Accumulation Of Pathogens Research Articles

Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters.

Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter-feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to the microbial ecology of pathogenic bacteria and their relationship with oyster hosts likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of Vibrio parahaemolyticus, Vibrio vulnificus, or fecal indicator bacteria. Site-specific environmental conditions significantly influenced microbial communities and potential pathogen concentrations in water. Oyster microbial communities, however, exhibited less variability in microbial community diversity and accumulation of target bacteria overall and were less impacted by environmental differences between sites. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated levels of potential pathogens. For example, increased levels of V. parahaemolyticus were associated with higher relative abundances of cyanobacteria, which could represent an environmental vector for Vibrio spp. transport, and with decreased relative abundance of Mycoplasma and other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters. IMPORTANCE Bacteria in the marine environment cause thousands of human illnesses annually. Bivalves are a popular seafood source and are important in coastal ecology, but their ability to concentrate pathogens from the water can cause human illness, threatening seafood safety and security. To predict and prevent disease, it is critical to understand what causes pathogenic bacteria to accumulate in bivalves. In this study, we examined how environmental factors and host and water microbial communities were linked to potential human pathogen accumulation in oysters. Oyster microbial communities were more stable than water communities, and both contained the highest concentrations of Vibrio parahaemolyticus at sites with warmer temperatures and lower salinities. High oyster V. parahaemolyticus concentrations corresponded with abundant cyanobacteria, a potential vector for transmission, and a decrease in potentially beneficial oyster microbes. Our study suggests that poorly understood factors, including host and water microbiota, likely play a role in pathogen distribution and pathogen transmission.

Effects of continuous melon cropping on rhizospheric fungal communities

Long-term continuous cropping of crops leads to soil degradation and a decrease in crop yield and quality. Continuous cropping obstacles are common with melon; however, the rhizosphere microbial community response to continuous cropping of melon remains poorly investigated. Here, we comparatively investigated the structure and function of the rhizospheric fungal community from melon greenhouses replanted for 0, 1, 2, and 3 years (CK, 1a, 2a, and 3a, respectively) using high-throughput absolute quantification sequencing. The results showed that the fungal abundance increased with continuous cropping duration, but the fungal diversity and richness decreased. The most dominant phyla were Ascomycota and Basidiomycota, and their absolute abundance increased continuously. At the genus level, Fusarium, Thanatephorus, and Plectosphaerella were the dominant genera, and their absolute abundance increased significantly (p＜ 0.05) with the continuous cropping duration. FUNGuild function prediction showed that continuous cropping caused the accumulation of endophyte‒plant pathogens and plant pathogens, which may accelerate soil-borne diseases of melon. Our results provide guidance for revealing the mechanism of continuous cropping obstacles in melon, which is important in evaluating the sustainability of this agricultural practice.

Effect of Lacticaseibacillus rhamnosus L8020 on the abundance of periodontal pathogens in individuals with intellectual disability: a randomized clinical trial.

Gingivitis refers to inflammation of the gingiva and its connective tissues. Research has revealed a higher prevalence of gingivitis in individuals with intellectual disability than in healthy individuals. Milk fermented with Lacticaseibacillus rhamnosus L8020 (L8020 yogurt) inhibits the accumulation of periodontal disease-related pathogens in vitro and alleviates the symptoms of periodontal disease. The aim of this study was to investigate the influence of L8020 yogurt on oral microbiota and the abundance of four periodontal pathogens (Tannerella forsythia, Porphyromonas gingivalis, Prevotella intermedia, and Treponema denticola) and on the microbiota in individuals with intellectual disability and gingivitis. Forty-one outpatients with intellectual disability participated in this study. To examine the effects of daily consumption of L8020 yogurt, the patients were randomly divided into L8020 (test group, n = 21) and placebo (n = 20) yogurt groups. All patients consumed 80 g of yogurt for 12 weeks. Oral examination was performed before the first intake of yogurt and dental plaque was collected before and after the intake of yogurt. DNA was extracted from dental plaque and subjected to next-generation sequencing. The relative abundance of T forsythia was significantly lower in the test group than in the placebo group. Additionally, the relative abundance of the four pathogens reduced after 84 days of consuming L8020 yogurt compared with that after consuming placebo yogurt. Mixing L rhamnosus L8020 with probiotic products that are consumed daily would be effective in suppressing the increase in periodontal disease-causing bacteria and beneficial for individuals with intellectual disability.

