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Anneberg TJ, Turcotte MM, Ashman TL. Plant neopolyploidy and genetic background differentiate the microbiome of duckweed across a variety of natural freshwater sources. Mol Ecol 2023; 32:5849-5863. [PMID: 37750335 DOI: 10.1111/mec.17142] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/06/2023] [Indexed: 09/27/2023]
Abstract
Whole-genome duplication has long been appreciated for its role in driving phenotypic novelty in plants, often altering the way organisms interface with the abiotic environment. Only recently, however, have we begun to investigate how polyploidy influences interactions of plants with other species, despite the biotic niche being predicted as one of the main determinants of polyploid establishment. Nevertheless, we lack information about how polyploidy affects the diversity and composition of the microbial taxa that colonize plants, and whether this is genotype-dependent and repeatable across natural environments. This information is a first step towards understanding whether the microbiome contributes to polyploid establishment. We, thus, tested the immediate effect of polyploidy on the diversity and composition of the bacterial microbiome of the aquatic plant Spirodela polyrhiza using four pairs of diploids and synthetic autotetraploids. Under controlled conditions, axenic plants were inoculated with pond waters collected from 10 field sites across a broad environmental gradient. Autotetraploids hosted 4%-11% greater bacterial taxonomic and phylogenetic diversity than their diploid progenitors. Polyploidy, along with its interactions with the inoculum source and genetic lineage, collectively explained 7% of the total variation in microbiome composition. Furthermore, polyploidy broadened the core microbiome, with autotetraploids having 15 unique bacterial taxa in addition to the 55 they shared with diploids. Our results show that whole-genome duplication directly leads to novelty in the plant microbiome and importantly that the effect is dependent on the genetic ancestry of the polyploid and generalizable over many environmental contexts.
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Affiliation(s)
- Thomas J Anneberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Martin M Turcotte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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2
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Pagliuso D, Pedro de Jesus Pereira J, Ulrich JC, Barbosa Cotrim ME, Buckeridge MS, Grandis A. Carbon allocation of Spirodela polyrhiza under boron toxicity. FRONTIERS IN PLANT SCIENCE 2023; 14:1208888. [PMID: 37528985 PMCID: PMC10388368 DOI: 10.3389/fpls.2023.1208888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/08/2023] [Indexed: 08/03/2023]
Abstract
Pectic polysaccharides containing apiose, xylose, and uronic acids are excellent candidates for boron fixation. Duckweeds are the fastest-growing angiosperms that can absorb diverse metals and contaminants from water and have high pectin content in their cell walls. Therefore, these plants can be considered excellent boron (B) accumulators. This work aimed to investigate the relationship between B assimilation capacity with apiose content in the cell wall of Spirodela polyrhiza subjected to different boric acid concentrations. Plants were grown for 7 and 10 days in ½ Schenck-Hildebrandt media supplemented with 0 to 56 mg B.L-1, the non-structural and structural carbohydrates, and related genes were evaluated. The results showed that B altered the morphology and carbohydrate composition of this species during plant development. The optimum B concentration (1.8 mg B.L-1) led to the highest relative growth and biomass accumulation, reduced starch, and high pectin and apiose contents, together with increased expression of UDP-apiose/UDP-xylose synthase (AXS) and 1,4-α-galacturonosyltransferase (GAUT). The toxic state (28 and 56 mg B.L-1) increased the hexose contents in the cell wall with a concomitant reduction of pectins, apiose, and growth. The pectin content of S. polyrhiza was strongly associated with its growth capacity and regulation of B content within the cells, which have AXS as an important regulator. These findings suggest that duckweeds are suitable for B remediation, and their biomass can be used for bioenergy production.
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Affiliation(s)
- Débora Pagliuso
- Laboratory of Plant Physiological Ecology, Department of Botany. Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - João Pedro de Jesus Pereira
- Laboratory of Plant Physiological Ecology, Department of Botany. Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | | | - Marcos S. Buckeridge
- Laboratory of Plant Physiological Ecology, Department of Botany. Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Adriana Grandis
- Laboratory of Plant Physiological Ecology, Department of Botany. Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Oláh V, Appenroth KJ, Lam E, Sree KS. Sixth International Conference on Duckweed Research and Applications Presents Lemnaceae as a Model Plant System in the Genomics and Postgenomics Era. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112134. [PMID: 37299113 DOI: 10.3390/plants12112134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/08/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
The 6th International Conference on Duckweed Research and Applications (6th ICDRA) was organized at the Institute of Plant Genetics and Crop Plant Research (IPK) located in Gatersleben, Germany, from 29 May to 1 June 2022. The growing community of duckweed research and application specialists was noted with participants from 21 different countries including an increased share of newly integrated young researchers. The four-day conference focused on diverse aspects of basic and applied research together with practical applications of these tiny aquatic plants that could have an enormous potential for biomass production.
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Affiliation(s)
- Viktor Oláh
- Department of Botany, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | | | - Eric Lam
- Department Plant Biology, Rutgers State University of New Jersey, New Brunswick, NJ 08901, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
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4
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Anneberg TJ, O'Neill EM, Ashman TL, Turcotte MM. Polyploidy impacts population growth and competition with diploids: multigenerational experiments reveal key life-history trade-offs. THE NEW PHYTOLOGIST 2023; 238:1294-1304. [PMID: 36740596 DOI: 10.1111/nph.18794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Ecological theory predicts that early generation polyploids ('neopolyploids') should quickly go extinct owing to the disadvantages of rarity and competition with their diploid progenitors. However, polyploids persist in natural habitats globally. This paradox has been addressed theoretically by recognizing that reproductive assurance of neopolyploids and niche differentiation can promote establishment. Despite this, the direct effects of polyploidy at the population level remain largely untested despite establishment being an intrinsically population-level process. We conducted population-level experiments where life-history investment in current and future growth was tracked in four lineage pairs of diploids and synthetic autotetraploids of the aquatic plant Spirodela polyrhiza. Population growth was evaluated with and without competition between diploids and neopolyploids across a range of nutrient treatments. Although neopolyploid populations produce more biomass, they reach lower population sizes and have reduced carrying capacities when growing alone or in competition across all nutrient treatments. Thus, contrary to individual-level studies, our population-level data suggest that neopolyploids are competitively inferior to diploids. Conversely, neopolyploid populations have greater investment in dormant propagule production than diploids. Our results show that neopolyploid populations should not persist based on current growth dynamics, but high potential future growth may allow polyploids to establish in subsequent seasons.
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Affiliation(s)
- Thomas J Anneberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Elizabeth M O'Neill
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Martin M Turcotte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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Sun Z, Zhao X, Li G, Yang J, Chen Y, Xia M, Hwang I, Hou H. Metabolic flexibility during a trophic transition reveals the phenotypic plasticity of greater duckweed (Spirodela polyrhiza 7498). THE NEW PHYTOLOGIST 2023; 238:1386-1402. [PMID: 36856336 DOI: 10.1111/nph.18844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
The greater duckweed (Spirodela polyrhiza 7498) exhibits trophic diversity (photoautotrophic, heterotrophic, photoheterotrophic, and mixotrophic growth) depending on the availability of exogenous organic carbon sources and light. Here, we show that the ability to transition between various trophic growth conditions is an advantageous trait, providing great phenotypic plasticity and metabolic flexibility in S. polyrhiza 7498. By comparing S. polyrhiza 7498 growth characteristics, metabolic acclimation, and cellular ultrastructure across these trophic modes, we show that mixotrophy decreases photosynthetic performance and relieves the CO2 limitation of photosynthesis by enhancing the CO2 supply through the active respiration pathway. Proteomic and metabolomic analyses corroborated that S. polyrhiza 7498 increases its intracellular CO2 and decreases reactive oxygen species under mixotrophic and heterotrophic conditions, which substantially suppressed the wasteful photorespiration and oxidative-damage pathways. As a consequence, mixotrophy resulted in a higher biomass yield than the sum of photoautotrophy and heterotrophy. Our work provides a basis for using trophic transitions in S. polyrhiza 7498 for the enhanced accumulation of value-added products.
