Stoichiometric homeostasis of N:P ratio drives species-specific symbiotic N fixation inhibition under N addition.

Introduction: Symbiotic N fixation inhibition induced by N supply to legumes is potentially regulated by the relative N and P availability in soil. However, the specific responses of different legume species to changes in N:P availability remain unclear, and must be better understood to optimize symbiotic N fixation inputs under N enrichment. This study investigated mechanisms by which soil N and P supply influence the symbiotic N fixation of eight legume species, to quantify the inter-specific differences, and to demonstrate how these differences can be determined by the stoichiometric homeostasis in N:P ratios (HN:P). Methods: Eight herbaceous legume species were grown separately in outdoor pots and treated with either no fertilizer (control), N fertilizer (14 g N m-2), P fertilizer (3.5 g P m-2) or both N and P fertilizer. Plant nutrients, stoichiometric characteristics, root biomass, non-structural carbohydrates (NSC), rhizosphere chemistry, P mobilization, root nodulation and symbiotic N fixation were measured. Results: N addition enhanced rhizosphere P mobilization but drove a loss of root biomass and root NSC via exudation of P mobilization compound (organic acid), especially so in treatments without P addition. N addition also induced a 2-14% or 14-36% decline in symbiotic N fixation per plant biomass by legumes in treatments with or without P addition, as a result of decreasing root biomass and root NSC. The changes in symbiotic N fixation were positively correlated with stoichiometric homeostasis of N:P ratios in intact plants without root nodules, regardless of P additions. Discussion: This study indicates that N addition can induce relative P limitations for growth, which can stimulate rhizosphere P mobilization at the expense of root biomass and carbohydrate concentrations, reducing symbiotic N fixation in legumes. Legume species that had less changes in plant N:P ratio, such as Lespedeza daurica and Medicago varia maintained symbiotic N fixation to a greater extent under N addition.

Trichoderma atroviride seed dressing influenced the fungal community and pathogenic fungi in the wheat rhizosphere.

Fusarium crown rot and wheat sharp eyespot are major soil-borne diseases of wheat, causing serious losses to wheat yield in China. We applied high-throughput sequencing combined with qPCR to determine the effect of winter wheat seed dressing, with either Trichoderma atroviride HB20111 spore suspension or a chemical fungicide consisting of 6% tebuconazole, on the fungal community composition and absolute content of pathogens Fusarium pseudograminearum and Rhizoctonia cerealis in the rhizosphere at 180 days after planting. The results showed that the Trichoderma and chemical fungicide significantly reduced the amount of F. pseudograminearum in the rhizosphere soil (p < 0.05), and also changed the composition and structure of the fungal community. In addition, field disease investigation and yield measurement showed that T. atroviride HB20111 treatment reduced the whiteheads with an average control effect of 60.1%, 14.9% higher than the chemical treatment; T. atroviride HB20111 increased yield by 7.7%, which was slightly more than the chemical treatment. Therefore, T. atroviride HB20111 was found to have the potential to replace chemical fungicides to control an extended range of soil-borne diseases of wheat and to improve wheat yield.

Plant growth-promoting rhizobacteria Burkholderia vietnamiensis B418 inhibits root-knot nematode on watermelon by modifying the rhizosphere microbial community.

