Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Peredo, E. L., & Cardon, Z. G. Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. Proceedings of the National Academy of Sciences of the United States of America, 117(29), 1(2020): 7438-17445, doi:10.1073/pnas.1906904117.Among green plants, desiccation tolerance is common in seeds and spores but rare in leaves and other vegetative green tissues. Over the last two decades, genes have been identified whose expression is induced by desiccation in diverse, desiccation-tolerant (DT) taxa, including, e.g., late embryogenesis abundant proteins (LEA) and reactive oxygen species scavengers. This up-regulation is observed in DT resurrection plants, mosses, and green algae most closely related to these Embryophytes. Here we test whether this same suite of protective genes is up-regulated during desiccation in even more distantly related DT green algae, and, importantly, whether that up-regulation is unique to DT algae or also occurs in a desiccation-intolerant relative. We used three closely related aquatic and desert-derived green microalgae in the family Scenedesmaceae and capitalized on extraordinary desiccation tolerance in two of the species, contrasting with desiccation intolerance in the third. We found that during desiccation, all three species increased expression of common protective genes. The feature distinguishing gene expression in DT algae, however, was extensive down-regulation of gene expression associated with diverse metabolic processes during the desiccation time course, suggesting a switch from active growth to energy-saving metabolism. This widespread downshift did not occur in the desiccation-intolerant taxon. These results show that desiccation-induced up-regulation of expression of protective genes may be necessary but is not sufficient to confer desiccation tolerance. The data also suggest that desiccation tolerance may require induced protective mechanisms operating in concert with massive down-regulation of gene expression controlling numerous other aspects of metabolism.Dr. Louise Lewis (University of Connecticut) provided F. rotunda and A. deserticola. Suzanne Thomas and Jordan Stark provided expert technical assistance. This work was supported by the NSF, Division of Integrative Organismal Systems (1355085 to Z.G.C.), and an anonymous donor (to Z.G.C.)

Dimension Reduction via Colour Refinement

Colour refinement is a basic algorithmic routine for graph isomorphism testing, appearing as a subroutine in almost all practical isomorphism solvers. It partitions the vertices of a graph into "colour classes" in such a way that all vertices in the same colour class have the same number of neighbours in every colour class. Tinhofer (Disc. App. Math., 1991), Ramana, Scheinerman, and Ullman (Disc. Math., 1994) and Godsil (Lin. Alg. and its App., 1997) established a tight correspondence between colour refinement and fractional isomorphisms of graphs, which are solutions to the LP relaxation of a natural ILP formulation of graph isomorphism. We introduce a version of colour refinement for matrices and extend existing quasilinear algorithms for computing the colour classes. Then we generalise the correspondence between colour refinement and fractional automorphisms and develop a theory of fractional automorphisms and isomorphisms of matrices. We apply our results to reduce the dimensions of systems of linear equations and linear programs. Specifically, we show that any given LP L can efficiently be transformed into a (potentially) smaller LP L' whose number of variables and constraints is the number of colour classes of the colour refinement algorithm, applied to a matrix associated with the LP. The transformation is such that we can easily (by a linear mapping) map both feasible and optimal solutions back and forth between the two LPs. We demonstrate empirically that colour refinement can indeed greatly reduce the cost of solving linear programs

Protocol for a state-wide ground water quality monitoring program and establishment of a ground water quality data clearinghouse

February, 2004.Includes bibliographical references (pages 31-34).Financed in part by the U.S. Department of the Interior, Geological Survey, through the Colorado Water Resources Research Institute, grant no. 1434HQ96GR02660/04

Simple Soil Tests for Onsite Evaluation of Soil Health in Orchards

This fact sheet describes the importance of soil health and best soil testing practices

Diel plant water use and competitive soil cation exchange interact to enhance NH4+ and K+ availability in the rhizosphere

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Plant and Soil 414 (2017): 33-51, doi:10.1007/s11104-016-3089-5.Hydro-biogeochemical processes in the rhizosphere regulate nutrient and water availability, and thus ecosystem productivity. We hypothesized that two such processes often neglected in rhizosphere models — diel plant water use and competitive cation exchange — could interact to enhance availability of K+ and NH4+, both high-demand nutrients. A rhizosphere model with competitive cation exchange was used to investigate how diel plant water use (i.e., daytime transpiration coupled with no nighttime water use, with nighttime root water release, and with nighttime transpiration) affects competitive ion interactions and availability of K+ and NH4+. Competitive cation exchange enabled low-demand cations that accumulate against roots (Ca2+, Mg2+, Na+) to desorb NH4+ and K+ from soil, generating non-monotonic dissolved concentration profiles (i.e. ‘hotspots’ 0.1–1 cm from the root). Cation accumulation and competitive desorption increased with net root water uptake. Daytime transpiration rate controlled diel variation in NH4+ and K+ aqueous mass, nighttime water use controlled spatial locations of ‘hotspots’, and day-to-night differences in water use controlled diel differences in ‘hotspot’ concentrations. Diel plant water use and competitive cation exchange enhanced NH4+ and K+ availability and influenced rhizosphere concentration dynamics. Demonstrated responses have implications for understanding rhizosphere nutrient cycling and plant nutrient uptake.This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research Terrestrial Ecosystem Science program under Award Number DE-SC0008182 to Z.G.C. and R.B.N

