The presence of plant-associated bacteria alters responses to N-acyl homoserine lactone quorum sensing signals that modulate nodulation

Bacteria use quorum sensing signaling for cell-to-cell communication, which is also important for their interactions with plant hosts. Quorum sensing via N-acyl-homoserine lactones (AHLs) is important for successful symbioses between legumes and nitrogen-fixing rhizobia. Previous studies have shown that plant hosts can recognize and respond to AHLs. Here, we tested whether the response of the model legume Medicago truncatula to AHLs from its symbiont and other bacteria could be modulated by the abundance and composition of plant-associated microbial communities. Temporary antibiotic treatment of the seeds removed the majority of bacterial taxa associated with M. truncatula roots and significantly altered the effect of AHLs on nodule numbers, but lateral root density, biomass, and root length responses were much less affected. The AHL 3-oxo-C14-HSL (homoserine lactone) specifically increased nodule numbers but only after the treatment of seeds with antibiotics. This increase was associated with increased expression of the early nodulation genes RIP1 and ENOD11 at 24 h after infection. A 454 pyrosequencing analysis of the plant-associated bacteria showed that antibiotic treatment had the biggest effect on bacterial community composition. However, we also found distinct effects of 3-oxo-C14-HSL on the abundance of specific bacterial taxa. Our results revealed a complex interaction between plants and their associated microbiome that could modify plant responses to AHLs

Root type is not an important driver of mycorrhizal colonisation in Brachypodium distachyon

Breeding for favourable root traits in food and energy crops should be considered in the context of interactions with soil biota, notably those that can increase the nutrient use efficiency of crops. Arbuscular mycorrhizal (AM) fungi can provide services to plants but a better understanding of the interactions between root traits and AM fungi is required to maximise these benefits. One source of intraspecific variation in root architecture is the allocation of resources to different root types. We hypothesized that different root types would have different traits and be colonised differently by AM fungi, either in the amount of colonisation or identity of colonisers. We studied communities colonising the seminal, coleoptile nodal and leaf nodal roots of seven Brachypodium distachyon accessions grown in three crop or pasture soils. Leaf nodal roots had low specific root length compared to coleoptile nodal and seminal roots, yet all three root types harboured similar AM fungal communities and levels of colonisation. Most of the variation in the AM fungal communities was explained by soil; significant proportions were explained by plant accession and root type but these effects were weak. Differential allocation of resources between root types is not a trait that could be selected to maximise beneficial interactions with AM fungi and we found no link between a root phenotypic trait (specific root length) and AM fungal colonisation. Accessions did vary in extent of colonisation by arbuscules, meaning B. distachyon may be a useful model to study mechanisms underlying the symbiotic interface and mycorrhizal growth response of cereals.This study was funded by an Australian Research Council grant DP140103936 to JR

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat

The rhizosphere microbiome is regulated by plant genotype, root exudates and environment. There is substantial interest in breeding and managing crops that host root microbial communities that increase productivity. The eudicot model species Arabidopsis has been used to investigate these processes, however a model for monocotyledons is also required. We characterized the rhizosphere microbiome and root exudates of Brachypodium distachyon, to develop it as a rhizosphere model for cereal species like wheat. The Brachypodium rhizosphere microbial community was dominated by Burkholderiales. However, these communities were also dependent on how tightly they were bound to roots, the root type they were associated with (nodal or seminal roots), and their location along the roots. Moreover, the functional gene categories detected in microorganisms isolated from around root tips differed from those isolated from bases of roots. The Brachypodium rhizosphere microbiota and root exudate profiles were similar to those reported for wheat rhizospheres, and different to Arabidopsis. The differences in root system development and cell wall chemistry between monocotyledons and eudicots may also influence the microorganism composition of these major plant types. Brachypodium is a promising model for investigating the microbiome of wheat

Root type is not an important driver of mycorrhizal colonisation in Brachypodium distachyon

Breeding for favourable root traits in food and energy crops should be considered in the context of interactions with soil biota, notably those that can increase the nutrient use efficiency of crops. Arbuscular mycorrhizal (AM) fungi can provide services to plants but a better understanding of the interactions between root traits and AM fungi is required to maximise these benefits.One source of intraspecific variation in root architecture is the allocation of resources to different root types. We hypothesized that different root types would have different traits and be colonised differently by AM fungi, either in the amount of colonisation or identity of colonisers. We studied communities colonising the seminal, coleoptile nodal and leaf nodal roots of seven Brachypodium distachyon accessions grown in three crop or pasture soils.Leaf nodal roots had low specific root length compared to coleoptile nodal and seminal roots, yet all three root types harboured similar AM fungal communities and levels of colonisation. Most of the variation in the AM fungal communities was explained by soil; significant proportions were explained by plant accession and root type but these effects were weak.Differential allocation of resources between root types is not a trait that could be selected to maximise beneficial interactions with AM fungi and we found no link between a root phenotypic trait (specific root length) and AM fungal colonisation. Accessions did vary in extent of colonisation by arbuscules, meaning B. distachyon may be a useful model to study mechanisms underlying the symbiotic interface and mycorrhizal growth response of cereals

