Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.

Gama-aminobutyric acid (GABA) is a natural functional amino acid. In the current study, Lactobacillus brevis TCCC13007, a high GABA-producing strain, was isolated from naturally pickled Chinese vegetables. A two-step cellular bioconversion process was established using L. brevis TCCC13007 for the production of GABA. First, L. brevis cells were grown anaerobically in 7% monosodium glutamate (MSG)-containing medium at an initial pH of 6.0 and a controlled pH of 4.6 for 16 to 66 h; approximately 38 g L(-1) of GABA was obtained after 66 h of fermentation at a conversion rate of 98.6%. In the second stage of the process, about 7.6 g L(-1) of GABA was produced three more times at a conversion rate of 92.2% using the same batch of resting cells in the substrate-containing buffer under optimized conditions. Thus, the total GABA yield reached 61 g L(-1). A model system for the biotransformation of MSG to GABA was established using L. brevis TCCC13007 resting cells. The reaction rates were found to follow the classic Michaelis-Menten equation at low substrate concentrations (<80 mM). Kinetic analysis of the biotransformation revealed that L. brevis TCCC13007 resting cells produced GABA similar to that produced by purified glutamate decarboxylase from L. brevis.

Summary• Plant production of methanol (MeOH) is a poorly understood aspect of metabolism, and understanding MeOH production in plants is crucial for modeling MeOH emissions. Here, we have examined the source of MeOH emissions from mature and immature leaves and whether pectin methylesterase (PME) activity is a good predictor of MeOH emission. We also investigated the significance of belowground MeOH production for mature leaf emissions.• We present measurements of MeOH emission, PME activity, and MeOH concentration in mature and immature tissues of tomato (Lycopersicon esculentum). We also present stable carbon isotopic signatures of MeOH emission and the pectin methoxyl pool.• Our results suggest that below-ground MeOH production was not the dominant contributor to daytime MeOH emissions from mature and immature leaves. Stable carbon isotopic signatures of mature and immature leaf MeOH were similar, suggesting that they were derived from the same pathway. Foliar PME activity was related to MeOH flux, but unexplained variance suggested PME activity could not predict emissions.• The data show that MeOH production and emission are complex and cannot be predicted using PME activity alone. We hypothesize that substrate limitation of MeOH synthesis and MeOH catabolism may be important regulators of MeOH emission.

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