The importance of the antagonistic potential in the management of populations of plant-parasitic nematodes in banana (<em>Musa</em> AAA) as influenced by agronomic factors

Plant-parasitic nematodes are a major obstacle to sustainable banana production around the world. The use of organic amendments was investigated as one method to stimulate organisms that are antagonistic to plant-parasitic nematodes. Nine different amendments; mill mud, mill ash (by-products from processing sugarcane), biosolids, municipal waste (MW) compost, banana residue, grass hay, legume hay, molasses and calcium silicate (CaSi) were applied in a glasshouse experiment. Significant suppression of Radopholus similis occurred in soils amended with legume hay, grass hay, banana residue and mill mud relative to untreated soil, which increased the nematode community structure index, indicating greater potential for predation. A field experiment was established to determine the changes in soil properties following applications of compost, grass hay, mill mud and mill ash. At the termination of the experiment there was significant increase in bunch size in the mill ash treatment relative to the untreated plants. Furthermore, in the soil treated with additional organic matter there was an increase in labile C, the number of omnivorous nematodes and lower proportion of plant-parasitic nematodes relative to the untreated soil. The suppression of plant-parasitic nematodes resulting from the addition of organic matter appeared to be the result of a combination of two factors; nematoxic compounds produced in the early degradation of the organic matter, followed by an increase in nematode antagonists favoured by an increase in soil fungal activity. A study was implemented on 10 banana plantations in north Queensland to determine differences in soil management, soil physical, chemical and nematode community properties. A principal component analysis could explain 61% of the variation between farms and identified the proportion of plant-parasitic nematodes, labile C, nitrate-N, and the number of fungal feeding nematodes as the most important soil factors. When used in combination the ratio of labile C and nitrate-N in the soil and the diversity of nematodes were able to explain 88.7% of the variation in the proportion of plant-parasitic nematodes in the soil. A similar survey of 21 banana plantations in Costa Rica using 34 soil variables was able to explain 71% of variation between plantations from five principle components. A bioassay of the soil collected, which was inoculated with R. similis, resulted in different populations of the nematode recovered from the different soils. The differences could be explained by soil pH, structure index and Zn using a multiple linear regression model, which explained 79.2% of the variation. Furthermore, the correlation of soil pH with nematode diversity suggested that pH was the factor limiting the biological suppression of R. similis in the Costa Rican banana plantations. The development of soils capable of suppressing plant-parasitic nematodes requires and understanding of soil constraints in the farming system. In Australia, soil C appeared to constrain antagonists, whereas, in Costa Rica low soil pH constrained the diversity of the soil nematode community. Management options to increase soil C in Australia and to increase soil pH in Costa Rica are necessary to develop a more favourable soil environment for the suppression of plant-parasitic nematodes by antagonistic soil organisms.Die Bedeutung des antagonistischen Potentials für die Kontrolle von Pflanzenparasitären Nematoden in Bananen (Musa AAA) und dessen Beeinflussung durch pflanzenbauliche Maßnahmen Der Pflanzen-parasitäre Nematode (PPN) Radopholus similis gehört weltweit zu den bedeutendsten Schädlingen nachhaltiger Bananenproduktion. Traditionell, wurden diese Schädlinge mit Nematiziden bekämpft. Deren Gebrauch ist jedoch mit einer Gefährdung landwirtschaftlichen Personals und einer Reduzierung der Biodiversität im Boden und dessen antagonistischem Potential verbunden. Deshalb ist ein besseres Verständnis der Faktoren, die das antagonistische Potential eines Bodens beeinflussen, unabdingbar. In der vorliegenden Arbeit wurden verschiedene organische Bodenzusätze auf die Stimulierung des antagonistischen Potentials gegen R. similis in Musa AAA untersucht. Gewächshausexperimente zeigten, dass Leguminosen Heu, Zuckermühlen-abfälle und Bananenrückstände als Bodenzusätze die Nematodendiversität erhöhte, die Anzahl an R. similis jedoch reduzierten. In Feldexperimenten konnte gezeigt werden, dass die Zugabe von Kompost, Heu, Nebenprodukten aus Zuckermühlen und Mühlenschlamm zu einer Erhöhung des instabilen Kohlenstoffs und omnivorer Nematoden, jedoch zu einer Verringerung von PPN führte. Eine Hauptkomponentenanalyse mit Zehn unterschiedlich bewirtschafteten Bananenplantagen in Nord-Queensland, Australien, identifizierte instabilen Kohlenstoff, Nitrat und die Anzahl fungivorer Nematoden als Hauptbodenfaktoren in Bezug auf ihr antagonistisches Potential gegenüber PPN und konnte 61% der Variation zwischen den Plantagen erklären. In Kombination erklärte das Verhältnis von instabilem Kohlenstoff zu Nitrat im Boden und die Nematodendiversität 88.7% der Variation an PPN zwischen den Plantagen. Eine ähnliche Studie in Costa Rica bei der 34 Bodenvariablen erhoben wurden konnte 71% der Variation zwischen den verschiedenen Böden in Bezug auf ihr antagonistisches Potential gegenüber PPN erklären. In bioassay´s mit diesen Böden zeigte sich, dass deren antagonistisches Potential vom pH-Wert, dem „Struktur- Index“ und Zink-Gehalt beeinflusst wurde und das sich mit Hilfe einer multiplen linearen Regression 79.2% der Variationen des antagonistischen Potentials zwischen den Böden erklären ließ. Darüberhinaus korrelierte der Boden pH mit der Nematodendiversität, was den Schluss zuließ, dass der Boden pH der limitierende Faktor biologisch suppressiver Böden in Costa Rica´s Bananenproduktion ist. Zusammenfassend konnte gezeigt werden, dass das antagonistische Potential gegenüber PPN von verschiedenen Faktoren beeinflusst wird. Während in Australien instabiles Kohlenstoff der limitierende Faktor war, ist in Costa Rica der Boden pH entscheidend für Nematodendiversität und einhergehende Suppresion von PPN. Eine Steigerung des instabilen Kohlenstoffs in Australiens Böden und eine Erhöhung des Boden pH in Costa Rica scheinen deshalb notwendig um suppresive Böden mit hohem antagonisten Potential gegen PPN wie R. similis zu schaffen