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Affiliation(s)
- Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Zhou Y, Stepanenko A, Kishchenko O, Xu J, Borisjuk N. Duckweeds for Phytoremediation of Polluted Water. PLANTS (BASEL, SWITZERLAND) 2023; 12:589. [PMID: 36771672 PMCID: PMC9919746 DOI: 10.3390/plants12030589] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/28/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Tiny aquatic plants from the Lemnaceae family, commonly known as duckweeds, are often regarded as detrimental to the environment because of their ability to quickly populate and cover the surfaces of bodies of water. Due to their rapid vegetative propagation, duckweeds have one of the fastest growth rates among flowering plants and can accumulate large amounts of biomass in relatively short time periods. Due to the high yield of valuable biomass and ease of harvest, duckweeds can be used as feedstock for biofuels, animal feed, and other applications. Thanks to their efficient absorption of nitrogen- and phosphate-containing pollutants, duckweeds play an important role in the restorative ecology of water reservoirs. Moreover, compared to other species, duckweed species and ecotypes demonstrate exceptionally high adaptivity to a variety of environmental factors; indeed, duckweeds remove and convert many contaminants, such as nitrogen, into plant biomass. The global distribution of duckweeds and their tolerance of ammonia, heavy metals, other pollutants, and stresses are the major factors highlighting their potential for use in purifying agricultural, municipal, and some industrial wastewater. In summary, duckweeds are a powerful tool for bioremediation that can reduce anthropogenic pollution in aquatic ecosystems and prevent water eutrophication in a simple, inexpensive ecologically friendly way. Here we review the potential for using duckweeds in phytoremediation of several major water pollutants: mineral nitrogen and phosphorus, various organic chemicals, and heavy metals.
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Affiliation(s)
- Yuzhen Zhou
- School of Life Science, Huaiyin Normal University, Huai’an 223300, China
| | - Anton Stepanenko
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Olena Kishchenko
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Jianming Xu
- School of Life Science, Huaiyin Normal University, Huai’an 223300, China
| | - Nikolai Borisjuk
- School of Life Science, Huaiyin Normal University, Huai’an 223300, China
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Zhao X, Yang J, Li X, Li G, Sun Z, Chen Y, Chen Y, Xia M, Li Y, Yao L, Hou H. Identification and expression analysis of GARP superfamily genes in response to nitrogen and phosphorus stress in Spirodela polyrhiza. BMC PLANT BIOLOGY 2022; 22:308. [PMID: 35751022 PMCID: PMC9233324 DOI: 10.1186/s12870-022-03696-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/13/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND GARP transcription factors perform critical roles in plant development and response to environmental stimulus, especially in the phosphorus (P) and nitrogen (N) sensing and uptake. Spirodela polyrhiza (giant duckweed) is widely used for phytoremediation and biomass production due to its rapid growth and efficient N and P removal capacities. However, there has not yet been a comprehensive analysis of the GRAP gene family in S. polyrhiza. RESULTS We conducted a comprehensive study of GRAP superfamily genes in S. polyrhiza. First, we investigated 35 SpGARP genes which have been classified into three groups based on their gene structures, conserved motifs, and phylogenetic relationship. Then, we identified the duplication events, performed the synteny analysis, and calculated the Ka/Ks ratio in these SpGARP genes. The regulatory and co-expression networks of SpGARPs were further constructed using cis-acting element analysis and weighted correlation network analysis (WGCNA). Finally, the expression pattern of SpGARP genes were analyzed using RNA-seq data and qRT-PCR, and several NIGT1 transcription factors were found to be involved in both N and P starvation responses. CONCLUSIONS The study provides insight into the evolution and function of GARP superfamily in S. polyrhiza, and lays the foundation for the further functional verification of SpGARP genes.
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Affiliation(s)
- Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaozhe Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yimeng Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yixian Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lunguang Yao
- Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North Diversion Project of Henan Province, Collaborative Innovation Center of Water Security for Water Source Region of Mid-Line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang, 473061, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Peršić V, Antunović Dunić J, Domjan L, Zellnig G, Cesar V. Time Course of Age-Linked Changes in Photosynthetic Efficiency of Spirodela polyrhiza Exposed to Cadmium. FRONTIERS IN PLANT SCIENCE 2022; 13:872793. [PMID: 35693160 PMCID: PMC9175006 DOI: 10.3389/fpls.2022.872793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Short-term assessment of adverse effects is essential for populations exposed to higher risk of environmental pollution. This study presents the time course of physiological and morphological changes attributed to cadmium, emphasizing age-linked differences in the susceptibility of photosynthetic apparatus of Spirodela polyrhiza fronds exposed to different cadmium concentrations. A four-frond colony represented by mother, daughter, and granddaughter plants was exposed to cadmium concentrations for 6, 24, and 72 h to establish its effect on different generations of the great duckweed. The duration of cadmium exposure accounted for the most variation in chlorophyll content as the most influential variable, and after 72 h, frond responsiveness was a function of cadmium concentration. Carotenoid contents behaved slightly differently in fronds of different ages, with the oldest mother frond exhibiting accelerated senescence. Chlorophyll fluorescence measurements showed that cadmium affects different photosynthetic electron transport segments relative to the frond's chloroplast structure level. Photosynthesis of mother fronds exposed to low cadmium and daughter fronds exposed to high cadmium was determined by the functionality of primary electron acceptance at the PSII level. Mother plants exposed to higher cadmium concentrations were characterized by closed and inactive reaction centers, dissipated energy outflux, and inhibited photosynthesis. Young fronds exposed to low and high cadmium concentrations were characterized by increased non-reducing reaction centers and thermal phase reduction, with activated dissipative mechanisms at high cadmium concentrations. Cadmium-induced changes in the ultrastructure of chloroplasts were visible after 6 h of exposure to lowest concentrations, with gradual degradation of the thylakoid system as the fronds aged. Younger fronds responded to cadmium more dynamically through molecular, physiological, and anatomical changes and tolerated a more reduced electron transport chain under given conditions than older fronds.
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Affiliation(s)
- Vesna Peršić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | | | - Lucija Domjan
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | | | - Vera Cesar
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
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Lam E, Michael TP. Wolffia, a minimalist plant and synthetic biology chassis. TRENDS IN PLANT SCIENCE 2022; 27:430-439. [PMID: 34920947 DOI: 10.1016/j.tplants.2021.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/13/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
A highly simplified species for genome engineering would facilitate rational design of a synthetic plant. A candidate species is the aquatic, non-grass monocot wolffia (Wolffia australiana) in the Lemnaceae family. Commonly known as watermeal, wolffia is a rootless ball of several thousand cells the size of a pinhead and the fastest growing plant known on Earth. Its extreme morphological reduction is coupled to transposon-mediated streamlining of its transcriptome, which represents a core set of nonredundant protein coding genes. Despite its body plan and transcriptome being highly specialized for continuous growth, wolffia retains cell types relevant to higher plants. Systems level studies with this species could enable the creation of a defined biological chassis for synthetic plant construction.
