Neobodo
Neobodo are diverse protists belonging to the eukaryotic supergroup Excavata. They are Kinetoplastids in the subclass Bodonidae. They are small, free-living, heterotrophic flagellates with two flagella of unequal length used to create a propulsive current for feeding.[3] As members of Kinetoplastids, they have an evident kinetoplast[4] There was much confusion and debate within the class Kinetoplastid and subclass Bodonidae regarding the classification of the organism, but finally the new genera Neobodo was proposed by Keith Vickerman.[5] Although they are one of the most common flagellates found in freshwater, they are also able to tolerate saltwater[6] Their ability to alternate between both marine and freshwater environments in many parts of the world give them a “cosmopolitan” character.[6] Due to their relatively microscopic size ranging between 4–12 microns, they are further distinguished as heterotrophic nanoflagellates.[3] This small size ratio limits them as bacterivores that swim around feeding on bacteria attached to surfaces or in aggregates.[3]
Etymology
The prefix ‘Neo-’ comes from the ancient Greek word for ‘neos’ which signifies 'young'. Attaching the prefix to the original bodonid species, neobodo literally means a “new” bodonid species.[5]
History of Knowledge
The order Neobodonida was proposed by a researcher, Keith Vickerman, based on significant characteristics that differed from the original bodonid species.[5] Differing characteristics included: being phagotrophic, Polykinetoplastic/eukinetoplastic, biflagellate with usually both flagella lacking hairs, having a posterior flagellum attached to the body or free of it, and having an apical cytostome.[5] Many Neobodo species derived from Bodo species, and by recognizing these differences, they were tentatively assigned to the new genus Neobodo by adding the ‘neo’ prefix.[5] Through studies on the ultrastructure of Bodo designis, researchers discovered the possession of a ‘microtubular prism’ supporting the cytostome–cytopharynx, as well as a significantly different feeding apparatus from other bodonids, thus proposing the new species as Neobodo designis.[5] Through this discovery, they were proposed as the type species of the new genus Neobodo.[5] Neobodo have very close connections with Kinetoplastid protists. Kinetoplastid protists belong together with euglenids and diplonemids, to the phylum Euglenozoa, and are grouped in the class Kinetoplastea.[5] The name of kinetoplastid is derived from the presence of a characteristic structure called the kinetoplast which is a mass of concentrated extranuclear DNA within a mitochondrion.[5] In the past, kinetoplastids were classified into two major suborder groups via morphology-based taxonomic criteria: either as parasitic uniflagellate trypanosomatids, or biflagellate bodonids.[5] Originally, Vickerman proposed two families, Bodonidae and Cryptobiidae, but later on re-unified all bodonids within the single family, Bodonidae.[5] Based on comparisons of RNA sequences and molecular phylogenetic analyses, it was suggested that the trypanosomatids also emerged from within the bodonids.[5] Moreover, recent research of deep-sea hydrothermal vent samples at the Mid-Atlantic Ridge and analysis via PCR amplification reported several new kinetoplastid-like sequences.[5] Researchers David Moreira, Purificacion Lopez-Garcıa, and Keith Vickerman analyzed the phylogeny of these kinetoplastids and found a much more stable phylogeny that supported the monophyly of groups that typically emerged as polyphyletic in the trees rooted using the traditional, distant outgroup sequences.[5] As a result, the classification of the class Kinetoplastea was divided as two new subclasses:
- Prokinetoplastina -containing various bodonid species, and
- Metakinetoplastina -including the Trypanosomatida and three additional new orders:
Through this process, Neobodo was created as a new genus, along with the revision of the classification of species formerly included in the genus Bodo and the amendment of the genus Parabodo.[5]
Description
The new genus Neobodo is characterized as solitary phagotrophic flagellates with a single discrete eukinetoplast. They are known for having an apical cytostome and cytopharynx supported by a prismatic rod of microtubules.[5]
