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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.

The analysis of environmental DNA (eDNA) is a powerful and non-invasive method for monitoring the presence of species in ecosystems. However, ecologists and laboratory staff can find it challenging to use eDNA analysis software effectively due to the unfamiliar command-line interfaces used by many of these packages. Therefore, we developed the eDNA-container app, a free and open-source software package that provides a simple user-friendly interface for eDNA analysis. The application is based on the popular QIIME2 library and is distributed as a Docker image. The use of Docker makes it compatible with a wide range of operating systems and facilitates the reproducible analysis of data across different laboratories. The application includes a point-and-click user interface for selecting sequencing files, configuring parameters, and accessing the results. Key pipeline outputs, such as sequence quality plots, denoising, and ASV generation statistics, are automatically included in a PDF report. This open-source and freely available analysis package should be a valuable tool for scientists using eDNA in biodiversity and biosecurity applications.

Background and aims Biodegradation of polycyclic aromatic hydrocarbons (PAHs) is accelerated in the presence of plants, due to the stimulation of rhizosphere microbes by plant exudates (nonspecific enhancement). However, plants may also recruit specific microbial groups in response to PAH stress (specific enhancement). In this study, plant effects on the development of rhizosphere microbial communities in heterogeneously contaminated soils were assessed for three grasses (ryegrass, red fescue and Yorkshire fog) and four legumes (white clover, chickpea, subterranean clover and red lentil). Methods Plants were cultivated using a split-root model with their roots divided between two independent pots containing either uncontaminated soil or PAH-contaminated soil (pyrene or phenanthrene). Microbial community development in the two halves of the rhizosphere was assessed by T-RFLP (bacterial and fungal community) or DGGE (bacterial community), and by 16S rRNA gene tag-pyrosequencing. Results In legume rhizospheres, the microbial community structure in the uncontaminated part of the split-root model was significantly influenced by the presence of PAH-contamination in the other part of the root system (indirect effect), but this effect was not seen for grasses. In the contaminated rhizospheres, Verrucomicrobia and Actinobacteria showed increased populations, and there was a dramatic increase in Denitratisoma numbers, suggesting that this genus may be important in rhizoremediation processes. Conclusion Our results show that Trifolium and other legumes respond to PAH-contamination stress in a systemic manner, to influence the microbial diversity in their rhizospheres.

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.

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.

Application of biochar to soil may stabilize soil organic carbon (SOC), concomitantly increasing nutrient retention. However, the interactive effect of biochar and nutrients on SOC and the underlying microbial mechanisms remain poorly understood, particularly in intensively managed forests where decarbonization is substantial after converting from natural forests. This 80-day incubation experiment aimed to quantify native SOC mineralization as affected by biochar (B) and nutrients [nitrogen (N) or phosphorus (P)], linking to the chemical composition of SOC, soil microbial community composition, and enzyme activities within a subtropical Moso bamboo ( Phyllostachys edulis ) forest soil. Results presented that compared to the control (nil-nutrient), nutrients (N, P, and NP) significantly destabilized native SOC [positive priming effect (PE); 20–98% increase in SOC mineralization], whereas such destabilization effect was significantly reduced by biochar (6.0–19%). The positive PE by nutrient was due to the increases in O-alkyl C, microbial biomass C, available mineral N, soil pH, β-glucosidase, and invertase activities. Meanwhile, the greater PE by N than P could be attributed to (i) decreases in diversity of bacterial and fungal communities; and (ii) increases in the relative abundances of microbial taxa such as Bacilli, Planctomycetes, and Alphaproteobacteria. Importantly, biochar’s stabilization effect was because biochar not only lowered NH 4 + -N and NO 3 − -N and β-glucosidase activity, but also increased the activity of C-fixing enzyme (RubisCO) and polyphenol oxidase activity. Furthermore, biochar significantly decreased soil O-alkyl C that possibly resulted in less labile SOC mineralization, but increased aromatic C resulting in lower fungal diversity. We conclude that the biochar significantly reduces the destabilization effects of nutrients on SOC, highlighting that the biochar application is an effective approach to mitigate soil CO 2 emissions within subtropical forest.

