A Jakobid Flagellate Isolated from Desert Soil with A
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Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from rsob.royalsocietypublishing.org desert soil with a bacteria-like, but bloated mitochondrial genome Ju¨rgen F. H. Strassert1, Denis V. Tikhonenkov1,2, Jean-Franc¸ois Pombert3, Research Martin Kolisko1, Vera Tai1, Alexander P. Mylnikov2 and Patrick J. Keeling1 Cite this article: Strassert JFH, Tikhonenkov 1Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada DV, Pombert J-F, Kolisko M, Tai V, Mylnikov AP, 2Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia 3 Keeling PJ. 2016 Moramonas marocensis gen. Department of Biology, Illinois Institute of Technology, Chicago, IL, USA nov., sp. nov.: a jakobid flagellate isolated A new jakobid genus has been isolated from Moroccan desert soil. The cyst- from desert soil with a bacteria-like, but forming protist Moramonas marocensis gen. nov., sp. nov. has two anteriorly bloated mitochondrial genome. Open Biol. 6: inserted flagella of which one points to the posterior cell pole accompanying 150239. the ventral feeding groove and is equipped with a dorsal vane—a feature typi- http://dx.doi.org/10.1098/rsob.150239 cal for the Jakobida. It further shows a flagellar root system consisting of singlet microtubular root, left root (R1), right root (R2) and typical fibres associated with R1 and R2. The affiliation of M. marocensis to the Jakobida was confirmed by molecular phylogenetic analyses of the SSU rRNA gene, five nuclear genes Received: 10 November 2015 and 66 mitochondrial protein-coding genes. The mitochondrial genome has Accepted: 25 January 2016 the high number of genes typical for jakobids, and bacterial features, such as the four-subunit RNA polymerase and Shine–Dalgarno sequences upstream of the coding regions of several genes. The M. marocensis mitochondrial genome encodes a similar number of genes as other jakobids, but is unique in its very large genome size (greater than 264 kbp), which is three to four Subject Area: times higher than that of any other jakobid species investigated yet. This cellular biology/genomics/microbiology/ increase seems to be due to a massive expansion in non-coding DNA, creating molecular biology/structural biology/ a bloated genome like those of plant mitochondria. systems biology Keywords: Moramonas, Moramonadidae, Jakobida, 1. Introduction mitochondrion, bloated genome The protist group Jakobida (‘jakobids’, within the Excavata) consists of free-living, heterotrophic flagellates that can be found globally distributed in a broad variety of aerobic and anaerobic environments (seawater, freshwater, soil). The small cells Author for correspondence: with a length of less than 15 mm bear two anteriorly inserted flagella of which one Ju¨rgen F. H. Strassert is directed posteriorly (posterior flagellum) and associated with a ventral groove, e-mail: [email protected] where bacteria and other food particles get ingested [1–4]. Cysts have been docu- mented for some species (e.g. [4,5]). Unique features of the Jakobida comprise (i) a posterior flagellum with a dorsal vane, (ii) a dorsal fan of microtubules that arise close to the basal body of the anterior flagellum and (iii) a characteristic structure of the non-microtubular fibre, which is dorsally associated with the left microtub- ular root [4,6]. The monophyletic nature of this group remained unresolved by molecular phylogenetic studies using the SSU rRNA as marker gene alone, but evidence for a common ancestry came recently from analyses of multi-protein datasets (cf. [4,7–11]), suggesting Jakobida as a sister group to a cluster consisting of Euglenozoa, Heterolobosea and Tsukubamonadida (altogether named as ‘Discoba’ [9]). This cluster includes some of the best-known protist species, such as the freshwater flagellates Euglena spp. (e.g. [12]) or the vertebrate parasites Trypanosoma spp. (e.g. [13]), but to date not even a dozen species of jakobids have been discovered, much less formally described. & 2016 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. Despite the lack of known diversity, jakobids have attracted a For ultrastructure descriptions, a terminology according 2 great deal of attention due to their mitochondrial genomes, to Simpson & Patterson [3] and Yubuki et al. [22,23] is used. rsob.royalsocietypublishing.org which have been shown to share more characteristics in common with bacteriathan anyother known mitochondrial gen- 2.3. Genome sequencing, assembly and annotation omes. They encode the largest number of genes known (more than 90 assignable genes; more than 60 protein-coding genes), Cells of M. marocensis were harvested following peak abun- usually including rpoA–D, which encode a bacteria-like, four- dance in culture. Two sampling strategies were used. The subunit RNA polymerase that in other eukaryotes