Neobodo cells are usually elongate and elliptical in shape and somewhat inflexible.[4] They range from 4 to 12 microns long, but are mostly 6 to 9 microns.[4] They have a nucleus near the middle of the cell and two unequal, heterodynamic flagella emerging from a shallow, subapical pocket.[4] The anterior flagellum appears inactive and just wraps around the anterior part of the cell. It is about the same length or slightly shorter than the cell.[4] It is held forward with a single anterior curve that is held perpendicular to the substrate and curves back over the rostrum.[4] The acronematic posterior flagellum is trailed and sometimes forms an undulating membrane.[4] It is typically directed straight behind the cell and is about 2 to 4 times the length of the cell.[4] The proximal part of the posterior flagellum is accompanied with a paraxial rod and sometimes non-tubular mastigonemes.[5] The cells use their posterior flagellum and rotate around their longitudinal axes to swim and glide along in rapid darts of straight lines.[7]
Along with their two flagella, they have two nearly parallel basal bodies.[4] They also house discoid shaped mitochondrial cristae and a compact kinetoplast (a DNA-containing granule located within a single mitochondrion) that is associated with the flagellar bases.[4] The kinetoplasts are naked, but the cytoskeletal microtubules beneath the cell membrane are developed.[4] They have a cytoplasm usually filled with symbiotic bacteria and small glycosomes that possess glycolytic enzymes.[4] Although sexual reproduction is unknown and cysts have not been found to date, they are able to reproduce asexually by means of binary fission.[4]
Habitat and Ecology
Bodonid flagellates (class Kinetoplastea) are abundant, free-living bacterivores that occur in a wide variety of environments including freshwater, soil and marine habitats ranging from the tropics to the Arctic.[6] Neobodo is one of the most common flagellates in freshwater environments, but can also tolerate marine environments with low salinities of 3–4 ppt.[4] Strains of Neobodo species isolated from different environments fall exclusively into marine and freshwater lineages.[6] Studies show that Neobodo is a complex and ancient species with a major marine clade nested among older freshwater clades.[7] This suggests that these lineages were constrained physiologically from moving between these environments for most of their long history.[7] Their broad physiological tolerance enables them to easily interchange between marine and freshwater environments, which gives them a cosmopolitan characteristic and a wide ecological tolerance.[6] Recent evidence for Neobodo designis suggested notable divergence between freshwater and marine strains and all strains exhibited extensive genetic diversity.[7] Epifluorescent microscopy studies reported the abundance of several heterotrophic nanoflagellate groups (including bodonids) in the euphotic zone of different marine areas.[3] Areas include the Mediterranean Sea, Norwegian Sea, the Indian Ocean and around the Antarctic Peninsula.[3] Throughout the numerous oceans, large fractions of small heterotrophic flagellates with few morphological features remain unidentified.[3] Therefore there is a high possibility that there are many bodonids among the unidentified that have not yet been studied.[3]
Although Neobodo are surface organisms, typically found in surface waters, studies have shown their ability to tolerate deep water conditions.[6] Due to advection or attachment to sinking particles, microbes from the surface of the ocean are continuously transported to deeper areas.[6] The vast majority of the marine environment consists of dark, cold, high-pressure environments, which increases with depth.[6] When cultures of Neobodo were isolated from surface waters and were put in different deep-sea temperatures and pressures, the abundance of protists declined in all treatments, with a significantly greater rate of mortality under combined cold temperature and high pressure conditions than in the cold temperature-only conditions.[6] However, an average of 6.1% of N. designis cells survived in the high pressure treatments, indicating that some fraction of sinking protists can survive transport to the deep ocean.[6] In addition, after a period of acclimation, positive growth rates were measured in some cases.[6] This suggests that surface-adapted flagellates can not only survive under deep-sea conditions but are able to reproduce and potentially provide seed populations in cold, high-pressure environments.[6] Although Neobodo are not abundant in the deep oceans, they are capable of surviving in the deep waters, tolerating high pressure and low temperature conditions.[6]
Feeding
