Taxonomic and functional diversity of cultured seed associated microbes of the cucurbit family

Abstract

BackgroundEndophytes are microbes that colonize plant internal tissues without causing disease. In particular, seed-associated endophytes may be vectors for founder microbes that establish the plant microbiome, which may subsequently contribute beneficial functions to their host plants including nutrient acquisition and promotion of plant growth. The Cucurbitaceae family of gourds (e.g., cucumbers, melons, pumpkin, squash), including its fruits and seeds, is widely consumed by humans. However, there is limited data concerning the taxonomy and functions of seed-associated endophytes across the Cucurbitaceae family. Here, bacteria from surface-sterilized seeds of 21 curcurbit varieties belonging to seven economically important species were cultured, classified using 16S rRNA gene sequencing, and subjected to eight in vitro functional tests.ResultsIn total, 169 unique seed-associated bacterial strains were cultured from selected cucurbit seeds. Interestingly, nearly all strains belonged to only two phyla (Firmicutes, Proteobacteria) and only one class within each phyla (Bacilli, γ-proteobacteria, respectively). Bacillus constituted 50 % of all strains and spanned all tested cucurbit species. Paenibacillus was the next most common genus, while strains of Enterobacteriaceae and lactic acid bacteria were also cultured. Phylogenetic trees showed limited taxonomic clustering of strains by host species. Surprisingly, 33 % of strains produced the plant hormone, indole-3-acetic acid (auxin), known to stimulate the growth of fruits/gourds and nutrient-acquiring roots. The next most common nutrient acquisition traits in vitro were (in rank order): nitrogen fixation/N-scavenging, phosphate solubilisation, siderophore secretion, and production of ACC deaminase. Secretion of extracellular enzymes required for nutrient acquisition, endophyte colonization and/or community establishment were observed. Bacillus strains had the potential to contribute all tested functional traits to their hosts.ConclusionThe seeds of economically important cucurbits tested in this study have a culturable core microbiota consisting of Bacillus species with potential to contribute diverse nutrient acquisition and growth promotion activities to their hosts. These microbes may lead to novel seed inoculants to assist sustainable food production. Given that cucurbit seeds are consumed by traditional societies as a source of tryptophan, the precursor for auxin, we discuss the possibility that human selection inadvertently facilitated auxin-mediated increases in gourd size.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0743-2) contains supplementary material, which is available to authorized users.

Seed-resident microbiomes of leguminous and gramineous grasses are related to host stress tolerance

“…factors [24,25,47]. Except genetic background, the seven grass seeds in our study also have different seed weight, morphological structure and geographic location; all of these factors have been reported to influence seed microbiome structure [47].…”

“…factors [24,25,47]. Except genetic background, the seven grass seeds in our study also have different seed weight, morphological structure and geographic location; all of these factors have been reported to influence seed microbiome structure [47]. The gramineous Avena sativa seed were significantly differentwith Elymus sibiricus and Elymus dahuricus in seed weight, morphological structure (Table 1; Additional file 1: Figure S1), which may be the main factors driving the difference of their microbial structures.…”

Draft Genome Sequences of Six Strains of Lactococcus lactis (Phylum Firmicutes ), Spanning the Seeds of Cucumis sativus L. (Cucumber), Cucumis melo L. (Cantaloupe), and Cucurbita pepo var. turbinate (Acorn Squash)

“…turbinate (acorn squash) were surface sterilized and then gently ground in 50 mM Na 2 HPO 4 buffer using autoclaved mortars. To isolate seed-associated endophytes, the ground seed suspensions were cultured by streaking onto peptone-dextrose agar (PDA), Reasoner's 2A (R2A) agar, and LGI agar ( 5 ) plates and then incubated for up to 7 days at 28°C ( 6 ). Six strains of L. lactis (EKM101L, EKM102L, EKM201L, EKM203L, EKM501L, and EKM502L) were isolated and identified using the 16S rRNA universal primer pair 799F/1492R, and the gene sequences were deposited in GenBank (accession numbers KT281324 , KT281446 , KT281325 , KT281327 , KT281328 , and KT281329 , respectively) ( 6 ).…”

Alternative Medicine for Hair Loss

“…Pumpkin seed oil (PSO, family Cucurbitaceae) has been used for treating symptomatic benign prostatic hyperplasia through its inhibitory effect on 5α-reductase and antiandrogenic effect [60,61]. In a randomized, double-blind, placebo-controlled study, self-rated improvement score, and self-rated satisfaction scores in the PSO-treated group were higher compared with the placebo group after oral administration of PSO at dosage of 400 mg/day for 24 weeks.…”