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Summary Flooding represents a major threat to global agricultural productivity and food security, but plants are capable of deploying a suite of adaptive responses that can lead to short‐ or longer‐term survival to this stress. One cellular pathway thought to help coordinate these responses is via flooding‐triggered Ca²⁺signaling.We have mined publicly available transcriptomic data from Arabidopsis subjected to flooding or low oxygen stress to identify rapidly upregulated, Ca²⁺‐related transcripts. We then focused on transporters likely to modulate Ca²⁺signals. Candidates emerging from this analysis includedAUTOINHIBITED Ca²⁺ATPASE 1andCATION EXCHANGER 2. We therefore assayed mutants in these genes for flooding sensitivity at levels from growth to patterns of gene expression and the kinetics of flooding‐related Ca²⁺changes.Knockout mutants inCAX2especially showed enhanced survival to soil waterlogging coupled with suppressed induction of many marker genes for hypoxic response and constitutive activation of others.CAX2mutants also generated larger and more sustained Ca²⁺signals in response to both flooding and hypoxic challenges.CAX2 is a Ca²⁺transporter located on the tonoplast, and so these results are consistent with an important role for vacuolar Ca²⁺transport in the signaling systems that trigger flooding response. 

Gravity is a powerful element in shaping plant development, with gravitropism, the oriented growth response of plant organs to the direction of gravity, leading to each plant’s characteristic form both above and below ground. Despite being conceptually simple to follow, monitoring a plant’s directional growth responses can become complex as variation arises from both internal developmental cues as well as effects of the environment. In this protocol, we discuss approaches to gravitropism assays, focusing on automated analyses of root responses. For Arabidopsis, we recommend a simple 90􏰁 rotation using seedlings that are 5–8 days old. If images are taken at regular intervals and the environmental metadata is recorded during both seedling development and gravitropic assay, these data can be used to reveal quantitative kinetic patterns at distinct stages of the assay. The use of software that analyzes root system parameters and stores this data in the RSML format opens up the possibility for a host of root parameters to be extracted to characterize growth of the primary root and a range of lateral root phenotypes. 

Plants possess a systemic signaling system whereby local stimuli can lead to rapid, plant-wide responses. In addition to the redistribution of chemical messengers that range from RNAs and peptides to hormones and metabolites, a communication system acting through the transmission of electrical, Ca2+, reactive oxygen species and potentially even hydraulic signals has also been discovered. This latter system can propagate signals across many cells each second and researchers are now beginning to uncover the molecular machineries behind this rapid communications network. Thus, elements such as the reactive oxygen species producing NAPDH oxidases and ion channels of the two pore channel, glutamate receptor-like and cyclic nucleotide gated families are all required for the rapid propagation of these signals. Upon arrival at their distant targets, these changes trigger responses ranging from the production of hormones, to changes in the levels of primary metabolites and shifts in patterns of gene expression. These systemic responses occur within seconds to minutes of perception of the initial, local signal, allowing for the rapid deployment of plant-wide responses. For example, an insect starting to chew on just a single leaf triggers preemptive antiherbivore defenses throughout the plant well before it has a chance to move on to the next leaf on its menu.