Artificial Organelles with Digesting Characteristics: Imitating Simplified Lysosome- and Macrophage-Like Functions by Trypsin-Loaded Polymersomes.

Defects in cellular protein/enzyme encoding or even in organelles are responsible for many diseases. For instance, dysfunctional lysosome or macrophage activity results in the unwanted accumulation of biomolecules and pathogens implicated in autoimmune, neurodegenerative, and metabolic disorders. Enzyme replacement therapy (ERT) is a medical treatment that replaces an enzyme that is deficient or absent in the body but suffers from short lifetime of the enzymes. Here, this work proposes the fabrication of two different pH-responsive and crosslinked trypsin-loaded polymersomes as protecting enzyme carriers mimicking artificial organelles (AOs). They allow the enzymatic degradation of biomolecules to mimic simplified lysosomal function at acidic pH and macrophage functions at physiological pH. For optimal working of digesting AOs in different environments, pH and salt composition are considered the key parameters, since they define the permeability of the membrane of the polymersomes and the access of model pathogens to the loaded trypsin. Thus, this work demonstrates environmentally controlled biomolecule digestion by trypsin-loaded polymersomes also under simulated physiological fluids, allowing a prolonged therapeutic window due to protection of the enzyme in the AOs. This enables the application of AOs in the fields of biomimetic therapeutics, specifically in ERT for dysfunctional lysosomal diseases.

An Antimicrobial Fabric Using Nano-Herbal Encapsulation of Essential Oils.

Lab coats are widely used in biohazard laboratories and healthcare facilities as protective garments to prevent direct exposure to pathogens, spills, and burns. These cotton-based protective coats provide ideal conditions for microbial growth and attachment sites due to their porous nature, moisture-holding capacity, and retention of warmth from the user's body. Several studies have demonstrated the survival of pathogenic bacteria on hospital garments and lab coats, acting as vectors of microbial transmission. A common approach to fix these problems is the application of antimicrobial agents in textile finishing, but concerns have been raised due to the toxicity and environmental effects of many synthetic chemicals. The ongoing pandemic has also opened a window for the investigation of effective antimicrobials and eco-friendly and toxic-free formulations. This study uses two natural bioactive compounds, carvacrol and thymol, encapsulated in chitosan nanoparticles, which guarantee effective protection against four human pathogens with up to a 4-log reduction (99.99%). These pathogens are frequently detected in lab coats used in biohazard laboratories. The treated fabrics also resisted up to 10 wash cycles with 90% microbial reduction, which is sufficient for the intended use. We made modifications to the existing standard fabric tests to better represent the typical scenarios of lab coat usage. These refinements allow for a more accurate evaluation of the effectiveness of antimicrobial lab coats and for the simulation of the fate of any accidental microbial spills that must be neutralized within a short time. Further studies are recommended to investigate the accumulation of pathogens over time on antimicrobial lab coats compared to regular protective coats.

Turning Garlic into a Modern Crop: State of the Art and Perspectives.

Garlic is cultivated worldwide for the value of its bulbs, but its cultivation is challenged by the infertility of commercial cultivars and the accumulation of pathogens over time, which occurs as a consequence of vegetative (clonal) propagation. In this review, we summarize the state of the art of garlic genetics and genomics, highlighting recent developments that will lead to its development as a modern crop, including the restoration of sexual reproduction in some garlic strains. The set of tools available to the breeder currently includes a chromosome-scale assembly of the garlic genome and multiple transcriptome assemblies that are furthering our understanding of the molecular processes underlying important traits like the infertility, the induction of flowering and bulbing, the organoleptic properties and resistance to various pathogens.

Evaluating response mechanisms of soil microbiomes and metabolomes to Bt toxin additions