Burkholderia vietnamiensis B418 is a multifunctional plant growth-promoting rhizobacteria (PGPR) strain with nitrogen-fixing and phosphate-solubilizing capability which can be employed for root-knot nematode (RKN) management on various crops and vegetables. Here we investigated the control efficacy of B. vietnamiensis B418 inoculation against RKN on watermelon, applied either alone or combined with nematicides fosthiazate or avermectin, and their effects on bacterial and fungal microbiomes in rhizosphere soil. The results of field experiments showed individual application of B418 displayed the highest control efficacy against RKN by 71.15%. The combinations with fosthiazate and avermectin exhibited slight incompatibility with lower inhibitory effects of 62.71% and 67.87%, respectively, which were still notably higher than these nematicides applied separately. Analysis of microbiome assemblages revealed B418 inoculation resulted in a slight reduction for bacterial community and a significant increment for fungal community, suggesting that B418 could compete with other bacteria and stimulate fungal diversity in rhizosphere. The relative abundance of Xanthomonadales, Gemmatimonadales and Sphingomonadales increased while that of Actinomycetales reduced with B418 inoculation. The predominate Sordariomycetes of fungal community decreased dramatically in control treatment with B418 inoculation whereas there were increments in fosthiazate and avermectin treatments. Additionally, nitrogen (N) cycling by soil microbes was estimated by quantifying the abundance of microbial functional genes involved in N-transformation processes as B418 has the capability of N-fixation. The copy number of N-fixing gene nifH increased with B418 inoculation, and the highest increment reached 35.66% in control treatment. Our results demonstrate that B. vietnamiensis B418 is an effective biological nematicide for nematode management, which acts through the modulation of rhizosphere microbial community.

Rhizobial diversity is associated with inoculation history at a two-continent scale.

A total of 120 Mesorhizobium strains collected from the central dry zone of Myanmar were analyzed in a pot experiment to evaluate nodulation and symbiotic effectiveness (SE%) in chickpea plants. Phylogenetic analyses revealed all strains belonged to the genus Mesorhizobium according to 16-23S rDNA IGS and the majority of chickpea nodulating rhizobia in Myanmar soils were most closely related to M. gobiense, M. muleiense, M. silamurunense, M. tamadayense and M. temperatum. Around two-thirds of the Myanmar strains (68%) were most closely related to Indian strain IC-2058 (CA-181), which is also most closely related to M. gobiense. There were no strains that were closely related to the cognate rhizobial species to nodulate chickpea: M. ciceri and M. mediterraneum. Strains with diverse 16S-23S rDNA IGS shared similar nodC and nifH gene sequences with chickpea symbionts. Detailed sequence analysis of nodC and nifH found that the strains in Myanmar were somewhat divergent from the group including M. ciceri and were more closely related to M. muleiense and IC-2058. A cross-continent analysis between strains isolated in Australia compared with Myanmar found that there was little overlap in species, where Australian soils were dominated with M. ciceri, M. temperatum and M. huakuii. The only co-occurring species found in both Myanmar and Australia were M. tamadayense and M. silumurunense. Continued inoculation with CC1192 may have reduced diversity of chickpea strains in Australian soils. Isolated strains in Australian and Myanmar had similar adaptive traits, which in some cases were also phylogenetically related. The genetic discrepancy between chickpea nodulating strains in Australia and Myanmar is not only due to inoculation history but to adaptation to soil conditions and crop management over a long period, and there has been virtually no loss of symbiotic efficiency over this time in strains isolated from soils in Myanmar.

Ability to produce indole acetic acid is associated with improved phosphate solubilising activity of rhizobacteria.

Indole acetic acid (IAA) can upregulate genes encoding enzymes responsible for the synthesis of carboxylates involved in phosphorus (P) solubilisation. Here, we investigated whether IAA and its precursor affect the P-solubilising activity of rhizobacteria. A total of 841 rhizobacteria were obtained using taxonomically selective and enrichment isolation methods. Phylogenetic analysis revealed 15 genera of phosphate solubilising bacteria (PSB) capable of producing a wide range of IAA concentrations between 4.1 and 67.2 µg mL-1 in vitro. Addition of L-tryptophan to growth media improved the P-solubilising activity of PSB that were able to produce IAA greater than 20 µg mL-1. This effect was connected to the drop of pH and release of a high concentration of carboxylates, comprising α-ketoglutarate, cis-aconitate, citrate, malate and succinate. An increase in production of organic acids rather than IAA production per se appears to result in the improved P solubilisation in PSB.

