Rhodotorula benthica sp. nov. and Rhodotorula calyptogenae sp. nov., novel yeast species from animals collected from the deep-sea floor, and Rhodotorula lysiniphila sp. nov., which is related phylogenetically

Nagahama, Takahiko; Hamamoto, Makiko; Nakase, Takashi; Horikoshi, Koki

doi:10.1099/ijs.0.02395-0

Cited by 51 publications

(23 citation statements)

References 20 publications

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“…4). Fungi haplotype KT2-C is probably red yeast, possibly a member of the genus Rhodotorula, a ubiquitous deep-sea fungus previously isolated from the Japan, Palau-Yap, and Mariana Trenches (Nagahama et al 2001(Nagahama et al , 2003. Fungal clone TT1-C exhibited 98% sequence similarity with the ascomycete Peziza phyllogena, and most top BLAST returns belonged to this genus.…”

Section: Resultsmentioning

confidence: 99%

“…Microeukaryotes appear pervasive in the gut contents of this species, indicating that adults ingest sediment. Diatoms are likely surface-derived detritus, although the fungi and some alveolate species (particularly the predatory ciliates) may be autochthonous (Takami et al 1997;Lopez-Garcia et al 2003;Nagahama et al 2003). The detection of S. schellenbergi DNA from the guts of two H. dubia specimens was an extraordinary result.…”

Section: Discussionmentioning

confidence: 95%

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Extreme food webs: Foraging strategies and diets of scavenging amphipods from the ocean’s deepest 5 kilometers

Blankenship

Levin

2007

Limnology & Oceanography

106

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We explore hypotheses that alternate foraging strategies, diet, or nutrient partitioning could help explain the success of scavenging Lysianassoids (Amphipoda) in hadal oligotrophic trenches (depths of 6-11 km) by examining the nutritional strategies of four lysianassoid species (Eurythenes gryllus, Scopelocheirus schellenbergi, Hirondellea dubia, and Uristes sp. nov.) collected with baited traps (6.3-10.8 km) from the oligotrophic Tonga and Kermadec Trenches (southwest Pacific Ocean). Diets and foraging strategies were examined by use of (1) the nascent DNA-based analysis of hindgut contents, which provides a 'snapshot' of recently ingested organisms, and (2) natural abundance isotopic signatures, which reflect the source of nutrition and relative trophic position. The scavenging guild exhibits remarkable trophic plasticity, and each amphipod species employs alternate foraging modes, including detrivory or predation, to supplement necrophagy. The nutritional strategies of some species appear to shift with age, depth, and even between trenches. Thus, there is no single ubiquitous hadal food web; rather it is influenced by depth and overlying surface productivity. Isotopic data suggest that coexisting species partition the dietary items, providing evidence of competition among members of the scavenging guild. The extreme foraging flexibility of scavenging amphipods may ultimately contribute to their success in severely foodlimited hadal ecosystems.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 95%

Extreme food webs: Foraging strategies and diets of scavenging amphipods from the ocean’s deepest 5 kilometers

Blankenship

Levin

2007

Limnology & Oceanography

106

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“…Bar, 0.01 substitution per site. The isoprenoid chain numbers of major ubiquinone were cited in Yamada and Kondo (1973), Suzuki and Nakase (1986), , Bai et al (2001), Nagahama et al (2001Nagahama et al ( , 2003, Hamamoto et al (2002), Zhao et al (2002). NDs show that Co-Q systems are not determined. of these species.…”

Section: Variation In the Secondary Structure Of The C1 Helix Derivedmentioning

confidence: 99%

“…However, a relationship among these species was not supported by most of the phylogenetic trees published previously. Some new species have recently been described in this clade (Bai et al, 2001;Hamamoto et al, 2002;Nagahama et al, 2001Nagahama et al, , 2003. As the approach for investigating the issues mentioned above, we determined and analyzed partial sequences of 18S rDNAs domains, elongation factor (EF)-1a, the D1/D2 region of 26S rDNA and the ITS.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic relationship within the Erythrobasidium clade: Molecular phylogenies, secondary structure, and intron positions inferred from partial sequences of ribosomal RNA and elongation factor-1α genes

