Methodology Papers -Papers that present different methodological approaches that can be used to investigate problems in a relevant scientific field and to encourage innovation.
Recently, metal oxides and magnesium hydroxide nanoparticles (NPs) with high surface-to-volume ratios were shown to possess antibacterial properties with applications in biomedicine and agriculture. To assess recent observations from field trials on tomatoes showing resistance to pathogen attacks, porous micron-scale particles composed of nano-grains of MgO were hydrated and sprayed on the leaves of healthy tomato (Solanum lycopersicum) plants in a 20-day program. The results showed that the spray induced (a) a modest and selective stress gene response that was consistent with the absence of phytotoxicity and the production of salicylic acid as a signalling response to pathogens; (b) a shift of the phylloplane microbiota from near 100% dominance by Gram (−) bacteria, leaving extremophiles and cyanobacteria to cover the void; and (c) a response of the fungal leaf phylloplane that showed that the leaf epiphytome was unchanged but the fungal load was reduced by about 70%. The direct microbiome changes together with the low level priming of the plant’s immune system may explain the previously observed resistance to pathogen assaults in field tomato plants sprayed with the same hydrated porous micron-scale particles.
The genetic material of Vitis varieties is crucial for the wine sector. In addition, genomic technologies applied in vitis germplasm characterization are important for the conservation of indigenous genetic reservoirs. Until recently the most common method to genetically identify vitis varieties was the use of Simple Sequence Repeats (SSR) along with SNP chips. Yet, with the progress in Next Generation Sequencing (NGS) technologies and the reduced sequencing cost per base, a twist in plant species genetic identification methods has occurred. Among them, the low coverage Whole-Genome Sequencing (lcWGS) method with downstream bioinformatic analysis for variant discovery and phylogenetic characterization is gaining scientific attention. In this dataset, shotgun sequencing data of two different Greek Vitis varieties, 'Razaki' and 'Vlachiko' are presented. Vitis cultivars were collected from the Aristotle University of Thessaloniki's (AUTH) ampelographic collection and have been previously phenotypically and genetically characterized. WGS libraries were sequenced on an IlluminaⓇ NovaSeq 6000 platform with the IlluminaⓇ NovaSeq 6000 S2 Reagent Kit (300 cycles). Raw sequence data used for analysis are available in NCBI under the Sequence Read Archive (SRA), with BioProject ID PRJNA805368. Reads were aligned to the reference genome of Vitis vinifera available from the EnsemblPlants database and formal analysis was conducted with the Genome Analysis Toolkit 4 (GATK4) pipeline. Data can be used to enrich our knowledge related to the genetic background of vitis cultivars and can also serve as a threshold in the scientific community towards the construction of a genomic database of vitis cultivars.
Obesity and type 2 diabetes are characterized by low-grade systemic inflammation and glucose intolerance, which can be partially controlled with nutritional interventions. Protein-containing nutritional supplements possess health-promoting benefits. Herein, we examined the effect of dietary supplementation with protein hydrolysates derived from fish sidestreams on obesity and diabetes, utilizing a mouse model of High-Fat Diet-induced obesity and type 2 diabetes. We examined the effect of protein hydrolysates from salmon and mackerel backbone (HSB and HMB, respectively), salmon and mackerel heads (HSH and HMH, respectively), and fish collagen. The results showed that none of the dietary supplements affected weight gain, but HSH partially suppressed glucose intolerance, while HMB and HMH suppressed leptin increase in the adipose tissue. We further analyzed the gut microbiome, which contributes to the metabolic disease implicated in the development of type 2 diabetes, and found that supplementation with selected protein hydrolysates resulted in distinct changes in gut microbiome composition. The most prominent changes occurred when the diet was supplemented with fish collagen since it increased the abundance of beneficial bacteria and restricted the presence of harmful ones. Overall, the results suggest that protein hydrolysates derived from fish sidestreams can be utilized as dietary supplements with significant health benefits in the context of type 2 diabetes and diet-induced changes in the gut microbiome.
Goat farming is a significant livestock sector in Greece, which holds the largest population of goats in the European Union. This population is mainly composed of the Eghoria and Skopelos indigenous breeds, the first of which is characterized by great phenotypic diversity, while the second presents a more uniform phenotype. Both breeds are characterized by high levels of genetic diversity. However, data regarding their genetic structure are scarce, usually concerning a limited number of genetic loci. Here, we present the first whole genome sequencing data generated for 14 indigenous Greek goats. In total, 66.5 Gb of data were produced on a NovaSeq. 6000 Illumina sequencer, corresponding to 3.18X average coverage. After quality filtering, >99.7% of sequences mapped successfully to the goat reference genome. Variant calling identified approximately 14 million autosomal variants of high-quality. These data can be used for the genetic improvement of the national herd through selective breeding schemes and, subsequently, improve the sustainability of the sector.
