Culturable bacterial microflora associated with nectarine fruit and their potential for control of brown rot

Diversity of Culture Microorganisms from Portuguese Sweet Cherries

Consumers today seek safe functional foods with proven health-promoting properties. Current evidence shows that a healthy diet can effectively alleviate oxidative stress levels and reduce inflammatory markers, thereby preventing the occurrence of many types of cancer, hypertension, and cardiovascular and neurological pathologies. Nevertheless, as fruits and vegetables are mainly consumed fresh, they can serve as vectors for the transmission of pathogenic microorganisms associated with various disease outbreaks. As a result, there has been a surge in interest in the microbiome of fruits and vegetables. Therefore, given the growing interest in sweet cherries, and since their microbial communities have been largely ignored, the primary purpose of this study is to investigate their culturome at various maturity stages for the first time. A total of 55 microorganisms were isolated from sweet cherry fruit, comprising 23 bacteria and 32 fungi species. Subsequently, the selected isolates were molecularly identified by amplifying the 16S rRNA gene and ITS region. Furthermore, it was observed that the communities became more diverse as the fruit matured. The most abundant taxa included Pseudomonas and Ralstonia among the bacteria, and Metschnikowia, Aureobasidium, and Hanseniaspora among the fungi.

Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.

The Microbiome of the ‘Williams’ Pear Variety Grown in the Organic Orchard and Antifungal Activity by the Autochthonous Bacterial and Yeast Isolates

The total diversity of bacterial and fungal communities associated with the phyllosphere (fruits and leaves) of the ‘Williams’ pear variety was analyzed in two phenological stages during fruit development and maturation. The antagonistic potential of autochthonous bacterial and yeast isolates against phytopathogenic fungi was also evaluated. A metabarcoding approach revealed Pantoea, Sphingomonas, Hymenobacter, Massilia, and Pseudomonas as dominant bacterial constituents of the pear phyllosphere, whilst most abundant among the fungal representatives identified were Metschnikowia, Filobasidium, Aureobasidiumpullulans, Botrytis cinerea, and Taphrina. The traditional culturable approach revealed that the Pseudomonas genus with P. graminis, P. putida, and P. congelans was most prevalent. The most frequently cultivated fungal representatives belonged to the genus Fusarium with six identified species. A broad range of the antagonistic activity was detected for the Hannaella luteola and Metschnikowia pulcherrima yeasts, significantly affecting the growth of many fungal isolates in the range of 53–70%. Fusarium sporotrichioides was the most susceptible fungal isolate. The autochthonous antagonistic yeasts H. luteola and M. pulcherrima might be powerful biological control agents of postharvest diseases caused by Fusarium spp. and common pathogens like Monilinia laxa, Botrytis cinerea, Alternaria tenuissima, and Cladosporium cladosporioides.

Microbial Diversity of Psychrotolerant Bacteria Isolated from Wild Flora of Andes Mountains and Patagonia of Chile towards the Selection of Plant Growth-Promoting Bacterial Consortia to Alleviate Cold Stress in Plants

Cold stress decreases the growth and productivity of agricultural crops. Psychrotolerant plant growth-promoting bacteria (PGPB) may protect and promote plant growth at low temperatures. The aims of this study were to isolate and characterize psychrotolerant PGPB from wild flora of Andes Mountains and Patagonia of Chile and to formulate PGPB consortia. Psychrotolerant strains were isolated from 11 wild plants (rhizosphere and phyllosphere) during winter of 2015. For the first time, bacteria associated with Calycera, Orites, and Chusquea plant genera were reported. More than 50% of the 130 isolates showed ≥33% bacterial cell survival at temperatures below zero. Seventy strains of Pseudomonas, Curtobacterium, Janthinobacterium, Stenotrophomonas, Serratia, Brevundimonas, Xanthomonas, Frondihabitans, Arthrobacter, Pseudarthrobacter, Paenarthrobacter, Brachybacterium, Clavibacter, Sporosarcina, Bacillus, Solibacillus, Flavobacterium, and Pedobacter genera were identified by 16S rRNA gene sequence analyses. Ten strains were selected based on psychrotolerance, auxin production, phosphate solubilization, presence of nifH (nitrogenase reductase) and acdS (1-aminocyclopropane-1-carboxylate (ACC) deaminase) genes, and anti-phytopathogenic activities. Two of the three bacterial consortia formulated promoted tomato plant growth under normal and cold stress conditions. The bacterial consortium composed of Pseudomonas sp. TmR5a & Curtobacterium sp. BmP22c that possesses ACC deaminase and ice recrystallization inhibition activities is a promising candidate for future cold stress studies.

The current status on the taxonomy of Pseudomonas revisited: An update

The genus Pseudomonas described in 1894 is one of the most diverse and ubiquitous bacterial genera which encompass species isolated worldwide. In the last years more than 70 new species have been described, which were isolated from different environments, including soil, water, sediments, air, animals, plants, fungi, algae, compost, human and animal related sources. Some of these species have been isolated in extreme environments, such as Antarctica or Atacama desert, and from contaminated water or soil. Also, some species recently described are plant or animal pathogens. In this review, we revised the current status of the taxonomy of genus Pseudomonas and the methodologies currently used for the description of novel species which includes, in addition to the classic ones, new methodologies such as MALDI-TOF MS, MLSA and genome analyses. The novel Pseudomonas species described in the last years are listed, together with the available genome sequences of the type strains of Pseudomonas species present in different databases.

Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane

BACKGROUND

Knowledge on the culturable bacteria and foodborne pathogen presence on pears is important for understanding the impact of postharvest practices on food safety assurance. Pear fruit bacteria were investigated from the point of harvest, following chlorine drenching and after controlled atmosphere (CA) storage to assess the impact on natural bacterial populations and potential foodborne pathogens.