Neobodo are free-living and active microbial predators that swim around and feed on prey in aquatic ecosystems.[7] As free-living flagellates, they are the most important bacterivorous forms in aquatic environments.[4] Neobodo, like other bodonids, are heterotrophic flagellates (HF) which are a very diverse and heterogeneous group of protists with a size range between 1 and 450 microns.[3] They play an essential role in aquatic and terrestrial food webs as major consumers of bacterial biomass.[3] The predator to prey size ratio limits the maximal size difference between bacteria and their predator: Neobodo.[3] The marine environment presents additional constraints, imposed by the typical small size and low abundance of bacteria.[3] In these conditions, physical and hydrodynamic considerations theoretically restrict Neobodo’s feeding to graze on small bacteria, typically within the nanoplankton.[3] Most bacterivorous protists in the marine pelagic zone are generally in the size range of 2–5 microns and are classified as a functional group called heterotrophic nanoflagellates.[3] The predominance of heterotrophic nanoflagellates as marine bacterivores has been confirmed by manipulations with size-fractionated natural assemblages and by direct observation of protists with ingested fluorescent bacteria.[3] More specifically, Neobodo are interception feeders, meaning they feed on bacteria attached to surfaces/biofilms or in aggregates. They press their mouth against food and are often aided by a pseudopod-like structure (pharynx) to detach bacteria.[3] Within this feeding mechanism, further variability in terms of feeding behavior and selection strategies can be observed among different species.[3]
Practical importance
Despite the ecological and evolutionary significance of these organisms, many of their biological and pathological features are currently unknown. Through metatranscriptomics using RNA-seq technology combined with field-emission microscopy the virulence factors of a recently described genus of Neobodonida that is considered to be responsible for Ascidian Soft Tunic Syndrome (AsSTS) was revealed.[8] AsSTS is a disease of the edible ascidian, Halocynthia roretzi, which has done enormous damage to the Korean and Japanese aquaculture.[8] AsSTS is characterized by changes in the tunic (the outermost barrier against the environment), including elasticity loss and subsequent rupture leading to thinner bundled tunic fibers and coarser tunic matrices.[8] However, the pathogenesis is unclear and is still an area of research.[8]
List of species (or of lower taxonomic units)
Despite the considerable interest in free-living bodonids, their true biodiversity has most likely been grossly underestimated by simple light microscopy, as it does not differentiate most ‘species’ very well.[7] rRNA gene primers were used to test Neobodo’s global distribution and genetic diversity.[7] The non-overlap between environmental DNA sequences and those from cultures suggests that there are hundreds, possibly thousands, of different rRNA gene sequences of free-living Neobodo species globally.[7] Some of the species identified to date are:
- Neobodo designis
- Neobodo cf. designis
- Neobodo curvifilus
- Neobodo saliens
- Neobodo sp. KL
- Neobodo borokensis
References
- ^ a b c d e f g h i j k l m n o p "Neobodo". biolib.cz. Retrieved 25 April 2018.
- ^ a b c d e f "Neobodo". NCBI taxonomy. Bethesda, MD: National Center for Biotechnology Information. Retrieved 19 April 2018.
- ^ a b c d e f g h i j k l m n o p Kirchman, D. 2008: Microbial ecology of the oceans / [edited by] David L. Kirchman. (2nd ed.).
- ^ a b c d e f g h i j k l m n o Tikhonenkov, D. V., Janouškovec, J., Keeling, P. J., and Mylnikov, A. P. 2016: The Morphology, Ultrastructure and SSU rRNA Gene Sequence of a New Freshwater Flagellate, Neobodo borokensis n. sp. (Kinetoplastea, Excavata). The Journal Of Eukaryotic Microbiology, 63 :220–232. DOI:10.1111/jeu.12271
- ^ a b c d e f g h i j k l m n o p q Moreira, David, et al. 2004: An Updated View of Kinetoplastid Phylogeny Using Environmental Sequences and a Closer Outgroup: Proposal for a New Classification of the Class Kinetoplastea. International Journal of Systematic and Evolutionary Microbiology, 54: 1861–75. DOI:10.1099/ijs.0.63081-0
- ^ a b c d e f g h i j k l m Morgan-Smith, D., Garrison, C. E., and Bochdansky, A. B. 2013: Mortality and survival of cultured surface-ocean flagellates under simulated deep-sea conditions. Journal of Experimental Marine Biology and Ecology, 445: 13–20. DOI: 10.1016/j.jembe.2013.03.017
- ^ a b c d e f g h Von Der Heyden, S., and Cavalier-Smith, T. 2005: Culturing and Environmental DNA Sequencing Uncover Hidden Kinetoplastid Biodiversity and a Major Marine Clade within Ancestrally Freshwater Neobodo Designis. International Journal of Systematic and Evolutionary Microbiology, 55: 2605–2621. DOI: 10.1099/ijs.0.63606-0
- ^ a b c d Jang, H.B., Kim, Y. K., Del Castillo, C. S., Nho, S. W., Cha, I. S., and Park, S. B. 2012: RNA-Seq-Based Metatranscriptomic and Microscopic Investigation Reveals Novel Metalloproteases of Neobodo sp. as Potential Virulence Factors for Soft Tunic Syndrome in Halocynthia roretzi. PLoS ONE, 7(12): e52379. DOI: 10.1371/journal.pone.0052379