has been first (whole culture) consisted of 7 ml raw culture, while for replaced by a nucleus-encoded, single-subunit, viral enzyme the second (sorted cells) the same amount of culture was [14–18]. Other typical bacterial features include Shine–Dalgarno used, but the ratio between target cells and bacteria (prey translation initiation motifs upstream of the coding regions (not organisms) was improved by using a BD FACSAria Cell in Jakoba libera) as well as similarities in gene order shared with Sorter. The cells were separated from the medium with Open Biol. some a-proteobacterial operons [14–18]. These characteristics centrifugal filters (Vivaclear Mini 0.8 mm PES, Sartorius) have led to the idea that jakobids may represent one of the and subsequently resuspended in the lysis buffer. Genomic earliest-branching eukaryotic lineages [14]. DNA was extracted using the MasterPure Complete DNA 6 : 150239 In this study, we combined morphological and molecu- Purification Kit (Epicentre). lar phylogenetic data to describe a newly isolated flagellate, Genomic libraries were prepared with the Nextera Moramonas marocensis gen. nov., sp. nov., and determine its phy- DNA Sample Prep Kit (Illumina) and sequenced at McGill logenetic position within the Jakobida. To examine the diversity University and Ge´nome Que´bec Innovation Centre (MiSeq, of jakobid mitochondrial genomes, we also sequenced its mito- PE, 300 bases). All reads were trimmed with SICKLE v. 1.33 chondrial (mt) DNA, which shares bacterial features found in [24] using a quality and sequence length threshold of 25 and other jakobids, but is dramatically different in its overall form 150, respectively. After removing transposon sequences, fil- and size. tered reads of both approaches (whole culture and sorted cells, with each roughly 3 mio paired end reads and 0.85 mio single reads) were combined and tested for the best k-mer 2. Material and methods value using KMERGENIE v. 1.6950 [25]. The combined reads were assembled with RAY v. 2.1.1 [26] and a k-mer of 31 yield- 2.1. Sampling and culturing ing 283 893 contigs. Contigs belonging to M. marocensis were detected by BLASTN and TBLASTN searches using Jakobida A sample of desert soil was collected by A. A. Abramov (Insti- nucleic acid and protein sequences respectively as query (see tute of Physicochemical and Biological Problems in Soil below) and the contigs as reference BLAST database [27]. Science, Russia) in March 2007 near Zagora City, Morocco, a Correct assignments were assured by reciprocal BLAST small valley separated from the Sahara by a mountain ridge searches against the entire non-redundant NCBI database. 0 00 0 00 (coordinates: 30819 50.0 N, 5850 17.0 W). The sample (in a After mapping the reads back to the selected contigs using sterile plastic tube) was stored for several years in the dark at BOWTIE2 v. 2.2.4 [28], the assembly was further visually 21 21 108C. Pratt medium (0.1 g l KNO3, 0.01 g l MgSO4 Â 7 reviewed and checked for chimeric sequences and duplicated 21 21 H2O, 0.1 g l K2HPO4 Â 3H2O, 0.001 g l FeCl3 Â 6H2O; regions with UGENE v. 1.16.2 [29]. Furthermore, in order to pH ¼ 6.5–7.5 [19]) was added to the sample in April 2013 detect potential repeated regions, additional self similarity and a single cell of M. marocensis was isolated with a micropip- dot plots of the contigs with different word sizes were calcu- ette and transferred to a new Petri dish. The culture was lated (not shown). We did not attempt to extend/join the then propagated and maintained in Petri dishes filled with contigs by PCR. Pratt medium and Pseudomonas fluorescens bacteria as food. The SSU rRNA gene was found with BLASTN searches M. marocensis is stored at 108C in the collection of protozoan against publicly available jakobid SSU rRNA genes. To obtain cultures at the Institute for Biology of Inland Waters, Russia. the nucleus-encoded protein-coding genes for actin, a-tubulin, b-tubulin, elongation factor 2 (EF2) and heat shock protein 90 2.2. Microscopy (HSP90), the following steps were conducted for each gene: (i) BLASTP searches using Jakobida protein sequences as Light microscopy was done with a Zeiss Axio Scope A1. query (kindly provided by R. Kamikawa [8]) and translated For scanning electron microscopy (SEM), flagellates were M. marocensis contigs as BLAST database; (ii) aligning of poten- fixed for 10 min in 2% glutaraldehyde in 0.1 M cacodylate tial candidates against orthologues from Jakobida and other buffer (pH 7.2), washed using the same buffer, and carefully taxa with L-INS-i implemented in MAFFT v. 7.215 [30]; attached to a polycarbonate filter by filtration (diameter: (iii) alignment trimming with TRIMAl v. 1.4 [31]; and (iv) phylo- 24 mm; pore size: 1 mm). The attached cells were then genetic tree calculation with RAXML v. 7.4.2 [32] using -f a -m dehydrated in a graded series of ethanol and acetone.