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Affiliation(s)
- Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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10
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Masavang S, Winckler P, Tira-Umphon A, Phahom T. New insights into moisture sorption characteristics, nutritional composition, and antioxidant and morphological properties of dried duckweed [Wolffia arrhiza (L.) Wimm]. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:2135-2143. [PMID: 34601730 DOI: 10.1002/jsfa.11555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/23/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Duckweed has been considered as an alternative future food material as a result of its high nutritional values, although it also has a high moisture content resulting in a short shelf life. Moisture sorption isotherms are used to design dehydration and storage conditions to prolong the shelf life food products. To date, information regarding the sorption isotherm of duckweed has not been reported. Scanning electron microscopy (SEM) is frequently used to study food microstructure. However, this technique has to be performed under high-vacuum conditions and takes a long time. In the present study, two-photon imaging microscopy was selected to investigate the microstructure of dried duckweed instead of SEM. RESULTS Among five sorption isotherm models, the Peleg model gave the highest goodness of fit. The monolayer moisture content (M0 ) of duckweed was in the range 7.43-7.92% dry basis (d.b.) and 8.87-8.86% d.b. for the GAB and BET multilayer kinetic models, respectively. The moisture changing behavior at each relative humidity step could be described by two exponential and reaction order kinetics. A clear cell structure (hexagonal shape) and stomata, as well as structural images (both 2D and 3D), were obtained using the two-photon microscopy technique. CONCLUSION The Peleg model best described the moisture sorption behaviors of dried duckweed and the shape of sorption isotherms were classified as type III isotherm. The M0 of dried duckweed ranged from 7.43 to 8.86% d.b. Two-photon microscopy was a potent tool for investigating the microstructure and composition of dried duckweed. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Supuksorn Masavang
- Department of Food Science and Technology, Faculty of Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
| | - Pascale Winckler
- Plateforme Dimacell/Imagerie spectroscopique UMR Procédés Alimentaires et Microbiologiques Equipe Procédés Microbiologiques et Biotechnologiques, AgroSup Dijon Nord, Dijon, France
| | - Arak Tira-Umphon
- School of Crop Production Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Traiphop Phahom
- University of Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
- School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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Characterization of Various Subunit Combinations of ADP-Glucose Pyrophosphorylase in Duckweed (Landoltia punctata). BIOMED RESEARCH INTERNATIONAL 2022; 2022:5455593. [PMID: 35309169 PMCID: PMC8927976 DOI: 10.1155/2022/5455593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/24/2022] [Indexed: 11/17/2022]
Abstract
Background Landoltia punctata can be used as renewable and sustainable biofuel feedstock because it can quickly accumulate high starch levels. ADP-glucose pyrophosphorylase (AGPase) catalyzes the first committed step during starch biosynthesis in higher plants. The heterotetrameric structure of plant AGPases comprises pairs of large subunits (LSs) and small subunits (SSs). Although several studies have reported on the high starch accumulation capacity of duckweed, no study has explored the underlying molecular accumulation mechanisms and their linkage with AGPase. Therefore, this study focused on characterizing the roles of different L. punctate AGPases. Methodology. Expression patterns of LpAGPs were determined through comparative transcriptome analyses, followed by coexpressing their coding sequences in Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Nicotiana tabacum. Results Comparative transcriptome analyses showed that there are five AGPase subunits encoding cDNAs in L. punctata (LpAGPS1, LpAGPS2, LpAGPL1, LpAGPL2, and LpAGPL3). Nutrient starvation (distilled water treatment) significantly upregulated the expression of LpAGPS1, LpAGPL2, and LpAGPL3. Coexpression of LpAGPSs and LpAGPLs in Escherichia coli generated six heterotetramers, but only four (LpAGPS1/LpAGPL3, LpAGPS2/LpAGPL1, LpAGPS2/LpAGPL2, and LpAGPS2/LpAGPL3) exhibited AGPase activities and displayed a brownish coloration upon exposure to iodine staining. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays validated the interactions between LpAGPS1/LpAGPL2, LpAGPS1/LpAGPL3, LpAGPS2/LpAGPL1, LpAGPS2/LpAGPL2, and LpAGPS2/LpAGPL3. All the five LpAGPs were fusion-expressed with hGFP in Arabidopsis protoplasts, and their green fluorescence signals were uniformly localized in the chloroplast, indicating that they are plastid proteins. Conclusions This study uncovered the cDNA sequences, structures, subunit interactions, expression patterns, and subcellular localization of AGPase. Collectively, these findings provide new insights into the molecular mechanism of fast starch accumulation in L. punctata.
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12
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Acosta K, Appenroth KJ, Borisjuk L, Edelman M, Heinig U, Jansen MAK, Oyama T, Pasaribu B, Schubert I, Sorrels S, Sree KS, Xu S, Michael TP, Lam E. Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era. THE PLANT CELL 2021; 33:3207-3234. [PMID: 34273173 PMCID: PMC8505876 DOI: 10.1093/plcell/koab189] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/18/2021] [Indexed: 05/05/2023]
Abstract
The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society's pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.
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Affiliation(s)
- Kenneth Acosta
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Klaus J Appenroth
- Plant Physiology, Matthias Schleiden Institute, University of Jena, Jena 07737, Germany
| | - Ljudmilla Borisjuk
- The Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben D-06466, Germany
| | - Marvin Edelman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uwe Heinig
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marcel A K Jansen
- School of Biological, Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Cork T23 TK30, Ireland
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Buntora Pasaribu
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Ingo Schubert
- The Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben D-06466, Germany
| | - Shawn Sorrels
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
| | - Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Münster 48149, Germany
| | | | - Eric Lam
- Author for correspondence: (E.L.), (T.P.M.)
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13
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Yang GL, Yang MX, Lv SM, Tan AJ. The effect of chelating agents on iron plaques and arsenic accumulation in duckweed (Lemna minor). JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126410. [PMID: 34157466 DOI: 10.1016/j.jhazmat.2021.126410] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Iron plaques have been found to limit the phytoremediation efficiency by reducing iron solubility, while chelating agents can increase the bioavailability of iron from Fe plaques to numerous terrestrial plants. However, the effects of chelating agents on Fe plaques along the As accumulation in aquatic plants remain unknown. In this study, the effects of five chelating agents (EDTA, DTPA, NTA, GLDA, and CA) on the As (As(III) or As(V)), phosphate, and iron uptake by iron plaques and duckweed (Lemna minor) were examined. The results showed that the chelating agents increased the As accumulation in L. minor plants by desorbing and mobilizing As from Fe plaques. The desorption rates of As(V) (As(III)) from the Fe plaques by the chelating agents were 5.26-8.77% (8.70-15.02%), and the plants/DCB extract ratios of As(V) (As(III)) increased from 2.63 ± 0.13 (1.97 ± 0.06) to the peak value of 3.38 ± 0.21 (2.70 ± 0.14) upon adding chelating agents. Besides, the addition of chelating agents increased the uptake of P and Fe by L. minor plants. This work provides a theoretical basis for the remediation of As-contaminated waters by duckweed with the help of chelating agents.
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Affiliation(s)
- Gui-Li Yang
- College of Life Sciences, Guizhou University, Guiyang 550025, China.
| | - Ming-Xing Yang
- Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Shi-Ming Lv
- College of Animal Science, Guizhou University, Guiyang 50025, China
| | - Ai-Juan Tan
- College of Life Sciences, Guizhou University, Guiyang 550025, China.
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14
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Jiang M, Wang P, Xu L, Ye X, Fan H, Cheng J, Chen J. In silico analysis of glycosyltransferase 2 family genes in duckweed ( Spirodela polyrhiza) and its role in salt stress tolerance. Open Life Sci 2021; 16:583-593. [PMID: 34179502 PMCID: PMC8216227 DOI: 10.1515/biol-2021-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/27/2021] [Accepted: 05/22/2021] [Indexed: 11/15/2022] Open
Abstract
Plant glycosyltransferase 2 (GT2) family genes are involved in plant abiotic stress tolerance. However, the roles of GT2 genes in the abiotic resistance in freshwater plants are largely unknown. We identified seven GT2 genes in duckweed, remarkably more than those in the genomes of Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, Nymphaea tetragona, Persea americana, Zostera marina, and Ginkgo biloba, suggesting a significant expansion of this family in the duckweed genome. Phylogeny resolved the GT2 family into two major clades. Six duckweed genes formed an independent subclade in Clade I, and the other was clustered in Clade II. Gene structure and protein domain analysis showed that the lengths of the seven duckweed GT2 genes were varied, and the majority of GT2 genes harbored two conserved domains, PF04722.12 and PF00535.25. The expression of all Clade I duckweed GT2 genes was elevated at 0 h after salt treatment, suggesting a common role of these genes in rapid response to salt stress. The gene Sp01g00794 was highly expressed at 12 and 24 h after salt treatment, indicating its association with salt stress resilience. Overall, these results are essential for studies on the molecular mechanisms in stress response and resistance in aquatic plants.
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Affiliation(s)
- Mingliang Jiang
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
| | - Ligang Xu
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
| | - Hongxiang Fan
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Junxiang Cheng
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jinting Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
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15
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Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs EL, Sree KS, Appenroth KJ, Fuchs J, Jupe F, Sandoval JP, Krasileva KV, Borisjuk L, Mockler TC, Ecker JR, Martienssen RA, Lam E. Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome Res 2021; 31:225-238. [PMID: 33361111 PMCID: PMC7849404 DOI: 10.1101/gr.266429.120] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/16/2020] [Indexed: 11/24/2022]
Abstract
Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.
