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.

Low soil fertility commonly limits growth and yield production of common bean (Phaseolus vulgaris L.) in tropical regions. Impacts of nutrient limitations on production volume are well studied and are a major factor in reducing crop yields. This study characterised the impact of reduced nutrient supply on carbon assimilation and nutrient content of leaf, phloem sap and reproductive tissues of common bean grown in a controlled environment in order to detect chemical markers for changes in nutritional content. Leaf gas exchange measurements were undertaken over plant development to characterise changes to carbon assimilation under reduced nutrient supply. Samples of leaf, phloem sap and pod tissue of common bean were analysed for carbon isotope discrimination, mineral nutrient content, and amino acid concentration. Despite declines in nutrient availability leading to decreased carbon assimilation and reductions in yield, amino acid concentration was maintained in the pod tissue. Common bean can maintain the nutritional content of individual pods under varying nutrient availabilities demonstrating the resilience of processes determining the viability of reproductive tissues.

Thermal stress reduces plant growth and development, resulting in considerable economic losses in crops such as soybeans. Nitric oxide (NO) in plants is associated with tolerance to various abiotic stresses. Nevertheless, there are few studies of the range of observed effects of NO in modulating physiological and metabolic functions in soybean plants under high temperature. In the present study, we investigated the effects of sodium nitroprusside (SNP, NO donor), on anatomical, physiological, biochemical, and metabolic processes of soybean plants exposed to high temperature. Soybean plants were grown in soil: sand (2:1) substrate in acclimatized growth chambers. At developmental V3 stage, plants were exposed to two temperatures (25 °C and 40 °C) and SNP (0 and 100 μM), in a randomized block experimental design, with five replicates. After six days, we quantified NO concentration, leaf anatomy, gas exchange, chlorophyll a fluorescence, photosynthetic pigments, lipid peroxidation, antioxidant enzyme activity, and metabolite profiles. Higher NO concentration in soybean plants exposed to high temperature and SNP showed increased effective quantum yields of photosystem II (PSII) and photochemical dissipation, thereby maintaining the photosynthetic rate. Under high temperature, NO also promoted greater activity of ascorbate peroxidase and peroxidase activity, avoiding lipid peroxidation of cell membranes, in addition to regulating amino acid and organic compound levels. These results suggest that NO prevented damage caused by high temperature in soybean plants, illustrating the potential to mitigate thermal stress in cultivated plants.

Chickpea is the second-most-cultivated legume globally, with India and Australia being the two largest producers. In both of these locations, the crop is sown on residual summer soil moisture and left to grow on progressively depleting water content, finally maturing under terminal drought conditions. The metabolic profile of plants is commonly, correlatively associated with performance or stress responses, e.g., the accumulation of osmoprotective metabolites during cold stress. In animals and humans, metabolites are also prognostically used to predict the likelihood of an event (usually a disease) before it occurs, e.g., blood cholesterol and heart disease. We sought to discover metabolic biomarkers in chickpea that could be used to predict grain yield traits under terminal drought, from the leaf tissue of young, watered, healthy plants. The metabolic profile (GC-MS and enzyme assays) of field-grown chickpea leaves was analysed over two growing seasons, and then predictive modelling was applied to associate the most strongly correlated metabolites with the final seed number plant⁻¹. Pinitol (negatively), sucrose (negatively) and GABA (positively) were significantly correlated with seed number in both years of study. The feature selection algorithm of the model selected a larger range of metabolites including carbohydrates, sugar alcohols and GABA. The correlation between the predicted seed number and actual seed number was R² adj = 0.62, demonstrating that the metabolic profile could be used to predict a complex trait with a high degree of accuracy. A previously unknown association between D-pinitol and hundred-kernel weight was also discovered and may provide a single metabolic marker with which to predict large seeded chickpea varieties from new crosses. The use of metabolic biomarkers could be used by breeders to identify superior-performing genotypes before maturity is reached.

Eucalyptus globulus, commonly known as blue gum or southern blue gum, is a tall, evergreen tree endemic to southeastern Australia. E. globulus is grown extensively in plantations to improve the sustainability of timber and fibre production across Australia. Sustainable forest management practices necessitate the consideration of ‘off-site’ carbon and ecological footprints. Pursuing optimal supplemental nutrient application and maximum growth rates is therefore critical to the establishment of a sustainable timber and fibre production industry. Biological indicators that can predict growth responses are therefore of extreme value. We investigated the carbon isotope abundance of wood cellulose (δ¹³C_cel) in E. globulus to determine potential relationships with the carbon isotope abundance of phloem sap (δ¹³C_phl) where the trees were subjected to different level of nutrient availability. This study also sought to determine the effect of nutrient additions on the growth of the E. globulus and to quantify the relationship between the volumetric growth of wood and δ¹³C_cel. Phloem sap and wood cores were collected from trees within study plots which were subjected to seven nutrient treatments over a two-year period in a monoculture E. globulus plantation in South Australia. Phloem sap was collected using the razor blade technique and wood cores were collected using a stem borer. The carbon isotope abundance (δ¹³C) of phloem sap and wood grown in the radial direction of the stem were determined. The basic and dry densities of wood were determined, and their relationships with phloem and wood δ¹³C were established. The δ¹³C_phl was significantly correlated with δ¹³C_cel. The relationship between δ¹³C_cel and the wood density of the respective wood sections was significant but did not consistently show the same pattern. There was no significant variation in basic density observed along the radial direction of the stem wood of the short-rotation E. globulus trees. A positive correlation was observed between δ¹³C_cel and the wood basic density, but the relationship was not consistent along the radial direction of the stem. However, positive correlations were observed between δ¹³C_cel and the air-dry density of respective wood sections. The relationship between phloem and wood δ¹³C and the relationship between δ¹³C and wood density along the radial direction of the stem needs to be considered while monitoring forest growth under nutrient- and water-limited conditions.