22 research outputs found
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.)
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 â diel plant water use and competitive cation exchange â 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. âhotspotsâ 0.1â1 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 âhotspotsâ, and day-to-night differences in water use controlled diel differences in âhotspotâ 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 1â4 and 20â35 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
Modelled hydraulic redistribution by sunflower (Helianthus annuusâ L.) matches observed data only after including night-time transpiration
Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Plant, Cell & Environment 37 (2014): 899-910, doi:10.1111/pce.12206.The movement of water from moist to dry soil layers through the root systems of plants, referred
to as hydraulic redistribution (HR), occurs throughout the world and is thought to influence
carbon and water budgets and ecosystem functioning. The realized hydrologic, biogeochemical,
and ecological consequences of HR depend on the amount of redistributed water, while the
ability to assess these impacts requires models that correctly capture HR magnitude and timing.
Using several soil types and two eco-types of sunflower (Helianthus annuus L.) in split-pot
experiments, we examined how well the widely used HR modeling formulation developed by
Ryel et al. (2002) matched experimental determination of HR across a range of water potential
driving gradients. H. annuus carries out extensive nighttime transpiration, and though over the
last decade it has become more widely recognized that nighttime transpiration occurs in multiple
species and many ecosystems, the original Ryel et al. (2002) formulation does not include the
effect of nighttime transpiration on HR. We developed and added a representation of nighttime
transpiration into the formulation, and only then was the model able to capture the dynamics and
magnitude of HR we observed as soils dried and nighttime stomatal behavior changed, both
influencing HR.This work was supported by a NOAA Climate and Global Change Postdoctoral
Fellowship to RBN, administered by the University Corporation for Atmospheric Research, by a
grant from the Andrew W. Mellon Foundation to NMH, and by DOE Terrestrial Ecosystem
Science grant ER65389 to ZGC and RBN.2014-10-2
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Systems Biology 5 Suppl 2 (2011): S15, doi:10.1186/1752-0509-5-S2-S15.The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval. We extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified. The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsaThis research is partially
supported by the National Science Foundation (NSF) DMS-1043075 and OCE
1136818
Toward a predictive understanding of Earthâs microbiomes to address 21st century challenges
© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 7 (2016): e00714-16, doi:10.1128/mBio.00714-16.Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.E.L.B. is supported by the Genomes-to-Watersheds Subsurface Biogeochemical
Research Scientific Focus Area, and T.R.N. is supported by
ENIGMA-Ecosystems and Networks Integrated with Genes and Molecular
Assemblies (http://enigma.lbl.gov) Scientific Focus Area, funded by
the U.S. Department of Energy (US DOE), Office of Science, Office of
Biological and Environmental Research under contract no. DE-AC02-
05CH11231 to Lawrence Berkeley National Laboratory (LBNL). M.E.M.
is also supported by the US DOE, Office of Science, Office of Biological
and Environmental Research under contract no. DE-AC02-05CH11231.
Z.G.C. is supported by National Science Foundation Integrative Organismal
Systems grant #1355085, and by US DOE, Office of Biological and
Environmental Research grant # DE-SC0008182 ER65389 from the Terrestrial
Ecosystem Science Program. M.J.B. is supported by R01 DK
090989 from the NIH. T.J.D. is supported by the US DOE Office of Scienceâs
Great Lakes Bioenergy Research Center, grant DE-FC02-
07ER64494. J.L.G. is supported by Alfred P. Sloan Foundation G 2-15-14023. R.K. is supported by grants from the NSF (DBI-1565057) and
NIH (U01AI24316, U19AI113048, P01DK078669, 1U54DE023789,
U01HG006537). K.S.P. is supported by grants from the NSF DMS-
1069303 and the Gordon & Betty Moore Foundation (#3300)
The green algal underground : evolutionary secrets of desert cells
Author Posting. © American Institute of Biological Sciences, 2008. This article is posted here by permission of American Institute of Biological Sciences for personal use, not for redistribution. The definitive version was published in BioScience 58 (2008): 114-122, doi:10.1641/B580206.Microscopic, unicellular, free-living green algae are found in desert microbiotic crusts worldwide. Although morphologically simple, green algae in desert crusts have recently been found to be extraordinarily diverse, with membership spanning five green algal classes and encompassing many taxa new to science. This overview explores this remarkable diversity and its potential to lead to new perspectives on the diversity and evolution of green plants. Molecular systematic and physiological data gathered from desert taxa demonstrate that these algae are long-term members of desert communities, not transient visitors from aquatic habitats. Variations in desiccation tolerance and photophysiology among these algae include diverse evolutionary innovations that developed under selective pressures in the desert. Combined with the single embryophyte lineage to which more familiar terrestrial green plants belong, multiple desert green algal lineages provide independent evolutionary units that may enhance understanding of the evolution and ecology of eukaryotic photosynthetic life on land.This work was supported by
grants from the National Aeronautics and Space Administration,
Exobiology Program (EXB02-0042-0054) to L. A. L.
and Z. G. C., from the National Science Foundation (DEB-
0529737) to L. A. L., and from the University of Connecticut
Research Foundation to Z. G. C
Extraction of high-quality, high-molecular-weight DNA depends heavily on cell homogenization methods in green microalgae
© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stark, J. R., Cardon, Z. G., & Peredo, E. L. Extraction of high-quality, high-molecular-weight DNA depends heavily on cell homogenization methods in green microalgae. Applications in Plant Sciences, 8(3), (2020): e11333, doi:10.1002/aps3.11333.Premise
New sequencing technologies have facilitated genomic studies in green microalgae; however, extracting highâquality DNA is often a bottleneck for longâread sequencing.
Methods and Results
Here, we present a lowâcost, highly transferrable method for the extraction of highâmolecularâweight (HMW), highâpurity DNA from microalgae. We first determined the effect of sample preparation on DNA quality using three homogenization methods: manual grinding using a miniâpestle, automatic grinding using a vortex adapter, and grinding in liquid nitrogen. We demonstrated the versatility of grinding in liquid nitrogen followed by a modified cetyltrimethylammonium bromide (CTAB) extraction across a suite of aquaticâ and desertâevolved algal taxa. Finally, we tested the protocol's robustness by doubling the input material to increase yield, producing per sample up to 20 ÎŒg of highâpurity DNA longer than 21.2 kbp.
Conclusions
All homogenization methods produced DNA within acceptable parameters for purity, but only liquid nitrogen grinding resulted in HMW DNA. The optimization of cell lysis while minimizing DNA shearing is therefore crucial for the isolation of DNA for longâread genomic sequencing because template DNA length strongly affects read output and length.The authors thank Dr. Louise Lewis (University of Connecticut) for providing Flechtneria rotunda and Acutodesmus deserticola, and Suzanne Thomas for expert technical assistance. This work was supported by the National Science Foundation, Division of Integrative Organismal Systems (1355085 to Z.G.C.) and an anonymous donor (to Z.G.C.)