Correction to: Neighbourhood stories: role of neighbour identity,spatial location and order of arrival in legume and non-legume initial interactions

Background and aims

We characterized fungal endophytes of seeds of invasive, non-native Phragmites from three sites in the Great Lakes region to determine if fungal symbiosis could contribute to invasiveness through their effects on seed germination and seedling growth.

Methods

Field-collected seeds were surface sterilized and plated on agar to culture endophytes for ITS sequencing. Prevalence of specific endophytes from germinated and non-germinated seeds, and from seedlings, was compared.

Results

One-third of 740 seeds yielded endophyte isolates. Fifteen taxa were identified with Alternaria sp. representing 54% of all isolates followed by Phoma sp. (21%) and Penicillium corylophilum (12%). Overall germination of seeds producing an isolate (36%) was significantly higher than seeds not producing an isolate (20%). Penicillium in particular was strongly associated with increased germination of seeds from one site. Sixty-three isolates and 11 taxa were also obtained from 30 seedlings where Phoma, Penicillium and Alternaria respectively were most prevalent. There was a significant effect of isolating an endophyte from the seed on seedling growth.

Conclusions

These results suggest that many endophyte taxa are transmitted in seeds and can increase seed germination and seedling growth of invasive Phragmites. The role of fungal endophytes in host establishment, growth and invasiveness in nature requires further research.

     

Metabolomic analysis of tomato seed germination

Introduction

Seed germination is inherently related to seed metabolism, which changes throughout its maturation, desiccation and germination processes. The metabolite content of a seed and its ability to germinate are determined by underlying genetic architecture and environmental effects during development.

Objective

This study aimed to assess an integrative approach to explore genetics modulating seed metabolism in different developmental stages and the link between seed metabolic- and germination traits.

Methods

We have utilized gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) metabolite profiling to characterize tomato seeds during dry and imbibed stages. We describe, for the first time in tomato, the use of a so-called generalized genetical genomics (GGG) model to study the interaction between genetics, environment and seed metabolism using 100 tomato recombinant inbred lines (RILs) derived from a cross between Solanum lycopersicum and Solanum pimpinellifolium.

Results

QTLs were found for over two-thirds of the metabolites within several QTL hotspots. The transition from dry to 6 h imbibed seeds was associated with programmed metabolic switches. Significant correlations varied among individual metabolites and the obtained clusters were significantly enriched for metabolites involved in specific biochemical pathways.

Conclusions

Extensive genetic variation in metabolite abundance was uncovered. Numerous identified genetic regions that coordinate groups of metabolites were detected and these will contain plausible candidate genes. The combined analysis of germination phenotypes and metabolite profiles provides a strong indication for the hypothesis that metabolic composition is related to germination phenotypes and thus to seed performance.

     

Does dormancy protect seeds against attack by the pathogenic fungus <Emphasis Type="Italic">Fusarium tricinctum</Emphasis> in a semiarid grassland of Northwest China?

Aims

Soil fungal pathogens can result in the failure of seedling establishment, but the effects of fungicide applications on seed/seedling survival have differed among studies. We assumed that the variation may relate to seed dormancy/germination characteristics and hypothesized that nondormant germinating seeds are more likely to be killed by fungal pathogens than dormant seeds.

Methods

Dormant and nondormant seeds of Stipa bungeana and Lespedeza davurica were inoculated with a pathogenic fungus Fusarium tricinctum under laboratory and field conditions. The outcomes of seed/seedling fate and other parameters were evaluated.

Results

In the laboratory, nondormant seeds inoculated with F. tricinctum developed white tufts of mycelium on the radicles of germinating seeds causing them to quickly die, but dormant seeds remained intact. In contrast, in the field inoculation with F. tricinctum did not cause higher mortality of nondormant than dormant seeds but resulted in higher percentages of seedling death before they emerged from soil than the controls.

Conclusions

Our results suggest that dormancy protects seeds from being attacked by some pathogens by preventing germination, but the protection is lost once germination has commenced. Further study involving various plant species with more seeds is needed to assess the generality of this pathogen-seed interaction hypothesis.

