First Report of Streptomyces stelliscabiei Causing Potato Common Scab in Michigan

Potato (Solanum tuberosum L.) common scab can be caused by multiple Streptomyces spp., with S. scabies as a predominant species (2,3). However, according to our survey in August 2007, many symptomatic potato tubers did not have S. scabies in Michigan. To identify the pathogen, potato tubers with scab symptoms were collected from two fields in Michigan, and Streptomyces spp. were isolated using Streptomyces selective medium (STR) (2). Pure cultures of the isolates were obtained by transferring single colonies and incubation at 28°C on STR. Three isolates, designated HER21, HER24, and HER26, were identified as Streptomyces stelliscabiei based on morphological and physiological characterization (1). Bacterial cultures were prepared in liquid yeast malt extract at 28°C on an incubator shaker at 150 rpm. Genomic DNA was extracted from the cultures and used as a template for PCR with species-specific primers for Streptomyces spp. (4). The isolates gave a positive PCR reaction with primers Stel3 and T2st2 for S. stelliscabiei, but negative for any other Streptomyces spp. reported as pathogenic to potato. The 16S rRNA genes were amplified using primers previously reported (4) and amplicons were sequenced and submitted to GenBank (Accession Nos. HM018115, HM018116, and HM018117 for the three isolates, respectively). BLAST analysis of these sequences against the NCBI GenBank database determined these sequences to have 99 to 100% sequence identity with S. stelliscabiei sequences such as Accession No. FJ546728 (4). These isolates were all confirmed by PCR, using the same conditions described above, to have txtAB, nec1, and tomA genes (4), which are associated with pathogenicity of scab-causing Streptomyces spp. To complete Koch's postulates, cell suspensions of the isolates were mixed in vermiculate media (3) at a final concentration of 106 colony-forming units/ml, which were used as inocula. Potato (cv Snowden) tubers were incubated in sterilized potting mix in a growth chamber at 25°C until the seed germinated. Each potato seedling was transferred to a new pot in the greenhouse. Two weeks later, the potting mix was infested with the bacterial spore suspensions of either HER21, HER24, or HER26, with five pots per isolate. Potting mix with only media or media with S. scabies isolate 49173 were used as negative and positive controls, respectively. Three months later, potato tubers were harvested and evaluated for scab symptoms (3). The experiment was done twice. Potato tubers inoculated with either S. stelliscabiei or S. scabies exhibited superficial, raised, or pitted scabby symptoms, and no symptoms were observed on tubers grown in noninfested potting mix. Disease index values from the combined trials averaged 0, 37.8, 26.5, 11.1, and 30.5% for negative control and isolates HER21, HER24, HER26, and 49173, respectively. The pathogen was reisolated from the lesions and confirmed identical to the original isolate by DNA sequences. To our knowledge, this is the first report of S. stelliscabiei causing potato common scab in Michigan (4). References: (1) K. Bouchek-Mechiche et al. Int. J. Syst. Evol. Microbiol. 50:91, 2000. (2) Conn et al. Plant Dis. 82:631, 1998. (3) Hao et al. Plant Dis. 93:1329, 2009. (4) L. A. Wanner. Am. J. Potato Res. 86:247, 2009.

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Characterization of a New Streptomyces Strain, DS3024, That Causes Potato Common Scab

Plant Disease ◽

10.1094/pdis-93-12-1329 ◽

2009 ◽

Vol 93 (12) ◽

pp. 1329-1334 ◽

Cited By ~ 19

Author(s):

J. J. Hao ◽

Q. X. Meng ◽

J. F. Yin ◽

W. W. Kirk

Keyword(s):

