Pseudomonas hormoni sp. nov., a plant hormone producing bacterium isolated from Arctic grass, Ellesmere Island, Canada.

Bacterial strain G20-18T was previously isolated from the rhizosphere of an Arctic grass on Ellesmere Island, Canada and was characterized and described as Pseudomonas fluorescens. However, new polyphasic analyses coupled with phenotypic, phylogenetic and genomic analyses reported here demonstrate that the affiliation to the species P. fluorescens was incorrect. The strain is Gram-stain-negative, rod-shaped, aerobic and displays growth at 5-25 °C (optimum, 20-25 °C), at pH 5-9 (optimum, pH 6-7) and with 0-4 % NaCl (optimum, 2 % NaCl). The major fatty acids are C16 : 0 (35.6 %), C17 : 0 cyclo ω7c (26.3 %) and summed feature C18 : 1/C18 : 1 ω7c (13.6 %). The respiratory quinones were determined to be Q9 (93.5 %) and Q8 (6.5 %) and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strain G20-18T was shown to synthesize cytokinin and auxin plant hormones and to produce 1-aminocyclopropane-1-carboxylate deaminase. The DNA G+C content was determined to be 59.1 mol%. Phylogenetic analysis based on the 16S rRNA gene and multilocus sequence analysis (concatenated 16S rRNA, gyrB, rpoB and rpoD sequences) showed that G20-18T was affiliated with the Pseudomonas mandelii subgroup within the genus Pseudomonas. Comparisons of the G20-18T genome sequence and related Pseudomonas type strain sequences showed an average nucleotide identity value of ≤93.6 % and a digital DNA-DNA hybridization value of less than 54.4 % relatedness. The phenotypic, phylogenetic and genomic data support the hypothesis that strain G20-18T represents a novel species of the genus Pseudomonas. As strain G20-18T produces or modifies hormones, the name Pseudomonas hormoni sp. nov. is proposed. The type strain is G20-18T (=LMG 33086T=NCIMB 15469T).

Health Status of Ready-to-Plant Grapevine Nursery Material in Canada Regarding Crown Gall and Description of the First Allorhizobium vitis Strain OP-G1 Isolated from British Columbia.

Crown gall disease of grapevines caused by Allorhizobium vitis causes significant damage to vineyards in cold-climate viticulture areas such as Canada and the northern United States. Introduction of the disease into vineyards occurs mainly through planting of infected but asymptomatic nursery material. Because A. vitis is not a regulated pest for import into Canada, no information on the health status of nursery material destined for import into Canada has previously been collected. This study evaluated the health status of ready-to-plant nursery material from domestic and international nurseries in regard to crown gall by determining the abundance of A. vitis in different plant sections via Droplet Digital PCR technology. In addition, different rootstocks from one nursery were compared. Results showed that A. vitis was present in planting material from all nurseries tested. The bacteria were nonuniformly distributed in dormant nursery material, and there was no difference in abundance between the rootstocks tested. In addition, the first A. vitis strain OP-G1 isolated from galls in British Columbia is described. Results showed that a minimum of 5,000 bacterial OP-G1 cells were needed for symptom expression, suggesting that the initiation of symptom development is not based on presence of bacteria in nursery material alone; a minimum threshold is needed, and environmental conditions need to be met.

Soil organic carbon in irrigated agricultural systems: A meta-analysis.