     

Beneficial role of endophytes in biofortification of Zn in wheat genotypes varying in nutrient use efficiency grown in soils sufficient and deficient in Zn

Background and aim

Most of the food grains show deficiency of zinc. The study was carried out to evaluate the role of endophytes in the fortification of Zn in wheat genotypes with different nutrient use efficiency and in soils deficient and sufficient for Zn.

Methods

Two zinc solubilizing endophytes (Bacillus subtilis DS-178 and Arthrobacter sp. DS-179) were used to inoculate low and high Zn accumulating genotypes in soils sufficient and deficient in Zn.

Results

The data on different root morphological parameters, yield and accumulation of Zn indicated distinct variations among genotypes; soil types and also among the endophytes inoculated, un-inoculated and chemical fertilizer treatments. In general, the amount of Zn in grains due to inoculation of endophytes was 2 folds higher as compared to un-inoculated control. The low and high Zn accumulating genotypes responded in an almost identical manner to endophyte inoculation, irrespective of the soil types.

Conclusion

Zn solubilizing endophytes can enhance the translocation and enrichment of Zn to grains in wheat genotypes, irrespective of their different nutrient use efficiency (Zn). This approach can be integrated into the modern strategies for biofortification.

     

A fungal endophyte defensive symbiosis affects plant-nematode interactions in cotton

Background and aims

Most investigations of fungi as nematode antagonists have focused on their interactions with nematodes in the soil. This study tested a foliar-isolated endophytic Phialemonium inflatum for its effects against the root-knot nematode as an endophyte in cotton using a seed treatment inoculation.

Methods

Cotton seeds were inoculated with P. inflatum spore suspensions prior to planting. Nematode infection and reproduction were quantified at Day 12 and 6 weeks after nematode egg inoculation, respectively. To establish whether the observed negative effects on nematodes were due to P. inflatum in the soil or as an endophyte in the plant, we also applied a soil fungicide treatment at the seedling stage to kill the fungi outside the plant.

Results

Persistent suppression of nematode penetration and galling, as well as subsequent reproduction, were observed in endophyte-treated plants independent of fungicide treatment, consistent with an endophytic mode of nematode suppression; and these negative effects did not depend on the concentration of fungal inoculum used to treat to the seed.

Conclusions

Our study highlights a novel role for P. inflatum as part of a plant-fungal defensive symbiosis in cotton, as well as the need for a broader understanding of endophyte-plant-nematode ecological interactions.

     

Quantification of plant water uptake by water stable isotopes in rice paddy systems

Aims

Maintaining variation in germination response provides a selective advantage, by spreading risk during recruitment. In fire-prone regions, physically dormant (PY) species vary their response to dormancy-breaking fire-related heat cues at the intra-population level. However little is known about physiologically dormant (PD) species, which respond to smoke cues. These contrasting dormancy types reflect different evolutionary developmental pathways and we considered whether intra-population variation in germination of Boronia floribunda (PD) occurs in response to smoke.

Methods

Seeds were collected from individual plants. We assessed germination magnitude and rate of seeds from each individual in response to a single aerosol smoke treatment, and three concentrations of smoke water, using replicate seed lots in temperature-controlled incubators.

Results

The magnitude and onset of germination differed significantly among individuals in response to the same smoke treatment. Seeds from different individuals varied in their sensitivity to smoke water concentration, with some responding to very low doses, and others obligated to high doses.

Conclusions

Variation in germination response to smoke highlights a mechanism by which PD species spread risk, by allowing some seeds to emerge quickly, while others remain dormant in the soil seed bank. The similarity to heat-cued variation displayed by PY species suggests that this could represent a convergent functional response.

     

Community structure and diversity of endophytic bacteria in seeds of three consecutive generations of <Emphasis Type="Italic">Crotalaria pumila</Emphasis> growing on metal mine residues

Aims

We investigated the possible transgenerational transfer of bacterial seed endophytes across three consecutive seed generations of Crotalaria pumila growing on a metal mining site in Mexico.

Methods

Seeds were collected during three successive years in the semi-arid region of Zimapan, Mexico. Total communities of seed endophytes were investigated using DNA extraction from surface sterilized seeds and 454 pyrosequencing of the V5-V7 hypervariable regions of the 16S rRNA gene.

