved germination and seedling vigor (11% increases) as compared to un-inoculated control. Rhizoscanning of these seedlings showed an increase in various root growth parameters. Wheat inoculation with selected strain MS16 showed pronounced effect on grain yield in pot (38.5% increase) and field (17-18% increase) experiments compared to non-inoculated control. Root colonization by PSB through Florescent in situ Hybridization and Confocal Laser Scanning Microscopy confirmed their rhizosphere competence in soil. BOX-PCR confirmed the re-isolated colonies of Pseudomonas sp. MS16. The results indicated that gluconic acid producing Pseudomonas sp. MS16 from un-explored soils may be cost effective and environment friendly candidate to improve plant growth and phosphorous uptake by wheat plants.
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Affiliation(s)
- Muhammad Suleman
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Sumera Yasmin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Maria Rasul
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Mahreen Yahya
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Babar Manzoor Atta
- Plant Breeding and Genetics Division, Nuclear Institute for Food and Agriculture (NIFA), Peshawar, Pakistan
| | - Muhammad Sajjad Mirza
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
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Garcia E, Moura L, Abelleira A, Aguín O, Ares A, Mansilla P. Characterization of Pseudomonas syringae pv. actinidiae biovar 3 on kiwifruit in north-west Portugal. J Appl Microbiol 2018; 125:1147-1161. [PMID: 29877004 DOI: 10.1111/jam.13943] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/11/2018] [Accepted: 05/25/2018] [Indexed: 12/23/2022]
Abstract
AIMS Bacterial kiwifruit canker disease, caused by Pseudomonas syringae pv. actinidiae (Psa) was detected in north-west Portugal in 2010, and has since caused significant losses. The objectives of this work were to characterize the Portuguese population(s) of Psa and to define the actual prevalence of Psa biovars in the most productive kiwifruit region in Portugal. METHODS AND RESULTS Isolates obtained from Actinidia deliciosa orchards were characterized by morphological, biochemical, physiological, fatty acids and molecular tests (PCR, BOX-PCR, duplex-PCR, multiplex-PCR and RFLP), phaseolotoxin, housekeeping and effector genes and pathogenicity. Results established that only Psa biovar 3 is present in the north-west of Portugal, despite phenotypic and genetic variability among the isolates. CONCLUSIONS This work provides new information on P. syringae pv. actinidiae (Psa) genetic profile in Portugal, indicating for the first time, that two genetically different subpopulations of Psa biovar 3 are present. SIGNIFICANCE AND IMPACT OF THE STUDY A new subpopulation of Psa biovar 3 was found for the first time in Portugal, contributing to increase knowledge about this population worldwide and to support further understanding of the impact of Psa.
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Affiliation(s)
- E Garcia
- Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Refóios, Ponte de Lima, Portugal
| | - L Moura
- Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Refóios, Ponte de Lima, Portugal.,Mountain Research Centre (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios, Ponte de Lima, Portugal
| | - A Abelleira
- Estación Fitopatolóxica Areeiro, Diputación Pontevedra, Pontevedra, Spain
| | - O Aguín
- Estación Fitopatolóxica Areeiro, Diputación Pontevedra, Pontevedra, Spain
| | - A Ares
- Estación Fitopatolóxica Areeiro, Diputación Pontevedra, Pontevedra, Spain
| | - P Mansilla
- Estación Fitopatolóxica Areeiro, Diputación Pontevedra, Pontevedra, Spain
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Pizzolante G, Durante M, Rizzo D, Di Salvo M, Tredici SM, Tufariello M, De Paolis A, Talà A, Mita G, Alifano P, De Benedetto GE. Characterization of two Pantoea strains isolated from extra-virgin olive oil. AMB Express 2018; 8:113. [PMID: 29992518 PMCID: PMC6039349 DOI: 10.1186/s13568-018-0642-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/05/2018] [Indexed: 11/10/2022] Open
Abstract
The olive oil is an unfavorable substrate for microbial survival and growth. Only few microorganisms use olive oil fatty acids as carbon and energy sources, and survive in the presence of olive oil anti-microbial components. In this study, we have evaluated the occurrence of microorganisms in 1-year-stored extra-virgin olive oil samples. We detected the presence of bacterial and yeast species with a recurrence of the bacterium Stenotrophomonas rhizophila and yeast Sporobolomyces roseus. We then assayed the ability of all isolates to grow in a mineral medium supplemented with a commercial extra-virgin olive oil as a sole carbon and energy source, and analyzed the utilization of olive oil fatty acids during their growth. We finally focused on two bacterial isolates belonging to the species Pantoea septica. Both these isolates produce carotenoids, and one of them synthesizes bioemulsifiers enabling the bacteria to better survive/growth in this unfavorable substrate. Analyses point to a mixture of glycolipids with glucose, galactose and xylose as carbohydrate moieties whereas the lipid domain was constituted by C6-C10 β-hydroxy carboxylic acids.
