scholarly journals Good and bad lettuce leaf microbes? Unravelling the genetic architecture of the microbiome to inform plant breeding for enhanced food safety and reduced food waste

2021 ◽  
Author(s):  
Annabelle Damerum ◽  
Elizabeth C Arnold ◽  
Villo Bernad ◽  
Hazel K Smith ◽  
Gail Taylor
Keyword(s):  
Bacterial Diversity ◽  
Food Waste ◽  
Genetic Architecture ◽  
Leaf Surface ◽  
Surface Characteristics ◽  
Surface Hydrophobicity ◽  
Human Pathogens ◽  
Host Genotype ◽  
Spoilage Bacteria ◽  
Bacterial Microbiome

Lettuce is a high value food crop, consumed raw around the world. Engineering of the leaf microbiome could provide significant benefits for enhanced crop yield and stress resistance and help to reduce food waste caused by microbial spoilage. Lettuce leaves also act as a vector for human pathogens, implicated in several high-profile food-borne disease outbreaks. Since host genotype helps determine microbiome composition, we hypothesize that leaf surface traits can be defined that associate with "good" bacterial microbiomes providing benefits to the crop and that "bad" microbiomes, where spoilage organisms and human pathogens are abundant, can also be associated to underlying leaf genetics, providing key targets for future crop breeding. Using a Recombinant Inbred Line (RIL) population, we show that cultivated and wild parental genotypes differ with reduced bacterial diversity, larger leaves and fewer, larger stomata, smaller epidermal cells and more hydrophilic leaf surfaces found in the cultivated compared to wild lettuce. Functional analysis of the associated microbiome revealed increased abundance of genes associated with disease virulence for the cultivated lettuce genotype, suggesting domestication has had broad impacts on leaf and associated bacterial microbiome traits. We defined the core lettuce bacterial microbiome from 171 RILs, comprised of 45 taxa in the phyla Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi and Deinococcus-Thermus. Leaf surface characteristics important in influencing bacterial diversity and abundance were identified as stomatal size (length and width), epidermal cell area and number and leaf surface hydrophobicity of the abaxial leaf surface. Quantitative trait loci (QTL) for leaf surface traits, frequently mapped alongside those for the extended phenotype of bacterial taxa abundance, including for human pathogens Campylobacter spp., Escherichia-Shigella spp., Clostridium spp. (LG 4, 5 and 6) and spoilage bacteria, Pseudomonas spp. (LG 1, 3, 4, 6 and 9). Candidate genes underlying these QTL were enriched in GO terms for cell wall assembly and modification, defence response, hormone-mediated signalling and biosynthesis and anatomical structure development. This work provides the first insight into the genetic architecture of host surface traits in a leafy crop alongside the mapped genetic architecture of bacterial communities and has identified areas of the lettuce genome as important targets for future microbiome engineering.

scholarly journals Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome

2017 ◽  
Author(s):  
Laura B. Dickson ◽  
Amine Ghozlane ◽  
Stevenn Volant ◽  
Christiane Bouchier ◽  
Laurence Ma ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Geographic Origin ◽  
Low Complexity ◽  
Genetic Effects ◽  
Microbiota Composition ◽  
Vector Biology ◽  
Human Pathogens ◽  
Host Genotype ◽  
Bacterial Microbiome ◽  
Laboratory Colonies

AbstractBackgroundHost-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six recent laboratory colonies of Aedes aegypti representing the geographical range and genetic diversity of the species.ResultsWe found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographic origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.ConclusionsOur finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.