Over the last 200 years, conversion of non-cultivated land for agriculture has substantially reduced global soil organic carbon (SOC) stocks in upper soil layers. Nevertheless, practices such as no- or reduced tillage, application of organic soil amendments, and maintenance of continuous cover can increase SOC in agricultural fields. While these management practices have been well studied, the effects on SOC of cropping systems that incorporate irrigation are poorly understood. Given the large, and expanding, agricultural landbase under irrigation across the globe, this is a critical knowledge gap for climate change mitigation. We undertook a systematic literature review and subsequent meta-analysis of data from studies that examined changes in SOC on irrigated agricultural sites through time. We investigated changes in SOC by climate (aridity), soil texture, and irrigation method with the following objectives: (i) to examine the impact of irrigated agriculture on SOC storage; and (ii) to identify the conditions under which irrigated agriculture is most likely to enhance SOC. Overall, irrigated agriculture increased SOC stocks by 5.9%, with little effect of study length (2-47 years). However, changes in SOC varied by climate and soil depth, with the greatest increase in SOC observed on irrigated semi-arid sites at the 0-10 cm depth (14.8%). Additionally, SOC increased in irrigated fine- and medium-textured soils but not coarse-textured soils. Furthermore, while there was no overall change to SOC in flood/furrow irrigated sites, SOC tended to increase in sprinkler irrigated sites, and decrease in drip irrigated sites, especially at depths below 10 cm. This work sheds light on the nuances of SOC change across irrigated agricultural systems, highlights the importance of studying SOC storage in deeper soils, and will help guide future research on the impacts of irrigated agriculture on SOC.

Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison with quantitative real-time PCR and validation of assays in vineyard soil.

Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared with those of quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada, over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK, and nosZII increased with time and the soil C/N ratio and NH4+-N concentration affected total archaea and archaeal amoA negatively. The results, compared with those of other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.

Efficacy of Pseudomonas fluorescens for control of Mucor rot of apple during commercial storage and potential modes of action.

The ability of Pseudomonas fluorescens isolates 1-112, 2-28, and 4-6, to control Mucor piriformis (Mucor rot) on Gala, McIntosh, Ambrosia, and Spartan apple cultivars in commercial cold storage and their possible mechanisms of action were investigated. Isolates 1-112 and 2-28 provided significant levels of disease control on McIntosh and Spartan apples, while isolate 4-6 provided control of Mucor rot on Gala and Spartan apples, compared with control fruits after 15 weeks of storage at 0 °C. Mycelial growth of M. piriformis was markedly inhibited by cell-free supernatant and volatile organic compounds produced by P. fluorescens isolates, in vitro. In filter-sterilized apple juice, living cells of all 3 P. fluorescens isolates or their metabolites significantly inhibited spore germination by 99.8% and 61.6%, on average, respectively. Electron microscopy indicated that all 3 isolates of P. fluorescens colonized the hyphae of M. piriformis, but only isolate 1-112 was observed to colonize M. piriformis spores in vitro. In the wounds of apple, all 3 isolates formed a biofilm on the fungal hyphae and on the fruit tissue. Potential mechanisms of antagonism utilized by P. fluorescens against M. piriformis may include competition for nutrients and space, production of inhibitory metabolites and volatiles, and biofilm formation, leading to inhibition of spore germination and mycelial growth.

Pseudomonads contribute to regulation of Pratylenchus penetrans (Nematoda) populations on apple.

Inoculation with antagonistic soil microorganisms has shown potential to suppress replant disease of apple in orchard soils. Pseudomonas spp. may have the potential to reduce Pratylenchus penetrans populations on apple. Pseudomonas spp. were isolated from the rhizosphere of sweet cherry and screened for antagonistic characteristics. Two highly antagonistic Pseudomonas isolates, P10-32 and P10-42, were evaluated for growth promotion of apple seedlings, suppression of P. penetrans populations, and root colonization in soil from three orchards. During the isolate screening, Pseudomonas fluorescens P10-32 reduced in vitro growth of fungal pathogens, had protease activity, had capacity to produce pyrrolnitrin, suppressed P. penetrans populations, and increased plant biomass. Pseudomonas fluorescens P10-42 reduced in vitro growth of fungal pathogens, had protease activity, suppressed P. penetrans populations, and increased plant biomass. In potted orchard soil, inoculating apple with P. fluorescens P10-32 suppressed P. penetrans populations in one of the three soils examined. Inoculation with P. fluorescens P10-42 improved plant growth in two of the soils and suppressed P. penetrans abundance in one soil. In one of the soils, P. fluorescens P10-42 was detected on the roots 56 days postinoculation. Overall, we conclude that Pseudomonas spp. play a role in suppressing P. penetrans on apple in orchard soil.

Quantification of Agrobacterium vitis from Grapevine Nursery Stock and Vineyard Soil using Droplet Digital PCR.