Impact of carbon farming practices on soil carbon in northern New South Wales

This study sought to quantify the influence of 'carbon farming' practices on soil carbon stocks, in comparison with conventional grazing and cropping, in northern New South Wales. The study had two components: assessment of impacts of organic amendments on soil carbon and biological indicators in croplands on Vertosols of the Liverpool Plains; and assessment of the impact of grazing management on soil carbon in Chromosols of the Northern Tablelands. The organic amendment sites identified for the survey had been treated with manures, composts, or microbial treatments, while the conventional management sites had received only chemical fertilisers. The rotational grazing sites had been managed so that grazing was restricted to short periods of several days, followed by long rest periods (generally several months) governed by pasture growth. These were compared with sites that were grazed continuously. No differences in total soil carbon stock, or soil carbon fractions, were observed between sites treated with organic amendments and those treated with chemical fertiliser. There was some evidence of increased soil carbon stock under rotational compared with continuous grazing, but the difference was not statistically significant. Similarly, double-stranded DNA (dsDNA) stocks were not significantly different in either of the management contrasts, but tended to show higher values in organic treatments and rotational grazing. The enzymatic activities of β-glucosidase and leucine-aminopeptidase were significantly higher in rotational than continuous grazing but statistically similar for the cropping site treatments. Relative abundance and community structure, measured on a subset of the cropping sites, showed a higher bacteria : fungi ratio and provided evidence that microbial process rates were significantly higher in chemically fertilised sites than organic amendment sites, suggesting enhanced mineralisation of organic matter under conventional management. The higher enzyme activity and indication of greater efficiency of microbial populations on carbon farming sites suggests a greater potential to build soil carbon under these practices. Further research is required to investigate whether the indicative trends observed reflect real effects of management

A sterile hydroponic system for characterising root exudates from specific root types and whole-root systems of large crop plants

Abstract Background Plant roots release a variety of organic compounds into the soil which alter the physical, chemical and biological properties of the rhizosphere. Root exudates are technically challenging to measure in soil because roots are difficult to access and exudates can be bound by minerals or consumed by microorganisms. Exudates are easier to measure with hydroponically-grown plants but, even here, simple compounds such as sugars and organic acids can be rapidly assimilated by microorganisms. Sterile hydroponic systems avoid this shortcoming but it is very difficult to maintain sterility for long periods especially for larger crop species. As a consequence, studies often use small model species such as Arabidopsis to measure exudates or use seedlings of crop plants which only have immature roots systems. Results We developed a simple hydroponic system for cultivating large crop plants in sterile conditions for more than 30 days. Using this system wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) plants were grown in sterile conditions for 30 days by which time they had reached the six-leaf stage and developed mature root systems with seminal, nodal and lateral roots. To demonstrate the utility of this system we characterized the aluminium-activated exudation of malate from the major types of wheat roots for the first time. We found that all root types measured released malate but the amounts were two-fold greater from the seminal and nodal axile roots compared with the lateral roots. Additionally, we showed that this sterile growth system could be used to collect exudates from intact whole root systems of barley. Conclusions We developed a simple hydroponic system that enables cereal plants to be grown in sterile conditions for longer periods than previously recorded. Using this system we measured, for the first time, the aluminium-activated efflux of malate from the major types of wheat roots. We showed the system can also be used for collecting exudates from intact root systems of 30-day-old barley plants. This hydroponic system can be modified for various purposes. Importantly it enables the study of exudates from crop species with mature root systems

Bacterial community in the bulk soil (BS) and in the loosely-bound (LB) and tightly-bound (TB) fractions of the Brachypodium Bd21-3 rhizosphere, revealed with 16S pyrosequencing.

<p>(A) NMDS ordination plot (based on Bray-Curtis similarity), where each point represents the bacterial community in a soil/rhizosphere fraction for one plant. (B) Abundance of bacterial phyla in the bulk soil and rhizosphere (Proteobacteria is further classified into classes). (C) Bacterial Orders that are significantly different in abundance between the sample groups (different lower case letters indicate ANOVA <i>P</i><0.05). Only Orders with >10% relative abundance in any sample type are shown. Means are shown ± SE (n = 4–5).</p

Impact of carbon farming practices on soil carbon in northern New South Wales

This study sought to quantify the influence of 'carbon farming' practices on soil carbon stocks, in comparison with conventional grazing and cropping, in northern New South Wales. The study had two components: assessment of impacts of organic amendments on soil carbon and biological indicators in croplands on Vertosols of the Liverpool Plains; and assessment of the impact of grazing management on soil carbon in Chromosols of the Northern Tablelands. The organic amendment sites identified for the survey had been treated with manures, composts, or microbial treatments, while the conventional management sites had received only chemical fertilisers. The rotational grazing sites had been managed so that grazing was restricted to short periods of several days, followed by long rest periods (generally several months) governed by pasture growth. These were compared with sites that were grazed continuously. No differences in total soil carbon stock, or soil carbon fractions, were observed between sites treated with organic amendments and those treated with chemical fertiliser. There was some evidence of increased soil carbon stock under rotational compared with continuous grazing, but the difference was not statistically significant. Similarly, double-stranded DNA (dsDNA) stocks were not significantly different in either of the management contrasts, but tended to show higher values in organic treatments and rotational grazing. The enzymatic activities of β-glucosidase and leucine-aminopeptidase were significantly higher in rotational than continuous grazing but statistically similar for the cropping site treatments. Relative abundance and community structure, measured on a subset of the cropping sites, showed a higher bacteria:fungi ratio and provided evidence that microbial process rates were significantly higher in chemically fertilised sites than organic amendment sites, suggesting enhanced mineralisation of organic matter under conventional management. The higher enzyme activity and indication of greater efficiency of microbial populations on carbon farming sites suggests a greater potential to build soil carbon under these practices. Further research is required to investigate whether the indicative trends observed reflect real effects of management