Effects of Metal Stress on Visible/Near-Infrared Reflectance Spectra of Vegetation

2011 ◽  
Vol 347-353 ◽  
pp. 2735-2738 ◽  
Author(s):  
Guang Yu Chi ◽  
Yi Shi ◽  
Xin Chen ◽  
Jian Ma ◽  
Tai Hui Zheng
Keyword(s):  
Heavy Metal ◽  
Structural Changes ◽  
Near Infrared ◽  
Leaf Surface ◽  
Spectral Response ◽  
Spectral Characteristics ◽  
Surface Characteristics ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Near Infrared Reflectance

Vegetation which suffers from heavy metal stresses can cause changes of leaf color, shape and structural changes. The spectral characteristics of vegetation leaves is related to leaf thickness, leaf surface characteristics, the content of water, chlorophyll and other pigments. So the eco-physiology changes of plants can be reflected by spectral reflectance. Studies on the spectral response of vegetation to heavy metal stress can provide a theoretical basis for remote sensing monitoring of metal pollution in soils. In recent decades, there are substantial amounts of literature exploring the effects of heavy metals on vegetation spectra.

scholarly journals Bovine Colostrum for Human Consumption - Improving Microbial Quality and Maintaining Bioactive Characteristics through Processing

2021 ◽  
Author(s):  
Sylvia Fasse ◽  
Jarmo Alarinta ◽  
Björn Frahm ◽  
Gun Wirtanen
Keyword(s):  
Heat Treatment ◽  
Large Scale ◽  
Bovine Colostrum ◽  
Raw Material ◽  
Human Consumption ◽  
Microbial Quality ◽  
Scale Production ◽  
Human Pathogens ◽  
Spoilage Bacteria

The purpose of bovine colostrum, being the milk secreted by a cow after giving birth, is to transfer passive immunity to the calf. The calves have an insufficient immune system as they lack immunoglobulins (Igs). Subsequently, the supply of good quality bovine colostrum is obligatory. The quality of colostrum is classified by low bacterial counts and adequate Ig concentrations. Bacterial contamination can contain a variety of human pathogens or high counts of spoilage bacteria, which becomes more challenging with emerging use of bovine colostrum as food and food supplements. There is also a growing risk for the spread of zoonotic diseases originating from bovines. For this reason, processing based on heat treatment or other feasible techniques are required. This review provides an overview of literature on the microbial quality of bovine colostrum and processing methods to improve its microbial quality and keep its nutritional values as food. The highlights of this review are: high quality colostrum is a valuable raw material in food products and supplements, the microbial safety of bovine colostrum is increased using appropriate processing, suitable effective heat-treatment, which does not destroy the high nutrition value of colostrum, the heat treatment processes are cost-effective compared to other methods, and heat treatment can be performed in both small- and large-scale production

scholarly journals Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences

2021 ◽  
Author(s):  
Grace A. Blackwell ◽  
Martin Hunt ◽  
Kerri M. Malone ◽  
Leandro Lima ◽  
Gal Horesh ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Dna Sequences ◽  
Anthropogenic Activities ◽  
Research Priorities ◽  
Specific Gene ◽  
Human Pathogens ◽  
Public Health Agencies ◽  
European Nucleotide Archive ◽  
National Public Health ◽  
And Function

ABSTRACTThe open sharing of genomic data provides an incredibly rich resource for the study of bacterial evolution and function, and even anthropogenic activities such as the widespread use of antimicrobials. Whilst these archives are rich in data, considerable processing is required before biological questions can be addressed. Here, we assembled and characterised 661,405 bacterial genomes using a uniform standardised approach, retrieved from the European Nucleotide Archive (ENA) in November of 2018. A searchable COBS index has been produced, facilitating the easy interrogation of the entire dataset for a specific gene or mutation. Additional MinHash and pp-sketch indices support genome-wide comparisons and estimations of genomic distance. An analysis on this scale revealed the uneven species composition in the ENA/public databases, with just 20 of the total 2,336 species making up 90% of the genomes. The over-represented species tend to be acute/common human pathogens. This aligns with research priorities at different levels from individuals with targeted but focused research questions, areas of focus for the funding bodies or national public health agencies, to those identified globally as priority pathogens by the WHO for their resistance to front and last line antimicrobials. Understanding the actual and potential biases in bacterial diversity depicted in this snapshot, and hence within the data being submitted to the public sequencing archives, is essential if we are to target and fill gaps in our understanding of the bacterial kingdom.

scholarly journals The Dysbiosis and Inter-Kingdom Synergy Model in Oropharyngeal Candidiasis, a New Perspective in Pathogenesis