Results

The communities consisted of an average of 75 operational taxonomic units (OTUs); richness and diversity did not change across years. Methylobacterium, Staphylococcus, Corynebacterium, Propionibacterium and eight other OTUs constituted >60% of the community in each generation. The microbiome was dominated by Methylobacterium (present in >80% of samples). Functions associated with the microbiome were C and N fixation, oxidative phosphorylation and photosynthesis activity.

Conclusions

The bacterial endophytic communities were similar across three consecutive seed generations. Among the core microbiome Methylobacterium strains were the most abundant and they can contribute to nutrient acquisition, plant growth promotion and stress resilience to their host in metal contaminated mine residues. Identification of the seed microbiome of C. pumila may lead to novel and more efficient inoculants for microbe-assisted phytoremediation.

     

Identification of an oleosin-like gene in seagrass seeds

Objective

To investigate the oil body protein and function in seeds of mature seagrass, Thalassia hemprichii.

Results

Seeds of mature seagrass T. hemprichii when stained with a fluorescent probe BODIPY showed the presence of oil bodies in intracellular cells. Triacylglycerol was the major lipid class in the seeds. Protein extracted from seagrass seeds was subjected to immunological cross-recognition with land plant seed oil body proteins, such as oleosin and caleosin, resulting in no cross-reactivity. An oleosin-like gene was found in seagrass seeds. Next generation sequencing and sequence alignment indicated that the deduced seagrass seed oleosin-like protein has a central hydrophobic domain responsible for their anchoring onto the surface of oil bodies. Phylogenetic analysis showed that the oleosin-like protein was evolutionarily closer to pollen oleosin than to seed oleosins.

Conclusion

Oil body protein found in seagrass seeds represent a distinct class of land seed oil body proteins.

     

<Emphasis Type="Italic">Epichloë</Emphasis> exudates promote in vitro and in vivo arbuscular mycorrhizal fungi development and plant growth

Background and aims

We studied, through exudates employment, the effect of Epichloë (endophytic fungi), both independently and in association with Bromus auleticus (grass), on arbuscular mycorrhizal fungi (AMF) colonization, host and neighbouring plants biomass production and soil changes.

Methods

Through in vitro and greenhouse experiments, Epichloë endophytes effect on AMF development was evaluated. In vitro studies of exudates effect on Gigaspora rosea and Rhizophagus intraradices were performed using root or endophyte exudates. A 6-month greenhouse experiment was conducted to determine Bromus auleticus endophytic status effect and endophyte exudates role in biomass production, neighbouring plants mycorrhizal colonization and soil properties.

Results

Endophyte exudates and E+ plant root exudates promoted in vitro AMF development in the pre-infective stage of G. rosea and in carrot root culture mycelium of R. intraradices in a dose-response relationship, while control media and E- plants exudates had no effect. R. intraradices colonization and plant growth was clearly increased by endophytes and their exudates.

Conclusions

This is the first work evidencing the direct effect of Epichloë endophytes and infected plants root exudates on AMF extramatrical development. While higher levels of AMF colonization were observed in E+ plants, no clear effect was detected in neighbouring plants colonization, plant biomass or soil properties.

     

A quantitative analysis of root distortion from contrasting wheat cropping systems

Aims

Bacterial ACC deaminase is one of the key tools to ameliorate plant stress by lowering ethylene level in plants. The effects of ACC deaminase-producing bacteria on the volatile profiles in plants have not been examined to date. To address this, we performed metabolic profiling of volatiles in carrots following inoculation of the bacteria producing ACC deaminase.

Methods

We isolated ACC deaminase-producing bacteria from the inner part of the fruits and vegetables grown on organic farms by culturing on ACC-containing media, and screened them with PCR for the acdS gene, mungbean growth assay, and in vitro ACC deaminase activity. The isolated endophytes were evaluated for their ability to alter volatile profiles in carrots.

Results

Eleven bacterial strains possessing the activity to cleave ACC were selected among the 60 isolates grown on the medium containing ACC as a sole N source. Three of them that belonged to Pseudomonas could reduce the levels of (E)-2-hexenal and the other green leaf volatiles (GLVs) and terpenoids in the carrot leaves following inoculation of the seeds.