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Affiliation(s)
- Graziano Pizzolante
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni 165, 73100 Lecce, Italy
| | - Miriana Durante
- Istituto di Scienze Delle Produzioni Alimentari-CNR, Via Provinciale Monteroni 165, 73100 Lecce, Italy
| | - Daniela Rizzo
- Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of Salento, Lecce, Italy
| | - Marco Di Salvo
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni 165, 73100 Lecce, Italy
| | - Salvatore Maurizio Tredici
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni 165, 73100 Lecce, Italy
| | - Maria Tufariello
- Istituto di Scienze Delle Produzioni Alimentari-CNR, Via Provinciale Monteroni 165, 73100 Lecce, Italy
| | - Angelo De Paolis
- Istituto di Scienze Delle Produzioni Alimentari-CNR, Via Provinciale Monteroni 165, 73100 Lecce, Italy
| | - Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni 165, 73100 Lecce, Italy
| | - Giovanni Mita
- Istituto di Scienze Delle Produzioni Alimentari-CNR, Via Provinciale Monteroni 165, 73100 Lecce, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni 165, 73100 Lecce, Italy
| | - Giuseppe Egidio De Benedetto
- Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of Salento, Lecce, Italy
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Blaiotta G, Murru N, Di Cerbo A, Romano R, Aponte M. Production of probiotic bovine salami using Lactobacillus plantarum 299v as adjunct. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:2285-2294. [PMID: 28990658 DOI: 10.1002/jsfa.8717] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/08/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Five probiotic lactobacilli were tested, alone or in combination with two commercial starters, to select the most suitable strain for a probiotic bovine salami production. Lactobacillus plantarum 299v was used with both starters, to make salami according to a traditional recipe. Salami obtained by using just the starters and by spontaneous fermentation, served as control. Microbial dynamics, as well as the main physico-chemical parameters, were monitored throughout ripening. The survival of probiotic 299v was confirmed by strains' tracking by means of RAPD-PCR coupled to a culture-independent approach PCR-DGGE-based. RESULTS The results showed a remarkable viability of the probiotic strain even after 60 days of storage. Experimental salami exhibited the same level of sensory acceptance of control salami, were hygienically safe, and characterised by pH, weight loss and microbiological loads within the ranges conventionally advocated for optimal fermented sausages. CONCLUSION Outcomes indicate the workable possibility of using second-quality beef cuts for probiotic salami production. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Giuseppe Blaiotta
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, (NA), Italy
| | - Nicoletta Murru
- Dipartimento di Medicina Veterinaria e Produzione Animali, Universita degli Studi di Napoli Federico II, Naples, Italy
| | - Alessandro Di Cerbo
- Dipartimento di Chirurgia Generale e Specialità Chirurgiche, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Raffaele Romano
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, (NA), Italy
| | - Maria Aponte
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, (NA), Italy
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Newberry EA, Babu B, Roberts PD, Dufault NS, Goss EM, Jones JB, Paret ML. Molecular Epidemiology of Pseudomonas syringae pv. syringae Causing Bacterial Leaf Spot of Watermelon and Squash in Florida. PLANT DISEASE 2018; 102:511-518. [PMID: 30673490 DOI: 10.1094/pdis-07-17-1002-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
From 2013 to 2014, bacterial leaf spot epidemics incited by Pseudomonas syringae pv. syringae affected an estimated 3,000 ha of watermelon and squash in Florida, and caused foliar blighting and transplant losses in severely affected fields. To investigate the diversity of the causal agent, we isolated 28 P. syringae strains from diseased plants grown in 10 Florida and Georgia counties over the course of 2 years. Strains were confirmed as P. syringae through sequence analysis of the 16S ribosomal RNA, phenotypic, and biochemical profiling; however, 20 displayed an atypical phenotype by exhibiting nonfluorescent activity on King's medium B agar and being negative for ice-nucleating activity. Multilocus sequence analysis and BOX polymerase chain reaction revealed the presence of two haplotypes among the collected strains that grouped into two distinct clades within P. syringae phylogroup 2. Pathogenicity testing showed that watermelon, cantaloupe, and squash seedlings were susceptible to a majority of these strains. Although both haplotypes were equally virulent on cantaloupe, they differed in virulence on watermelon and squash. The distribution of one haplotype in 9 of 10 Florida and Georgia counties sampled indicated that these epidemics were associated with the recent introduction of a novel clonal P. syringae lineage throughout major watermelon production areas in Florida.
