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Article: Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere.

Handakumbura, Pubudu P / Rivas Ubach, Albert / Battu, Anil K

mSystems

2021 Volume 6, Issue 5, Page(s) e0076521

Abstract: Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the rhizosphere microbiome. These ... ...

Abstract	Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the rhizosphere microbiome. These interactions affect plant fitness and performance, soil health, and the belowground carbon budget. Exploring and understanding the molecular mechanisms governing ecosystem responses via rhizosphere interactions allow the rational and sustainable design of future ecosystems. However, visualizing the plant root system architecture with spatially resolved root exudate and microbiome profiles along the root in its native state remains an ambitious grand challenge in rhizosphere biology. To address this challenge, we developed a three-dimensional (3D) root cartography platform to accurately visualize molecular and microbial constituents and their interactions in the root-rhizosphere zone.
Language	English
Publishing date	2021-09-14
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00765-21
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Article: Light-Dependence of Formate (C

Jardine, Kolby J / Lei, Joseph / Som, Suman / Souza, Daisy / Clendinen, Chaevien S / Mehta, Hardeep / Handakumbura, Pubudu / Bill, Markus / Young, Robert P

Plants (Basel, Switzerland)

2022 Volume 11, Issue 16

Abstract: Although apparent light inhibition of leaf day respiration is a widespread reported phenomenon, the mechanisms involved, including utilization of alternate respiratory pathways and substrates and light inhibition of TCA cycle enzymes are under active ... ...

Abstract	Although apparent light inhibition of leaf day respiration is a widespread reported phenomenon, the mechanisms involved, including utilization of alternate respiratory pathways and substrates and light inhibition of TCA cycle enzymes are under active investigation. Recently, acetate fermentation was highlighted as a key drought survival strategy mediated through protein acetylation and jasmonate signaling. Here, we evaluate the light-dependence of acetate transport and assimilation in
Language	English
Publishing date	2022-08-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants11162080
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Article: Light-Dependence of Formate (C1) and Acetate (C2) Transport and Oxidation in Poplar Trees

Jardine, Kolby J. / Lei, Joseph / Som, Suman / Souza, Daisy / Clendinen, Chaevien S. / Mehta, Hardeep / Handakumbura, Pubudu / Bill, Markus / Young, Robert P.

Plants. 2022 Aug. 09, v. 11, no. 16

2022

Abstract	Although apparent light inhibition of leaf day respiration is a widespread reported phenomenon, the mechanisms involved, including utilization of alternate respiratory pathways and substrates and light inhibition of TCA cycle enzymes are under active investigation. Recently, acetate fermentation was highlighted as a key drought survival strategy mediated through protein acetylation and jasmonate signaling. Here, we evaluate the light-dependence of acetate transport and assimilation in Populus trichocarpa trees using the dynamic xylem solution injection (DXSI) method developed here for continuous studies of C1 and C2 organic acid transport and light-dependent metabolism. Over 7 days, 1.0 L of [¹³C]formate and [¹³C₂]acetate solutions were delivered to the stem base of 2-year old potted poplar trees, while continuous diurnal observations were made in the canopy of CO₂, H₂O, and isoprene gas exchange together with δ¹³CO₂. Stem base injection of 10 mM [¹³C₂]acetate induced an overall pattern of canopy branch headspace ¹³CO₂ enrichment (δ¹³CO₂ +27‰) with a diurnal structure in δ¹³CO₂ reaching a mid-day minimum followed by a maximum shortly after darkening where δ¹³CO₂ values rapidly increased up to +12‰. In contrast, 50 mM injections of [¹³C]formate were required to reach similar δ¹³CO₂ enrichment levels in the canopy with δ¹³CO₂ following diurnal patterns of transpiration. Illuminated leaves of detached poplar branches pretreated with 10 mM [¹³C₂]acetate showed lower δ¹³CO₂ (+20‰) compared to leaves treated with 10 mM [¹³C]formate (+320‰), the opposite pattern observed at the whole plant scale. Following dark/light cycles at the leaf-scale, rapid, strong, and reversible enhancements in headspace δ¹³CO₂ by up to +60‰ were observed in [¹³C₂]acetate-treated leaves which showed enhanced dihydrojasmonic acid and TCA cycle intermediate concentrations. The results are consistent with acetate in the transpiration stream as an effective activator of the jasmonate signaling pathway and respiratory substrate. The shorter lifetime of formate relative to acetate in the transpiration stream suggests rapid formate oxidation to CO₂ during transport to the canopy. In contrast, acetate is efficiently transported to the canopy where an increased allocation towards mitochondrial dark respiration occurs at night. The results highlight the potential for an effective integration of acetate into glyoxylate and TCA cycles and the light-inhibition of citrate synthase as a potential regulatory mechanism controlling the diurnal allocation of acetate between anabolic and catabolic processes.
Keywords	Populus trichocarpa ; acetates ; acetylation ; canopy ; carbon dioxide ; citrate (si)-synthase ; drought ; fermentation ; formates ; gas exchange ; headspace analysis ; isoprene ; jasmonic acid ; leaves ; mitochondria ; oxidation ; transpiration ; tricarboxylic acid cycle ; xylem
Language	English
Dates of publication	2022-0809
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants11162080
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Article ; Online: Distinct Preflowering Drought Tolerance Strategies of