Current detection methodologies for Agrobacterium vitis, causing crown gall of grapevines, are time intensive and lack the ability to quantify pathogen abundance in nursery stock and soil. Information on pathogen abundance is a key component to develop management strategies. The aim of this study was to develop a rapid and sensitive quantification assay for grapevine nursery stock and vineyard soil via droplet digital polymerase chain reaction targeting the virA gene. DNA isolated from roots of dormant grapevines originating from nurseries in Germany, California, and Ontario were tested for virA abundance. Bacterial numbers varied with grapevine origin; plants from California had the highest numbers. In addition, rhizosphere soil from two vineyards in the Okanagan valley in British Columbia was tested over a growing season. Sampling time during the season did not affect virA gene abundance. The older vineyard had higher soil A. vitis populations than the younger vineyard. The assay developed here has potential for use in national clean plant programs to prevent import of infected grapevine nursery stock and to test vineyard soil for abundance of the pathogen before planting.

Which items on the distress thermometer problem list are the most distressing?

PURPOSE: The importance of distress identification and management in oncology has been established. We examined the relationship between distress and unmet bio-psychosocial needs, applying advanced statistical techniques, to identify which needs have the closest relationship to distress. METHODS: Oncology outpatients (n = 1066) undergoing QUICATOUCH screening in an Australian cancer centre completed the distress thermometer (DT) and problem list (PL). Principal component analysis (PCA), logistic regression and classification and regression tree (CART) analyses tested the relationship between DT score (at a cut-off point of 4) and PL items. RESULTS: Sixteen items were reported by <5 % of participants. PCA analysis identified four major components. Logistic regression analysis indicated three of these component scores, and four individual items (20 items in total) demonstrated a significant independent relationship with distress. The best CART model contained only two PL items: 'worry' and 'depression'. CONCLUSIONS: The DT and PL function as intended, quantifying negative emotional experience (distress) and identifying bio-psychosocial sources of distress. We offer two suggestions to minimise PL response time whilst targeting PL items most related to distress, thereby increasing clinical utility. To identify patients who might require specialised psychological services, we suggest the DT followed by a short, case-finding instrument for patients over threshold on the DT. To identify other important sources of distress, we suggest using a modified PL of 14 key items, with the 15th item 'any other problem' as a simple safety net question. Shorter times for patient completion and clinician response to endorsed PL items will maximise acceptance and clinical utility.

Extended pleurectomy decortication and chemotherapy versus chemotherapy alone for pleural mesothelioma (MARS 2): a phase 3 randomised controlled trial.

BACKGROUND: Extended pleurectomy decortication for complete macroscopic resection for pleural mesothelioma has never been evaluated in a randomised trial. The aim of this study was to compare outcomes after extended pleurectomy decortication plus chemotherapy versus chemotherapy alone. METHODS: MARS 2 was a phase 3, national, multicentre, open-label, parallel two-group, pragmatic, superiority randomised controlled trial conducted in the UK. The trial took place across 26 hospitals (21 recruiting only, one surgical only, and four recruiting and surgical). Following two cycles of chemotherapy, eligible participants with pleural mesothelioma were randomly assigned (1:1) to surgery and chemotherapy or chemotherapy alone using a secure web-based system. Individuals aged 16 years or older with resectable pleural mesothelioma and adequate organ and lung function were eligible for inclusion. Participants in the chemotherapy only group received two to four further cycles of chemotherapy, and participants in the surgery and chemotherapy group received pleurectomy decortication or extended pleurectomy decortication, followed by two to four further cycles of chemotherapy. It was not possible to mask allocation because the intervention was a major surgical procedure. The primary outcome was overall survival, defined as time from randomisation to death from any cause. Analyses were done on the intention-to-treat population for all outcomes, unless specified. This study is registered with ClinicalTrials.gov, NCT02040272, and is closed to new participants. FINDINGS: Between June 19, 2015, and Jan 21, 2021, of 1030 assessed for eligibility, 335 participants were randomly assigned (169 to surgery and chemotherapy, and 166 to chemotherapy alone). 291 (87%) participants were men and 44 (13%) women, and 288 (86%) were diagnosed with epithelioid mesothelioma. At a median follow-up of 22·4 months (IQR 11·3-30·8), median survival was shorter in the surgery and chemotherapy group (19·3 months [IQR 10·0-33·7]) than in the chemotherapy alone group (24·8 months [IQR 12·6-37·4]), and the difference in restricted mean survival time at 2 years was -1·9 months (95% CI -3·4 to -0·3, p=0·019). There were 318 serious adverse events (grade ≥3) in the surgery group and 169 in the chemotherapy group (incidence rate ratio 3·6 [95% CI 2·3 to 5·5], p<0·0001), with increased incidence of cardiac (30 vs 12; 3·01 [1·13 to 8·02]) and respiratory (84 vs 34; 2·62 [1·58 to 4·33]) disorders, infection (124 vs 53; 2·13 [1·36 to 3·33]), and additional surgical or medical procedures (15 vs eight; 2·41 [1·04 to 5·57]) in the surgery group. INTERPRETATION: Extended pleurectomy decortication was associated with worse survival to 2 years, and more serious adverse events for individuals with resectable pleural mesothelioma, compared with chemotherapy alone. FUNDING: National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (15/188/31), Cancer Research UK Feasibility Studies Project Grant (A15895).