The accumulation and persistence of Bt toxins in soils from Bt plants and Bt biopesticides may result in environmental hazards such as adverse impacts on soil microorganisms. However, the dynamic relationships among exogenous Bt toxins, soil characteristics, and soil microorganisms are not well understood. Cry1Ab is one of the most commonly used Bt toxins and was added to soils in this study to evaluate subsequent changes in soil physiochemical properties, microbial taxa, microbial functional genes, and metabolites profiles via 16S rRNA gene pyrosequencing, high-throughput qPCR, metagenomic shotgun sequencing, and untargeted metabolomics. Higher additions of Bt toxins led to higher concentrations of soil organic matter (SOM), ammonium (NH+4-N), and nitrite (NO2--N) compared against controls without addition after 100 days of soil incubation. High-throughput qPCR analysis and shotgun metagenomic sequencing analysis revealed that the 500 ng/g Bt toxin addition significantly affected profiles of soil microbial functional genes involved in soil carbon (C), nitrogen (N), and phosphorus (P) cycling after 100 days of incubation. Furthermore, combined metagenomic and metabolomic analyses indicated that the 500 ng/g Bt toxin addition significantly altered low molecular weight metabolite profiles of soils. Importantly, some of these altered metabolites are involved in soil nutrient cycling, and robust associations were identified among differentially abundant metabolites and microorganisms due to Bt toxin addition treatments. Taken together, these results suggest that higher levels of Bt toxin addition can alter soil nutrients, probably by affecting the activities of Bt toxin-degrading microorganisms. These dynamics would then activate other microorganisms involved in nutrient cycling, finally leading to broad changes in metabolite profiles. Notably, the addition of Bt toxins did not cause the accumulation of potential microbial pathogens in soils, nor did it adversely affect the diversity and stability of microbial communities. This study provides new insights into the putative mechanistic associations among Bt toxins, soil characteristics, and microorganisms, providing new understanding into the ecological impacts of Bt toxins on soil ecosystems.

Recent Research on Municipal Sludge as Soil Fertilizer in China: a Review.

Due to the annual increase in wastewater treatment in most Chinese cities, a major environmental issue has arisen: safe treatment, disposal, and recycling of municipal sludge. Municipal sludge has a high content of carbon and essential nutrients for plant growth; hence, it has gained interest among researchers as a soil fertilizer. This study discusses the potential usage of municipal sludge as soil fertilizer (indicators include nitrogen (N), phosphorus (P), and trace elements) along with its shortcomings and drawbacks (potentially toxic elements (PTEs), organic matter (OM), pathogens, etc.) as well as reviews the latest reports on the role of municipal sludge in land use. The use of municipal sludge as a soil fertilizer is a sustainable management practice and a single application of sludge does not harm the environment. However, repeated use of sludge may result in the accumulation of harmful chemicals and pathogens that can enter the food chain and endanger human health. Therefore, long-term field studies are needed to develop ways to eliminate these adverse effects and make municipal sludge available for agricultural use.

CRISPRa-mediated transcriptional activation of the SlPR-1 gene in edited tomato plants

With the continuous deterioration of arable land due to an ever-growing population, improvement of crops and crop protection have a fundamental role in maintaining and increasing crop productivity. Alternatives to the use of pesticides encompass the use of biological control agents, generation of new resistant crop cultivars, the application of plant activator agrochemicals to enhance plant defenses, and the use of gene editing techniques, like the CRISPR-Cas system. Here, we test the hypothesis that epigenome editing, via CRISPR activation (CRISPRa), activate tomato plant defense genes to confer resistance against pathogen attack. We provide evidence that edited tomato plants for the PATHOGENESIS-RELATED GENE 1 gene (SlPR-1) show enhanced disease resistance to Clavibacter michiganensis subsp. michiganensis infection. Resistance was assessed by evaluating disease progression and symptom appearance, pathogen accumulation, and changes in SlPR-1 gene expression at different time points. We determined that CRISPRa-edited plants develop enhanced disease-resistant to the pathogen without altering their agronomic characteristics and, above all, preventing the advancement of disease symptoms, stem canker, and plant death.

Constructed wetlands as hotspots of antibiotic resistance genes and pathogens: Evidence from metagenomic analysis in Chinese rural areas

In rural China, many constructed wetlands (CWs) have been developed to treat rural wastewater sustainably. However, due to the scarce information on those rural CWs, it is difficult to analyze the biological contaminants within those systems, such as antibiotic resistance genes (ARGs) and pathogens. Based on the data collected from two pilot-scale, one-year-observed CWs, for the first time, this study explored the accumulation of ARGs and pathogens using the metagenomic sequencing approach and SourceTracker analysis under different hydraulic loading rates. The Shannon index of ARGs in the effluent surpassed the level found in the influent. The DESeq2 analysis showed that up to 21.49% of the total pathogen species had increased relative abundance in the effluent compared with the influent. By combining the contribution of substrate and rhizosphere, the CW became a more influencing factor for ARGs and pathogens contamination than the influent. The network analysis revealed a critical but latent fact that the development of antibiotic-resistant pathogens is highly likely to be triggered by the co-occurrence of ARGs and pathogens. Collectively, from the aspect of biological risk, our study showed that CWs alone might not be an ideal solution for improving wastewater treatment in rural China.