A model suite of green algae within the Scenedesmaceae for investigating contrasting desiccation tolerance and morphology

Author Posting. © The Company of Biologists, 2018. This article is posted here by permission of The Company of Biologists for personal use, not for redistribution. The definitive version was published in Journal of Cell Science 131 (2018): jcs212233, doi:10.1242/jcs.212233.Microscopic green algae inhabiting desert microbiotic crusts are remarkably diverse phylogenetically, and many desert lineages have independently evolved from aquatic ancestors. Here we worked with five desert and aquatic species within the family Scenedesmaceae to examine mechanisms that underlie desiccation tolerance and release of unicellular versus multicellular progeny. Live cell staining and time-lapse confocal imaging coupled with transmission electron microscopy established that the desert and aquatic species all divide by multiple (rather than binary) fission, although progeny were unicellular in three species and multicellular (joined in a sheet-like coenobium) in two. During division, Golgi complexes were localized near nuclei, and all species exhibited dynamic rotation of the daughter cell mass within the mother cell wall at cytokinesis. Differential desiccation tolerance across the five species, assessed from photosynthetic efficiency during desiccation/rehydration cycles, was accompanied by differential accumulation of intracellular reactive oxygen species (ROS) detected using a dye sensitive to intracellular ROS. Further comparative investigation will aim to understand the genetic, ultrastructural and physiological characteristics supporting unicellular versus multicellular coenobial morphology, and the ability of representatives in the Scenedesmaceae to colonize ecologically diverse, even extreme, habitats.This work was supported by the National Science Foundation, Division of Integrative Organismal Systems [1355085 to Z.G.C.], an anonymous donor [to Z.G.C.], the Marine Biological Laboratory [to M.B.] and the Environmental and Molecular Sciences Laboratory (EMSL) [48938 to Z.G.C.], a Department of Energy, Office of Science User Facility sponsored by the Office of Biological and Environmental Research, located at Pacific Northwest National Laboratory.2019-04-1

Better to light a candle than curse the darkness : illuminating spatial localization and temporal dynamics of rapid microbial growth in the rhizosphere

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Plant Science 4 (2013): 323, doi:10.3389/fpls.2013.00323.The rhizosphere is a hotbed of microbial activity in ecosystems, fueled by carbon compounds from plant roots. Basic questions about the location and dynamics of plant-spurred microbial growth in the rhizosphere are difficult to answer with standard, destructive soil assays mixing a multitude of microbe-scale microenvironments in a single, often sieved, sample. Soil microbial biosensors designed with the luxCDABE reporter genes fused to a promoter of interest enable continuous imaging of the microbial perception of (and response to) environmental conditions in soil. We used the common soil bacterium Pseudomonas putida KT2440 as host to plasmid pZKH2 containing a fusion between the strong constitutive promoter nptII and luxCDABE (coding for light-emitting proteins) from Vibrio fischeri. Experiments in liquid media demonstrated that high light production by KT2440/pZKH2 was associated with rapid microbial growth supported by high carbon availability. We applied the biosensors in microcosms filled with non-sterile soil in which corn (Zea mays L.), black poplar (Populus nigra L.), or tomato (Solanum lycopersicum L.) was growing. We detected minimal light production from microbiosensors in the bulk soil, but biosensors reported continuously from around roots for as long as six days. For corn, peaks of luminescence were detected 1–4 and 20–35 mm along the root axis behind growing root tips, with the location of maximum light production moving farther back from the tip as root growth rate increased. For poplar, luminescence around mature roots increased and decreased on a coordinated diel rhythm, but was not bright near root tips. For tomato, luminescence was dynamic, but did not exhibit a diel rhythm, appearing in acropetal waves along roots. KT2440/pZKH2 revealed that root tips are not always the only, or even the dominant, hotspots for rhizosphere microbial growth, and carbon availability is highly variable in space and time around roots. - See more at: http://journal.frontiersin.org/Journal/10.3389/fpls.2013.00323/full#sthash.Bv7U0hD6.dpufNSF DEB Ecosystems grant #0415938 to Zoe G.Cardon and Daniel J. Gage, and an U.S. EPA Science to Achieve Results (STAR) Fellowship #91633901-0 to Patrick M. Herron

Strategies for Managing Soil Fertility and Health in Organic Orchards - A Fact Sheet

This fact sheet is a report of research to provide fruit growers with locally adapted advice and solutions for managing soil fertility in certified organic stone-fruits.It includes information of transitioning to organic management; building soil organic matter and providing appropriate nutrients, including phosphorus, potassium, seconary nutrients and trace elements; soil testing; cover crops; mulches; and possible organic management systems