Depression screening in stroke: a comparison of alternative measures with the structured diagnostic interview for the diagnostic and statistical manual of mental disorders, fourth edition (major depressive episode) as criterion standard.

BACKGROUND AND PURPOSE: Screening tools for depression and psychological distress commonly used in medical settings have not been well validated in stroke populations. We aimed to determine the accuracy of common screening tools for depression or distress in detecting caseness for a major depressive episode compared with a clinician-administered structured clinical interview for Diagnostic and Statistical Manual of Mental Disorders Fourth Edition as the gold standard. METHODS: Seventy-two participants ≥3 weeks poststroke underwent a diagnostic interview for major depressive episode and completed the Patient Health Questionnaire-2 and -9, Hospital Anxiety and Depression Scale, Beck Depression Inventory-II, Distress Thermometer, and Kessler-10. Internal consistency, sensitivity, specificity, likelihood ratios, and posttest probabilities were calculated. Each measure was validated against the gold standard using receiver operating characteristic curves with comparison of the area under the curve for all measures. RESULTS: Internal consistency ranged from acceptable to excellent for all measures (Cronbach α=0.78-0.94). Areas under the curve (95% CI) for the Patient Health Questionnaire-2, Patient Health Questionnaire-9, Hospital Anxiety and Depression Scale depression and total score, Beck Depression Inventory-II, and Kessler-10 ranged from 0.80 (0.69-0.89) for the Kessler-10 to 0.89 (0.79-0.95) for the Beck Depression Inventory-II with no significant differences between measures. The Distress Thermometer had an area under the curve (95% CI) of 0.73 (0.61-0.83), significantly smaller than the Beck Depression Inventory-II (P<0.05). CONCLUSIONS: Apart from the Distress Thermometer, selected scales performed adequately in a stroke population with no significant difference between measures. The Patient Health Questionnaire-2 would be the most useful single screen given free availability and the shortest number of items.

Phytohormone production and colonization of canola (Brassica napus L.) roots by Pseudomonas fluorescens 6-8 under gnotobiotic conditions.

Pseudomonas fluorescens 6-8, a rhizosphere isolate previously shown to enhance root elongation of canola ( Brassica napus L.), was characterized for its ability to produce indole-3-acetic acid and cytokinins in pure culture and in the rhizosphere of canola under gnotobiotic conditions in comparison with the cytokinin-producing strain P. fluorescens G20-18 and its mutant CNT2. Strain 6-8 produced isopentenyl adenosine, zeatin riboside, and dihydroxyzeatin riboside at levels similar to those of G20-18, but only very low concentrations of indole-3-acetic acid. In a gnotobiotic assay canola inoculated with 6-8 and G20-18 had higher concentrations of isopentenyl adenosine and zeatin riboside in the rhizosphere and greater root length than the noninoculated control. The ability of strain 6-8 to colonize canola roots was assessed following transformation with the green fluorescent protein and inoculation onto canola seed in a gnotobiotic assay. Higher populations of strain 6-8 were observed on the proximal region of the root closest to the seed than on the mid and distal portions 9 days after seed inoculation. The ability of P. fluorescens 6-8 to produce cytokinins, colonize the roots of canola seedlings, and enhance root elongation may contribute to its ability to survive in the rhizosphere and may benefit seedling growth.