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Affiliation(s)
- Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Evan Ernst
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nolan Hartwick
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Philomena Chu
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Douglas Bryant
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Stefan Ortleb
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Erin L Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye, Kerala 671316, India
| | | | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Florian Jupe
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Justin P Sandoval
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Ljudmylla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Joseph R Ecker
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Robert A Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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16
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Yang GL, Feng D, Liu YT, Lv SM, Zheng MM, Tan AJ. Research Progress of a Potential Bioreactor: Duckweed. Biomolecules 2021; 11:biom11010093. [PMID: 33450858 PMCID: PMC7828363 DOI: 10.3390/biom11010093] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 02/01/2023] Open
Abstract
Recently, plant bioreactors have flourished into an exciting area of synthetic biology because of their product safety, inexpensive production cost, and easy scale-up. Duckweed is the smallest and fastest-growing aquatic plant, and has advantages including simple processing and the ability to grow high biomass in smaller areas. Therefore, duckweed could be used as a new potential bioreactor for biological products such as vaccines, antibodies, pharmaceutical proteins, and industrial enzymes. Duckweed has made a breakthrough in biosynthesis as a chassis plant and is being utilized for the production of plenty of biological products or bio-derivatives with multiple uses and high values. This review summarizes the latest progress on genetic background, genetic transformation system, and bioreactor development of duckweed, and provides insights for further exploration and application of duckweed.
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Affiliation(s)
- Gui-Li Yang
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
| | - Dan Feng
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
| | - Yu-Ting Liu
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
| | - Shi-Ming Lv
- College of Animal Science, Guizhou University, Guiyang 550025, China;
| | - Meng-Meng Zheng
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
| | - Ai-Juan Tan
- College of Life Sciences, Guizhou University, Guiyang 550025, China; (G.-L.Y.); (D.F.); (Y.-T.L.); (M.-M.Z.)
- Key Laboratory of Conservation and Germplasm Innovation of Mountain Plant Resources, Ministry of Education, Guiyang 550025, China
- Correspondence: ; Tel.: +86-1376-513-6919
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17
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Ekperusi AO, Nwachukwu EO, Sikoki FD. Assessing and Modelling the Efficacy of Lemna paucicostata for the Phytoremediation of Petroleum Hydrocarbons in Crude Oil-Contaminated Wetlands. Sci Rep 2020; 10:8489. [PMID: 32444776 PMCID: PMC7244528 DOI: 10.1038/s41598-020-65389-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/04/2020] [Indexed: 11/16/2022] Open
Abstract
The potentials of the invasive duckweed species, Lemna paucicostata to remove pollutants from aquatic environment was tested in a constructed wetlands as an ecological based system for the phytoremediation of petroleum hydrocarbons in crude oil-contaminated waters within 120 days. Total petroleum hydrocarbons in wetlands and tissues of duckweed were analyzed using gas chromatography with flame ionization detector following established methods while the experimental data were subjected to the first-order kinetic rate model to understand the remediation rate of duckweed in wetlands. L. paucicostata effected a significant (F = 253.405, P < 0.05) removal of hydrocarbons from wetlands reaching 97.91% after 120 days. Assessment on the transport and fate of hydrocarbons in duckweed indicated that L. paucicostata bioaccumulated less than 1% and significantly biodegraded 97.74% of hydrocarbons in wetlands at the end of the study. The experimental data reasonably fitted (r2 = 0.938) into the first-order kinetic rate model. From the result of the study, it is reasonable to infer that L. paucicostata is an effective aquatic macrophyte for the removal of petroleum hydrocarbons in moderately polluted waters.
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Affiliation(s)
- Abraham Ogheneruemu Ekperusi
- Africa Centre of Excellence, Centre for Oilfield Chemicals Research, Institute of Petroleum Studies, University of Port Harcourt, Choba, Rivers State, Nigeria.
- Department of Marine Environment & Pollution Control, Faculty of Marine Environmental Management, Nigeria Maritime University, Okerenkoko, Delta State, Nigeria.
| | - Eunice Oluchi Nwachukwu
- Department of Plant Science & Biotechnology, Faculty of Science, University of Port Harcourt, Choba, Rivers State, Nigeria
| | - Francis David Sikoki
- Department of Animal & Environmental Biology, Faculty of Science, University of Port Harcourt, Choba, Rivers State, Nigeria
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18
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Miranda AF, Kumar NR, Spangenberg G, Subudhi S, Lal B, Mouradov A. Aquatic Plants, Landoltia punctata, and Azolla filiculoides as Bio-Converters of Wastewater to Biofuel. PLANTS (BASEL, SWITZERLAND) 2020; 9:E437. [PMID: 32244834 PMCID: PMC7238415 DOI: 10.3390/plants9040437] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/17/2022]
Abstract
The aquatic plants, Azolla filiculoides, and Landoltia punctate, were used as complementing phytoremediators of wastewater containing high levels of phosphate, which simulates the effluents from textile, dyeing, and laundry detergent industries. Their complementarities are based on differences in capacities to uptake nitrogen and phosphate components from wastewater. Sequential treatment by L. punctata followed by A. filiculoides led to complete removal of NH4, NO3, and up to 93% reduction of PO4. In experiments where L. punctata treatment was followed by fresh L. punctata, PO4 concentration was reduced by 65%. The toxicity of wastewater assessed by shrimps, Paratya australiensis, showed a four-fold reduction of their mortality (LC50 value) after treatment. Collected dry biomass was used as an alternative carbon source for heterotrophic marine protists, thraustochytrids, which produced up to 35% dry weight of lipids rich in palmitic acid (50% of total fatty acids), the key fatty acid for biodiesel production. The fermentation of treated L. punctata biomass by Enterobacter cloacae yielded up to 2.14 mol H2/mole of reduced sugar, which is comparable with leading terrestrial feedstocks. A. filiculoides and L. punctata can be used as a new generation of feedstock, which can treat different types of wastewater and represent renewable and sustainable feedstock for bioenergy production.
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Affiliation(s)
- Ana F. Miranda
- School of Sciences, RMIT University, Bundoora West Campus, Bundoora VIC 3083, Australia;
| | - N. Ram Kumar
- The Energy and Resources Institute, New Delhi 110 003, India; (N.R.K.); (S.S.); (B.L.)
| | - German Spangenberg
- AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora VIC 3083, Australia;
- School of Applied Systems Biology, La Trobe University, Bundoora VIC 3086, Australia
| | - Sanjukta Subudhi
- The Energy and Resources Institute, New Delhi 110 003, India; (N.R.K.); (S.S.); (B.L.)
| | - Banwari Lal
- The Energy and Resources Institute, New Delhi 110 003, India; (N.R.K.); (S.S.); (B.L.)
| | - Aidyn Mouradov
- School of Sciences, RMIT University, Bundoora West Campus, Bundoora VIC 3083, Australia;
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19
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Acosta K, Xu J, Gilbert S, Denison E, Brinkman T, Lebeis S, Lam E. Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome. PLoS One 2020; 15:e0228560. [PMID: 32027711 PMCID: PMC7004381 DOI: 10.1371/journal.pone.0228560] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/19/2020] [Indexed: 12/20/2022] Open
Abstract
Culture-independent characterization of microbial communities associated with popular plant model systems have increased our understanding of the plant microbiome. However, the integration of other model systems, such as duckweed, could facilitate our understanding of plant microbiota assembly and evolution. Duckweeds are floating aquatic plants with many characteristics, including small size and reduced plant architecture, that suggest their use as a facile model system for plant microbiome studies. Here, we investigated the structure and assembly of the duckweed bacterial microbiome. First, a culture-independent survey of the duckweed bacterial microbiome from different locations in New Jersey revealed similar phylogenetic profiles. These studies showed that Proteobacteria is a dominant phylum in the duckweed bacterial microbiome. To observe the assembly dynamics of the duckweed bacterial community, we inoculated quasi-gnotobiotic duckweed with wastewater effluent from a municipal wastewater treatment plant. Our results revealed that duckweed strongly shapes its bacterial microbiome and forms distinct associations with bacterial community members from the initial inoculum. Additionally, these inoculation studies showed the bacterial communities of different duckweed species were similar in taxa composition and abundance. Analysis across the different duckweed bacterial communities collected in this study identified a set of "core" bacterial taxa consistently present on duckweed irrespective of the locale and context. Furthermore, comparison of the duckweed bacterial community to that of rice and Arabidopsis revealed a conserved taxonomic structure between the duckweed microbiome and the terrestrial leaf microbiome. Our results suggest that duckweeds utilize similar bacterial community assembly principles as those found in terrestrial plants and indicate a highly conserved structuring effect of leaf tissue on the plant microbiome.
