Isolation of Bacteria of the Family Enterobacteriaceae from Plant Tissues

Phenotypic and genotypic characterization of endophytic bacteria associated with transgenic and non-transgenic soybean plants

Endophytic bacteria isolated from non-transgenic and transgenic Roundup Ready® glyphosate-resistant (GR) soybean plants were investigated to analyze the correspondence between phenotypic and genotypic characteristics and to determine whether or not the strains could be grouped based on the source of isolation in transgenic or non-transgenic plants, respectively. Most of the strains recovered from GR plants have shown the ability for plant growth promotion (PGP) by means of IAA production and inorganic phosphate solubilization, and 100% of the strains showed great motility (swarm or swim); in addition, 90% of the strains were able to metabolize the majority of carbon sources tested. GR soybean fields showed higher endophytes abundance than non-transgenic; however, analyzing the phylogenetic trees constructed using the partial 16SrRNA gene sequences, higher diversity was observed in non-transgenic soybean fields. Overall the majority of isolated endophytes could utilize multiple patterns of carbon sources and express resistance to antibiotics, while isolates varied widely in the PGP ability. The greater pattern and frequency of utilization of carbon sources and frequency and intensity of antibiotic resistance compared with PGP ability within the soybean endophytes community suggest that carbon sources metabolism and antibiotic resistance confer a greater relative fitness benefit than PGP ability. In conclusion, cluster analysis of the phenotypes and 16SrRNA gene sequences reveals lack of correspondence between the pattern of bacterial isolates and the transgenic character of plants, and the heterogeneity of clustering suggested that various adaptive processes, such as stress response, could have contributed to generate phenotypic variability to enhance endophytes overall fitness.

Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits

The plant microbiome is a key determinant of plant health and productivity, and changes in the plant microbiome can alter the tolerance to biotic and abiotic stresses and the quality of end produce. Little is known about the microbial diversity and its effect on carbohydrate metabolism in ripe fruits. In this study, we aimed to understand the diversity and function of microorganisms in relation to carbohydrate metabolism of ripe watermelon fruits. We used 16S metagenomics and RNAseq metatranscriptomics for analysis of red (PI459074, Congo, and SDRose) and yellow fruit-flesh cultivars (PI227202, PI435990, and JBush) of geographically and metabolically diverse watermelon cultivars. Metagenomics data showed that Proteobacteria were abundant in SDRose and PI227202, whereas Cyanobacteria were most abundant in Congo and PI4559074. In the case of metatranscriptome data, Proteobacteria was the most abundant in all cultivars. High expression of genes linked to infectious diseases and the expression of peptidoglycan hydrolases associated to pathogenicity of eukaryotic hosts was observed in SDRose, which could have resulted in low microbial diversity in this cultivar. The presence of GH28, associated with polygalacturonase activity in JBush and SDRose could be related to cell wall modifications including de-esterification and depolymerization, and consequent loss of galacturonic acid and neutral sugars. Moreover, based on the KEGG annotation of the expressed genes, nine α-galactosidase genes involved in key processes of galactosyl oligosaccharide metabolism, such as raffinose family were identified and galactose metabolism pathway was reconstructed. Results of this study underline the links between the host and fruit-associated microbiome in carbohydrate metabolism of the ripe fruits. The cultivar difference in watermelon reflects the quantum and diversity of the microbiome, which would benefit watermelon and other plant breeders aiming at the holobiont concept to incorporate associated microbiomes in breeding programs.

Wastewater reuse in irrigation: a microbiological perspective on implications in soil fertility and human and environmental health

The reuse of treated wastewater, in particular for irrigation, is an increasingly common practice, encouraged by governments and official entities worldwide. Irrigation with wastewater may have implications at two different levels: alter the physicochemical and microbiological properties of the soil and/or introduce and contribute to the accumulation of chemical and biological contaminants in soil. The first may affect soil productivity and fertility; the second may pose serious risks to the human and environmental health. The sustainable wastewater reuse in agriculture should prevent both types of effects, requiring a holistic and integrated risk assessment. In this article we critically review possible effects of irrigation with treated wastewater, with special emphasis on soil microbiota. The maintenance of a rich and diversified autochthonous soil microbiota and the use of treated wastewater with minimal levels of potential soil contaminants are proposed as sine qua non conditions to achieve a sustainable wastewater reuse for irrigation.

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.

Bacteria colonizing root nodules of wild legumes exhibit virulence-associated properties of mammalian pathogens

Bacteria not proficient in nitrogen fixing symbiosis were proven able to invade root nodules of three wild legumes of the genus Hedysarum in Algeria and to be multiplying in these in place of the natural rhizobium symbionts. The involved species featured taxa known as human pathogens including: Enterobacter cloacae, Enterobacter kobei, Escherichia vulneris, Pantoea agglomerans and Leclercia adecarboxylata. A direct screening of the phenotypic determinants of virulence using human cultured cells tested positive for the traits of cytotoxicity, vital stain exclusion and adhesion to epithelia. Antibiogram analyses revealed also a complex pattern of multiple antibiotic resistances. The data suggest that legume root nodules can be a site of survival and of active multiplication for populations of mammalian pathogens, which could thus alternate between the target animal and a number of neutral plant hosts. The worldwide distribution of as yet uninvestigated legumes raises the concern that these represent a general niche that could enhance the hazards posed by microorganisms of clinical nature.

Plants as a habitat for beneficial and/or human pathogenic bacteria

Non-plant pathogenic endophytic bacteria can promote plant growth, improve nitrogen nutrition, and, in some cases, are human pathogens. Recent work in several laboratories has shown that enteric bacteria are common inhabitants of the interior of plants. These observations led to the experiments that showed the entry into plants of enteric human pathogens such as Salmonella and E. coli O157:H7. The extent of endophytic colonization by strains is regulated by plant defenses and several genetic determinants necessary for this interior colonization in endophytic bacteria have been identified. The genomes of four endophytic bacteria now available should promote discovery of other genes that contribute to this phenotype. Common virulence factors in plant and animal pathogens have also been described in bacteria that can infect both plant and animal models. Future directions in all of these areas are proposed.