Conclusions

The isolated endophytes with ACC deaminase activity could alter the composition of volatiles in plants, probably through lowering ethylene level in the plant.

     

Disease protection and allelopathic interactions of seed-transmitted endophytic pseudomonads of invasive reed grass (<Emphasis Type="Italic">Phragmites australis</Emphasis>)

Background and aims

Non-native Phragmites australis (haplotype M) is an invasive grass that decreases biodiversity and produces dense stands. We hypothesized that seeds of Phragmites carry microbes that improve seedling growth, defend against pathogens and maximize capacity of seedlings to compete with other plants.

Methods

We isolated bacteria from seeds of Phragmites, then evaluated representatives for their capacities to become intracellular in root cells, and their effects on: 1.) germination rates and seedling growth, 2.) susceptibility to damping-off disease, and 3.) mortality and growth of competitor plant seedlings (dandelion (Taraxacum officionale F. H. Wigg) and curly dock (Rumex crispus L.)).

Results

Ten strains (of 23 total) were identified and characterized; seven were identified as Pseudomonas spp. Strains Sandy LB4 (Pseudomonas fluorescens) and West 9 (Pseudomonas sp.) entered root meristems and became intracellular. These bacteria improved seed germination in Phragmites and increased seedling root branching in Poa annua. They increased plant growth and protected plants from damping off disease. Sandy LB4 increased mortality and reduced growth rates in seedlings of dandelion and curly dock.

Conclusions

Phragmites plants associate with endophytes to increase growth and disease resistance, and release bacteria into the soil to create an environment that is favorable to their seedlings and less favorable to competitor plants.

     

Fertilization,soil and plant community characteristics determine soil microbial activity in managed temperate grasslands

Background and aims

Contaminated soils can impede germination and growth of selected plant species, restricting effective phytoremediation strategies. The purpose of the present study was to enhance the germination and growth of saltgrass [Distichlis spicata (L.) Greene] by evaluating the efficacy of certain seed pretreatments and soil amendments.

Methods

Ten seed pretreatment methods, two amendments, three soil depths and five saline levels were tested under greenhouse conditions.

Results

Saltgrass germination and growth were negatively correlated with increasing salinity levels when NaCl > 85.6 mM. Among ten seed pretreatments (stratification + Proxy 24 h, hot water + Proxy 24 h, stratification, hot water + Proxy 48 h, Proxy 48 h, Proxy 24 h, hot water, scarification, gibberellins, and KMnO₄), the two best methods were stratification + Proxy 24 h and hot water + Proxy 24 h for enhancing saltgrass germination, with the latter pretreatment being especially useful because of its shorter preparation time and high germination rates. Proxy is a commercial ethephon product. Potting soil (5.0 cm depth) was found to be the best amendment for saltgrass germination and growth in hydrocarbon-contaminated soils.

Conclusion

We conclude that direct seeding of saline soils contaminated with petroleum hydrocarbons is a feasible phytoremediation strategy provided that appropriate seed pretreatments and amendments are utilized.

     

A novel method for single-grain-based metabolic profiling of Arabidopsis seed

Introduction

In plant metabolomics, metabolite contents are often normalized by sample weight. However, accurate weighing of very small samples, such as individual Arabidopsis thaliana seeds (approximately 20 µg), is difficult, which may lead to irreproducible results.

Objectives

We aimed to establish alternative normalization methods for seed-grain-based comparative metabolomics of A. thaliana.

Methods

Arabidopsis thaliana seeds were assumed to have a prolate spheroid shape. Using a microscope image of each seed, the lengths of major and minor axes were measured by fitting a projected 2-dimensional shape of each seed as an ellipse. Metabolic profiles of individual diploid or tetraploid A. thaliana seeds were measured by our highly sensitive protocol (“widely targeted metabolomics”) that uses liquid chromatography coupled with tandem quadrupole mass spectrometry. Mass spectrometric analysis of 1 µL of solution extract identified more than 100 metabolites. The data were normalized by various seed-size measures, including seed volume (single-grain-based analysis). For comparison, metabolites were extracted from 4 mg of diploid and tetraploid A. thaliana seeds and their metabolic profiles were analyzed by normalization of weight (weight-based analysis).