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Affiliation(s)
- Kenneth Acosta
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Jenny Xu
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Elizabeth Denison
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Thomas Brinkman
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sarah Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey, United States of America
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20
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Liu Y, Wang Y, Xu S, Tang X, Zhao J, Yu C, He G, Xu H, Wang S, Tang Y, Fu C, Ma Y, Zhou G. Efficient genetic transformation and CRISPR/Cas9-mediated genome editing in Lemna aequinoctialis. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2143-2152. [PMID: 30972865 PMCID: PMC6790374 DOI: 10.1111/pbi.13128] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/03/2019] [Accepted: 04/08/2019] [Indexed: 05/13/2023]
Abstract
The fast growth, ease of metabolic labelling and potential for feedstock and biofuels production make duckweeds not only an attractive model system for understanding plant biology, but also a potential future crop. However, current duckweed research is constrained by the lack of efficient genetic manipulation tools. Here, we report a case study on genome editing in a duckweed species, Lemna aequinoctialis, using a fast and efficient transformation and CRISPR/Cas9 tool. By optimizing currently available transformation protocols, we reduced the duration time of Agrobacterium-mediated transformation to 5-6 weeks with a success rate of over 94%. Based on the optimized transformation protocol, we generated 15 (14.3% success rate) biallelic LaPDS mutants that showed albino phenotype using a CRISPR/Cas9 system. Investigations on CRISPR/Cas9-mediated mutation spectrum among mutated L. aequinoctialis showed that most of mutations were short insertions and deletions. This study presents the first example of CRISPR/Cas9-mediated genome editing in duckweeds, which will open new research avenues in using duckweeds for both basic and applied research.
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Affiliation(s)
- Yu Liu
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Yu Wang
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Shuqing Xu
- Institute for Evolution and BiodiversityUniversity of MünsterMünsterGermany
| | - Xianfeng Tang
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Jinshan Zhao
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
| | - Changjiang Yu
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Guo He
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Hua Xu
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Shumin Wang
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Yali Tang
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Chunxiang Fu
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Yubin Ma
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Gongke Zhou
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
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21
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Barbosa Neto A, Morais M, Dutra E, Calsa Junior T. Biological diversity of Lemna aequinoctialis Welw. isolates influences biomass production and wastewater phytoremediation. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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22
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Ekperusi AO, Sikoki FD, Nwachukwu EO. Application of common duckweed (Lemna minor) in phytoremediation of chemicals in the environment: State and future perspective. CHEMOSPHERE 2019; 223:285-309. [PMID: 30784736 DOI: 10.1016/j.chemosphere.2019.02.025] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 05/18/2023]
Abstract
Over the past 50 years, different strategies have been developed for the remediation of polluted air, land and water. Driven by public opinion and regulatory bottlenecks, ecological based strategies are preferable than conventional methods in the treatments of chemical effluents. Ecological systems with the application of microbes, fungi, earthworms, plants, enzymes, electrode and nanoparticles have been applied to varying degrees in different media for the remediation of various categories of pollutants. Aquatic macrophytes have been used extensively for the remediation of pollutants in wastewater effluents and aquatic environment over the past 30 years with the common duckweed (L. minor) as one of the most effective macrophytes that have been applied for remediation studies. Duckweed has shown strong potentials for the phytoremediation of organic pollutants, heavy metals, agrochemicals, pharmaceuticals and personal care products, radioactive waste, nanomaterials, petroleum hydrocarbons, dyes, toxins, and related pollutants. This review covers the state of duckweed application for the remediation of diverse aquatic pollutants and identifies gaps that are necessary for further studies as we find pragmatic and sound ecological solutions for the remediation of polluted environment for sustainable development.
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Affiliation(s)
- Abraham O Ekperusi
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemicals Research, Institute of Petroleum Studies, University of Port Harcourt, Choba, Rivers State, Nigeria; Department of Marine Environment & Pollution Control, Faculty of Marine Environmental Management, Nigeria Maritime University, Okerenkoko, Delta State, Nigeria.
| | - Francis D Sikoki
- Department of Animal & Environmental Biology, Faculty of Science, University of Port Harcourt, Choba, Rivers State, Nigeria
| | - Eunice O Nwachukwu
- Department of Plant Science & Biotechnology, Faculty of Science, University of Port Harcourt, Choba, Rivers State, Nigeria
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23
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Kreider AN, Fernandez Pulido CR, Bruns MA, Brennan RA. Duckweed as an Agricultural Amendment: Nitrogen Mineralization, Leaching, and Sorghum Uptake. JOURNAL OF ENVIRONMENTAL QUALITY 2019; 48:469-475. [PMID: 30951113 DOI: 10.2134/jeq2018.05.0207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Excessive N and P in surface waters can promote eutrophication (algae-dominated, low-O waters), which decreases water quality and aquatic life. Duckweed (Lemnaceae), a floating aquatic plant, rapidly absorbs N and P from water and its composition shows strong potential as a soil amendment. Therefore, it may be used to transfer N and P from eutrophic water bodies to agricultural fields. In this work, dried duckweed was incorporated into agricultural soil in microcosm, column, and field tests to evaluate biological N cycling, nutrient retention, and crop yield compared with compost, diammonium phosphate (DAP), and an amendment-free control. In microcosm tests, 25 ± 13% of duckweed N was mineralized, providing on average less mineral N than DAP (107 ± 21%), but more than compost (11 ± 12%). In columns, duckweed treatments leached only 2% of the N added, significantly less than DAP, which leached 60% of its N. Compared with the control, DAP leached significantly more phosphate (78%), whereas duckweed and compost treatments leached less (56 and 27%, respectively). Crop yield, as well as runoff N and P, were measured in field tests growing forage sorghum [ (L.) Moench.]. Although less total N was applied to duckweed plots than to DAP plots (75 vs. 130 kg ha, respectively), duckweed was found to retain 30% more total mineral N in a tilled agricultural field than DAP, while supporting a comparable yield. These tests indicate that duckweed may provide a sustainable source of N and P for agriculture.
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24
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Yang GL, Fang Y, Xu YL, Tan L, Li Q, Liu Y, Lai F, Jin YL, Du AP, He KZ, Ma XR, Zhao H. Frond transformation system mediated by Agrobacterium tumefaciens for Lemna minor. PLANT MOLECULAR BIOLOGY 2018; 98:319-331. [PMID: 30298427 DOI: 10.1007/s11103-018-0778-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
The Lemnaceae, known as duckweed, the smallest flowering aquatic plant, shows promise as a plant bioreactor. For applying this potential plant bioreactor, establishing a stable and efficient genetic transformation system is necessary. The currently favored callus-based method for duckweed transformation is time consuming and genotype limited, as it requires callus culture and regeneration, which is inapplicable to many elite duckweed strains suitable for bioreactor exploitation. In this study, we attempted to establish a simple frond transformation system mediated by Agrobacterium tumefaciens for Lemna minor, one of the most widespread duckweed species in the world. To evaluate the feasibility of the new transformation system, the gene CYP710A11 was overexpressed to improve the yield of stigmasterol, which has multiple medicinal purposes. Three L. minor strains, ZH0055, D0158 and M0165, were transformed by both a conventional callus transformation system (CTS) and the simple frond transformation system (FTS). GUS staining, PCR, quantitative PCR and stigmasterol content detection showed that FTS can produce stable transgenic lines as well as CTS. Moreover, compared to CTS, FTS can avoid the genotype constraints of callus induction, thus saving at least half of the required processing time (CTS took 8-9 months while FTS took approximately 3 months in this study). Therefore, this transformation system is feasible in producing stable transgenic lines for a wide range of L. minor genotypes.
