Assessment of Morphological Variation in Irish Brassica oleracea Species

This study aimed at assessing the morphological variation in 25 accessions of an Irish collection of Brassica oleracea using 44 morphological traits. The morphological traits showed a pronounced variation among accessions. Vegetative preflowering and maturity traits revealed higher variation than seedling traits. Of the 44 morphological descriptors used, 28 were significantly different and proved useful in examining diversity and differentiating among accessions studied. Principal component analysis (PCA) showed variation among accessions, where 87.24% of the total variation in the morphological data was separated on the first five components, indicating a high degree of correlation among traits studied. Cluster analysis grouped the 25 accessions into 4 main groups, corresponding to kales, cauliflowers, cabbages and sprouts, and also showed a sort of correlation between clustering pattern and eco-geographical distribution of the accessions. Furthermore, this study identified 9 highly diverse accessions, providing opportunities for optimising parental sources in future breeding programs to develop new or more productive Brassica varieties. Morphological traits were deemed useful for assessing the diversity and relationships in Irish Brassica oleracea species

Genetic diversity and population structure of Brassica oleracea germplasm in Ireland using SSR markers

The most economically important Brassica oleracea species is endangered in Ireland, with no prior reported genetic characterization studies. This study assesses the genetic diversity, population structure and relationships of B. oleracea germplasm in Ireland using microsatellite (SSRs) markers. A total of 118 individuals from 25 accessions of Irish B. oleracea were genotyped. The SSR loci used revealed a total of 47 alleles. The observed heterozygosity (0.699) was higher than the expected one (0.417). Moreover, the average values of fixation indices (F) were negative, indicating excess of heterozygotes in all accessions. Polymorphic information content (PIC) values of SSR loci ranged from 0.27 to 0.66, with an average of 0.571, and classified 10 loci as informative markers (PIC\u3e0.5) to differentiate among the accessions studied. The genetic differentiation among accessions showed that 27.1% of the total genetic variation was found among accessions, and 72.9% of the variation resided within accessions. The averages of total heterozygosity (H(T)) and intra-accession genetic diversity (H(S)) were 0.577 and 0.442, respectively. Cluster analysis of SSR data distinguished among kale and Brussels sprouts cultivars. This study provided a new insight into the exploitation of the genetically diverse spring cabbages accessions, revealing a high genetic variation, as potential resources for future breeding programs. SSR loci were effective for differentiation among the accessions studied

Development of a GFP‐based biosensor for detecting the bioavailability and biodegradation of polychlorinated biphenyls (PCBs)