Results

A small number of metabolites showed statistically significant differences in the single-grain-based analysis compared to weight-based analysis. A total of 17 metabolites showed statistically different accumulation between ploidy types with similar fold changes in both analyses.

Conclusion

Seed-size measures obtained by microscopic imaging were useful for data normalization. Single-grain-based analysis enables evaluation of metabolism of each seed and elucidates the metabolic profiles of precious bioresources by using small amounts of samples.

     

A seed-recruited microbiome protects developing seedlings from disease by altering homing responses of <Emphasis Type="Italic">Pythium aphanidermatum</Emphasis> zoospores

Aims

We investigated potential mechanisms by which a seed microbiome recruited from vermicomposted dairy manure alters Pythium aphanidermatum zoospore mediated pathogenesis in cucumber.

Methods

Bioassays were conducted to measure arrival of zoospores at the seed surface via qPCR and subsequent seedling disease incidence. Seed exudates were collected at relevant time points for use in zoospore microscopy assays. Metabolomic analysis was used to characterize seed exudates.

Results

Microbes recruited by the germinating seed from a disease suppressive substrate within 8 hours of sowing prevented zoospore arrival at the seed surface, modified seed exudates and reduced disease incidence. In vitro exposure to microbially modified seed exudates altered zoospore homing responses and reduced both encystment and germination compared to control exudates. Combining modified and control exudates failed to restore zoospore attraction to levels observed with control exudates. Observed zoosporolytic activity of the modified exudates was unique to the ethyl acetate fraction and metabolomic analysis revealed several putative zoosporolytic compounds present at higher relative abundance when compared to control exudates.

Conclusions

The observed disease suppression was likely due to the production of a specific zoosporolytic compound or set of compounds in the spermosphere by one or more members of the seed-recruited vermicompost microbiome.

     

Biocrusts enhance soil fertility and <Emphasis Type="Italic">Bromus tectorum</Emphasis> growth,and interact with warming to influence germination

Background and aims

Biocrusts are communities of cyanobacteria, mosses, and/or lichens found in drylands worldwide. Biocrusts are proposed to enhance soil fertility and productivity, but simultaneously act as a barrier to the invasive grass, Bromus tectorum, in western North America. Both biocrusts and B. tectorum are sensitive to climate change drivers, yet how their responses might interact to affect dryland ecosystems is unclear.

Methods

Using mesocosms with bare soil versus biocrust cover, we germinated B. tectorum seeds collected from warmed, warmed + watered, and ambient temperature plots within a long-term climate change experiment on the Colorado Plateau, USA. We characterized biocrust influences on soil fertility and grass germination, morphology, and chemistry.

Results

Biocrusts increased soil fertility and B. tectorum biomass, specific leaf area (SLA), and root:shoot ratios. Germination rates were unaffected by mesocosm cover-type. Biocrusts delayed germination timing while also interacting with the warmed treatment to advance, and with the warmed + watered treatment to delay germination.

Conclusions

Biocrusts promoted B. tectorum growth, likely through positive influence on soil fertility which was elevated in biocrust mesocosms, and interacted with seed treatment-provenance to affect germination. Understanding how anticipated losses of biocrusts will affect invasion dynamics will require further investigation of how plant plasticity/adaptation to specific climate drivers interact with soil and biocrust properties.

     

Soil micro-food web interactions and rhizosphere priming effect

Background

Seeds host bacterial inhabitants but only a limited knowledge is available on which taxa inhabit seed, which niches could be colonized, and what the routes of colonization are.

Scope

Within this commentary, a discussion is provided on seed bacterial inhabitants, their taxa, and from where derive the seed colonizers.

Conclusions

Seeds/and grains host specific bacteria deriving from the anthosphere, carposphere, or from cones of gymnosperms and inner tissues of plants after a long colonization from the soil to reproductive organs.