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Affiliation(s)
- Gui-Li Yang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
| | - Ya-Liang Xu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Tan
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
| | - Qi Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Lai
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan-Ling Jin
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
| | - An-Ping Du
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
| | - Kai-Ze He
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China
| | - Xin-Rong Ma
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Hai Zhao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
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25
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Hoang PNT, Michael TP, Gilbert S, Chu P, Motley ST, Appenroth KJ, Schubert I, Lam E. Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:670-684. [PMID: 30054939 DOI: 10.1111/tpj.14049] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/29/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Duckweeds are the fastest growing angiosperms and have the potential to become a new generation of sustainable crops. Although a seed plant, Spirodela polyrhiza clones rarely flower and multiply mainly through vegetative propagation. Whole-genome sequencing using different approaches and clones yielded two reference maps. One for clone 9509, supported in its assembly by optical mapping of single DNA molecules, and one for clone 7498, supported by cytogenetic assignment of 96 fingerprinted bacterial artificial chromosomes (BACs) to its 20 chromosomes. However, these maps differ in the composition of several individual chromosome models. We validated both maps further to resolve these differences and addressed whether they could be due to chromosome rearrangements in different clones. For this purpose, we applied sequential multicolor fluorescence in situ hybridization (mcFISH) to seven S. polyrhiza clones, using 106 BACs that were mapped onto the 39 pseudomolecules for clone 7498. Furthermore we integrated high-depth Oxford Nanopore (ON) sequence data for clone 9509 to validate and revise the previously assembled chromosome models. We found no major structural rearrangements between these seven clones, identified seven chimeric pseudomolecules and Illumina assembly errors in the previous maps, respectively. A new S. polyrhiza genome map with high contiguity was produced with the ON sequence data and genome-wide synteny analysis supported the occurrence of two Whole Genome Duplication events during its evolution. This work generated a high confidence genome map for S. polyrhiza at the chromosome scale, and illustrates the complementarity of independent approaches to produce whole-genome assemblies in the absence of a genetic map.
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Affiliation(s)
- Phuong N T Hoang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, D-06466, Germany
- Dalat University, Lamdong Province, Vietnam
| | | | - Sarah Gilbert
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Philomena Chu
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | | | - Klaus J Appenroth
- Department of Plant Physiology, Matthias-Schleiden-Institute, Friedrich-Schiller- University of Jena, Jena, D-07743, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, D-06466, Germany
| | - Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
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26
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Chu P, Wilson GM, Michael TP, Vaiciunas J, Honig J, Lam E. Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes. PLANT MOLECULAR BIOLOGY 2018; 98:219-231. [PMID: 30191440 DOI: 10.1007/s11103-018-0774-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/23/2018] [Indexed: 05/13/2023]
Abstract
Leveraging the heightened levels of polymorphism in NB-ARC-related protein encoding genes in higher plants, a bioinformatic pipeline was created to identify regions in this gene family from sequenced plant genomes that exhibit fragment length or single nucleotide differences in different accessions of the same species. Testing this approach with the aquatic plant Spirodela polyrhiza demonstrated its superior performance in comparison with currently available genotyping technologies based on PCR amplification. Rapid and economical genotyping tools that can reliably distinguish species and intraspecific variations in plants can be powerful tools for biogeographical and ecological studies. Clones of the cosmopolitan duckweed species, Spirodela polyrhiza, are difficult to distinguish morphologically due to their highly abbreviated architecture and inherently low levels of sequence variation. The use of plastidic markers and generic Amplification Fragment Length Polymorphism approaches have met with limited success in resolving clones of S. polyrhiza from diverse geographical locales. Using whole genome sequencing data from nine S. polyrhiza clones as a training set, we created an informatic pipeline to identify and rank polymorphic regions from nuclear-encoded NB-ARC-related genes to design markers for PCR, Sanger sequencing (barcoding), and fragment length analysis. With seven primer sets, we found 21 unique fingerprints from a set of 23 S. polyrhiza clones. However, three of these clones share the same fingerprint and are indistinguishable by these markers. These primer sets can also be used as interspecific barcoding tools to rapidly resolve S. polyrhiza from the closely related S. intermedia species without the need for DNA sequencing. Our work demonstrates a general approach of using hyper-polymorphic loci within genomes as a resource to produce facile tools that can have high resolving power for genotyping applications.
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Affiliation(s)
- Philomena Chu
- Department of Plant Biology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ, 08901-8520, USA
| | - Glen M Wilson
- Department of Mathematics, University of Oslo, Postboks 1053, 0316 OSLO, Blindern, Norway
| | | | - Jennifer Vaiciunas
- Department of Plant Biology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ, 08901-8520, USA
| | - Joshua Honig
- Department of Plant Biology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ, 08901-8520, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers University, 59 Dudley Rd., New Brunswick, NJ, 08901-8520, USA.
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27
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Borisjuk N, Peterson AA, Lv J, Qu G, Luo Q, Shi L, Chen G, Kishchenko O, Zhou Y, Shi J. Structural and Biochemical Properties of Duckweed Surface Cuticle. Front Chem 2018; 6:317. [PMID: 30094233 PMCID: PMC6070633 DOI: 10.3389/fchem.2018.00317] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 07/09/2018] [Indexed: 01/10/2023] Open
Abstract
The plant cuticle, which consists of cutin and waxes, forms a hydrophobic coating covering the aerial surfaces of all plants. It acts as an interface between plants and their surrounding environment whilst also protecting them against biotic and abiotic stresses. In this research, we have investigated the biodiversity and cuticle properties of aquatic plant duckweed, using samples isolated from four different locations around Hongze lake in Jiangsu province, China. The samples were genotyped using two chloroplast markers and nuclear ribosomal DNA markers, which revealed them as ecotypes of the larger duckweed, Spirodela polyrhiza. Duckweed cuticle properties were investigated by compositional analysis using Gas Chromatography coupled with Mass Spectroscopy (GC-MS) Flame Ionization Detector (GC-FID), and ultrastructural observation by cryo-Scanning Electron Microscopy (cryo-SEM). Cuticle compositional analysis indicated that fatty acids and primary alcohols, the two typical constituents found in many land plant cuticle, are the major duckweed wax components. A large portion of the duckweed wax fraction is composed of phytosterols, represented by campesterol, stigmasterol, sitosterol and their common precursor squalene. The cryo-SEM observation uncovered significant differences between the surface structures of the top air-facing and bottom water-facing sides of the plant fronds. The top side of the fronds, containing multiple stomata complexes, appeared to be represented by a rather flat waxy film sporadically covered with wax crystals. Underneath the waxy film was detected a barely distinguished nanoridge net, which became distinctly noticeable after chloroform treatment. On the bottom side of the fronds, the large epidermal cells were covered by the well-structured net, whose sections became narrower and sharper under cryo-SEM following chloroform treatment. These structural differences between the abaxial and adaxial sides of the fronds evidently relate to their distinct physiological roles in interacting with the contrasting environments of sunlight/air and nutrients/water. The unique structural and biochemical features of Spirodela frond surfaces with their rapid reproductive cycle and readily availability genome sequence, make duckweed an attractive monocot model for studying the fundamental processes related to plant protection against ultraviolet irradiation, pathogens and other environmental stresses.
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Affiliation(s)
- Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Science, Huaiyin Normal University, Huaian, China
| | - Anton A. Peterson
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Science, Huaiyin Normal University, Huaian, China
| | - Jiyang Lv
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guorun Qu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Luo
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Science, Huaiyin Normal University, Huaian, China
| | - Olena Kishchenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Science, Huaiyin Normal University, Huaian, China
| | - Yuzhen Zhou
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Science, Huaiyin Normal University, Huaian, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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28
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Miranda AF, Liu Z, Rochfort S, Mouradov A. Lipid production in aquatic plant Azolla at vegetative and reproductive stages and in response to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 124:117-125. [PMID: 29366971 DOI: 10.1016/j.plaphy.2018.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/13/2018] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
The aquatic plant Azolla became increasingly popular as bioenergy feedstock because of its high growth rate, production of biomass with high levels of biofuel-producing molecules and ability to grow on marginal lands. In this study, we analysed the contribution of all organs of Azolla to the total yield of lipids at vegetative and reproductive stages and in response to stress. Triacylglycerol-containing lipid droplets were detected in all (vegetative and reproductive) organs with the highest level in the male microsporocarps and microspores. As a result, significantly higher total yields of lipids were detected in Azolla filiculoides and Azolla pinnata at the reproductive stage. Starving changed the yield and composition of the fatty acid as a result of re-direction of carbon flow from fatty acid to anthocyanin pathways. The composition of lipids, in regard the length and degree of unsaturation of fatty acids, in Azolla meets most of the important requirements for biodiesel standards. The ability of Azolla to grow on wastewaters, along with their high productivity rate, makes it an attractive feedstock for the production of biofuels.