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Affiliation(s)
- E A Newberry
- North Florida Research and Education Center, University of Florida, Quincy
| | - B Babu
- North Florida Research and Education Center, University of Florida, Quincy
| | - P D Roberts
- Southwest Florida Research and Education Center, University of Florida, Immokalee
| | - N S Dufault
- Department of Plant Pathology, University of Florida, Gainesville
| | - E M Goss
- Department of Plant Pathology, University of Florida, Gainesville
| | - J B Jones
- Department of Plant Pathology, University of Florida, Gainesville
| | - M L Paret
- North Florida Research and Education Center, University of Florida, Quincy
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Li Y, Xu G, Lin C, Wang X, Piao CG. Aureimonas populi sp. nov., isolated from poplar tree bark. Int J Syst Evol Microbiol 2018; 68:487-491. [DOI: 10.1099/ijsem.0.002479] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yong Li
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Guangtang Xu
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Caili Lin
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xizhuo Wang
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Chun-gen Piao
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
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46
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Marek-Kozaczuk M, Wdowiak-Wróbel S, Kalita M, Chernetskyy M, Deryło K, Tchórzewski M, Skorupska A. Host-dependent symbiotic efficiency of Rhizobium leguminosarum bv. trifolii strains isolated from nodules of Trifolium rubens. Antonie van Leeuwenhoek 2017; 110:1729-1744. [PMID: 28791535 PMCID: PMC5676844 DOI: 10.1007/s10482-017-0922-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/29/2017] [Indexed: 11/28/2022]
Abstract
Trifolium rubens L., commonly known as the red feather clover, is capable of symbiotic interactions with rhizobia. Up to now, no specific symbionts of T. rubens and their symbiotic compatibility with Trifolium spp. have been described. We characterized the genomic diversity of T. rubens symbionts by analyses of plasmid profiles and BOX-PCR. The phylogeny of T. rubens isolates was inferred based on the nucleotide sequences of 16S rRNA and two core genes (atpD, recA). The nodC phylogeny allowed classification of rhizobia nodulating T. rubens as Rhizobium leguminosarum symbiovar trifolii (Rlt). The symbiotic efficiency of the Rlt isolates was determined on four clover species: T. rubens, T. pratense, T. repens and T. resupinatum. We determined that Rlt strains formed mostly inefficient symbiosis with their native host plant T. rubens and weakly effective (sub-optimal) symbiosis with T. repens and T. pratense. The same Rlt strains were fully compatible in the symbiosis with T. resupinatum. T. rubens did not exhibit strict selectivity in regard to the symbionts and rhizobia closely related to Rhizobium grahamii, Rhizobium galegae and Agrobacterium radiobacter, which did not nodulate Trifolium spp., were found amongst T. rubens nodule isolates.
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Affiliation(s)
- Monika Marek-Kozaczuk
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland.
