Characterizing microbial communities associated with disease-suppressive soil is an important first step toward understanding the potential of microbiota to protect crops against plant pathogens. In the present study, we compared microbial communities in suppressive- and conducive-soils associated with Fusarium wilt disease in a vanilla long-term continuous cropping system. Suppressive soil was associated with higher fungal diversity and lower bacterial diversity. The fungal phyla Zygomycota and Basidiomycota, and the bacterial phyla Acidobacteria, Verrucomicrobia, Actinobacteria and Firmicutes were strongly enriched in the suppressive soil. Notably, suppressive soil was dominated by the fungal genus Mortierella, accounting for 37% of the total fungal sequences. The hyper-dominance of Mortierella spp. in suppressive soil suggests that this taxon may serve as an indicator and enhancer of Fusarium wilt disease suppression in vanilla. In addition, Molecular Ecological Network analysis revealed that fungal communities were more connected and showed more co-occurrence relationships in the suppressive versus conducive soils. Our results indicate that fungal communities may be important in the development of soil suppressiveness against vanilla Fusarium wilt disease.

Distinct roles for soil fungal and bacterial communities associated with the suppression of vanilla Fusarium wilt disease

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

Different Continuous Cropping Spans Significantly Affect Microbial Community Membership and Structure in a Vanilla-Grown Soil as Revealed by Deep Pyrosequencing

Addition of organic material, such as crop straw mulch in most soils is considered a strategy for sustainable agricultural production. We conducted a two-year experiment in 2015 and 2016 to determine changes in soil biochemical properties and maize yield in response to treatment with wheat-straw mulch. The treatments consisted of the addition of different levels of wheat-straw mulch (S1: 0, S2: 2500, S3: 5000 kg ha−1). Soil samples from four depths (0.1, 0.2, 0.3, and 0.4 m) were collected and analyzed. Soil enzymes, such as invertase, phosphatase, urease, and catalase, were significantly higher in the S3 treatment than in the S1 treatment. Values were greater for the samples collected at 0.1 m soil depth than those collected from deeper soil layers. Regarding soil properties, soil organic carbon (SOC), available nitrogen (AN), available phosphorus (AP), total nitrogen (TN), total phosphorus (TP), and soil water content (SWC) were significantly higher in S3 at 0–0.1 m soil depth than in other treatments. Compared with the (S1), an average increase in SOC, AN, AP, TN, TP, and SWC in 0–0.4 m soil depth with full straw mulch (S3), were 32.4, 31.9, 32.0, 11.8, 16.7, and 18.5%, higher, respectively. On average, urease, phosphatase, invertase, and catalase increased by 15.1, 11.0, 88.4, and 24.0%, respectively in the S3 treatment compared with that in the S1 treatment at 0–0.1 m depth, and decreased with increasing soil depth. The S3 treatment had increased grain yield (7%), biomass yield (28%), and water use efficiency (8%), compared with the S1 treatment. Overall, our results suggested that the S3 straw mulch treatment (5000 kg ha−1) could be used to sustain maize productivity and promote a better relationship between soil enzymes and soil properties in the semi-arid conditions of the Guanzhong area.

Changes in soil enzymes, soil properties, and maize crop productivity under wheat straw mulching in Guanzhong, China

Background: The wild relatives of crops represent a major source of valuable traits for crop improvement. These resources are threatened by habitat destruction, land use changes, and other factors, requiring their urgent collection and long-term availability for research and breeding from ex situ collections. We propose a method to identify gaps in ex situ collections (i.e. gap analysis) of crop wild relatives as a means to guide efficient and effective collecting activities. Methodology/Principal Findings: The methodology prioritizes among taxa based on a combination of sampling, geographic, and environmental gaps. We apply the gap analysis methodology to wild taxa of the Phaseolus genepool. Of 85 taxa, 48 (56.5%) are assigned high priority for collecting due to lack of, or under-representation, in genebanks, 17 taxa are given medium priority for collecting, 15 low priority, and 5 species are assessed as adequately represented in ex situ collections. Gap ‘‘hotspots’’, representing priority target areas for collecting, are concentrated in central Mexico, although the narrow endemic nature of a suite of priority species adds a number of specific additional regions to spatial collecting priorities. Conclusions/Significance: Results of the gap analysis method mostly align very well with expert opinion of gaps in ex situ collections, with only a few exceptions. A more detailed prioritization of taxa and geographic areas for collection can be achieved by including in the analysis predictive threat factors, such as climate change or habitat destruction, or by adding additional prioritization filters, such as the degree of relatedness to cultivated species (i.e. ease of use in crop breeding). Furthermore, results for multiple crop genepools may be overlaid, which would allow a global analysis of gaps in ex situ collections of the world’s plant genetic resources.