Ogden, Aaron J / Abdali, Shadan / Engbrecht, Kristin M / Zhou, Mowei / Handakumbura, Pubudu P

International journal of molecular sciences

2020 Volume 21, Issue 24

Abstract: Drought is the largest stress affecting agricultural crops, resulting in substantial reductions in yield. Plant adaptation to water stress is a complex trait involving changes in hormone signaling, physiology, and morphology. Sorghum ( ...

Abstract	Drought is the largest stress affecting agricultural crops, resulting in substantial reductions in yield. Plant adaptation to water stress is a complex trait involving changes in hormone signaling, physiology, and morphology. Sorghum (
MeSH term(s)	Droughts ; Flowers/genetics ; Flowers/physiology ; Gene Expression Regulation, Plant ; Genotype ; Plant Proteins/metabolism ; Proteome/analysis ; Proteome/metabolism ; Sorghum/genetics ; Sorghum/physiology ; Stress, Physiological ; Subcellular Fractions/metabolism
Chemical Substances	Plant Proteins ; Proteome
Language	English
Publishing date	2020-12-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21249706
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Article ; Online: Metabotyping as a Stopover in Genome-to-Phenome Mapping.

Handakumbura, Pubudu P / Stanfill, Bryan / Rivas-Ubach, Albert / Fortin, Dan / Vogel, John P / Jansson, Christer

Scientific reports

2019 Volume 9, Issue 1, Page(s) 1858

Abstract: Predicting phenotypic expression from genomic and environmental information is arguably the greatest challenge in today's biology. Being able to survey genomic content, e.g., as single-nucleotide polymorphism data, within a diverse population and predict ...

Abstract	Predicting phenotypic expression from genomic and environmental information is arguably the greatest challenge in today's biology. Being able to survey genomic content, e.g., as single-nucleotide polymorphism data, within a diverse population and predict the phenotypes of external traits, represents the holy grail across genome-informed disciplines, from personal medicine and nutrition to plant breeding. In the present study, we propose a two-step procedure in bridging the genome to phenome gap where external phenotypes are viewed as emergent properties of internal phenotypes, such as molecular profiles, in interaction with the environment. Using biomass accumulation and shoot-root allometry as external traits in diverse genotypes of the model grass Brachypodium distachyon, we established correlative models between genotypes and metabolite profiles (metabotypes) as internal phenotypes, and between metabotypes and external phenotypes under two contrasting watering regimes. Our results demonstrate the potential for employing metabotypes as an integrator in predicting external phenotypes from genomic information.
MeSH term(s)	Algorithms ; Biomass ; Brachypodium/genetics ; Chromosome Mapping ; Genetic Association Studies ; Genome, Plant ; Genomics ; Genotype ; Mass Spectrometry ; Metabolomics ; Phenotype ; Plant Roots ; Plant Shoots ; Polymorphism, Single Nucleotide ; Principal Component Analysis
Language	English
Publishing date	2019-02-12
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-38483-0
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Article ; Online: Transcriptional Regulation of Grass Secondary Cell Wall Biosynthesis: Playing Catch-Up with Arabidopsis thaliana.