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Mykhaylo Chernetskyy
- The Botanic Garden of Maria Curie-Skłodowska University, Sławinkowska 3, 20-810, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Anna Skorupska
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
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Wdowiak-Wróbel S, Marek-Kozaczuk M, Kalita M, Karaś M, Wójcik M, Małek W. Diversity and plant growth promoting properties of rhizobia isolated from root nodules of Ononis arvensis. Antonie van Leeuwenhoek 2017; 110:1087-1103. [PMID: 28500544 PMCID: PMC5511607 DOI: 10.1007/s10482-017-0883-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/28/2017] [Indexed: 12/05/2022]
Abstract
This is the first report describing isolates from root nodules of Ononis arvensis (field restharrow). The aim of this investigation was to describe the diversity, phylogeny, and plant growth promoting features of microsymbionts of O. arvensis, i.e., a legume plant growing in different places of the southern part of Poland. Twenty-nine bacterial isolates were characterized in terms of their phenotypic properties, genome fingerprinting, and comparative analysis of their 16S rRNA, nodC and acdS gene sequences. Based on the nodC and 16S rRNA gene phylogenies, the O. arvensis symbionts were grouped close to bacteria of the genera Rhizobium and Mesorhizobium, which formed monophyletic clusters. The acdS gene sequences of all the isolates tested exhibited the highest similarities to the corresponding gene sequences of genus Mesorhizobium strains. The presence of the acdS genes in the genomes of rhizobia specific for O. arvensis implies that these bacteria may promote the growth and development of their host plant in stress conditions. The isolated bacteria showed a high genomic diversity and, in the BOX-PCR reaction, all of them (except three) exhibited DNA fingerprints specific only for them. Our studies showed that restharrow isolates formed effective symbiotic interactions with their native host (O. arvensis) and Ononis spinosa but not with Trifolium repens and Medicago sativa belonging to the same tribe Trifolieae as Ononis species and not with Lotus corniculatus, representing the tribe Loteae.
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Affiliation(s)
- Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, Maria Curie -Skłodowska University, Akademicka 19 St., 20-033, Lublin, Poland.
| | - Monika Marek-Kozaczuk
- Department of Genetics and Microbiology, Maria Curie -Skłodowska University, Akademicka 19 St., 20-033, Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, Maria Curie -Skłodowska University, Akademicka 19 St., 20-033, Lublin, Poland
| | - Magdalena Karaś
- Department of Genetics and Microbiology, Maria Curie -Skłodowska University, Akademicka 19 St., 20-033, Lublin, Poland
| | - Magdalena Wójcik
- Department of Genetics and Microbiology, Maria Curie -Skłodowska University, Akademicka 19 St., 20-033, Lublin, Poland
| | - Wanda Małek
- Department of Genetics and Microbiology, Maria Curie -Skłodowska University, Akademicka 19 St., 20-033, Lublin, Poland
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Krongdang S, Evans JD, Pettis JS, Chantawannakul P. Multilocus sequence typing, biochemical and antibiotic resistance characterizations reveal diversity of North American strains of the honey bee pathogen Paenibacillus larvae. PLoS One 2017; 12:e0176831. [PMID: 28467471 PMCID: PMC5415181 DOI: 10.1371/journal.pone.0176831] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 04/18/2017] [Indexed: 11/18/2022] Open
Abstract
Paenibacillus larvae is a Gram positive bacterium and the causative agent of the most widespread fatal brood disease of honey bees, American foulbrood (AFB). A total of thirty-three independent Paenibacillus larvae isolates from various geographical origins in North America and five reference strains were investigated for genetic diversity using multilocus sequence typing (MLST). This technique is regarded to be a powerful tool for epidemiological studies of pathogenic bacteria and is widely used in genotyping assays. For MLST, seven housekeeping gene loci, ilvD (dihydroxy-acid dyhydrogenase), tri (triosephosphate isomerase), purH (phospharibosyl-aminoimidazolecarboxamide), recF (DNA replication and repair protein), pyrE (orotate phosphoribosyltransferase), sucC (succinyl coenzyme A synthetase β subunit) and glpF (glycerol uptake facilitator protein) were studied and applied for primer designs. Previously, ERIC type DNA fingerprinting was applied to these same isolates and the data showed that almost all represented the ERIC I type, whereas using BOX-PCR gave an indication of more diversity. All isolates were screened for resistance to four antibiotics used by U.S. beekeepers, showing extensive resistance to tetracycline and the first records of resistance to tylosin and lincomycin. Our data highlight the intraspecies relationships of P. larvae and the potential application of MLST methods in enhancing our understanding of epidemiological relationships among bacterial isolates of different origins.