The rhizospheric bacterial diversity of Fritillaria taipaiensis under single planting pattern over five years

Rhizospheric microorganisms can profoundly influence the nutritional status of soil and the growth of plant. To reveal the change on the bacterial diversity in the rhizosphere of Fritillaria taipaiensis under long-term single planting, the bacterial community structure in the rhizospheric soils of F. taipaiensis with different cultivation years from 1 to 5 were analyzed. The result showed the Chao1 and the ACE indices of the bacterial community had no significant difference among samples while the Shannon and Simpson indices declined with the cutivation year; the intra group beta diversity of the rhizospheric bacteria increased after a initial decline with the cultivation year; in the sample with 1 year of cultivation, the dominant bacterial genera were mainly the species that can improve the soil nutrient status and promote plant growth while with the increase of cultivation year, the dominant genera in samples then gradually reflected the pathogen accumulation and soil nutrient status deterioration; pH was the most significant factor affected by the bacterial community composition. These results indicated long term continuous cropping changed the bacterial community structure and soil nutritional status in the F. taipaiensis rhizospheric soils, which could badly affect its growth.

Effects of different soil moisture on the growth, quality, and root rot disease of organic Panax notoginseng cultivated under pine forests

The under-forest economy in the agroforestry system can improve land use efficiency, protect ecological environment, and promote arable land sustainable development. However, the effects of soil moisture in the forest and irrigation strategies on the healthy growth of intercropping crops are still incomplete. Here, considering the organic Panax notoginseng cultivated under pine forests (PPF) as the research object, we explored the effects of different soil moisture on the physiological state, yield, quality and disease occurrence of PPF. Our results suggested that 80–85% and 95–100% field capacity (FC) treatments were more conducive to increased photosynthetic rate and biomass accumulation of PPF, but 50–55% and 65–70% FC treatments were more conducive to the accumulation of saponins in PPF leaves. Notably, the root rot index of PPF was highest under 95–100% FC (19.51) treatment, significantly higher than that under 65–70% FC (8.44) and 80–85% FC (10.21) treatments. Further, the rhizosphere microorganisms of PPF under different soil moisture treatments were sequenced, and the sequencing data analysis revealed that high soil moisture (95–100% FC) could destroy the microbial diversity balance and cause the accumulation of pathogens (Fusarium oxysporum and Ilyonectria radicicola), leading to a high incidence of root rot. The incidence of PPF root rot was negatively correlated with rhizosphere microbial diversity. Overall, our results highlight that the quantitative irrigation (80–85% FC) is conducive to maintaining the balance between yield, saponin content and disease occurrence of PPF, providing a practical basis for PPF irrigation strategy and promoting the sustainable development of PPF agroforestry system.

Assessing soil microbes that drive fairy ring patterns in temperate semiarid grasslands

BackgroundFairy rings occur in diverse global biomes; however, there is a critical knowledge gap regarding drivers of fairy rings in grassland ecosystems. Grassland fairy rings are characterized belowground by an expanding mycelial front and aboveground by vigorous vegetation rings that develop concentrically with each growing season. We evaluated fairy ring dynamics in a field study conducted in semiarid grasslands to elucidate above- and belowground interactions driving distinct vegetation patterns. We followed this initial field investigation with a complementary greenhouse experiment, using soils collected from specific fairy ring zones (inside, ring-edge, outside) to examine plant-soil-microbial interactions under controlled conditions. We selected Leymus chinensis (a dominant grass) as our model plant species to assess the role of diverse fairy ring microbial communities on plant growth and nutrition.ResultsIn our field study, plants on the ring-edge produced greater shoot biomass with higher concentrations of N and P, compared to plants inside the ring or adjacent (outside) controls. Soil microbial community biomarkers indicate shifts in relative microbial biomass as fairy rings expand. Inside the ring, plant roots showed greater damage from pathogenic fungi, compared to outside or ring-edge. Our greenhouse experiment confirmed that inoculation with live ring-edge soil generally promoted plant growth but decreased shoot P concentration. Inoculation with soil collected from inside the ring increased root pathogen infection and reduced shoot biomass.ConclusionWe propose that soil microbial activity within ring-edges promotes plant growth via mobilization of plant-available P or directed stimulation. However, as the ring expands, L. chinensis at the leading edge may increase pathogen accumulation, resulting in reduced growth at the center of the ring in subsequent growing seasons. Our results provide new insights into the plant-soil-microbial dynamics of fairy rings in grasslands, helping to elucidate these mysterious vegetation patterns.