2019 ◽  
Vol 5 (4) ◽  
pp. 87 ◽  
Author(s):  
Martinna Bertolini ◽  
Anna Dongari-Bagtzoglou
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Species ◽  
Oral Microbiota ◽  
Oropharyngeal Candidiasis ◽  
Bacterial Microbiome ◽  
Significant Enrichment ◽  
Enterococcal Species ◽  
New Perspective ◽  
Mucosal Candidiasis ◽  
The Relationship

As more information emerges on oral microbiota using advanced sequencing methodologies, it is imperative to examine how organisms modulate the capacity of each other to colonize or trigger infection. Most mouse models of oral C. albicans infection have focused on interactions with single bacterial species. Thus, little is known about the microbiome-mediated interactions that control the switch of C. albicans from commensalism to infection. Evidence is accumulating that in immunosuppression where mucosal candidiasis is more prevalent, there is an altered oral bacterial microbiome with reduced diversity, but not an altered mycobiome. Oropharyngeal candidiasis in immunosuppressed humans and mice is associated with a further reduction in oral bacterial diversity and a dysbiotic shift with significant enrichment of streptococcal and enterococcal species. Our recent studies in a cancer chemotherapy mouse model supported the combined profound effect of immunosuppression and C. albicans in reducing oral bacterial diversity and provided the first direct evidence that these changes contribute to pathogenesis, representing dysbiosis. There is still a gap in understanding the relationship between Candida and the oral bacterial microbiome. We propose that certain oral commensal bacteria contribute to fungal pathogenesis and we identify gaps in our understanding of the mechanisms involved in this cooperative virulence.

Different leaf surface characteristics of three grape cultivars affect leaf optical properties as measured with fibre optics: possible implication in stress tolerance

1999 ◽  
Vol 26 (1) ◽  
pp. 47 ◽  
Author(s):  
G. Karabourniotis ◽  
J. F. Bornman ◽  
V. Liakoura
Keyword(s):  
Leaf Surface ◽  
Relative Concentration ◽  
Light Attenuation ◽  
Surface Characteristics ◽  
Ultraviolet B ◽  
The Other ◽  
Visible Radiation ◽  
Fibre Optics ◽  
Young Leaves ◽  
Grape Cultivars

Young leaves of three grape cultivars having different surface characteristics (cv. Athiri, pubescent; cv. Soultanina, glabrous green; and cv. Fraoula, glabrous red-brown) only during the early stages of their development, were used to investigate the potential, differential effect of a trichome layer or a pigmented epidermis on the light microenvironment within the mesophyll. The penetration of forward propagated 310, 360 and 430 nm radiation into the leaf tissues was monitored using a quartz fibre-optic microprobe. The mesophyll of the young leaves of Athiri was much better protected from ultraviolet-A, ultraviolet-B and high visible radiation compared to the other two cultivars. Abaxial, as well as adaxial trichome layers attenuated almost all incident radiation at 310 nm and 360 nm and a considerable part of the blue light (430 nm). No significant differences in light attenuation from epidermal and mesophyll layers between the other two cultivars were observed. The adaxial epidermis of young and dehaired leaves of cv. Athiri was largely ineffective in absorbing the incident ultraviolet- B radiation. In addition, the dehaired lamina of such leaves exhibited 80% lower relative concentration of ultraviolet-absorbing compounds per leaf surface area, compared to leaves of similar ontogenetic stage in the cv. Soultanina. It is proposed that the occurrence of a dense trichome layer in young leaves, besides other proposed functions, may play a protective role against not only ultraviolet radiation damage, but also against high insolation. This protection could be advantageous under stress conditions during leaf development.

