Composition of the Microbiomes from Spinach Seeds Infested or Noninfested with Peronospora effusa or Verticillium dahliae (original) (raw)
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Diversity of the spinach ( Spinacia oleracea ) spermosphere and phyllosphere bacterial communities
FEMS Microbiology Letters, 2013
The bacterial diversity of seeds, transmission of bacteria from seed to phyllosphere, and fate of seed-transmitted bacteria on mature plants are poorly characterized. Understanding the dynamics of microbial communities is important for finding bio-control or mitigation strategies for human and plant pathogens. Bacterial populations colonizing spermosphere and phyllosphere of spinach (Spinacia oleracea) seedlings and plants were characterized using pyrosequencing of 16S rRNA gene amplicons. Spinach seed microbiota was composed of three bacterial phyla: Proteobacteria, Firmicutes and Actinobacteria, belonging to > 250 different operational taxonomic units (OTUs). Seed and cotyledon bacterial communities were similar in richness and diversity. Richness of 3-4 leaf-stage of development plants increased markedly to > 850 OTUs classified within 11 phyla. Although some bacterial OTUs were detected on seeds, cotyledons and plants, the breadth of new sequences indicates the importance of multiple sources outside the seed in shaping phyllosphere community. Most classified sequences were from previously undescribed taxa, highlighting the benefits of pyrosequencing in describing seed diversity and phyllosphere bacterial communities. Bacterial community richness increased from 250 different OTUs for spinach seeds and cotyledons, to 800 OTUs for seedlings. To our knowledge this is the first comprehensive characterization of the spinach microbiome, complementing previous culture-based and clone library studies.
Diversity, 2011
Modern molecular ecology techniques were used to demonstrate the effects of plant genotype and environmental conditions prior to harvest on the spinach epiphytic bacterial community. Three cultivars of spinach with different leaf topographies were collected at three different periods during the fall growing season. Leaf surface topography had an effect on diversity and number of culturable bacteria on the phylloepiphtyic community of spinach. Savoy cultivars, which had larger surface area and more stomata and glandular trichomes, where bacterial aggregates were observed, featured more diverse communities with increased richness and larger bacterial populations compared to flat-leaved cultivars. Bacterial community richness was compared using denaturant gradient gel electrophoresis (DGGE), while abundance was quantified using 16s rRNA primers for major phyla. The most diverse communities, both in richness and abundance, were observed during the first sampling period, immediately following a period of rapid spinach growth. Exposure to lower air and soil temperatures and decreased precipitation resulted in significantly reduced bacterial population size and bacterial community richness OPEN ACCESS Diversity 2011, 3 722 in November and December. This study describes the effect of the plant characteristics and environmental conditions that affect spinach microbiota population size and diversity, which might have implications in the survival of food and plant bacterial pathogens.
2011
Modern molecular ecology techniques were used to demonstrate the effects of plant genotype and environmental conditions prior to harvest on the spinach epiphytic bacterial community. Three cultivars of spinach with different leaf topographies were collected at three different periods during the fall growing season. Leaf surface topography had an effect on diversity and number of culturable bacteria on the phylloepiphtyic community of spinach. Savoy cultivars, which had larger surface area and more stomata and glandular trichomes, where bacterial aggregates were observed, featured more diverse communities with increased richness and larger bacterial populations compared to flat-leaved cultivars. Bacterial community richness was compared using denaturant gradient gel electrophoresis (DGGE), while abundance was quantified using 16s rRNA primers for major phyla. The most diverse communities, both in richness and abundance, were observed during the first sampling period, immediately following a period of rapid spinach growth. Exposure to lower air and soil temperatures and decreased precipitation resulted in significantly reduced bacterial population size and bacterial community richness OPEN ACCESS Diversity 2011, 3 722 in November and December. This study describes the effect of the plant characteristics and environmental conditions that affect spinach microbiota population size and diversity, which might have implications in the survival of food and plant bacterial pathogens.
XXVIII International Horticultural Congress on Science and Horticulture for People (IHC2010): International Symposium on Environmental, Edaphic, and Genetic Factors Affecting Plants, Seeds and Turfgrass, 2012
Recent disease outbreaks associated with vegetables, especially fresh spinach, have alarmed consumers, caused economic losses for vegetable producers, and raised questions about how pathogens are transmitted. Little is known about bacteria associated with seeds and the contributions of the seed to the endophytic and epiphytic communities of the leaves (phyllosphere). The bacterial populations of spinach seed and on leaves of seedlings after seed germination, and from developing plants were compared using DGGE, to assess bacterial community richness, and real-time PCR to compare the abundance of select phyla (total bacteria, Actinobacteria, Bacteroidetes, Firmicutes, α-Proteobacteria and β-Proteobacteria). To determine the effect of environment, the plants were grown in field and growth chambers. Vertical transmission of bacterial community members was evident; the developmental stage of the plant affected the richness and abundance of select bacterial phyla. The bacterial richness of plants grown in the two environments was not affected. However, overall numbers of bacteria were higher in field-grown samples in comparison to those produced in growth chambers. A statistically significant interaction was seen between growth stage and environment with each of the selected phyla. Bacteria populations colonizing cotyledons were smaller than those of mature leaves, but the differences were not significant with the 3-4 leaf-stage plants. The culturable populations of bacteria on seeds (~5 log CFU/g) were significantly smaller than determined using real time PCR (~7 log copies). This study highlights the importance of vertical transmission on the bacterial community colonizing plants and suggests that plants have adapted to transfer bacteria which are beneficial to their growth through the seed, possibly within the seed coat, embryo, or layers of endosperm.