     

Identity of plant,lichen and moss species connects with microbial abundance and soil functioning in maritime Antarctica

Background and aims

Plant breeding activities shape the rhizosphere microbiome but less is known about the relationship of both with the seed microbiome. We analyzed the composition of bacterial communities of seeds and rhizospheres of Styrian oil pumpkin genotypes in comparison to bulk soil to elucidate specific microbial signatures to support a concept involving plant-microbe interactions in breeding strategies.

Methods

The seed and rhizosphere microbiomes of 14 genotypes of oilseed pumpkin and relatives were analyzed using a 16S rRNA gene amplicon sequencing approach, which was assessed by bioinformatics and statistical methods.

Results

All analyzed microhabitats were characterized by diverse bacterial communities, but the relative proportions of phyla and the overall diversity was different. Seed microbiomes were characterized by the lowest diversity and dominant members of Enterobacteriaceae including potential pathogens (Erwinia, Pectobacterium). Potential plant-beneficial bacteria like Lysobacter, Paenibacillus and Lactococcus contributed to the microbial communities in significant abundances. Interestingly, strong genotype-specific microbiomes were detected for seeds but not for the rhizospheres.

Conclusions

Our study indicates a strong impact of the Cucurbita pepo genotype on the composition of the seed microbiome. This should be considered in breeding of new cultivars that are more capable of exploiting beneficial indigenous microbial communities.

     

Niches and routes of transmission of <Emphasis Type="Italic">Xanthomonas citri</Emphasis> pv. <Emphasis Type="Italic">fuscans</Emphasis> to bean seeds

Aims

Seeds are vectors of a diversified microbiota including plant pathogens. To better understand transmission of common bacterial blight (CBB) agents to bean seeds, we analyzed the role of non-pathogenic xanthomonads on seed transmission efficiency and investigated the location of Xanthomonas citri pv. fuscans (Xcf) into seeds and plantlets.

Methods

Competition between CBB and NP strains was initially assessed in vitro and then extended in planta to monitor the impact of co-inoculation on Xcf seed transmission. Moreover, location of Xcf strains in seeds and seedlings was visualized using a combination of gfp-tagged strain and DOPE-FISH/CSLM.

Results

Whereas CBB agent growth was inhibited in vitro by some seed-borne non-pathogenic xanthomonads strains, these strains did not transmit efficiently to seed through floral pathway and did not affect Xcf seed transmission. Xcf cells were observed entering seed through vascular elements and parenchyma of funiculus, but also micropyle and testa. Xcf cells were observed, moreover, among other bacteria on radicle surfaces, especially tip, in cotyledons, and plumules.

Conclusions

CBB agents are more efficient than non-pathogenic xanthomonads in using the floral route to colonize seeds. CBB agents are located within different niches in the seed tissues up to the embryonic axis.

     

Three symbionts involved in interspecific plant-soil feedback: epichloid endophytes and mycorrhizal fungi affect the performance of rhizobia-legume symbiosis

Aims

Plants interact by modifying soil conditions in plant-soil feedback processes. Foliar endophytes of grasses exert multiple effects on host rhizosphere with potential consequences on plant-soil feedback. Here, we hypothesize that the grass-endophyte symbiosis impairs soil symbiotic potential, and in turn influences legume performance and nitrogen acquisition.

Methods

Soil was conditioned in pots, growing Lolium multiflorum with or without the fungal endophyte Epichloë and with or without arbuscular mycorrhizal fungi (AMF). Then, Trifolium repens grew in all types of conditioned soils with high or low rhizobia availability.

Results

Endophyte soil conditioning reduced AMF spores number and rhizobial nodules (?27 % and ?38 %, respectively). Seedling survival was lower in endophyte-conditioned soil and higher in mycorrhizal soils (?27 % and +24 %, respectively). High rhizobia-availability allowed greater growth and nitrogen acquisition, independent of soil conditioning. Low rhizobia-availability allowed both effects only in endophyte-conditioned soil.

Conclusion

Endophyte-induced changes in soil (i) hindered symbiotic potential by reducing AMF spore availability or rhizobia nodulation, (ii) impaired legume survival irrespective of belowground symbionts presence, but (iii) mimicked rhizobia effects, enhancing growth and nitrogen fixation in poorly nodulated plants. Our results show that shoot and root symbionts can be interactively involved in interspecific plant-soil feedback.