Anti-adhesion properties of aminopropanol derivative with N-alkylaryl radical KVM-194 against Pseudomonas aeruginosa

2020 ◽  
Vol 2 (1) ◽  
pp. 34-41
Author(s):  
Nataliia HRYNCHUK ◽  
Tetiana BUKHTIAROVA ◽  
Daria DUDIKOVA ◽  
Nina VRYNCHANU ◽  
Vira NEDASHKIVSKA ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Cell Surface Hydrophobicity ◽  
Surface Characteristics ◽  
Surface Hydrophobicity ◽  
Clinical Strain ◽  
Bacterial Cells ◽  
Adhesion Properties ◽  
Minimal Inhibitory Concentrations ◽  
Pre Treatment ◽  
Antibiofilm Agents

Introduction. The present study assessed Pseudomonas aeruginosa surface characteristics, motility and adhesion properties under the influence of 1-[4-(1,1,3,3-tetra methyl butyl) phenoxy]-3-(N-benzyl hexa methylene iminium)-2-propanol chloride (KVM-194). Material and methods. The clinical strain P. aeruginosa 449 was used in the study. The cell surface hydrophobicity (CSH) was evaluated by adhesion to solvent (MATS test). Swimming, swarming and twitching motility of P. aeruginosa were studied by standard methods in media with different agar contents. Cells ability to adhere to polystyrene was assessed by the Christensen method. The effect of KVM-194, meropenem and ciprofloxacin on hydrophobicity and motility was evaluated both at 0.5 or 2.0 minimal inhibitory concentrations (MIC), while on adhesion abilities – only 0.5×MIC. Results. It was shown that 0.5× MIC KVM-194 reduced CSH of P. aeruginosa (by 16%, p˂0.05), affected swimming motility, and decreased its adhesion to polystyrene. The most pronounced changes in adhesion properties were recorded after 3-5 hours of pre-treatment with this compound. Moreover, it was proven that sub-MICs of meropenem and ciprofloxacin did not alter bacterial cells hydrophobicity and had no significant influence on P. aeruginosa motility and adhesion properties. Conclusions. The present study suggested that KVM-194 affected the initial steps of   P. aeruginosa biofilm formation and thus had tremendous potential for new antibiofilm agents’ development.

Bacterial Diversity in Rhipicephalus sanguineus (Acari: Ixodidae) from Two States in Nigeria

2021 ◽  
Vol 56 (2) ◽  
pp. 256-271
Author(s):  
Desmond Onyeka Agwunobi ◽  
Joshua Kamani ◽  
Hongyuan Zheng ◽  
Lida Guo ◽  
Zhijun Yu ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Tick Species ◽  
High Throughput Sequencing ◽  
Rhipicephalus Sanguineus ◽  
Pathogen Transmission ◽  
Sequencing Platform ◽  
Bacterial Microbiome ◽  
Community Profile ◽  
Plateau State ◽  
Abundant Genus

Abstract Rhipicephalus sanguineus (Latreille) is the most widely distributed tick species globally and plays a major role in tick-borne pathogen transmission among canine populations. The microbial community of this tick has not been characterized previously in Nigeria. Thus, in this study, the bacterial diversity in R. sanguineus collected from two states in Nigeria was explored using 16S rRNA high-throughput sequencing (IonS5TM XL sequencing platform). Three hundred genera (although 18 groups belong to unidentified genera) of bacteria belonging to 22 phyla were detected after pooling and sequencing, indicating a diverse bacterial community profile. At the phylum level, Actinobacteria (47.39%) was the most abundant phylum in the Benue state samples, followed by Proteobacteria (43.87%) and Firmicutes (8.21%), whereas Fusobacteria (38.14%) was the most abundant phylum in Plateau state samples, followed by Bacteroidetes (17.57%) and Firmicutes (17.54%). Proteobacteria accounts for 17% of samples from Plateau state. In general, Cetobacterium (35.86%) was the most abundant genus, followed by an unidentified genus under Corynebacteriaceae (29.94%) and Stenotrophomonas (19.52%). Coxiella spp., one common endosymbiont found in various tick species, was present in R. sanguineus. This study provides a baseline of knowledge of the bacterial microbiome of R. sanguineus in Nigeria. Nonpathogenic bacteria species were prevalent, and not much is known about their role. Thus, their composition, functional, and ecologic implications merit further investigation because this will aid in the subsequent management of ticks and tick-borne diseases.

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