RESULTS

Salmonella spp. and Listeria monocytogenes were detected on freshly harvested fruit in season one. During season one, chemical drenching and CA storage did not have a significant effect on the bacterial load of orchard pears, except for two farms where the populations were lower 'after CA storage'. During season two, bacterial populations of orchard pears from three of the four farms increased significantly following drenching; however, the bacterial load decreased 'after CA storage'. Bacteria isolated following enumeration included Enterobacteriaceae, Microbacteriaceae, Pseudomonadaceae and Bacillaceae, with richness decreasing 'after drench' and 'after CA storage'.

CONCLUSION

Salmonella spp. and L. monocytogenes were not detected after postharvest practices. Postharvest practices resulted in decreased bacterial species richness. Understanding how postharvest practices have an impact on the viable bacterial populations of pear fruit will contribute to the development of crop-specific management systems for food safety assurance. © 2016 Society of Chemical Industry.

Yeasts associated with plums and their potential for controlling brown rot after harvest

Bacterial and yeast antagonists isolated from fruit surfaces have been effective in controlling various post-harvest diseases, and several microbial antagonists have been developed into commercial products. Our knowledge of the fruit microbial community, with the exception of grapes, apples and some citrus fruit, is rudimentary and the potential of the resident yeasts for biocontrol remains largely unknown. We determined the occurrence of yeasts on plum surfaces during fruit development from the pre-hardening stage until harvest for 2 years. A total of 16 species from 13 genera were isolated. Species from three genera, basidiomycetes Rhodotorula (29.5%) and Sporidiobolus (24.7%) and the dimorphic ascomycete genus Aureobasidium (24.7%), constituted 78.7% of all isolations and were recovered throughout fruit development, while Cryptococcus spp. constituted only 6.2% of the total plum isolates. The yeast community in the final sampling was significantly different from the first three samplings, reflecting a rapidly changing fruit habitat during the maturation of fruit. For example, Hanseniaspora, Pichia, Zygosaccharomyces and Wickerhamomyces occurred only on the most mature fruit. Screening of the yeasts for antagonistic activity against Monilinia fructicola, a fungus that causes brown rot, revealed a range of biocontrol activities. Several isolates provided complete control of the decay on plums, challenged with a pathogen suspension of 10(3) conidia/ml and > 90% of control on fruit inoculated with the pathogen at a concentration 10 times higher. Some of the best antagonists included A. pullulans and R. phylloplana. Populations of both of these antagonists increased rapidly by several orders of magnitude in wounds of plums incubated at 24ºC and 4ºC. Our results indicate that plum surfaces harbour several yeast species, with excellent potential for use in biological control of brown rot of stone fruits.

Phenotype microarray technology and its application in industrial biotechnology

Phenotype microarray (PM) technology provides an insight into the metabolic profiling of microbial cells within 96-well plate system. The PM assay allows for cells to be assessed for utilisation of nutrients or sensitivity to toxic compounds. The assay utilises a redox sensitive tetrazolium dye which becomes irreversibly reduced upon detection of cellular metabolic output, detection is synchronous with a colour change from colourless to purple. Output from PM technology can be measured visually or quantified by reader the absorbance in each well. PM technology has highlighted differences in growth requirements, nutrient utilisation, sensitivity to toxins, and genetic diversity in bacteria, fungi and mammalian cells.

Endophytic fungi from plums (Prunus domestica) and their antifungal activity against Monilinia fructicola

Enophytic fungi were isolated from plum (Prunus domestica) leaves, identified with ITS1 and ITS4 primers, and their antagonistic activity was tested against Monilinia fructicola, which causes brown rot, blossom blight, and twig blight of stone fruits, and Colletotrichum gloeosporioides, which causes anthracnose on a variety of fruit crops. The production of antifungal compounds was determined in agar-diffusion and volatile inverted-plate tests. A total of 163 fungi were recovered from 30 plum trees, representing 22 cultivars. Twenty-nine morphotypes were detected, but only 14 species were identified genetically. The most frequently isolated species was Phaeosphaeria nodorum, constituting 86.5% of the total isolates. Four isolates produced inhibitory volatiles to M. fructicola; however, no isolate produced volatiles inhibitory to C. gloeosporioides. The volatiles produced by these fungi were identified as ethyl acetate, 3-methyl-1-butanol, acetic acid, 2-propyn-1-ol, and 2-propenenitrile. The fungal volatiles inhibited growth and reduced width of the hyphae, and caused disintegration of the hyphal content. This is the first study describing fungal endophytes in stone fruits. The P. nodorum strains producing inhibitory volatiles could play a significant role in reduction of M. fructicola expansion in plum tissues. Potential of these strains for biological control of this pathogen on stone fruits warrants further investigation.

Changes in bacterial composition of zucchini flowers exposed to refrigeration temperatures

Microbial spoilage is one of the main factors affecting the quality of fresh fruits and vegetables, leading to off-flavor, fermented aroma, and tissue decay. The knowledge of microbial growth kinetics is essential for estimating a correct risk assessment associated with consuming raw vegetables and better managing the development of spoilage microorganisms. This study shows, for the first time, that only a part of total microbial community, originally present on fresh harvested female zucchini flowers, was able to adapt itself to refrigerated conditions. Through the study of microbial growth kinetics it was possible to isolate forty-four strains belonging to twenty-two species of the genera Acinetobacter, Arthrobacter, Bacillus, Enterobacter, Erwinia, Klebsiella, Pantoea, Pseudoclavibacter, Pseudomonas, Serratia, Staphylococcus, and Weissella, suggesting Enterobacteriaceae as potentially responsible for pistil spoilage.