Common Scab ◽

Potato Tubers ◽

North Central ◽

Thaxtomin A ◽

The North ◽

Streptomyces Spp ◽

Common Marker ◽

Central United States ◽

Potato Common Scab

A novel strain of Streptomyces (named DS3024) was isolated from a potato field in Michigan in 2006. The taxonomy of the organism was determined by morphology, biochemistry, and genetic analysis. Analysis of the 16S ribosomal RNA gene sequence indicated that the organism was most similar to an isolate of Streptomyces sp., ME02-6979.3a, which is not pathogenic to potato tubers but is distinct from other known pathogenic Streptomyces spp. Strain DS3024 has genes that encode thaxtomin synthetase (txtAB), which is required for pathogenicity and virulence, and tomatinase (tomA), which is a common marker for many pathogenic Streptomyces spp. However, the nec1 gene (associated with virulence in most pathogenic Streptomyces spp.) was not detected. The new strain was capable of growth at pH 4.5, caused necrosis on potato tuber slices, and produced thaxtomin A. In greenhouse experiments, DS3024 caused scab symptoms on potato tubers similar to those caused by Streptomyces scabies on tubers of potato cv. Atlantic, which is scab susceptible. We propose that DS3024 is a new strain of Streptomyces capable of causing common scab on potato tubers. The prevalence of this strain of Streptomyces in potato-producing areas in the north-central United States has not been determined.

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First Report of Streptomyces stelliscabiei Causing Potato Common Scab in Guizhou Province, China

Plant Disease ◽

10.1094/pdis-06-21-1242-pdn ◽

2021 ◽

Author(s):

Utpal Handique ◽

Ruofang Zhang ◽

Zhxin Zhang ◽

Zhiwen Feng ◽

Qinghua Sun ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenetic Trees ◽

Common Scab ◽

Disease Incidence ◽

Guizhou Province ◽

Rrna Gene ◽

Potato Tubers ◽

First Report ◽

Potato Common Scab

Potato (Solanum tuberosum L.) common scab can be caused by multiple pathogenic Streptomyces spp. worldwide. Potato tubers (cv. Favorita) with severe pitted common scab symptoms were observed at a small farm (2 hectares) during harvest in Anshun, Guizhou province in early May 2020. The disease incidence was around 10%, and symptomatic samples were collected to isolate the pathogen. Two isolates, ZR-IMU141 and ZR-IMU146 (Accession number MW995958 and MW995959 respectively), showed more than 99% sequence identity to S. stelliscabiei sequences (Accession No. HM018085). Five house-keeping genes for multi-locus sequence analyze (MLSA) of Streptomycetaceae were amplified, sequenced and uploaded to NCBI: atpD (MZ343164 and MZ343165), gyrB (MZ343162 and MZ343163), recA (MZ343166 and MZ343167), rpoB (MZ343168and MZ343169) and trpB (MZ343170 and MZ343171). All the genes show over 98% identity with S. stelliscabiei. Phylogenetic trees of 16S rRNA gene sequence and multi-locus sequence analysis (MLSA) were constructed. The two isolates contain pathogenicity genes txtAB, nec1, and tomA, which was confirmed by PCR. To complete Koch’s postulates, 9 potato seedlings (cv. Favorita, 15 centimeters high), were transferred to new pots and inoculated with spore suspensions of ZR-IMU141 and ZR-IMU146 (104 CFU/ml), or water as a negative control. Two months later, potato tubers inoculated with either ZR-IMU141 or ZR-IMU146 exhibited typical symptoms of potato common scab, such as superficial or deep, raised, pitted, or polygonal lesions like the field symptoms, but the negative controls remained asymptomatic. The pathogens were reisolated from the lesions and confirmed identical to the original isolate by 16s rRNA gene sequences. To our knowledge, this is the first report of S. stelliscabiei causing potato common scab in Guizhou province, China. We believe that this report will draw attention to the study and management of the increased pool of scab pathogens in China.

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Variability of the Sheep Lung Microbiota

Applied and Environmental Microbiology ◽

10.1128/aem.00540-16 ◽

2016 ◽

Vol 82 (11) ◽

pp. 3225-3238 ◽

Cited By ~ 27

Author(s):

Laura Glendinning ◽

Steven Wright ◽

Jolinda Pollock ◽

Peter Tennant ◽

David Collie ◽

...