18F-Fluoroestradiol PET in the evaluation of probable oligometastatic breast cancer.

Recent advances with specific PET tracer ligands, for example prostate-specific membrane antigen (PSMA)-based PET imaging, have substantially improved the sensitivity and specificity of PET imaging. 18F-Fluoroestradiol (FES) is a novel PET tracer that has been demonstrated to have high specificity for oestrogen receptor (ER) in breast cancer. This case describes the use of FES-PET to further characterise a solitary scapular lesion in a patient with locally advanced ER-positive breast cancer. In demonstrating FES avidity in the lesion, it was determined to represent metastatic disease, thus avoiding further biopsy with its associated morbidity. This case demonstrates the potential diagnostic utility of FES PET-CT in the management of ER-positive breast cancer patients with probable oligometastatic disease.

A high-quality genome of taro (Colocasia esculenta (L.) Schott), one of the world's oldest crops.

Taro (Colocasia esculenta (L.), Schott), from the Araceae family, is one of the oldest crops with important edible, medicinal, nutritional and economic value. Taro is a highly polymorphic species including diverse genotypes adapted to a broad range of environments, but the taro genome has rarely been investigated. Here, a high-quality chromosome-level genome of C. esculenta was assembled using data sequenced by Illumina, PacBio and Nanopore platforms. The assembled genome size was 2,405 Mb with a contig N50 of 400.0 kb and a scaffold N50 of 159.4 Mb. In total, 2,311 Mb (96.09%) of the contig sequences was anchored onto 14 chromosomes to form pseudomolecules, and 2,126 Mb (88.43%) was annotated as repetitive sequences. Of the 28,695 predicted protein-coding genes, 26,215 genes (91.4%) could be functionally annotated. On the basis of phylogenetic analysis using 769 genes, C. esculenta and Spirodela polyrhiza were placed on one branch of the tree that diverged approximately 73.23 million years ago. The synteny analyses showed that there have been two whole-genome duplication events in C. esculenta separated by a relatively short gap. According to comparative genome analysis, a larger number (1,189) of distinct gene families and long terminal repeats were enriched in C. esculenta. Our high-quality taro genome will provide valuable resources for further genetic, ecological and evolutionary analyses of taro or other species in the Araceae.

Nitrifying Microbes in the Rhizosphere of Perennial Grasses are Modified by Biological Nitrification Inhibition.

Soil nitrification (microbial oxidation of ammonium to nitrate) can lead to nitrogen leaching and environmental pollution. A number of plant species are able to suppress soil nitrifiers by exuding inhibitors from roots, a process called biological nitrification inhibition (BNI). However, the BNI activity of perennial grasses in the nutrient-poor soils of Australia and the effects of BNI activity on nitrifying microbes in the rhizosphere microbiome have not been well studied. Here we evaluated the BNI capacity of bermudagrass (Cynodon dactylon L.), St. Augustinegrass (Stenotaphrum secundatum (Walt.) Kuntze), saltwater couch (Sporobolus virginicus), seashore paspalum (Paspalum vaginatum Swartz.), and kikuyu grass (Pennisetum clandestinum) compared with the known positive control, koronivia grass (Brachiaria humidicola). The microbial communities were analysed by sequencing 16S rRNA genes. St. Augustinegrass and bermudagrass showed high BNI activity, about 80 to 90% of koronivia grass. All the three grasses with stronger BNI capacities suppressed the populations of Nitrospira in the rhizosphere, a bacteria genus with a nitrite-oxidizing function, but not all of the potential ammonia-oxidizing archaea. The rhizosphere of saltwater couch and seashore paspalum exerted a weak recruitment effect on the soil microbiome. Our results demonstrate that BNI activity of perennial grasses played a vital role in modulating nitrification-associated microbial populations.

Trichoderma harzianum Inoculation Reduces the Incidence of Clubroot Disease in Chinese Cabbage by Regulating the Rhizosphere Microbial Community.