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A Gap Analysis Methodology for Collecting Crop Genepools: A Case Study with Phaseolus Beans

Fusarium wilt disease is a growing problem in agriculture systems. Application of bio-fertilizers containing beneficial microbes represents a promising disease control strategy. However, the mechanisms underlying disease suppression remain elusive. Here, in order to assess the importance of direct antagonism and modified soil microbiota on suppression of Fusarium wilt disease, we conducted a pot experiment with chemical, organic and biologically enhanced fertilizers, we tracked the impact of those fertilizer amendments on disease incidence, and measured the pathogen density and changes in soil microbiota. Alterations in bacterial abundance and community structure after bio-fertilizers application were determined to be key factors in constraining the pathogen, Fusarium oxysporum. In particular, bio-fertilizer application increased the abundance of indigenous microbial groups with reported antifungal activity, such as Lysobacter spp., which could play a keystone role in controlling this pathogen. The microbes introduced in the bio-fertilizer treatments (e.g. Bacillus and Trichoderma spp.) induced suppressiveness via alteration of the soil microbiome rather than direct pathogen inhibition. These results contrast with the commonly held paradigm of disease suppression using beneficial microbes and open up new perspectives for the promotion of soil health. In addition to seeking antagonistic microbes based on their direct inhibitory activity, disease suppression may also be achieved by introducing keystone species that reshape soil microbiome structure and function.

Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome

Vanilla is naturally distributed in Mexico and parts of Central America and the history of origin of cultivated vanilla suggests that the entire stock outside Mexico may be from a single genetic source. In the present study, RAPD polymorphism was used to estimate the level of genetic diversity and interrelationships among different collections of Vanilla planifolia Andr., and few related species, including both leafy and leafless types such as V. tahitensis J.W.Moore, V. andamanica, Rolfe, V. pilifera Holtt., and V. aphylla Blume. Studies revealed that there are very limited variation within collections of V. planifolia, indicative of its narrow genetic base, and of the related species we tested, V. tahitensis is nearest to V. planifolia. The species studied are diverse and have a similarity ranging from 1.2 to 57.3 %. Of the sampled taxa, V. andamanica is the most divergent and there is also reasonable variability within its collections, indicating the possibility of natural seed set. A total of 82 polymorphic bands expressed in the RAPD profiles were used to generate a genetic distance matrix, which was then used in cluster analysis. Specific groupings were revealed by the cluster analysis whereby the leafless forms (V. aphylla, V. pilifera and the new species) and V. andamanica formed separate clusters. This is the first report of species interrelationship studies, including both cultivated and wild vanilla species.

Genetic variations and interrelationships in Vanilla planifolia and few related species as expressed by RAPD polymorphism

Correlation of metabolites in the leaf and berries of selected black pepper varieties.

A protocol for high frequency callus induction and plant regeneration from sunflower (Helianthus annuus L.) anthers is described. Different variables using Murashige & Skoog (MS) basal medium supplemented with 2.0 mg/l α-naphthaleneacetic acid (NAA) and 1.0 mg/l N6-benzyladenine (BA) were tested for their ability to enhance the frequency of anther callusing and subsequent embryogenesis. Of these, agar concentration, sucrose concentration, carbohydrate source had significant effect on callusing, while differences due to incubation under dark vs light conditions, cold pretreatment of capitula for 1 to 6 days prior to anther inoculation and genotype on callusing were non-significant. However, all these factors exerted highly significant influence on embryogenesis when calli from the various media were transferred to medium supplemented with 0.1 mg/l NAA and 0.5 mg/l BA. With the procedure developed, callusing as high as 100% and embryo formation at a frequency of 44% was achieved. Although complete embryos were formed the frequency of their conversion to whole plantlets was low (14.3%). Hence, the embryogenic pathway was bypassed to obtain multiple shoots by transferring embryogenic calli with developing embryos to MS medium supplemented with 0.5 mg/l BA. Elongated shoots rooted on half-strength MS medium supplemented with 0.5 mg/l NAA. Cytological analysis of embryogenic callus and somatic embryos revealed haploids at a frequency of 30% while that of rooted plants showed haploid regenerants at a frequency of 8.3%. Nevertheless, the frequency of putative haploid plants could be enhanced through mass multiplication using nodal explants of the regenerants.

Embryogenesis and plant regeneration in anther culture of sunflower (Helianthus annuus L.)

Sixteen Piper species, including P nigrum, have been collected from the 483 sites, majority from Western Ghats and maintained at the Indian Institute of Spices Research, Calicut Fifteen qualitative morphological characters of 16 wild species of southern India were studied and plotted for the hierarchical clustering, using SPSS software The cluster groups were compared using BIOCLIM model of DIVA-GIS to identify the areas or 'niches' where Piper species occur predominantly A grid of 50 × 50 km cells and a circular neighbourhood with a radius of 50 km to assign points to grid cells was used to map species richness and species diversity The highest richness grid was found to have 15-16 species, while the highest diversity value was found to be 18 to 3

K. V. Saji

Papers

Genetic variations and interrelationships in Vanilla planifolia and few related species as expressed by RAPD polymorphism

Correlation of metabolites in the leaf and berries of selected black pepper varieties.

Embryogenesis and plant regeneration in anther culture of sunflower (Helianthus annuus L.)

Biodiversity of Piper in South India - : application of GIS and cluster analysis

Effect of mulches on weed suppression and yield of ginger (Zingiber officinale Roscoe)