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Affiliation(s)
- Ana F Miranda
- School of Sciences, RMIT University, Melbourne, VIC, Australia.
| | - Zhiqian Liu
- AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, VIC 3083, Australia.
| | - Simone Rochfort
- AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, VIC 3083, Australia.
| | - Aidyn Mouradov
- School of Sciences, RMIT University, Melbourne, VIC, Australia.
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29
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Tao X, Fang Y, Huang MJ, Xiao Y, Liu Y, Ma XR, Zhao H. High flavonoid accompanied with high starch accumulation triggered by nutrient starvation in bioenergy crop duckweed (Landoltia punctata). BMC Genomics 2017; 18:166. [PMID: 28201992 PMCID: PMC5310006 DOI: 10.1186/s12864-017-3559-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 02/07/2017] [Indexed: 12/04/2022] Open
Abstract
Background As the fastest growing plant, duckweed can thrive on anthropogenic wastewater. The purple-backed duckweed, Landoltia punctata, is rich in starch and flavonoids. However, the molecular biological basis of high flavonoid and low lignin content remains largely unknown, as does the best method to combine nutrients removed from sewage and the utilization value improvement of duckweed biomass. Results A combined omics study was performed to investigate the biosynthesis of flavonoid and the metabolic flux changes in L. punctata grown in different culture medium. Phenylalanine metabolism related transcripts were identified and carefully analyzed. Expression quantification results showed that most of the flavonoid biosynthetic transcripts were relatively highly expressed, while most lignin-related transcripts were poorly expressed or failed to be detected by iTRAQ based proteomic analyses. This explains why duckweed has a much lower lignin percentage and higher flavonoid content than most other plants. Growing in distilled water, expression of most flavonoid-related transcripts were increased, while most were decreased in uniconazole treated L. punctata (1/6 × Hoagland + 800 mg•L-1 uniconazole). When L. punctata was cultivated in full nutrient medium (1/6 × Hoagland), more than half of these transcripts were increased, however others were suppressed. Metabolome results showed that a total of 20 flavonoid compounds were separated by HPLC in L. punctata grown in uniconazole and full nutrient medium. The quantities of all 20 compounds were decreased by uniconazole, while 11 were increased and 6 decreased when grown in full nutrient medium. Nutrient starvation resulted in an obvious purple accumulation on the underside of each frond. Conclusions The high flavonoid and low lignin content of L. punctata appears to be predominantly caused by the flavonoid-directed metabolic flux. Nutrient starvation is the best option to obtain high starch and flavonoid accumulation simultaneously in a short time for biofuels fermentation and natural products isolation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3559-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yang Fang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Meng-Jun Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China.,College of Life Science & Forestry, Chongqing University of Art & Science, Yongchuan, Chongqing, 402160, China
| | - Yao Xiao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yang Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Hai Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China.
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30
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Michael TP, Bryant D, Gutierrez R, Borisjuk N, Chu P, Zhang H, Xia J, Zhou J, Peng H, El Baidouri M, Ten Hallers B, Hastie AR, Liang T, Acosta K, Gilbert S, McEntee C, Jackson SA, Mockler TC, Zhang W, Lam E. Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:617-635. [PMID: 27754575 DOI: 10.1111/tpj.13400] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 05/15/2023]
Abstract
Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family.
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Affiliation(s)
- Todd P Michael
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
- IBIS Bioscience, Carlsbad, CA, USA
| | - Douglas Bryant
- IBIS Bioscience, Carlsbad, CA, USA
- Donald Danforth Center for Plant Science, St. Louis, MO, USA
| | - Ryan Gutierrez
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Nikolai Borisjuk
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Philomena Chu
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Hanzhong Zhang
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, China
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, China
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, China
| | - Moaine El Baidouri
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | | | | | - Kenneth Acosta
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | - Sarah Gilbert
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
| | | | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Todd C Mockler
- Donald Danforth Center for Plant Science, St. Louis, MO, USA
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, China
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA
| | - Eric Lam
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA
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Cao HX, Vu GTH, Wang W, Appenroth KJ, Messing J, Schubert I. The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution. THE NEW PHYTOLOGIST 2016; 209:354-363. [PMID: 26305472 DOI: 10.1111/nph.13592] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/03/2015] [Indexed: 06/04/2023]
Abstract
Duckweeds are aquatic monocotyledonous plants of potential economic interest with fast vegetative propagation, comprising 37 species with variable genome sizes (0.158-1.88 Gbp). The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. We selected physically mapped bacterial artificial chromosomes (BACs) containing Spirodela DNA inserts with little or no repetitive elements as probes for multicolor fluorescence in situ hybridization (mcFISH), using an optimized BAC pooling strategy, to validate its physical map and correlate it with its chromosome complement. By consecutive mcFISH analyses, we assigned the originally assembled 32 pseudomolecules (supercontigs) of the genomic sequences to the 20 chromosomes of S. polyrhiza. A Spirodela cytogenetic map containing 96 BAC markers with an average distance of 0.89 Mbp was constructed. Using a cocktail of 41 BACs in three colors, all chromosome pairs could be individualized simultaneously. Seven ancestral blocks emerged from duplicated chromosome segments of 19 Spirodela chromosomes. The chromosomally integrated genome of S. polyrhiza and the established prerequisites for comparative chromosome painting enable future studies on the chromosome homoeology and karyotype evolution of duckweed species.
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Affiliation(s)
- Hieu Xuan Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Giang Thi Ha Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Wenqin Wang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | | | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
- Faculty of Science and Central European Institute of Technology, Masaryk University, CZ-61137, Brno, Czech Republic
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Appenroth KJ, Sree KS, Fakhoorian T, Lam E. Resurgence of duckweed research and applications: report from the 3rd International Duckweed Conference. PLANT MOLECULAR BIOLOGY 2015; 89:647-654. [PMID: 26506824 DOI: 10.1007/s11103-015-0396-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
Duckweed, flowering plants in the Lemnaceae family, comprises the smallest angiosperms in the plant kingdom. They have some of the fastest biomass accumulation rates reported to date for plants and have the demonstrated ability to thrive on wastewater rich in dissolved organic compounds and thus could help to remediated polluted water resources and prevents eutrophication. With a high quality genome sequence now available and increased commercial interest worldwide to develop duckweed biomass for renewables such as protein and fuel, the 3rd International Duckweed Conference convened at Kyoto, Japan, in July of 2015, to update the community of duckweed researchers and developers on the progress in the field. In addition to sharing results and ideas, the conference also provided ample opportunities for new-comers as well as established workers in the field to network and create new aliances. We hope this meeting summary will also help to disseminate the key advances and observations that have been presented in this conference to the broader plant biology community in order to encourage increased cross-fertilization of ideas and technologies.
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Affiliation(s)
- Klaus-J Appenroth
- Institute of General Botany and Plant Physiology, University of Jena, 07743 Jena, Germany
| | - K Sowjanya Sree
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | | | - Eric Lam
- Department of Plant Biology and Pathology, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA.
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Van Hoeck A, Horemans N, Monsieurs P, Cao HX, Vandenhove H, Blust R. The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:188. [PMID: 26609323 PMCID: PMC4659200 DOI: 10.1186/s13068-015-0381-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/10/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production. Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools and industrial applications. Given the ecotoxic relevance and high potential for biomass production, whole-genome information of this cosmopolitan duckweed is needed. RESULTS The 472 Mbp assembly of the L. minor genome (2n = 40; estimated 481 Mbp; 98.1 %) contains 22,382 protein-coding genes and 61.5 % repetitive sequences. The repeat content explains 94.5 % of the genome size difference in comparison with the greater duckweed, Spirodela polyrhiza (2n = 40; 158 Mbp; 19,623 protein-coding genes; and 15.79 % repetitive sequences). Comparison of proteins from other monocot plants, protein ortholog identification, OrthoMCL, suggests 1356 duckweed-specific groups (3367 proteins, 15.0 % total L. minor proteins) and 795 Lemna-specific groups (2897 proteins, 12.9 % total L. minor proteins). Interestingly, proteins involved in biosynthetic processes in response to various stimuli and hydrolase activities are enriched in the Lemna proteome in comparison with the Spirodela proteome. CONCLUSIONS The genome sequence and annotation of L. minor protein-coding genes provide new insights in biological understanding and biomass production applications of Lemna species.