Two whole‐cell biosensors were constructed to detect the in situ biodegradation of polychlorinated biphenyl by chromosomal insertion of a mini‐Tn5‐Kmr‐Pm::gfp[mut3]‐T0‐T1 construct into P. fluorescens. In vitro tests showed that the expression of the Pm promoter depended on the growth phase of the biosensors and the concentration of chemical inducers; chlorinated benzoic acid derivatives. A linear relationship between the fluorescent intensity and the log10 concentration of the inducer was observed. One biosensor (F113L::1180gfp) had the ability to degrade PCBs to relevant chlorobenzoic acid derivatives and to induce expression of Gfp. The second biosensor (F113gfp), which cannot degrade PCBs, shows fluorescence after induction by chloro‐benzoic acid derivatives. By using these two biosensors, PCB degradation could be detected in vitro and in soil. Gfp pagrindo biosensorių tobulinimas polichlorintų bifenilų (PCBs) biotinkamumui ir biodegradacijai nustatyti Santrauka Sukonstruoti du ląsteliniai bioindikatoriai polichlorintų bifenilų in situ biodegradacijai nustatyti chromosominiu konstrukto mini-Tn5-KmF -Pm::gfp[mut3]-T0 -T1 įterpimo į P. fluorescens būdu. Bandymai dirbtinėmis sąlygomis parodė, kad Pm aktyviklio išraiška priklauso nuo bioindikatoriaus augimo fazės ir cheminių indikatorių koncentracijos, taip pat nuo chlorintų benzenkarboksirūgščių derinių. Nustatyta tiesinė priklausomybė tarp fluorescentų intensyvumo ir indikatorių log10 koncentracijos. Vienas iš bioindikatorių (F113L::1180gfp) galėjo degraduoti PCBs iki tinkamų chlorobenzenkarboksirūgščių derinių ir indukuoti Gfp išraišką. Antrasis bioindikatorius (F113gfp), kuris negali degraduoti PCBs, parodo fluorescentiškumą įvykus indukcijai pagal chloro-benzenkarboksirūgščių derinius. Naudojant šiuos du bioindikatorius, PCB degradacija gali būti nustatyta tiek dirbtinėmis sąlygomis, tiek dirvožemyje. Reikšminiai žodžiai: bioindikatoriai, Pseudomonas fluorescens F113, PCBs, rizosfera, šaknų kolonizacija. Совершенствование биосенсоров основы gfp для определения биосоответствия и биодеградации полихлорированных бифенилов (PCBs) Резюме Сконструированы два клеточных биоиндикатора для выявления на участке биодеградации полихлорированных бифенилов путем хромосомного введения мини-Tn5-Kmr-Pm::gfp[mut3]-T0-T1 в P. fluorescen. Испытания в искусственных условиях показали, что выражение активатора Pm зависит от фазы роста биоиндикатора и концентрации химических индикаторов, а также от сочетаний хлорированных бензойных кислот. Наблюдалась линейная зависимость между интенсивностью флуоресцентов и концентрации log10 индикаторов. Один из индикаторов (F113L::1180gfp) мог способствовать деградации PCBs в сочетания соответствующих хлор-бензойных кислот и индуцировать выражение Gfp. Другой биоиндикатор (F113gfp), который не может способствовать деградации PCBs, показал флуоресцентность после индикации по сочетаниям хлор-бензойных кислот. С использованием этих индикаций деградация PCB может наблюдаться лишь в искусственных условиях и лишь в почве. Ключевые слова: биоиндикаторы, Pseudomonas fluorescens F113, PCBs, ризосфера, корневая колонизация. First Published Online: 14 Oct 201

Field scale biodegradation of total petroleum hydrocarbons and soil restoration by Ecopiles: microbiological analysis of the process

Ecopiling is a method for biodegradation of hydrocarbons in soils. It derives from Biopiles, but phytoremediation is added to biostimulation with nitrogen fertilization and bioaugmentation with local bacteria. We have constructed seven Ecopiles with soil heavily polluted with hydrocarbons in Carlow (Ireland). The aim of the study was to analyze changes in the microbial community during ecopiling. In the course of 18 months of remediation, total petroleum hydrocarbons values decreased in 99 and 88% on average for aliphatics and aromatics, respectively, indicating a successful biodegradation. Community analysis showed that bacterial alfa diversity (Shannon Index), increased with the degradation of hydrocarbons, starting at an average value of 7.59 and ending at an average value of 9.38. Beta-diversity analysis, was performed using Bray-Curtis distances and PCoA ordination, where the two first principal components (PCs) explain the 17 and 14% of the observed variance, respectively. The results show that samples tend to cluster by sampling time instead of by Ecopile. This pattern is supported by the hierarchical clustering analysis, where most samples from the same timepoint clustered together. We used DSeq2 to determine the differential abundance of bacterial populations in Ecopiles at the beginning and the end of the treatment. While TPHs degraders are more abundant at the start of the experiment, these populations are substituted by bacterial populations typical of clean soils by the end of the biodegradation process. Similar results are found for the fungal community, indicating that the microbial community follows a succession along the process. This succession starts with a TPH degraders or tolerant enriched community, and finish with a microbial community typical of clean soil

Whole-Cell Fluorescent Biosensors for Bioavailability and Biodegradation of Polychlorinated Biphenyls

Whole-cell microbial biosensors are one of the newest molecular tools used in environmental monitoring. Such biosensors are constructed through fusing a reporter gene such as lux, gfp or lacZ, to a responsive promoter. There have been many reports of the applications of biosensors, particularly their use in assaying pollutant toxicity and bioavailability. This paper reviews the basic concepts behind the construction of whole-cell microbial biosensors for pollutant monitoring, and describes the applications of two such biosensors for detecting the bioavailability and biodegradation of Polychlorinated Biphenyls (PCBs)