Keyword(s):

Spatial Variability ◽

Dna Sequences ◽

Bacterial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Large Animal ◽

Local Factors ◽

Adult Sheep ◽

Sequencing Technologies ◽

Host Influence

ABSTRACTSequencing technologies have recently facilitated the characterization of bacterial communities present in lungs during health and disease. However, there is currently a dearth of information concerning the variability of such data in health both between and within subjects. This study seeks to examine such variability using healthy adult sheep as our model system. Protected specimen brush samples were collected from three spatially disparate segmental bronchi of six adult sheep (age, 20 months) on three occasions (day 0, 1 month, and 3 months). To further explore the spatial variability of the microbiotas, more-extensive brushing samples (n= 16) and a throat swab were taken from a separate sheep. The V2 and V3 hypervariable regions of the bacterial 16S rRNA genes were amplified and sequenced via Illumina MiSeq. DNA sequences were analyzed using the mothur software package. Quantitative PCR was performed to quantify total bacterial DNA. Some sheep lungs contained dramatically different bacterial communities at different sampling sites, whereas in others, airway microbiotas appeared similar across the lung. In our spatial variability study, we observed clustering related to the depth within the lung from which samples were taken. Lung depth refers to increasing distance from the glottis, progressing in a caudal direction. We conclude that both host influence and local factors have impacts on the composition of the sheep lung microbiota.IMPORTANCEUntil recently, it was assumed that the lungs were a sterile environment which was colonized by microbes only during disease. However, recent studies using sequencing technologies have found that there is a small population of bacteria which exists in the lung during health, referred to as the “lung microbiota.” In this study, we characterize the variability of the lung microbiotas of healthy sheep. Sheep not only are economically important animals but also are often used as large animal models of human respiratory disease. We conclude that, while host influence does play a role in dictating the types of microbes which colonize the airways, it is clear that local factors also play an important role in this regard. Understanding the nature and influence of these factors will be key to understanding the variability in, and functional relevance of, the lung microbiota.

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Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

Applied and Environmental Microbiology ◽

10.1128/aem.02157-10 ◽

2011 ◽

Vol 77 (7) ◽

pp. 2264-2274 ◽

Cited By ~ 285

Author(s):

Ji Young Jung ◽

Se Hee Lee ◽

Jeong Myeong Kim ◽

Moon Su Park ◽

Jin-Woo Bae ◽

...

Keyword(s):

Microbial Community ◽

Dna Sequences ◽

Leuconostoc Mesenteroides ◽

16S Rrna Genes ◽

Read Length ◽

Rrna Genes ◽

Genetic Profile ◽

Average Read Length ◽

Metabolic Potential ◽

Fermentation Products

ABSTRACTKimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera:Leuconostoc,Lactobacillus, andWeissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, theLeuconostoc mesenteroidessubsp.mesenteroidesATCC 8293 andLactobacillus sakeisubsp.sakei23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity toLeuconostoc mesenteroidesandLactobacillusgenes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.

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Isolation and Characterization of Plant-Pathogenic Streptomyces Species Associated with Common Scab-Infected Potato Tubers in Newfoundland

Phytopathology ◽

10.1094/phyto-05-15-0125-r ◽

2016 ◽

Vol 106 (2) ◽

pp. 123-131 ◽

Cited By ~ 15

Author(s):

Joanna K. Fyans ◽

Luke Bown ◽

Dawn R. D. Bignell

Keyword(s):

Common Scab ◽

Virulence Gene ◽

Potato Scab ◽

Potato Tubers ◽

Streptomyces Species ◽

Genus Streptomyces ◽

Thaxtomin A ◽

Streptomyces Spp ◽

Putative Virulence Gene ◽

Isolation And Characterization

Potato common scab (CS) is an economically important crop disease that is caused by several members of the genus Streptomyces. In this study, we characterized the plant-pathogenic Streptomyces spp. associated with CS-infected potato tubers harvested in Newfoundland, Canada. A total of 17 pathogenic Streptomyces isolates were recovered from potato scab lesions, of which eight were determined to be most similar to the known CS pathogen S. europaeiscabiei. All eight S. europaeiscabiei isolates were found to produce the thaxtomin A phytotoxin and to harbor the nec1 virulence gene, and most also carry the putative virulence gene tomA. The remaining isolates appear to be novel pathogenic species that do not produce thaxtomin A, and only two of these isolates were determined to harbor the nec1 or tomA genes. Of the non-thaxtomin-producing isolates, strain 11-1-2 was shown to exhibit a severe pathogenic phenotype against different plant hosts and to produce a novel, secreted phytotoxic substance. This is the first report documenting the plant-pathogenic Streptomyces spp. associated with CS disease in Newfoundland. Furthermore, our findings provide further evidence that phytotoxins other than thaxtomin A may also contribute to the development of CS by Streptomyces spp.

