Activation of the salicylic acid signalling pathway in wheat had no significant short-term impact on the diversity of root-associated microbiomes

Salicylic acid (SA) plays an important role in plant defence against biotrophic pathogens. Recent work with Arabidopsis thaliana mutants indicates an association between SA signalling and the diversity of root-associated microbial communities. This has led to the idea that activation of the SA pathway may help plants to rapidly recruit microbes that enhance stress tolerance and could be exploited as an approach to engineer beneficial plant microbiomes in agriculture. Nonetheless, unlike plants in natural environments, mutants with altered SA signalling constitutively express their phenotype. For this reason, we investigated whether transient activation of the SA pathway in wheat (Triticum aestivum) leads to rapid changes in the composition of root microbiomes. High throughput phylogenetic marker gene sequencing demonstrated that, 72 h post-treatment, SA had no significant effects on the richness, evenness and composition of bulk soil and root-associated microbiomes in two soil types. These findings indicate that the structure of wheat root-associated microbiomes did not undergo significant rapid changes in response to activation of the SA signalling pathway

Plant defence inducers rapidly influence the diversity of bacterial communities in a potting mix

Plant hormones and their functional analogues are used in agriculture to combat plant diseases and pests. These chemicals are generally targeted at shoots, but soils inevitably receive a dose during application. In this study, we used 16S rRNA gene amplicon pyrosequencing to determine whether the diversity of bacterial communities in a potting mix (referred here as 'model soil') is influenced by exposure to salicylic acid (SA), methyl jasmonate (MeJA), ethylene (ET) and abscisic acid (ABA). The number of operational taxonomic units (OTUs; richness) and Simpson's Diversity Index values (evenness) associated with each sample was not influenced by the hormone treatments, but changes in community composition were observed. Relative to the control, all hormones more than doubled the abundance of a Limnobacter population, ABA led to a four-fold increase in a Cellvibrio population, ET led to a c. 70% decrease in an Algoriphagus population, and MeJA and ABA applications halved the abundance of a Massilia population. These changes may influence plant productivity. (C) 2014 Elsevier B.V. All rights reserved

Jasmonic acid signalling and the plant holobiont

The plant holobiont – which is the plant and its associated microbiome – is increasingly viewed as an evolving entity. Some interacting microbes that compose the microbiome assist plants in combating pathogens and herbivorous insects. However, knowledge of the factors that influence the microbiome in the context of defence signalling pathways is still in its infancy. Recent research reported that changes in jasmonic acid (JA) and salicylic acid signalling affects the root microbiome of Arabidopsis thaliana. This review aims to present the hypothesis that the JA pathway represents a novel mechanism for microbiome engineering for improved holobiont fitness in agricultural systems

Effects of jasmonic acid signalling on the wheat microbiome differ between body sites

Jasmonic acid (JA) signalling helps plants to defend themselves against necrotrophic pathogens and herbivorous insects and has been shown to influence the root microbiome of Arabidopsis thaliana. In this study, we determined whether JA signalling influences the diversity and functioning of the wheat (Triticum aestivum) microbiome and whether these effects are specific to particular parts of the plant. Activation of the JA pathway was achieved via exogenous application of methyl jasmonate and was confirmed by significant increases in the abundance of 10 JA-signalling-related gene transcripts. Phylogenetic marker gene sequencing revealed that JA signalling reduced the diversity and changed the composition of root endophytic but not shoot endophytic or rhizosphere bacterial communities. The total enzymatic activity and substrate utilisation profiles of rhizosphere bacterial communities were not affected by JA signalling. Our findings indicate that the effects of JA signalling on the wheat microbiome are specific to individual plant compartments