Handakumbura, Pubudu P / Hazen, Samuel P

Frontiers in plant science

2012 Volume 3, Page(s) 74

Abstract: Secondary cell wall synthesis occurs in specialized cell types following completion of cell enlargement. By virtue of mechanical strength provided by a wall thickened with cellulose, hemicelluloses, and lignin, these cells can function as water- ... ...

Abstract	Secondary cell wall synthesis occurs in specialized cell types following completion of cell enlargement. By virtue of mechanical strength provided by a wall thickened with cellulose, hemicelluloses, and lignin, these cells can function as water-conducting vessels and provide structural support. Several transcription factor families regulate genes encoding wall synthesis enzymes. Certain NAC and MYB proteins directly bind to the SNBE and AC elements upstream of structural genes and other transcription factors. The most detailed model of this regulatory network is established predominantly for a eudicot, Arabidopsis thaliana. In grasses, both the patterning and the composition of secondary cell walls are distinct from that of eudicots. These differences suggest transcriptional regulation is similarly distinct. Putative rice and maize orthologs of several eudicot cell wall regulators genetically complement mutants of A. thaliana or result in wall defects when constitutively overexpressed; nevertheless, aside from a maize, ZmMYB31, and a switchgrass protein, PvMYB4, function has not been tested in a grass. Similar to the seminal work conducted in A. thaliana, gene expression profiling in maize, rice, and other grasses implicates additional genes as regulators. Characterization of these genes will continue to elucidate the relationship between the transcription regulatory networks of eudicots and grasses.
Language	English
Publishing date	2012-04-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X ; 1664-462X
ISSN (online)	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2012.00074
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Article ; Online: Activation of the plant mevalonate pathway by extracellular ATP.

Cho, Sung-Hwan / Tóth, Katalin / Kim, Daewon / Vo, Phuc H / Lin, Chung-Ho / Handakumbura, Pubudu P / Ubach, Albert Rivas / Evans, Sterling / Paša-Tolić, Ljiljana / Stacey, Gary

Nature communications

2022 Volume 13, Issue 1, Page(s) 450

Abstract: The mevalonate pathway plays a critical role in multiple cellular processes in both animals and plants. In plants, the products of this pathway impact growth and development, as well as the response to environmental stress. A forward genetic screen of ... ...

Abstract	The mevalonate pathway plays a critical role in multiple cellular processes in both animals and plants. In plants, the products of this pathway impact growth and development, as well as the response to environmental stress. A forward genetic screen of Arabidopsis thaliana using Ca
MeSH term(s)	Adenosine Triphosphate/pharmacology ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Calcium/metabolism ; Cytosol/metabolism ; Extracellular Space/chemistry ; Immunity, Innate/drug effects ; Kinetics ; Metabolic Networks and Pathways/drug effects ; Metabolome/genetics ; Mevalonic Acid/metabolism ; Mutation/genetics ; Phenotype ; Phosphorylation/drug effects ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Phosphotransferases (Alcohol Group Acceptor)/metabolism ; Plant Immunity/drug effects ; Protein Binding/drug effects ; Signal Transduction
Chemical Substances	Arabidopsis Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; Phosphotransferases (Alcohol Group Acceptor) (EC 2.7.1.-) ; mevalonate kinase (EC 2.7.1.36) ; Mevalonic Acid (S5UOB36OCZ) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2022-01-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28150-w
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Article ; Online: Evolutionary Variation in MADS Box Dimerization Affects Floral Development and Protein Abundance in Maize.

Abraham-Juárez, María Jazmín / Schrager-Lavelle, Amanda / Man, Jarrett / Whipple, Clinton / Handakumbura, Pubudu / Babbitt, Courtney / Bartlett, Madelaine

The Plant cell

2020 Volume 32, Issue 11, Page(s) 3408–3424

Abstract: Interactions between MADS box transcription factors are critical in the regulation of floral development, and shifting MADS box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation ... ...