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Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses

Plant Disease ◽

10.1094/pdis-07-11-0571 ◽

2012 ◽

Vol 96 (5) ◽

pp. 718-725 ◽

Cited By ~ 97

Author(s):

Noah Rosenzweig ◽

James M. Tiedje ◽

John F. Quensen ◽

Qingxiao Meng ◽

Jianjun J. Hao

Keyword(s):

Microbial Communities ◽

Common Scab ◽

Disease Suppression ◽

Rrna Gene ◽

Suppressive Soil ◽

Streptomyces Spp ◽

Potato Common Scab ◽

Order Of Magnitude ◽

Disease Suppressive Soil ◽

Conducive Soil

Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogenetically taxon-informative region of the 16S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobacter were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil.

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First Report of Dieback on Hybrid Rhododendrons Caused by Neofusicoccum luteum and N. parvum in Spain

Plant Disease ◽

10.1094/pdis-10-10-0723 ◽

2011 ◽

Vol 95 (2) ◽

pp. 221-221 ◽

Cited By ~ 6

Author(s):

C. Pintos Varela ◽

V. Redondo Fernández ◽

J. P. Mansilla Vázquez ◽

O. Aguín Casal

Keyword(s):

Dna Sequences ◽

Uv Light ◽

Morphological Characteristics ◽

Phytophthora Ramorum ◽

Malt Extract ◽

First Report ◽

Agar Plug ◽

Thin Walled ◽

Neofusicoccum Luteum

During the conducting of Phytophthora ramorum surveys at Galician public parks (northwestern Spain) in 2010, established Rhododendron spp. plants were observed to be exhibiting leaf spots and necrosis, shoot blight, and cankers and dieback of shoots and branches. Branches and leaves of affected rhododendrons contained pseudothecia with bitunicate asci and hyaline pseudoparaphyses, and pycnidia were observed within the same stromatic masses. Symptomatic samples were disinfested in 0.5% sodium hypochlorite for 3 min. Tissues were cut from the margin of lesions, placed onto malt extract agar amended with streptomycin (25 μg ml–1), and incubated at 25°C in the dark. Cultures displaying morphological characteristics associated with Botryosphaeriaceae species were subcultured on 2% water agar with sterilized Pinus pinaster needles as a substrate and incubated at 25°C under near-UV light to encourage pycnidial production (1). Single conidial cultures gave rise to two distinct colonies on potato dextrose agar (PDA) at 25°C. In type 1, isolates produced a sparse, aerial mycelium and a characteristic yellow pigment that was more intense after 3 days, thereafter becoming violaceous and gradually turning dark gray. Growth occurred in the range of 4 to 38°C with an optimum at 29°C. Conidia were hyaline, fusiform, aseptate, thin walled, and averaged 21.1 (14.3 to 25.0) × 5.7 (4.3 to 6.8) μm with a length/width (L/W) ratio of 3.7 ± 0.4 (n = 100). On the basis of these characteristics, isolates were identified as Neofusicoccum luteum (1,3). Colonies of type 2 produced a dense, white-to-yellowish mycelium that rapidly became gray followed by marked diurnal zonation. Mycelial growth occurred in the range of 6 to 38°C with an optimum at 29 to 30°C. Conidia were hyaline, elliptical or fusiform, aseptate, thin walled, and averaging 18.3 (14.1 to 20.7) × 5.8 (4.6 to 7.0) μm with a L/W ratio of 3.2 ± 0.4 (n = 100). These isolates were identified as N. parvum (1,2). Identity was confirmed by DNA sequences analysis of internal transcribed spacer (ITS) regions. Comparison of the sequences of type 1 and 2 showed 100% homology with N. luteum and N. parvum (GenBank Accession Nos. EU673311 and GU251146, respectively). Representative sequences were deposited at GenBank (Accession Nos. HQ197352 and HQ197351). Pathogenicity of each isolate of N. luteum and N. parvum was confirmed by inoculating four 3-year-old Rhododendron spp. seedlings grown in pots. Shallow cuts were made in three branches of each plant. A colonized 6-mm agar plug, removed from the margin of an actively growing colony, was inserted beneath the flap and sealed with Parafilm. Four control seedlings received only sterile PDA agar plugs. Plants were maintained at 26°C and 70% humidity for 21 days. Inoculated plants began showing symptoms after 3 days. Necrosis progressed quickly and bidirectionally from the wound, resulting in death of leaves and wilting of shoots. N. luteum and N. parvum were reisolated from all inoculated plants but not from the controls. To our knowledge, this is the first report of N. luteum and N. parvum on Rhododendron spp. in Spain. References: (1) P. W. Crous et al. Stud. Mycol. 55:235, 2006. (2) S. R. Pennycook et al. Mycotaxon 24:445, 1985. (3) A .J. L. Phillips et al. Sydowia 54:59, 2002.