Changes in microbial populations on fresh cut spinach
International Journal of Food Microbiology, 1996
The microbial populations found on fresh-cut spinach leaves that were stored in gas permeable bags at 10°C for 12 days were examined and identified. The microorganisms consisted of mesophilic aerobic bacteria, psychrotrophic bacteria, Pseudomonadaceae, Enterobacteriaceae, Micrococcaceae, lactic acid bacteria and yeasts. Populations of mesophiles, psychrotrophs, Pseudomonadaceae and Enterobacteriaceae increased sharply during the storage period. The initial populations were 107, 106, lo6 and lo4 CFU.g -' respectively.
Microbial communities of vegetable seeds and biocontrol microbes for seed treatment
Seed Science and Technology, 2022
Thirty-one species of vegetable seeds from Kyrgyzstan’s State Register were analysed for mycological and bacterial composition using various methods, from simple visual to molecular. The modified roll-towel method simultaneously assesses the degree of contamination and seed germination. Screening in agar medium allows analysis of species on the outer and inner surfaces of vegetable seeds that are not detected using the roll-towel method. As a result of the phytopathological examination, 15 fungal and three bacterial species were found. Direct DNA extraction and amplification of the universal 16S rRNA gene of diseased seeds was used to identify the plant pathogenic bacteria, which included Pseudomonas syringae, Pseudomonas savastanoi, Pseudomonas cerasi, Pectobacterium carotovorum, Xanthomonas oryzae, Erwinia sp. and others from the Proteobacteria phylum. For the coating of vegetable seeds, S. alfalfae CI-4 was selected. This strain had a beneficial double effect on the tested vegeta...
Environment and Ecology Research, 2024
Ubiquitous endophytes asymptomatically colonize intra- and intercellular plant tissues through a symbiotic association. These microbes adapt to their environment within the plant’s strict limits, grow, and produce specific compounds that promote the host's growth and maintain a stable symbiosis. Applications of endophytes include the production of pigments, enzymes, antimicrobials, biodegradation/bioremediation, and bioactive compounds that help mankind. A hypothesis could be that microbial diversity depends on the variety of microbes, their association patterns with the host, and the surrounding environment. Our objectives were to isolate, identify, and analyze the diversity of both bacteria and fungi from various parts of Basella alba and Basella rubra plants. We used conventional culture-based methods to grow bacteria and fungi on artificial media from the roots, stems, leaves, fruits, and seeds of B. alba and B. rubra. To identify and sequence the grown organisms, we used Internal Transcribed Sequence (ITS) 1 and 4 and 16S rRNA PCR, followed by Sanger’s sequencing methods. We manually calculated diversity measurements, such as Shannon's and Simpson's indices of diversity and species richness (SChao1). All the endophytic fungi identified belong to the phylum Ascomycetes, with three classes, nine orders, nine families, and 13 genera from B. alba, and three classes, five orders, eight families, and 13 genera from B. rubra. The most common class found was Dothideomycetes, followed by Eurotiomycetes and Sordariomycetes. In the phylum Firmicutes, genus Bacillus was identified from B. alba. From B. rubra, members of the phyla Firmicutes and Proteobacteria were identified. Bacillus was found in greater abundance in the leaf, stem, fruit, and seed, while Achromobacter was predominant in the root, and Clostridium in the leaf. On nutrient agar for bacteria and potato dextrose agar for fungi, 105 cultivable fungi and 49 bacteria were identified. Both plants harbored a diverse range of microbes.
New Phytologist, 2014
In order to address the hypothesis that seeds from ecologically and geographically diverse plants harbor characteristic epiphytic microbiota, we characterized the bacterial and fungal microbiota associated with Triticum and Brassica seed surfaces. The total microbial complement was determined by amplification and sequencing of a fragment of chaperonin 60 (cpn60). Specific microorganisms were quantified by qPCR. Bacteria and fungi corresponding to operational taxonomic units (OTU) that were identified in the sequencing study were isolated and their interactions examined. A total of 5477 OTU were observed from seed washes. Neither total epiphytic bacterial load nor community richness/evenness was significantly different between the seed types; 578 OTU were shared among all samples at a variety of abundances. Hierarchical clustering revealed that 203 were significantly different in abundance on Triticum seeds compared with Brassica. Microorganisms isolated from seeds showed 99-100% identity between the cpn60 sequences of the isolates and the OTU sequences from this shared microbiome. Bacterial strains identified as Pantoea agglomerans had antagonistic properties toward one of the fungal isolates (Alternaria sp.), providing a possible explanation for their reciprocal abundances on both Triticum and Brassica seeds. cpn60 enabled the simultaneous profiling of bacterial and fungal microbiota and revealed a core seed-associated microbiota shared between diverse plant genera.