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Affiliation(s)
- Arne Van Hoeck
- />Biosphere Impact Studies, SCK•CEN, Boeretang 200, 2400 Mol, Belgium
- />Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Nele Horemans
- />Biosphere Impact Studies, SCK•CEN, Boeretang 200, 2400 Mol, Belgium
- />Centre for Environmental Research, University of Hasselt, Universiteitslaan 1, 3590 Diepenbeek, Belgium
| | | | - Hieu Xuan Cao
- />Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, Germany
| | | | - Ronny Blust
- />Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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Huang M, Fang Y, Liu Y, Jin Y, Sun J, Tao X, Ma X, He K, Zhao H. Using proteomic analysis to investigate uniconazole-induced phytohormone variation and starch accumulation in duckweed (Landoltia punctata). BMC Biotechnol 2015; 15:81. [PMID: 26369558 PMCID: PMC4570701 DOI: 10.1186/s12896-015-0198-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Duckweed (Landoltia punctata) has the potential to remediate wastewater and accumulate enormous amounts of starch for bioethanol production. Using systematical screening, we determined that the highest biomass and starch percentage of duckweed was obtained after uniconazole application. Uniconazole contributes to starch accumulation of duckweed, but the molecular mechanism is still unclear. RESULTS To elucidate the mechanisms of high starch accumulation, in the study, the responses of L. punctata to uniconazole were investigated using a quantitative proteomic approach combined with physiological and biochemical analysis. A total of 3327 proteins were identified. Among these identified proteins, a large number of enzymes involved in endogenous hormone synthetic and starch metabolic pathways were affected. Notably, most of the enzymes involved in abscisic acid (ABA) biosynthesis showed up-regulated expression, which was consistent with the content variation. The increased endogenous ABA may up-regulate expression of ADP-glucose pyrophosphorylase to promote starch biosynthesis. Importantly, the expression levels of several key enzymes in the starch biosynthetic pathway were up-regulated, which supported the enzymatic assay results and may explain why there is increased starch accumulation. CONCLUSIONS These generated data linked uniconazole with changes in expression of enzymes involved in hormone biosynthesis and starch metabolic pathways and elucidated the effect of hormones on starch accumulation. Thus, this study not only provided insights into the molecular mechanisms of uniconazole-induced hormone variation and starch accumulation but also highlighted the potential for duckweed to be feedstock for biofuel as well as for sewage treatment.
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Affiliation(s)
- Mengjun Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Yang Fang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Yang Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Yanling Jin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Jiaolong Sun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Xinrong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Kaize He
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Hai Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041, China.
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Sree KS, Adelmann K, Garcia C, Lam E, Appenroth KJ. Natural variance in salt tolerance and induction of starch accumulation in duckweeds. PLANTA 2015; 241:1395-404. [PMID: 25693515 DOI: 10.1007/s00425-015-2264-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/06/2015] [Indexed: 05/10/2023]
Abstract
Ten of 34 tested duckweed clones showed relatively higher salt tolerance. Salinity stress induced high level of starch accumulation in these clones, making them potential feedstock candidates for biofuel production. Duckweeds are promising as a new generation of crop plants that requires minimal input while providing fast biomass production. Two important traits of interest that can impact on the economic viability of this system are their sensitivity to salt and the starch content of the harvested duckweed. We have surveyed 33 strains of duckweed selected from across all 5 genera and amongst 13 species to quantify the natural variance of these traits. We found that there are large ranges of intraspecific variations in salt tolerance, while all species examined accumulated more starch in response to the initial stages of salt stress. However, the magnitude of the change in starch content varied widely between strains. Our results suggest that specific duckweed clones can be cultivated under relatively saline conditions, while increasing salt in the medium before harvesting could be used to increase starch in duckweed biomass for bioethanol production.
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Affiliation(s)
- K Sowjanya Sree
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201303, India
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Liu Y, Fang Y, Huang M, Jin Y, Sun J, Tao X, Zhang G, He K, Zhao Y, Zhao H. Uniconazole-induced starch accumulation in the bioenergy crop duckweed (Landoltia punctata) I: transcriptome analysis of the effects of uniconazole on chlorophyll and endogenous hormone biosynthesis. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:57. [PMID: 25866562 PMCID: PMC4392464 DOI: 10.1186/s13068-015-0246-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/24/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND Duckweed is a novel aquatic bioenergy crop that is found ubiquitously throughout the world. Uniconazole plays an important role in improving crop production through the regulation of endogenous hormone levels. We found that a high quantity and quality of duckweed growth can be achieved by uniconazole application, although the mechanisms are unknown. RESULTS The fronds of Landoltia punctata were sprayed evenly with 800 mg/L uniconazole. The dry weight following treatment increased by 10% compared to the controls at 240 h. Endogenous cytokinin (CK) and abscisic acid (ABA) content both increased compared to the control, while the level of gibberellins (GAs) decreased. Additionally, gene expression profiling results showed that the expression of transcripts encoding key enzymes involved in endogenous CK and ABA biosynthesis were up-regulated, while the transcripts of key enzymes for GAs biosynthesis were down-regulated. On the other hand, chlorophyll a and chlorophyll b contents were both increased compared with the control. Moreover, the net photosynthetic rate was elevated to 25.6 μmol CO2/m(2)/s compared with the control value of 22.05 μmol CO2/m(2)/s. Importantly, the expression of some chlorophyll biosynthesis-related transcripts was up-regulated. CONCLUSION Uniconazole treatment altered endogenous hormone levels and enhanced chlorophyll content and net photosynthetic rate in duckweed by regulating key enzymes involved in endogenous hormone and chlorophyll biosynthesis. The alterations of endogenous hormones and the increase of chlorophyll and photosynthetic rate data support the increase of biomass and starch accumulation.
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Affiliation(s)
- Yang Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041 China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041 China
| | - Yang Fang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041 China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041 China
| | - Mengjun Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041 China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041 China
| | - Yanling Jin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041 China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041 China
| | - Jiaolong Sun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041 China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041 China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041 China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041 China
| | - Guohua Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041 China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041 China
| | - Kaize He
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041 China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041 China
| | - Yun Zhao
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064 China
| | - Hai Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Chengdu, 610041 China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, 610041 China
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Appenroth KJ, Crawford DJ, Les DH. After the genome sequencing of duckweed - how to proceed with research on the fastest growing angiosperm? PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17 Suppl 1:1-4. [PMID: 25571946 DOI: 10.1111/plb.12248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- K-J Appenroth
- Institute of Plant Physiology, Friedrich Schiller University, Dornburger Str. 159, 07743, Jena, Germany.
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Cao HX, Vu GTH, Wang W, Messing J, Schubert I. Chromatin organisation in duckweed interphase nuclei in relation to the nuclear DNA content. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17 Suppl 1:120-4. [PMID: 24853858 DOI: 10.1111/plb.12194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 03/13/2014] [Indexed: 05/23/2023]
Abstract
The accessibility of DNA during fundamental processes, such as transcription, replication and DNA repair, is tightly modulated through a dynamic chromatin structure. Differences in large-scale chromatin structure at the microscopic level can be observed as euchromatic and heterochromatic domains in interphase nuclei. Here, key epigenetic marks, including histone H3 methylation and 5-methylcytosine (5-mC) as a DNA modification, were studied cytologically to describe the chromatin organisation of representative species of the five duckweed genera in the context of their nuclear DNA content, which ranged from 158 to 1881 Mbp. All studied duckweeds, including Spirodela polyrhiza with a genome size and repeat proportion similar to that of Arabidopsis thaliana, showed dispersed distribution of heterochromatin signatures (5mC, H3K9me2 and H3K27me1). This immunolabelling pattern resembles that of early developmental stages of Arabidopsis nuclei, with less pronounced heterochromatin chromocenters and heterochromatic marks weakly dispersed throughout the nucleus.
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Affiliation(s)
- H X Cao
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Germany
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