Identifying built environment solutions, in Thai community hospital outpatient clinics, to prevent the spread of COVID-19

Due to the unprecedented outbreak of COVID-19 (Corona Virus Disease - 2019) healthcare facilities, including Thailand community hospitals were mandated to adjust their facilities to both medical and non-clinical areas to prevent the spread of the disease. The study aimed to identify problems focusing on the physical settings of out-patient departments (OPD) in community hospitals during the first Thailand COVID-19 outbreak in March 2020. Furthermore, the study focused on providing design suggestions for preventing the spread of respiratory infectious diseases. The study employed a two-step approach to data collection. First, physical setting observations of the OPD of the two hospital buildings. Second, interviews with 22 healthcare employees; 11 participants from the first hospital and 11 participants from the second hospital. Interviews were transcribed verbatim and analyzed using content analysis. Five main themes were identified: (1) factors leading to accumulation of pathogens, (2) measures for preventing the spread of respiratory diseases, (3) current services and physical settings of outpatient clinics, (4) guidelines for improving the physical setting of outpatient clinics and (5) prevention of accumulation of pathogens in OPD areas. Results indicate that not only improving the physical setting of the OPD areas is required, but a strict patient screening process and an organized building management programme should also be considered. Such actions with workflow management would have played important roles in preventing the spread of respiratory diseases during the first COVID-19 outbreak. The findings from the study contribute to both research and industry. For the research, the study contributes to three literature topics including hospital building evaluation and assessment techniques, hospital design, and design prevention for the spread of COVID-19. For industry, the study contributes to the future development of layout design that can prevent the spread of COVID-19 throughout Thai community hospitals.

Soil microbial legacies influence plant survival and growth in mine reclamation.

Plants alter soil biological communities, generating ecosystem legacies that affect the performance of successive plants, influencing plant community assembly and successional trajectories. Yet, our understanding of how microbe-mediated soil legacies influence plant establishment is limited for primary successional systems and forest ecosystems, particularly for ectomycorrhizal plants. In a two-phase greenhouse experiment using primary successional mine reclamation materials with or without forest soil additions, we conditioned soil with an early successional shrub with low mycorrhizal dependence (willow, Salix scouleriana) and a later-successional ectomycorrhizal conifer (spruce, Picea engelmannii × glauca). The same plant species and later-successional plants (spruce and/or redcedar, Thuja plicata, a mid- to late-successional arbuscular mycorrhizal conifer) were grown as legacy-phase seedlings in conditioned soils and unconditioned control soils. Legacy effects were evaluated based on seedling survival and biomass, and the abundance and diversity of root fungal symbionts and pathogens. We found negative intraspecific (same-species) soil legacies for willow associated with pathogen accumulation, but neutral to positive intraspecific legacies in spruce associated with increased mycorrhizal fungal colonization and diversity. Our findings support research showing that soil legacy effects vary with plant nutrient acquisition strategy, with plants with low mycorrhizal dependence experiencing negative feedbacks and ectomycorrhizal plants experiencing positive feedbacks. Soil legacy effects of willow on next-stage successional species (spruce and redcedar) were negative, potentially due to allelopathy, while ectomycorrhizal spruce had neutral to negative legacy effects on arbuscular mycorrhizal redcedar, likely due to the trees not associating with compatible mycorrhizae. Thus, positive biological legacies may be limited to scenarios where mycorrhizal-dependent plants grow in soil containing legacies of compatible mycorrhizae. We found that soil legacies influenced plant performance in mine reclamation materials with and without forest soil additions, indicating that initial restoration actions may potentially exert long-term effects on plant community composition, even in primary successional soils with low microbial activity.

Iron-enriched Aspergillus oryzae as an alternative to iron sulphate to limit iron accumulation, growth and motility of the enteric pathogen S. Typhimurium.