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

The biology of root lesion nematode (Pratylenchus thornei) in wheat (Triticum aestivum) fields in northern New South Wales

Root lesion nematode (Pratylenchus thornei) is a relatively new problem in the wheat growing areas of central and northern New South Wales. Despite this, the nematode has become endemic on heavy clay soils which have a long history of wheat production. The objectives of the research reported in this thesis were to investigate the influence of environmental factors on the population dynamics and distribution of P. thornei, and the tolerance and resistance of commercial cultivars and advanced breeding lines to the nematode. The population dynamics of the nematode were investigated in 1989, 1990 and 1991 by sampling a wheat field at monthly intervals. P. thornei populations remained static for a three month period following sowing, then increased in October. The increase in nematode populations was correlated with increases in soil temperature in 1989 and 1990. The influence of soil temperature on the multiplication and development of P. thornei was investigated in a growth chamber study at three temperatures; 10, 20 and 30 °C. Nematode populations developed slowly at 10 °C, increased rapidly and then declined at 30 °C and increased in an exponential pattern at 20 °C. In the 20 °C treatment wheat shoot growth was correlated to nematode populations, with increasing populations increasing shoot weight until nematodes exceeded 3000 per g of root. Root weights at 20 °C declined with increasing nematode populations. The distribution of P. thornei in a wheat field was investigated over two consecutive years in 1989 and 1990 by taking regular monthly samples 4 m apart on a 0.23 ha grid. The aggregation of the nematodes was close to random at the time of sowing, however, as the nematodes multiplied the distribution patterns became aggregated, with areas of very high populations. The areas of dense nematode populations could not be correlated to any plant or edaphic factor. However, the consistent seasonal nematode aggregation was shown to part of the nematode biology and allowed a sampling protocol to be developed which could be linked to sampling errors, depending on the precision of the field mean required. Twenty seven fields in northern NSW were sampled prior to sowing winter crops and again at harvest. Soil physical factors were not found to be correlated with initial nematode populations or multiplication of nematodes. However, the cropping history and the previous crop prior to sampling were found to be major factors influencing the initial population of nematodes at sowing. Continual cultivation of susceptible crops, such as wheat and legumes was found to increase the nematode population at the time of sowing. A study of thirty six cereal cultivars at two sites near Narrabri in northern NSW identified problems with the use of nematicides as a control when studying tolerance reactions of cereals. Differences in soil characteristics between the two sites and in genotype reactions to the nematicide were identified as the main causes of variation in cereal tolerance reactions to P. th o rn ei. Resistance to P. thornei was measured as the multiplication of nematodes from sowing to harvest. The initial population of nematodes at the time of sowing was identified as an important covariate influencing multiplication rates of the nematodes. Resistant cereals with good tolerance to P. thornei were identified as barley and durum wheat, as well as three breeding lines; SUN 289 A, SUN 290 B and SUN 277 A. From the studies of this thesis sustainable wheat production in northern NSW where P. thornei was identified as a potential problem was possible using an integrated management system. This involves crop rotation to non-host crops and quantifying nematode populations before sowing wheat crops to assess the risks of yield losses. As part of a management system wheat crops should be sown early to allow for maximum root development before nematodes multiply in warmer soils and where possible, tolerant and resistant wheat varieties grown