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The Genome and Phenome of the Green Alga Chloroidium Sp. UTEX

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The Genome and Phenome of the Green Alga Chloroidium Sp. UTEX RESEARCH ARTICLE The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization David R Nelson1,2*, Basel Khraiwesh1,2, Weiqi Fu1, Saleh Alseekh3, Ashish Jaiswal1, Amphun Chaiboonchoe1, Khaled M Hazzouri2, Matthew J O’Connor4, Glenn L Butterfoss2, Nizar Drou2, Jillian D Rowe2, Jamil Harb3,5, Alisdair R Fernie3, Kristin C Gunsalus2,6, Kourosh Salehi-Ashtiani1,2* 1Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; 2Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; 3Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany; 4Core Technology Platform, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; 5Department of Biology and Biochemistry, Birzeit University, Birzeit, Palestine; 6Center for Genomics and Systems Biology and Department of Biology, New York University, New York, United States Abstract To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero to 60 g/L and to grow heterotrophically on >40 distinct carbon sources. Assembly and annotation of genomic reads yielded a 52.5 Mbp genome with 8153 functionally annotated genes. Comparison with other sequenced green algae revealed *For correspondence: drn2@nyu. unique protein families involved in osmotic stress tolerance and saccharide metabolism that edu (DRN); [email protected] (KS-A) support phenomic studies. Our results reveal the robust and flexible biology utilized by a green Competing interests: The alga to successfully inhabit a desert coastline. authors declare that no DOI: 10.7554/eLife.25783.001 competing interests exist. Funding: See page 19 Received: 05 February 2017 Introduction Accepted: 15 June 2017 Green algae play important ecological roles as primary biomass producers and are emerging as via- Published: 17 June 2017 ble sources of commercial compounds in the food, fuel, and pharmaceutical industries. However, rel- Reviewing editor: Joerg atively few species of green algae have been characterized in depth at the genomic and Bohlmann, University of British metabolomic levels (Koussa et al., 2014; Salehi-Ashtiani et al., 2015; Chaiboonchoe et al., 2016). Columbia, Canada Also, recent genomics studies lack accompanying phenotype studies that could provide valuable context (Bochner, 2009; Chaiboonchoe et al., 2014). Analyses of this scope are necessary to better Copyright Nelson et al. This understand the ecology and physiology of microscopic algae (microphytes), both at the local and article is distributed under the global scales, and to optimize their cultivation and yield of bioproducts for industrial terms of the Creative Commons Attribution License, which applications (Abdrabu et al., 2016). Currently, species with superior growth characteristics for large- permits unrestricted use and scale cultivation remain understudied, under-developed, and under-exploited (Fu et al., 2016). redistribution provided that the Our study focuses on the green alga – formerly identified as Chloroidium sp. DN1 and acces- original author and source are sioned at the Culture Collection of Algae at the University of Texas at Austin (UTEX) as Chloroidium credited. sp. UTEX 3007, which we recently isolated in a screen for lipid-producing algae (Sharma et al., Nelson et al. eLife 2017;6:e25783. DOI: 10.7554/eLife.25783 1 of 24 Research article Genomics and Evolutionary Biology Plant Biology eLife digest Single-celled green algae, also known as green microalgae, play an important role for the world’s ecosystems, in part, because they can harness energy from sunlight to produce carbon-rich compounds. Microalgae are also important for biotechnology and people have harnessed them to make food, fuel and medicines. Green microalgae live in many types of habitats from streams to oceans, and they can also be found on the land, including in deserts. Like plants that live in the desert, these microalgae have likely evolved specific traits that allow them to live in these hot and dry regions. Yet, fewer scientists have studied microalgae compared to land plants, and until now it was not well understood how microalgae could survive in the desert. Nelson et al. analyzed green microalgae from different locations around the United Arab Emirates and found that one microalga, known as Chloroidium, is one of the most dominant algae in this area. This included samples from beaches, mangroves, desert oases, buildings and public fresh water sources. Chloroidium has a unique set of genes and proteins and grew particularly well in freshwater and saltwater. Rather than just harnessing sunlight, the microalgae were able to consume over 40 different varieties of carbon sources to produce energy. The microalgae also accumulated oily molecules with a similar composition to palm oil, which may help this species to