SAMN37359886
External Id
USDA Emerging Pest and Pathogen Research Unit
INSDC center name
2023-09-12T00:00:00Z
INSDC first public
2023-09-13T15:18:52.700Z
INSDC last update
SRS18873870
INSDC secondary accession
live
INSDC status
Microbe, viral or environmental
NCBI submission model
Microbe.1.0
NCBI submission package
SRS18873870
SRA accession
Paul Stodghill, USDA-ARS
biomaterial_provider
Stephen Stresow; Jo Ann Asselin
collected_by
2021
collection_date
Strain is HiVir- (non-pathogenic on onions) and Alt-. Small canes (diameter < 5mm) from a plant of Rubus sp. with disease symptoms, i.e. water-soaked and necrotic tissue, were collected near Ithaca, NY in the morning, placed in resealable plastic bags, and transported to the lab. The sample was cut into an approximately 3cm long piece and placed into a petri dish filled with 70% ethanol for 120 seconds. The piece was removed and allowed to air dry. In a laminar flow hood, a small portion of the stem that was connected to the petiole, including the parts of the petiole and leaf without necrosis, were cut into <5mm pieces using sterilized scissors and placed directly onto a plate of KB media and placed into an incubator at 28C for 40 hours. Cutting above the petri dish helped ensure that the pieces would fall onto the plate. The plate was dominated by a pale mucoid colony and was restreaked onto a plate with LB media and incubated at 28 C for 2 days. The original pale colony was a mixture of two colonies, which were streaked separately on LB plates and incubated at 28 C for 2 days. Two PCR reactions were performed using GYRB 1480F/2242R (Bonasera, et al., 2014) and 8UA/T5A (Bonasera, et al., 2017) primers. PCRs were cleaned and sent for Sanger Sequencing at the Cornell University Biotechnology Resource Center (BRC), Ithaca, NY. Strains were putatively identified as Pantoea agglomerans and Pseudomonas sp. The P.agglomerans strain was pursued for further investigation.
description
area of developed open space [ENVO:01000883]
env_broad_scale
USA: New York
geo_loc_name
stem [BTO:0001300]
host_tissue_sampled
Stephen Stresow, Jo Ann Asselin
identified_by
Rubus sp.
isolation_source
Pantoea agglomerans
http://purl.obolibrary.org/obo/NCBITaxon_549
organism
cell culture
sample_type
ROTS050421
strain
Microbe sample from Pantoea agglomerans
title