Excess unabsorbed iron in the gastrointestinal tract may select for enteric pathogens and increase the incidence and severity of infectious disease. Aspergillus oryzae (Ao) is a filamentous fungus that has the ability to accumulate and store large amounts of iron, and when used as a supplement or fortificant, has similar absorption to ferrous sulphate (FeSO4) in humans. The objective of this study was to determine the effect of iron-enriched Ao (Ao iron) compared with FeSO4 on iron accumulation, growth and motility of the Gram-negative enteric pathogen, S. Typhimurium. S. Typhimurium was cultured in media containing no added iron or 1 μM elemental iron as either Ao iron or FeSO4. S. Typhimurium cultured with FeSO4 accumulated more iron than those cultured with Ao iron. Genes regulated by the iron-activated transcriptional repressor, Fur, did not differ between control and Ao iron, but decreased in S. Typhimurium cultured with FeSO4 compared with both groups. Growth of S. Typhimurium was greater when cultured with FeSO4 compared with Ao iron and control. S. Typhimurium swam faster, had greater acceleration and travelled further when cultured with FeSO4 compared with Ao iron and control; swim speed, acceleration and distance travelled did not differ between Ao iron and control. These findings provide evidence that Ao iron reduces the virulence of a common enteric pathogen in vitro. Further research is required to determine whether iron-enriched Ao is a suitable iron supplement to improve iron delivery in areas with a high infection burden.

Deciphering the interactions between plant species and their main fungal root pathogens in mixed grassland communities

Abstract Plant diversity can reduce the risk of plant disease, but positive, and neutral effects have also been reported. These contrasting relationships suggest that plant community composition, rather than diversity per se, affects disease risk. Here, we investigated how the diversity and composition of plant communities drive root‐associated pathogen accumulation belowground. In a temperate grassland biodiversity experiment, containing 16 plant species (forbs and grasses), we determined the abundance of root‐associated fungal pathogens in individual plant species growing in monocultures and in four‐species mixtures through Illumina MiSeq amplicon sequencing. In the plant monocultures, we identified three major fungal pathogens that differed in host range: Paraphoma chrysanthemicola, associated with roots of forb species of the Asteraceae family, Slopeiomyces cylindrosporus, associated with grass species, and Rhizoctonia solani, associated with multiple forb and grass species. In mixtures, there was no significant reduction in relative abundance of these pathogens in their host species as compared to monocultures. However, in mixtures, there was a significant increase in relative abundance of each pathogen in several non‐host and host plant species. Across mixtures, plant community composition affected pathogen relative abundance in individual plant species. This effect was driven by the presence of a particular neighbouring plant species (depending on the pathogen), rather than functional group composition (i.e. grass/forb ratio) or averaged pathogen pressure (based on monocultures) of all neighbours. Specifically, the presence of neighbour host species Achillea millefolium significantly increased P. chrysanthemicola, but decreased R. solani relative abundance in several host and non‐host plant species in mixtures. Synthesis. Our results indicate that interactions between different plant species—both host and non‐hosts—and fungal pathogens underlie the effects of plant diversity on root pathogen abundance. Non‐host species may act as pathogen reservoirs in diverse plant communities, as they harboured certain pathogens in mixtures, but not in monocultures. Additionally, particular host species can strongly affect pathogen abundance in other (host and non‐host) plant species in plant mixtures, suggesting clear effects of species identity in the diversity–disease relationship. Below‐ground disease risk thus depends on plant community composition rather than diversity per se, via specific interactions between plant species and their root‐associated pathogens.

Leguminous cover crops and soya increased soil fungal diversity and suppressed pathotrophs caused by continuous cereal cropping.