survive in desert regions. A next step will be to develop biotechnological assets based on the information obtained. In the future, microalgae could be used to make an oil that represents an alternative to palm oil; this would reduce the demand for palm tree plantations, which pose a major threat to the natural environment. Moreover, understanding how microalgae can colonize a desert region will help us to understand the effects of climate change in the region. DOI: 10.7554/eLife.25783.002 2015). Its oleogenic properties, robust growth, and capacity to survive in a wide range of environ- mental conditions prompted us to carry out whole-genome sequencing and phenomic analyses. Genomic (Dataset 1) and phenomic (Dataset 2) datasets are available online at Dryad (Nelson et al., 2017). We discovered that this species accumulates palmitic acid that, in conjunction with other traits, may enable its survival in a desert climate. The mechanisms employed by desert extremophiles such as Chloroidium sp. UTEX 3007 to maintain cellular integrity despite the oxidative insults of a desert climate may yield insight into the biology of a key player in a desert ecosystem and may also provide resources for the production of highly thermo-oxido-stable oils for human use. One of the most important thermo-oxido-stable oils for human civilization is produced by the oil palm tree, Elaeis guineensisis (Barcelos et al., 2015). Palm oil’s distinguishing characteristics stem from its uniquely high concentrations of palmitic acid, which, due to its carbon chain length and lack of reactive double bonds, remains stable in conditions that destroy other longer and more unsatu- rated fatty acids. However, cultivation of trees for palm oil production has led to extensive destruc- tion of high-biodiversity rainforests and wetlands that threatens to expand around the globe (Abrams et al., 2016). In addition to the loss of unique and diverse flora and fauna (Labrie`re et al., 2015; Wich et al., 2014), clear-cutting these regions for palm oil plantations has devastated major carbon sinks (Yue et al., 2015) and caused intensive production of smoke pollution that affects mil- lions of people in densely populated areas (Bhardwaj et al., 2016; Vadrevu et al., 2014). Thus, an alternative source of palmitic acid could be valuable in terms of elevated product output, environ- mental preservation and a reduction of smoke pollution. Results We re-isolated Chloroidium strains from diverse locations around the UAE including coastal beaches, mangroves, and inland desert oases (Figure 1a–b). The frequent re-isolation of the species from these different habitats suggests a broad habitat range in the local, predominantly desert, region. Due to its ubiquitous occurrence and lipid accumulation phenotype (Figure 1c), we selected Chloroi- dium sp. UTEX 3007 for study as a well-adapted species within the UAE and a potential candidate species of interest for production of oil replacement products (Sharma et al., 2015). Nelson et al. eLife 2017;6:e25783. DOI: 10.7554/eLife.25783 2 of 24 Research article Genomics and Evolutionary Biology Plant Biology Figure 1. Geography and morphology of isolated Chloroidium strains. Chloroidium strains were isolated from samples taken from the indicated locations in (a) the UAE, and (b) within Abu Dhabi city specifically. Chloroidium strains were found in estuaries, mangrove forests, adhered to buildings, in municipal waters, etc. (c) Chloroidium sp. UTEX 3007 stained for lipid bodies with BODIPY 505/515 and observed by fluorescence microscopy (left column) and phase-contrast microscopy (right column). (I) Chloroidium sp. UTEX 3007 aplanospore displaying palmello-like morphology contrasted with a smaller vegetative cell, (II) two average-sized Chloroidium sp. UTEX 3007 cells can be seen in the upper right of the panel while a miniature, recently hatched from an autospore, can be seen in the lower left, (III) Stained oil stores excreted from a Chloroidium sp. UTEX 3007 cell, and (IV) a hatched, non-segregating autospore. DOI: 10.7554/eLife.25783.003 Bioreactor growth Chloroidium sp. UTEX 3007 reproduces via unequal autospores (2–8 cells/division); cells vary greatly in size from 1 to 12 mm in diameter (mean = 6 mm; Figure 2a) and exhibit ovoid morphology, parietal chloroplasts, and accumulation of prominent intracellular lipid deposits (Figures 1 and 2). Stationary phase is reached after ~2 weeks of growth in F/2 media (Figure 2). Chloroidium sp. UTEX 3007 showed robust growth in open pond simulators (OPSs), which generate a sinusoidal approximation Nelson et al. eLife 2017;6:e25783. DOI: 10.7554/eLife.25783 3 of 24 Research article Genomics and Evolutionary Biology Plant Biology Figure 2. Cell size, growth, and lipid accumulation in Chloroidium sp. UTEX 3007.(a) Cell size distribution of Chloroidium sp. UTEX 3007 in late log phase (14 days).
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