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First Report of Meloidogyne marylandi Infecting Bermudagrass in Oklahoma

Plant Disease ◽

10.1094/pdis-04-14-0399-pdn ◽

2014 ◽

Vol 98 (9) ◽

pp. 1286-1286 ◽

Cited By ~ 3

Author(s):

N. Walker

Keyword(s):

Cynodon Dactylon ◽

16S Rrna Genes ◽

Rrna Genes ◽

Similar Species ◽

Root Knot Nematode ◽

Putting Greens ◽

Egg Masses ◽

First Report ◽

Mean Width ◽

Ultradwarf Bermudagrass

Meloidogyne marylandi is a nematode commonly associated with turfgrasses and has been reported to occur in Texas and Arkansas (1,3). In the fall of 2013, a stand of ultradwarf bermudagrass (Cynodon dactylon × C. transvaalensis) plants in a sand-based, research putting green in Stillwater, Oklahoma, exhibited symptoms of decline. Roots of the affected plants had small galls and upon staining of the root system, numerous egg masses were evident. Egg masses were collected, placed in water, and the morphology of 20 hatched, second-stage juveniles were examined. The characteristics of the juveniles were: body length averaged 393.1 ± 19.87 (range: 361 to 425) μm, mean width averaged 16.6 ± 0.7 (15.6 to 17.8) μm, stylet lengths averaged 12.1 ± 0.7 (10.4 to 12.9) μm, dorsal gland orifice from stylet base averaged 2.9 ± 0.4 (2.5 to 3.6) μm, tail lengths averaged 53.7 ± 3.8 (46.2 to 60.4) μm, and the hyaline region of the tails averaged 10.4 ± 1.1 (8.4 to 12.7) μm. Genomic DNA was extracted from six females that were removed from roots. Amplification and sequencing of the mitochondrial DNA region between COII and 16S rRNA genes was performed with primers 1RNAF (5′-TACCTTTGACCAATCACGCT-3′) and CO11R (5′-GGTCAATGTTCAGAAATTTGTGG-3′) as previously described (2). A PCR product approximately 510 bp in length was obtained and sequenced at the Oklahoma State University Core Facility. Sequences were compared with those in NCBI's nucleotide database using BLAST and had 97% identity with two sequences from M. marylandi (KC473862.1 and KC473863.1) and the next most similar species being M. graminis (JN241898.1) with 83% identity. To our knowledge, this is the first report of the root-knot nematode M. marylandi in Oklahoma. As bermudagrass becomes more commonly used for putting greens in the turfgrass transition zone, M. marylandi may become a more common and damaging pathogen in the region. References: (1) A. A. Elmi et al. Grass For. Sci. 55:166, 2000. (2) M. A. McClure et al. Plant Dis. 96:635, 2012. (3) J. L. Starr et al. Nematrop. 37:43, 2007.

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The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR

Brazilian Journal of Biology ◽

10.1590/1519-6984.247529 ◽

2023 ◽

Vol 83 ◽

Author(s):

A. Belmok ◽

T. Rodrigues-Oliveira ◽

F.A.C. Lopes ◽

R.H. Krüger ◽

C.M. Kyaw

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Dna Sequences ◽

16S Rrna Genes ◽

Rrna Genes ◽

Universal Primers ◽

Rrna Gene ◽

Natural Habitats ◽

16S Rdna Pcr ◽

Archaeal Communities

Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

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First report of Streptomyces bottropensis causing potato common scab in Galicia, Spain

Plant Disease ◽

10.1094/pdis-11-17-1803-pdn ◽

2018 ◽

Vol 102 (7) ◽

pp. 1445 ◽

Cited By ~ 1

Author(s):

A. Sarwar ◽

Z. Latif ◽

C. Cabaleiro

Keyword(s):

Common Scab ◽

First Report ◽

Potato Common Scab

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