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Affiliation(s)
- Sasiprapa Krongdang
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jay D. Evans
- USDA-ARS, Bee Research Laboratory, Beltsville, MD, United States of America
| | - Jeffery S. Pettis
- USDA-ARS, Bee Research Laboratory, Beltsville, MD, United States of America
| | - Panuwan Chantawannakul
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Material Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
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Li Y, Wang SK, Xue H, Chang JP, Guo LM, Yang XQ. Corticicoccus populi gen. nov., sp. nov., a member of the family Staphylococcaceae, isolated from symptomatic bark of Populus × euramericana canker. Int J Syst Evol Microbiol 2017; 67:789-794. [DOI: 10.1099/ijsem.0.001602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yong Li
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Sheng-kun Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Han Xue
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Ju-pu Chang
- Puyang Academy of Forestry, Puyang 457000, PR China
| | - Li-min Guo
- Puyang Academy of Forestry, Puyang 457000, PR China
| | - Xu-qi Yang
- Puyang Academy of Forestry, Puyang 457000, PR China
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50
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Pizzolante G, Cordero C, Tredici SM, Vergara D, Pontieri P, Del Giudice L, Capuzzo A, Rubiolo P, Kanchiswamy CN, Zebelo SA, Bicchi C, Maffei ME, Alifano P. Cultivable gut bacteria provide a pathway for adaptation of Chrysolina herbacea to Mentha aquatica volatiles. BMC PLANT BIOLOGY 2017; 17:30. [PMID: 28249605 PMCID: PMC5333409 DOI: 10.1186/s12870-017-0986-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND A chemical cross-talk between plants and insects is required in order to achieve a successful co-adaptation. In response to herbivory, plants produce specific compounds, and feeding insects respond adequately7 to molecules produced by plants. Here we show the role of the gut microbial community of the mint beetle Chrysolina herbacea in the chemical cross-talk with Mentha aquatica (or watermint). RESULTS By using two-dimensional gas chromatography-mass spectrometry we first evaluated the chemical patterns of both M. aquatica leaf and frass volatiles extracted by C. herbacea males and females feeding on plants, and observed marked differences between males and females volatiles. The sex-specific chemical pattern of the frass paralleled with sex-specific distribution of cultivable gut bacteria. Indeed, all isolated gut bacteria from females belonged to either α- or γ-Proteobacteria, whilst those from males were γ-Proteobacteria or Firmicutes. We then demonstrated that five Serratia marcescens strains from females possessed antibacterial activity against bacteria from males belonging to Firmicutes suggesting competition by production of antimicrobial compounds. By in vitro experiments, we lastly showed that the microbial communities from the two sexes were associated to specific metabolic patterns with respect to their ability to biotransform M. aquatica terpenoids, and metabolize them into an array of compounds with possible pheromone activity. CONCLUSIONS Our data suggest that cultivable gut bacteria of Chrysolina herbacea males and females influence the volatile blend of herbivory induced Mentha aquatica volatiles in a sex-specific way.
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Affiliation(s)
- Graziano Pizzolante
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy
| | - Chiara Cordero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via Pietro Giuria n°9, 10125 Torino, Italy
| | - Salvatore M. Tredici
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy
| | - Davide Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy
| | - Paola Pontieri
- Dipartimento di Biologia, Sezione di Igiene, Institute of Biosciences and Bioresources-UOS Portici (IBBR-UOS Portici), CNR, Portici (NA) c/o, 80134 Naples, Italy
| | - Luigi Del Giudice
- Dipartimento di Biologia, Sezione di Igiene, Institute of Biosciences and Bioresources-UOS Portici (IBBR-UOS Portici), CNR, Portici (NA) c/o, 80134 Naples, Italy
| | - Andrea Capuzzo
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Quarello 15/A, 10135 Torino, Italy
| | - Patrizia Rubiolo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via Pietro Giuria n°9, 10125 Torino, Italy
| | - Chidananda N. Kanchiswamy
- Research and Innovation Centre Genomics and Biology of Fruit Crop Department, Fondazione Edmund Mach (FEM), Istituto Agrario San Michele (IASMA), Via Mach 1, 38010 San Michele all’Adige, TN Italy
| | - Simon A. Zebelo
- Department of Natural Sciences, University of Maryland Eastern Shore, 1117 Trigg Hall, Princess Anne, 21853 MD USA
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via Pietro Giuria n°9, 10125 Torino, Italy
| | - Massimo E. Maffei
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Quarello 15/A, 10135 Torino, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy
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