Purpose Durum wheat is sensitive of acid soils because it lacks effective genes for Al.sup.3+ tolerance. Previous research showed introgression of the TaMATE1B and TaALMT1 genes individually increased the Al.sup.3+ tolerance of durum wheat. Here we aimed to (a) combine the genes into a single durum line, (b) compare the various introgression lines and (c) establish the effectiveness of the introgressions in improving the acid soil tolerance in the field. Methods Durum wheat lines homozygous for Al.sup.3+-tolerant alleles of TaMATE1B and TaALMT1 were crossed to develop a line that incorporated both genes. The parental cultivar, lines with the individual genes and the line with both genes introgressed were screened for Al.sup.3+ tolerance by hydroponic and soil cultures in a growth cabinet. The lines were also assessed for biomass production and grain yield in the field on acid soils. Results The durum wheat lines with the various Al.sup.3+-tolerance genes introgressed performed better based on root growth than Jandaroi, the parental cultivar, in both hydroponic and soil assays when grown in a cabinet. The various introgression lines were tolerant of acid soils compared to Jandaroi when grown in the field as assessed by shoot biomass and grain yield. Conclusion The TaALMT1 and TaMATE1B genes improve the acid soil tolerance of durum wheat with indications that combining both genes is the most effective strategy. The various lines will be valuable to breeders who wish to enhance the acid soil tolerance of durum germplasm.

Durum wheat is sensitive of acid soils because it lacks effective genes for Al.sup.3+ tolerance. Previous research showed introgression of the TaMATE1B and TaALMT1 genes individually increased the Al.sup.3+ tolerance of durum wheat. Here we aimed to (a) combine the genes into a single durum line, (b) compare the various introgression lines and (c) establish the effectiveness of the introgressions in improving the acid soil tolerance in the field. Durum wheat lines homozygous for Al.sup.3+-tolerant alleles of TaMATE1B and TaALMT1 were crossed to develop a line that incorporated both genes. The parental cultivar, lines with the individual genes and the line with both genes introgressed were screened for Al.sup.3+ tolerance by hydroponic and soil cultures in a growth cabinet. The lines were also assessed for biomass production and grain yield in the field on acid soils. The durum wheat lines with the various Al.sup.3+-tolerance genes introgressed performed better based on root growth than Jandaroi, the parental cultivar, in both hydroponic and soil assays when grown in a cabinet. The various introgression lines were tolerant of acid soils compared to Jandaroi when grown in the field as assessed by shoot biomass and grain yield. The TaALMT1 and TaMATE1B genes improve the acid soil tolerance of durum wheat with indications that combining both genes is the most effective strategy. The various lines will be valuable to breeders who wish to enhance the acid soil tolerance of durum germplasm.

Purpose Durum wheat is sensitive of acid soils because it lacks effective genes for Al 3+ tolerance. Previous research showed introgression of the TaMATE1B and TaALMT1 genes individually increased the Al 3+ tolerance of durum wheat. Here we aimed to (a) combine the genes into a single durum line, (b) compare the various introgression lines and (c) establish the effectiveness of the introgressions in improving the acid soil tolerance in the field. Methods Durum wheat lines homozygous for Al 3+ -tolerant alleles of TaMATE1B and TaALMT1 were crossed to develop a line that incorporated both genes. The parental cultivar, lines with the individual genes and the line with both genes introgressed were screened for Al 3+ tolerance by hydroponic and soil cultures in a growth cabinet. The lines were also assessed for biomass production and grain yield in the field on acid soils. Results The durum wheat lines with the various Al 3+ -tolerance genes introgressed performed better based on root growth than Jandaroi, the parental cultivar, in both hydroponic and soil assays when grown in a cabinet. The various introgression lines were tolerant of acid soils compared to Jandaroi when grown in the field as assessed by shoot biomass and grain yield. Conclusion The TaALMT1 and TaMATE1B genes improve the acid soil tolerance of durum wheat with indications that combining both genes is the most effective strategy. The various lines will be valuable to breeders who wish to enhance the acid soil tolerance of durum germplasm.

Abstract The survival and effectiveness of a bioaugmentation strain in its target environment depend not only on physicochemical parameters in the soil but also on the physiological state of the inoculated organism. This study examined the effect of variations in inoculum pretreatment on the survival, metabolic activity (measured as rRNA content) and polycyclic aromatic hydrocarbon (PAH)-catabolic gene expression of Sphingobium yanoikuyae B1 in an aged PAH-contaminated soil. RNA denaturing gradient gel electrophoresis analysis showed stable colonization of PAH-contaminated soil by S. yanoikuyae B1 after four pretreatments (growth in complex or minimal medium, starvation, or acclimation to phenanthrene). By contrast, extractable CFUs decreased with time for all four treatments, and significantly faster for Luria Bertani-grown inocula, suggesting that these cells adhered strongly to soil particles while remaining metabolically active. Pretreatment of the inoculum had a dramatic effect on the expression of genes specific to the PAH-degradation pathway. The highest levels of bphC and xylE expression were seen for inocula that had been precultivated on complex medium, and degradation of PAHs was significantly enhanced in soils treated with these inocula. The results suggest that using complex media instead of minimal media for cultivating bioaugmentation inocula may improve the subsequent efficiency of contaminant biodegradation in the soil.