Abstract	Interactions between MADS box transcription factors are critical in the regulation of floral development, and shifting MADS box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation in protein-protein interactions affects MADS box protein function remains unknown. To assess the impact of changing MADS box protein-protein interactions on transcription factor function, we turned to the grasses, where interactions between B-class MADS box proteins vary. We tested the functional consequences of this evolutionary variability using maize (
MeSH term(s)	Chromatin Assembly and Disassembly ; Evolution, Molecular ; Flowers/genetics ; Flowers/growth & development ; Gene Expression Regulation, Plant ; Genetic Pleiotropy ; MADS Domain Proteins/genetics ; MADS Domain Proteins/metabolism ; Mutation ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plants, Genetically Modified ; Protein Multimerization ; Protein Processing, Post-Translational ; Ubiquitination ; Zea mays/genetics ; Zea mays/growth & development ; Zea mays/metabolism
Chemical Substances	MADS Domain Proteins ; Plant Proteins
Language	English
Publishing date	2020-09-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	623171-8
ISSN	1532-298X ; 1040-4651
ISSN (online)	1532-298X
ISSN	1040-4651
DOI	10.1105/tpc.20.00300
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Article: Antecedent conditions determine the biogeochemical response of coastal soils to seawater exposure

Sengupta, Aditi / Stegen, James C / Bond-Lamberty, Ben / Rivas-Ubach, Albert / Zheng, Jianqiu / Handakumbura, Pubudu P / Norris, Cooper / Peterson, Matthew J / Yabusaki, Steven B / Bailey, Vanessa L / Ward, Nicholas D

Soil biology & biochemistry. 2021 Feb., v. 153

2021

Abstract: Coastal landscapes are increasingly exposed to seawater due to sea level rise and extreme weather events. The biogeochemical responses of these vulnerable ecosystems are poorly understood, limiting our ability to predict how their role in local and ... ...

Abstract	Coastal landscapes are increasingly exposed to seawater due to sea level rise and extreme weather events. The biogeochemical responses of these vulnerable ecosystems are poorly understood, limiting our ability to predict how their role in local and global biogeochemical cycles will shift under future conditions. Here we evaluate how antecedent conditions influence the biogeochemical response of soil to seawater inundation events based on a 42-day laboratory incubation experiment with soils collected from a natural salinity gradient across a coastal floodplain. We quantified influences of seawater inundation on intact soil cores through high-frequency carbon dioxide (CO₂) and methane (CH₄) gas fluxes measurements as well as ultrahigh resolution characterization of organic matter chemistry and metabolites. Mean CO₂ and CH₄ fluxes were higher after inundation compared to control cores for soils that had low in situ electrical conductivity (EC). Soils with low in situ EC also exhibited significant shifts in organic matter profiles after inundation, with surficial soils (0–7.5 cm) becoming more enriched in phenolic compounds, compared to deeper soils (7.5–15 cm). The number of biochemical transformations inferred from mass spectrometry increased significantly after inundation for soils with low in situ EC. Our results suggest that seawater inundation of low-salinity terrestrial environments can lead to increased microbial activity and increasing likelihood of soil carbon release, with sites experiencing infrequent or new seawater exposure likely to be more sensitive to saltwater exposure relative to sites with more frequent exposure. We conclude that the biogeochemical impacts of future seawater exposure will be modulated by antecedent conditions associated with landscape position within coastal watersheds.
Keywords	carbon dioxide ; electrical conductivity ; floodplains ; landscape position ; mass spectrometry ; metabolites ; methane ; microbial activity ; organic matter ; saline water ; salinity ; sea level ; seawater ; soil biology ; soil carbon ; weather
Language	English
Dates of publication	2021-02
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2020.108104
Database	NAL-Catalogue (AGRICOLA)

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Article: Crops for Carbon Farming.

Jansson, Christer / Faiola, Celia / Wingler, Astrid / Zhu, Xin-Guang / Kravchenko, Alexandra / de Graaff, Marie-Anne / Ogden, Aaron J / Handakumbura, Pubudu P / Werner, Christiane / Beckles, Diane M

Frontiers in plant science

2021 Volume 12, Page(s) 636709

Abstract: Agricultural cropping systems and pasture comprise one third of the world's arable land and have the potential to draw down a considerable amount of atmospheric ... ...

Abstract	Agricultural cropping systems and pasture comprise one third of the world's arable land and have the potential to draw down a considerable amount of atmospheric CO
Language	English
Publishing date	2021-06-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2021.636709
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