Clubroot is a disease of cruciferous crops that causes significant economic losses to vegetable production worldwide. We applied high-throughput amplicon sequencing technology to quantify the effect of Trichodermaharzianum LTR-2 inoculation on the rhizosphere community of Chinese cabbage (Brassica rapa subsp. pekinensis cv. Jiaozhou) in a commercial production area. T. harzianum inoculation of cabbage reduced the incidence of clubroot disease by 45.4% (p < 0.05). The disease control efficacy (PDIDS) was 63%. This reduction in disease incidence and severity coincided with a drastic reduction in both the relative abundance of Plasmodiaphora brassicae, the causative pathogen of cabbage clubroot disease, and its copy number in rhizosphere soil. Pathogenic fungi Alternaria and Fusarium were also negatively associated with Trichoderma inoculation according to co-occurrence network analysis. Inoculation drastically reduced the relative abundance of the dominant bacterial genera Delftia and Pseudomonas, whilst increasing others including Bacillus. Our results demonstrate that T. harzianum LTR-2 is an effective biological control agent for cabbage clubroot, which acts through modulation of the soil and rhizosphere microbial community.

Near-Complete Genomes of Two Trichoderma Species: A Resource for Biological Control of Plant Pathogens.

Trichoderma species are widely used to control fungal and nematode diseases of crops. To date, only one complete Trichoderma genome has been sequenced, T. reesei QM6a, a model fungus for industrial enzyme production, while the species or strains used for biological control of plant diseases are only available as draft genomes. Previously, we demonstrated that two Trichoderma strains (T. afroharzianum and T. cyanodichotomus) provide effective control of nematode and fungal plant pathogens. Based on deep sequencing using Illumina and Pacbio platforms, we have assembled high-quality genomes of the above two strains, with contig N50 reaching 4.2 and 1.7 Mbp, respectively, which is greater than those of published draft genomes. The genome data will provide a resource to assist research on the biological control mechanisms of Trichoderma spp.

The preceding root system drives the composition and function of the rhizosphere microbiome.

BACKGROUND: The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production. RESULTS: This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65-87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3-24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched. CONCLUSIONS: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.

Plant Nitrogen and Phosphorus Resorption in Response to Varied Legume Proportions in a Restored Grassland.

An in-depth assessment of plant nutrient resorption can offer insights into understanding ecological processes and functional responses to biotic and abiotic changes in the environment. The legume proportion in a mixed grassland can drive changes in the soil environment and plant relationships, but little information is available regarding how the legume proportion influences plant nutrient resorption in mixed grasslands. In this study, three mixed communities of Leymus chinensis (Trin.) Tzvel. and Medicago sativa L. differing in legume proportion (Low-L, with 25% legume composition; Mid-L, with 50% legume composition; High-L, with 75% legume composition) were established with four replicates in a degraded grassland. Four years after establishing the mixed grassland, the quantity of biological N2 fixation by M. sativa, the availabilities of water and nitrogen (N) and phosphorus (P) in soil were examined, and the concentrations and resorption of leaf N and P for both species were measured during forage maturation and senescence. The results showed Mid-L had greater biological N2 fixation and soil N availability than Low-L and High-L, while the High-L had lower soil water and P availability, but a greater soil available N:P ratio compared with Low-L and Mid-L. Legume proportion did not alter N or P concentrations of mature leaves. However, in Mid-L N resorption was reduced by 8 to 16% for the two mixed-species compared with Low-L and High-L. High-L enhanced P resorption by 20 to 24% in both plant species compared with Low-L. The L. chinensis and M. sativa responded differently to varied legume proportion in terms of P resorption. It was concluded that legume proportion drove changes in soil nutrient availability of mixed communities, which primarily altered plant nutrient resorption during senescence, but had no influence on the nutrient concentrations of mature plants. A moderate legume proportion reduced N resorption, and increased senesced leaf N concentration of grass and legume species. The difference in P resorption by two mixed-species significantly changed the interspecific difference of senesced leaf P concentration and the N:P ratio with varied legume proportion.

Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis.

Astragalus membranaceus, also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from Astragalus membranaceus have been used to treat a wide range of illnesses, such as cardiovascular disease, type 2 diabetes, nephritis and cancers. Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of Astragalus membranaceus. Therefore, characterising the biosynthesis of bioactive compounds in Astragalus membranaceus, such as Astragalosides, Calycosin and Calycosin-7-O-ß-d-glucoside, is of particular importance for further genetic studies of Astragalus membranaceus. In this study, we reconstructed the Astragalus membranaceus full-length transcriptomes from leaf and root tissues using PacBio Iso-Seq long reads. We identified 27 975 and 22 343 full-length unique transcript models in each tissue respectively. Compared with previous studies that used short read sequencing, our reconstructed transcripts are longer, and are more likely to be full-length and include numerous transcript variants. Moreover, we also re-characterised and identified potential transcript variants of genes involved in Astragalosides, Calycosin and Calycosin-7-O-ß-d-glucoside biosynthesis. In conclusion, our study provides a practical pipeline to characterise the full-length transcriptome for species without a reference genome and a useful genomic resource for exploring the biosynthesis of active compounds in Astragalus membranaceus.

Accuracy and safety of ward based pleural ultrasound in the Australian healthcare system.

BACKGROUND AND OBJECTIVE: Ultrasound has been shown to improve the accuracy and safety of pleural procedures. Studies to date have been performed in large, specialized units, where pleural procedures are performed by a small number of highly specialized physicians. There are no studies examining the safety and accuracy of ultrasound in the Australian healthcare system where procedures are performed by junior doctors with a high staff turnover. METHODS: We performed a retrospective review of the ultrasound database in the Respiratory Department at the Royal Melbourne Hospital to determine accuracy and complications associated pleural procedures. RESULTS: A total of 357 ultrasounds were performed between October 2010 and June 2013. Accuracy of pleural procedures was 350 of 356 (98.3%). Aspiration of pleural fluid was successful in 121 of 126 (96%) of patients. Two (0.9%) patients required chest tube insertion for management of pneumothorax. There were no recorded pleural infections, haemorrhage or viscera puncture. CONCLUSION: Ward-based ultrasound for pleural procedures is safe and accurate when performed by appropriately trained and supported junior medical officers. Our findings support this model of pleural service care in the Australian healthcare system.

Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum.

Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a diverse range of annual and perennial Trifolium (clover) species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative rod, isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont predominated in the perennial grasslands of Glencoe Research Station, in Uruguay, to competitively nodulate its host, and fix atmospheric nitrogen. Here we describe the basic features of WSM2304, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a nitrogen fixing microsymbiont of a clover species from the American center of origin. We reveal that its genome size is 6,872,702 bp encoding 6,643 protein-coding genes and 62 RNA only encoding genes. This multipartite genome was found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four circular plasmids of size 1,266,105 bp, 501,946 bp, 308,747 bp and 257,956 bp.

Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers.

Rhizobium leguminosarum bv trifolii is a soil-inhabiting bacterium that has the capacity to be an effective nitrogen fixing microsymbiont of a diverse range of annual Trifolium (clover) species. Strain WSM1325 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from root nodules collected in 1993 from the Greek Island of Serifos. WSM1325 is produced commercially in Australia as an inoculant for a broad range of annual clovers of Mediterranean origin due to its superior attributes of saprophytic competence, nitrogen fixation and acid-tolerance. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a microsymbiont of annual clovers. We reveal that its genome size is 7,418,122 bp encoding 7,232 protein-coding genes and 61 RNA-only encoding genes. This multipartite genome contains 6 distinct replicons; a chromosome of size 4,767,043 bp and 5 plasmids of size 828,924 bp, 660,973 bp, 516,088 bp, 350,312 bp and 294,782 bp.