The enrichment of soil-borne fungal pathogens and a high input of mineral fertilizer in the continuous cropping of cereal crops have raised a concern about soil health deterioration. Conversion of continuous cereal cropping to a legume-involved system alters the soil fungal community. However, when a leguminous cover crop is grown with a succeeding legume grain crop such as soya (Glycine max L. Merril), the effects on the soil fungal community when two legumes are involved in the crop system remain unclear. Thus, the effects of the cover crop on the soil fungal community under a succession of soya and a succession of maize (Zea mays L.) were clarified: a continuous wheat (Triticum aestivum L.)–maize cropping system was converted to new rotation systems with three cover crop treatments: leguminous vetch (Vicia sativa L.), a mixture of vetch and rye (Secale cereale L.), and fallow, succeeded by soya or maize in this study. The soil fungal community at the harvest of soya and maize were determined using high-throughput sequencing of ITS2 amplicons. Compared to a wheat–maize rotation system, all of the new rotation systems that involved leguminous crops or fallow increased the soil fungal diversity and suppressed pathotrophs by reducing the soil NH4+, NO3−, available K, and available P concentrations. Different cover crops changed the fungal community composition, but their effect was overwhelmed by the strong effect of succeeding soya, which induced minor shifts among the cover crop treatments under soya than maize. The Vetch–Soya system exhibited the highest fungal diversity, which have been due to an increase of symbiotrophs. Replacing wheat with mixed vetch and rye most greatly suppressed the pathotrophs, and this suppression effect was stronger when succeeded by maize than by soya. These results showed the short-term benefits of legume–legume succession and legume–cereal mixed cover crops for increasing fungal diversity and suppressing pathotrophs. Further study is needed to examine the long-term effects of Vetch–Soya on the accumulation of legume-associated pathogens.

Preventing the spread of COVID-19 through environmental design in Thai community hospitals

The unprecedented outbreak of COVID-19 has had a tremendous negative impact on healthcare facilities, especially public hospitals. Thai community hospitals serve as primary care for COVID-19 patients. However, many hospital buildings were constructed in the 1990s and are now becoming outdated. Community hospitals faced many difficulties during the Thailand COVID-19 outbreak. To identify these difficulties this study focused on the physical settings of the community hospital’s outpatient departments (OPD) between 2020 and 2021. Furthermore, the study provided design suggestions for preventing the spread of respiratory infectious diseases. The study used a three-step process of data collection. The first was to observe the physical settings of the OPD buildings of the three hospitals. Secondly, interviews were conducted with thirty healthcare employees: 11 from the first hospital, 11 from the second hospital and 8 from the third hospital. Interviews were transcribed and analyzed using content analysis. Subsequently, the architectural design was produced based on observation and interview analysis. In the third step, the same thirty participants evaluated the architectural design through a focus group. Findings from the interviews led to four themes: 1) factors leading to the accumulation of pathogens, 2) measures for preventing the spread of respiratory diseases, 3) the effect of patient numbers on virus transmission, and 4) suggestions for improving the physical setting of OPDs. The analysis of the four themes led to the preliminary design recommendation, which was evaluated through a focus group, leading to suggestions for the improvement of thirteen areas. The analysis results showed that the participants were satisfied with the architectural design with additional minor recommendations. This study provided originality for the implementation and future development of hospital layout designs that can prevent the spread of COVID-19 throughout Thai community hospitals.

Phenological growth stage of tropical shallot (Allium cepa L. Aggregatum group) planted from seed in lowland area based on the BBCH scale

AbstractShallot (Allium cepa L. Aggregatum group) is an important Allium plant commonly grown in tropical countries, including Indonesia, and it is used as spice for daily cooking, medicine, cosmetics and dietary supplements. Since shallot is predominantly propagated vegetatively by bulbs, it augments pathogen accumulation which influences low seed bulb management as well as productivity. Hence, utilisation of seeds/True Seed Shallot (TSS) emerges an alternative propagation material. However, no information is available on the growth stages of shallot plants from TSS. The phenological growth stages of tropical shallot planted in lowland areas using seeds in accordance with the Biologische Bundesanstalt, Bundessortenamt nd CHemische Industrie (BBCH) scale are first described here. Five introduced TSS cultivars, that is, Tuk Tuk, Lokananta, Sanren, Maserati, Tropix and four landraces TSS cultivars, that is, Bima, Biru Lancor, Pancasona and Trisula, were used as planting materials to develop an extended numerical BBCH scale for the identification of different phenological growth stages of shallot from seed. The study was conducted in lowland areas under tropical conditions of Indonesia. Based on BBCH scale, phenology of tropical shallot from seed in lowland area exhibited five of the 10 principal stages (0–9): germination (stage 0), leaf development (stage 1), formation of lateral shoot/tiller of pseudostem (stage 2), development of bulb (harvestable vegetative part) (stage 4), and senescence (stage 9). The codification of the different growth stages is essential in determination of the correct timing for better crop management, particularly for transplanting, fertilisation, control of weeds, disease and pest, plant growth regulators application and harvest time. As an implication, these BBCH scales could be used in plant breeding activities to shorten the TSS life cycle.