Cytokinin production by Pseudomonas fluorescens G20-18 determines biocontrol activity against Pseudomonas syringae in Arabidopsis.

Plant beneficial microbes mediate biocontrol of diseases by interfering with pathogens or via strengthening the host. Although phytohormones, including cytokinins, are known to regulate plant development and physiology as well as plant immunity, their production by microorganisms has not been considered as a biocontrol mechanism. Here we identify the ability of Pseudomonas fluorescens G20-18 to efficiently control P. syringae infection in Arabidopsis, allowing maintenance of tissue integrity and ultimately biomass yield. Microbial cytokinin production was identified as a key determinant for this biocontrol effect on the hemibiotrophic bacterial pathogen. While cytokinin-deficient loss-of-function mutants of G20-18 exhibit impaired biocontrol, functional complementation with cytokinin biosynthetic genes restores cytokinin-mediated biocontrol, which is correlated with differential cytokinin levels in planta. Arabidopsis mutant analyses revealed the necessity of functional plant cytokinin perception and salicylic acid-dependent defence signalling for this biocontrol mechanism. These results demonstrate microbial cytokinin production as a novel microbe-based, hormone-mediated concept of biocontrol. This mechanism provides a basis to potentially develop novel, integrated plant protection strategies combining promotion of growth, a favourable physiological status and activation of fine-tuned direct defence and abiotic stress resilience.

Determining the efficacy of a pressure ulcer prevention program by collecting prevalence and incidence data: a unit-based effort.

Pressure ulcer prevention falls within the domain of nursing practice. When the results of a quality improvement survey indicated both an increase in the number of pressure ulcers and a higher prevalence than the national average, the nursing staff of a 500-bed Midwest hospital developed a pressure ulcer prevention program guided by the AHCPR guidelines. The literature supports collecting prevalence and incidence data as indicators of prevention program effectiveness, and the best indicator of the effectiveness of prevention strategies to reduce nosocomial pressure ulcers is incidence. Since the tracking mechanism was instituted, awareness of the results and impact of prevention measures increased; most nursing units experienced a 10% to 20% decrease in the incidence of pressure ulcers. Designing an efficient, timely, and practical method of retrieving pressure ulcer prevalence and incidence data provided a quality assurance method of monitoring the success of the program.

Isolation, selection, and characterization of beneficial rhizobacteria from pea, lentil, and chickpea grown in western Canada.

The use of beneficial soil microorganisms as agricultural inputs for improved crop production requires selection of rhizosphere-competent microorganisms with plant growth-promoting attributes. A collection of 563 bacteria originating from the roots of pea, lentil, and chickpea grown in Saskatchewan was screened for several plant growth-promoting traits, for suppression of legume fungal pathogens, and for plant growth promotion. Siderophore production was detected in 427 isolates (76%), amino-cyclopropane-1-carboxylic acid (ACC) deaminase activity in 29 isolates (5%), and indole production in 38 isolates (7%). Twenty-six isolates (5%) suppressed the growth of Pythium sp. strain p88-p3, 40 isolates (7%) suppressed the growth of Fusarium avenaceum, and 53 isolates (9%) suppressed the growth of Rhizoctonia solani CKP7. Seventeen isolates (3%) promoted canola root elongation in a growth pouch assay, and of these, 4 isolates promoted the growth of lentil and one isolate promoted the growth of pea. Fatty acid profile analysis and 16S rRNA sequencing of smaller subsets of the isolates that were positive for the plant growth-promotion traits tested showed that 39%-42% were members of the Pseudomonadaceae and 36%-42% of the Enterobacteriaceae families. Several of these isolates may have potential for development as biofertilizers or biopesticides for western Canadian legume crops.