Application of metatranscriptomics to soil environments

The activities of soil microbial communities are of critical importance to terrestrial ecosystem functioning. The mechanisms that determine the interactions between soil microorganisms, their environment and neighbouring organisms, however, are poorly understood. Due to advances in sequencing technologies, an increasing number of metagenomics studies are being conducted on samples from diverse environments including soils. This information has not only increased our awareness of the functional potential of soil microbial communities, but also constitutes powerful reference material for soil metatranscriptomics studies. Metatranscriptomics provides a snapshot of transcriptional profiles that correspond to discrete populations within a microbial community at the time of sampling. This information can indicate the potential activities of complex microbial communities and the mechanisms that regulate them. Here we summarise the technical challenges for metatranscriptomics applied to soil environments and discuss approaches for gaining biologically meaningful insight into these datasets

Rhizosphere Metatranscriptomics: Challenges and Opportunities

The interactions that occur between plant roots and soil microorganisms influence ecosystem function and stability, but are poorly understood. Metagenomics has revolutionized microbial ecology by facilitating the genomic characterization of microbial communities in the environment. This information has provided novel insight into the genes that are present in different environments and constitutes powerful reference material for studying microbial gene expression. Metatranscriptomics enables the characterization of community transcriptional patterns and is poised to advance understanding of plant and microbial gene expression. In this chapter, we discuss how metatranscriptomics could rapidly improve our understanding of plant-microbe interactions in soils

Strategic tillage increased the relative abundance of Acidobacteria but did not impact on overall soil microbial properties of a 19-year no-till Solonetz

Continuous no-till (NT) farming is widely practiced in Australia, but it is prone to weed infestation. Strategic tillage (ST) can be used to effectively control weeds; however, it is unclear whether ST influences soil microbial properties. We investigated whether one- or two-time tillage events using a chisel plough influence the soil microbial properties of an acidic Solonetz with 19-year NT management. Soil samples were collected from 0–10 and 10–20\ua0cm soil depths, 1\ua0year post-ST after a chickpea crop. Microbial biomass C (MBC) and N (MBN), community-level physiological profiling (CLPP, MicroResp™) and fluorescein diacetate as an indicator of total microbial activity (TMA) were determined in soil. The composition of soil microbial communities was profiled using terminal reaction fragment length polymorphism (T-RFLP) and 16S rRNA sequencing. Detection and DNA-based quantitation of ChitinaseA, nifH, amoA, narG, nirK and nosZ genes were used to assess ST effects on soil C and N cycling. Our results show that one- and two-time chisel did not change soil MBC/MBN, TMA or CLPP. Likewise, ST did not change the composition of soil microbial communities and the abundance of genes encoding enzymes involved in key steps of C and N reactions at either soil depth. However, one-time chisel increased relative abundance of Acidobacteria RB41 and Acidobacteria iii1-15, and two-time chisel slightly increased the average C utilisation, both at 10–20\ua0cm soil depth. This suggests that even after a cropping season of chickpea, ST effects on soil microbial properties of the NT Solonetz were negligible. One- and two-time chisel could potentially address the issues associated with long-term NT without impacting overall soil microbial properties

Location-Scale Rank Testing with Application in Quality Control

The best known and most used rank test for the location-scale problem is the Lepage (1971) test. The idea of Lepage is to use a statistic which is the sum of the squares of the standardized Wilcoxon and Ansari-Bradley statistics. There is also another rank test, due to Cucconi (1968) that is earlier but neither known in the literature nor applied in practice. The test is of interest since, contrary to the other location-scale tests, it is not a quadratic form of a test on location and a test on scale and it is easier to be computed than that of Lepage, and other tests. The Cucconi test is based on squared ranks and squared counter-ranks. It should be noted that the power of the Lepage test, contrary to that of the Cucconi test, has been widely studied, even recently. For this reason power and size of the Cucconi test are studied, and comparisons with the Lepage test are assessed. Simulations show that the test of Cucconi maintains the size very close to a and is more powerful than the Lepage test, and therefore should be taken into account as a better alternative. An application of the tests in the context of quality control and industrial statistics is discussed