The Good, the Bad, and the Useable Microbes within the Common Alder (<i>Alnus glutinosa</i>) Microbiome—Potential Bio-Agents to Combat Alder Dieback

Common Alder (Alnus glutinosa (L.) Gaertn.) is a tree species native to Ireland and Europe with high economic and ecological importance. The presence of Alder has many benefits including the ability to adapt to multiple climate types, as well as aiding in ecosystem restoration due to its colonization capabilities within disturbed soils. However, Alder is susceptible to infection of the root rot pathogen Phytophthora alni, amongst other pathogens associated with this tree species. P. alni has become an issue within the forestry sector as it continues to spread across Europe, infecting Alder plantations, thus affecting their growth and survival and altering ecosystem dynamics. Beneficial microbiota and biocontrol agents play a crucial role in maintaining the health and resilience of plants. Studies have shown that beneficial microbes promote plant growth as well as aid in the protection against pathogens and abiotic stress. Understanding the interactions between A. glutinosa and its microbiota, both beneficial and pathogenic, is essential for developing integrated management strategies to mitigate the impact of P. alni and maintain the health of Alder trees. This review is focused on collating the relevant literature associated with Alder, current threats to the species, what is known about its microbial composition, and Common Alder–microbe interactions that have been observed worldwide to date. It also summarizes the beneficial fungi, bacteria, and biocontrol agents, underpinning genetic mechanisms and secondary metabolites identified within the forestry sector in relation to the Alder tree species. In addition, biocontrol mechanisms and microbiome-assisted breeding as well as gaps within research that require further attention are discussed

AFLP Analysis of Genetic Diversity and Phylogenetic Relationships of Brassica Oleracea in Ireland

Brassica oleracea L. is one of the most economically important vegetable crop species of the genus Brassica L. This species is threatened in Ireland, without any prior reported genetic studies. The use of this species is being very limited due to its imprecise phylogeny and uncompleted genetic characterisation. The main objective of this study was to assess the genetic diversity and phylogenetic relationships of a set of 25 Irish B. oleracea accessions using the powerful amplified fragment length polymorphism (AFLP) technique. A total of 471 fragments were scored across all the 11 AFLP primer sets used, out of which 423 (89.8%) were polymorphic and could differentiate the accessions analysed. The dendrogram showed that cauliflowers were more closely related to cabbages than kales were, and accessions of some cabbage types were distributed among different clusters within cabbage subgroups. Approximately 33.7% of the total genetic variation was found among accessions, and 66.3% of the variation resided within accessions. The total genetic diversity (HT) and the intra-accessional genetic diversity (HS) were 0.251 and 0.156, respectively. This high level of variation demonstrates that the Irish B. oleracea accessions studied should be managed and conserved for future utilisation and exploitation in food and agriculture. In conclusion, this study addressed important phylogenetic questions within this species, and provided a new insight into the inclusion of four accessions of cabbages and kales in future breeding programs for improving varieties. AFLP markers were efficient for assessing genetic diversity and phylogenetic relationships in Irish B. oleracea species

Assessment of Biodegradation and Eco-Toxic Properties of Novel Starch and Gelatine Blend Bioplastics

To combat the release of petroleum-derived plastics into the environment the European Commission has adopted the EU plastics strategy, which aims for a complete ban on single-use plastics by 2030. Environmentally friendly and sustainable packaging like bioplastic is being up taken at significant levels by companies and consumers. In this study, the environmental impact of novel gelatine–starch blend bioplastics is investigated. The assessments included ecotoxicology with different species that can be found in marine and soil environments to simulate natural conditions. Microalgae, plant, and nematode species were chosen as these are representative of their habitats and are known for their sensitivity to pollutants. Degradation rates of these novel bioplastics were assessed as well as microbiome analysis of the soil before and after bioplastic degradation. The main findings of this study are that (i) the bioplastic generated can be fully biodegraded in soil environments at moderate conditions (20 °C) leaving no physical traces; (ii) bioplastic did not exhibit significantly adverse effects on any organisms assessed in this study; (iii) microbiome analysis of the soil after biodegradation showed a decrease in alpha diversity and a significant increase of Actinobacteria and Firmicutes phyla, which were dominative in the soil