Analysis of table olives microbiome using next-generation sequencing has enriched the available information about the microbial community composition of this popular fermented food. In this study, 16S and 18S rRNA sequencing was performed on table olives of five Greek popular cultivars, Halkidikis, Thassou, Kalamon, Amfissis, and Konservolia, fermented either by Greek style (in brine or salt-drying) or by Spanish style, in order to evaluate their microbial communities. Moreover, analytical methods were used to evaluate their biochemical properties. The prevailing bacterial species of all olives belonged to Lactobacillaceae, Leuconostocaceae, and Erwiniaceae families, while the most abundant yeasts were of the Pichiaceae family. Principal coordinates analysis showed a clustering of samples cured by salt-drying and of samples stored in brine, regardless of their cultivar. The biochemical evaluation of total phenol content, antioxidant activity, hydroxytyrosol, oleuropein, oleocanthal, and oleacein showed that salt-dried olives had low amounts of hydroxytyrosol, while Spanish-style green olives had the highest amounts of oleocanthal. All the other values exhibited various patterns, implying that more than one factor affects the biochemical identity of the final product. The protocols applied in this study can provide useful insights for the final product, both for the producers and the consumers.
Coastal aquaculture systems are complex environments with multiple microbial interactions that affect fish health and productivity. High-throughput amplicon sequencing is a valuable tool for identifying such bacterial communities and investigating the relationship between bacterial diversity and sustainability in these systems. In the present study, the seasonal dynamics of marine bacterial communities were assessed, in terms of diversity and composition, in three marine aquaculture farms in the northern Ionian Sea (western Greece) and a distant control site unaffected by aquaculture activities, using 16S rRNA amplicon metabarcoding. Results revealed that Proteobacteria, Bacteroidota, Cyanobacteria, and Verrucomicrobiota were the dominant phyla in the bacterial communities. Alpha diversity was significantly lower in the aquaculture farms compared to the control site. Season was the major factor driving bacterial community fluctuations. Comparative analysis between seasons revealed the presence of differentially abundant amplicon sequence variants (ASVs) in all pairwise comparisons, with the majority of them belonging to the phyla Bacteroidota (families Flavobacteriaceae, Cryomorphaceae) and Proteobacteria (family Rhodobacteraceae). Our study provides the first detailed description of bacterial communities present in Greek coastal aquaculture farms using amplicon metabarcoding analysis and expands our understanding of the impact of seasonality and environmental variables on marine bacterial community diversity and composition.
Sheep farming is a common agricultural practice in Greece, with many sheep populations belonging to Greek breeds. However, their genetic makeup remains relatively unexplored and limited information is available for their genetic variability. Here, we provide the first whole genome sequencing (WGS) data for six Greek sheep breeds, namely Chios, Kalarritiko, Karagouniko, Lesvos, Serres, and Thraki breeds. We performed variant discovery analysis on the data and identified 23,526,500 high-quality variants. The high average variant depth (148.7X ± 28.3) and low Single Nucleotide Polymorphism (SNP) density (1 variant per 111 bases) in the callset demonstrated the high quality of the data. The vast majority of the variants (97.46%) were located in non-coding regions, while a small percentage (1.32%) was positioned in exonic regions. The overall transition to transversion−Ti/Tv (2.449) and heterozygous to non-reference homozygous−Het/Hom (1.49) ratios further confirmed the callset’s high quality. This dataset comprises the first WGS data for six Greek sheep breeds, providing invaluable information to the Greek agricultural sector for the design and implementation of targeted breeding schemes, for traceability purposes, and for the overall enhancement of the sector, in terms of performance and sustainability.
Olive trees worldwide suffer from a number of devastating fungal diseases that affect production. One such serious disease is olive leaf spot caused by Venturia oleaginea. Recently, we applied magnesium hydroxide porous micron-scale particles (PMPs) on tomatoes and observed potent antimicrobial activity, reducing the fungal load of the treated phyllosphere. To assess the effectiveness of the compound on olive fungal disease, we applied it for two consecutive seasons. One particular olive tree exhibited extreme manifestations of fungal disease and was destined for removal. A single application of Mg(OH)2 PMP reversed all symptoms of the disease and eliminated the Venturia pathogen, curing the tree of disease. Venturia oleaginea appears to be exceptionally susceptible to treatment compared to other species in the fungal leaf community. The beneficial fungus Aureobasidium pullulans increased in relative abundance in all the sprayed trees. No toxicity and leaf loss were observed, and the compound retention exceeded 47 days. All trees sprayed showed drastic reductions in the total fungal load and compared favorably to the commercial copper compound. Spraying induced a moderate expression of key indicator genes associated with stress responses. No leaf chlorosis or shedding were observed. Overall, Mg(OH)2 PMP treatment appears to be a highly promising tool for combating plant fungal disease.