Nagahama

Hamamoto

Nakase

et al. 2006

J. Gen. Appl. Microbiol.

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Extensive investigations of molecular systematics in the basidiomycetous yeasts using the sequences of 26S rDNA (Fell et al., 2000) and internal transcribed spacers (ITSs) (Scorzetti et al., 2002) established that these molecular data are useful tools for the delineation of species. However, the phylogenetic relationships among some taxa derived from the analysis of 26S rDNA sequences were not always identical to those based on the ITS regions. In addition, many branches of the 26S rDNA-based tree were not confirmed statistically, and this was also true for the ITSbased tree. The Erythrobasidium clade (Fell et al., 2000) was an evolutionary lineage of the urediniomycetous yeasts that included Erythrobasidium hasegawianum as a representative species and the delimitation of this clade in the urediniomycetous yeasts was phenotypically supported by the lack of fuPhylogenetic relationship within the Erythrobasidium clade: Molecular phylogenies, secondary structure, and intron positions inferred from partial sequences of ribosomal RNA and elongation factor-1a a genes Phylogenetic relationships within the Erythrobasidium clade as a lineage of the urediniomycetous yeasts were examined using partial regions of 18S rDNA, 5.8S rDNA, 26S rDNA, internal transcribed spacers (ITSs), and elongation factor (EF)-1a a. Combined data analysis of all segments successfully yielded a reliable phylogeny and confirmed the cohesion of species characterized by Q-10(H 2 ) as a major ubiquinone. Differences in secondary structure predicted for a variable region in 26S rDNA corresponded to major divergences in the phylogenetic tree based on the primary sequence. The common presence of a shortened helix in this region was considered to be evidence of monophyly for species with Q-10(H 2 ), Sakaguchia dacryoides, Rhodotorula lactosa, and Rhodotorula lamellibrachiae, although it was not as strongly supported by the combined data tree. The information on intron positions in the EF-1a a gene had potential usefulness in the phylogenetic inference between closely related species.

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“…Previously, several new yeast species were isolated from deep-sea samples. These new deep-sea species were affiliated to the genera Kluyveromyces (Nagahama et al 1999), Cryptococcus (Nagahama et al 2003a), Rhodotorula (Nagahama et al 2001(Nagahama et al , 2003b(Nagahama et al , 2006 and Dipodascus (Nagahama et al 2008). Three yeast strains respectively identified as Mo39, MARY089 and CBS 5307 were isolated from an unidentified deep-sea coral near Rainbow hydrothermal vent, from water samples near Menez Gwen hydrothermal field and from the stomach of a marine fish.…”

Section: Introductionmentioning

confidence: 98%

Candida oceani sp. nov., a novel yeast isolated from a Mid-Atlantic Ridge hydrothermal vent (−2300 meters)

Burgaud

Arzur

Sampaio

et al. 2011

Antonie van Leeuwenhoek

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A novel species in the genus Candida was obtained from deep-sea hydrothermal fields on the Mid-Atlantic Ridge. Strains Mo39, MARY089 and CBS 5307, respectively, isolated from an unidentified deep-sea coral collected near Rainbow hydrothermal vent, from water samples near Menez Gwen hydrothermal field and from the stomach of a marine fish are considered as a novel taxon. Sequence similarities in the D1/D2 region of the 26S rRNA gene indicated that strains Mo39, MARY089 and CBS 5307 have for closest neighbors Candida spencermartinsiae, Candida taylorii, Candida atmosphaerica and Candida atlantica. The strains, respectively, differ from C. spencermartinsiae, C. taylorii, C. atmosphaerica andCandida atlantica by 4, 4.3, 4.3 and 4.7% in the D1/D2 domain. Strains Mo39, MARY089 and CBS 5307 were differentiated from others by differences in the ability to assimilate D: -Gluconate and in the ability to grow at relatively high temperature. Only strain Mo39 displays an optimal growth at 3% sea salts, indicating that this strain is clearly adapted to live in marine conditions. Sequence similarities between strains Mo39, MARY089 and CBS 5307 and related species and differences in the ability to utilize specific carbon compounds revealed that these strains represent a hitherto unknown species. Sexual reproduction was not observed in strains Mo39, MARY089 and CBS 5307. An anamorphic name Candida oceani sp. nov. is proposed for the type strain Mo39(T) (= CBS 11857(T) = DSM 23777(T)) and the two other strains MARY089 and CBS 5307. To our knowledge, this is the first description of a micro-eukaryotic organism including a strain isolated from a deep-sea coral near a hydrothermal ecosystem.

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Rhodotorula benthica sp. nov. and Rhodotorula calyptogenae sp. nov., novel yeast species from animals collected from the deep-sea floor, and Rhodotorula lysiniphila sp. nov., which is related phylogenetically

Cited by 51 publications

References 20 publications

Extreme food webs: Foraging strategies and diets of scavenging amphipods from the ocean’s deepest 5 kilometers

Extreme food webs: Foraging strategies and diets of scavenging amphipods from the ocean’s deepest 5 kilometers

Phylogenetic relationship within the Erythrobasidium clade: Molecular phylogenies, secondary structure, and intron positions inferred from partial sequences of ribosomal RNA and elongation factor-1α genes

Candida oceani sp. nov., a novel yeast isolated from a Mid-Atlantic Ridge hydrothermal vent (−2300 meters)

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