Category: Papers by CGEB labs

Characterization of a Deep-Branching Heterolobosean, Pharyngomonas turkanaensis n. sp., Isolated From a Non-Hypersaline Habitat, and Ultrastructural Comparison of Cysts and Amoebae Among Pharyngomonas Strains.

J Eukaryot Microbiol. 2015 Aug 20;

Authors: Park JS, Simpson AG

Abstract
An unusual heterolobosean amoeba, isolate LO, was isolated recently from a sample with a salinity of ~4‰, from Lake Turkana in East Africa. 18S rDNA phylogenies confirm that isolate LO branches among halophilic amoeboflagellates assigned to Pharyngomonas. We examined the ultrastructure of the amoeba and cyst stages of isolate LO, as well as the amoebae and cysts of Pharyngomonas kirbyi (isolates AS12B and SD1A). The amoebae of all three isolates lacked discrete dictyosomes and had discoidal/flattened mitochondrial cristae, but the mitochondria were not enrobed by rough endoplasmic reticulum. The cysts of all three isolates showed a thick, bipartite cyst wall, and lacked cyst pores. The cysts of isolate LO were distinct in that the ectocyst was very loose-fitting, and could contain ‘crypts’. No flagellate form of isolate LO has been observed to date, and a salinity-for-growth experiment showed that isolate LO can grow at 15‰ to 100‰ salinity, indicating that it is halotolerant. By contrast, other studied Pharyngomonas isolates are amoeboflagellates and true halophiles. Therefore, we propose isolate LO as a new species, Pharyngomonas turkanaensis n. sp. It is possible that P. turkanaensis descended from halophilic ancestors, and represents a secondary reestablishment of a physiology adapted for moderate salinity. This article is protected by copyright. All rights reserved.

PMID: 26291784 [PubMed – as supplied by publisher]

Characterization of a Deep-Branching Heterolobosean, Pharyngomonas turkanaensis n. sp., Isolated From a Non-Hypersaline Habitat, and Ultrastructural Comparison of Cysts and Amoebae Among Pharyngomonas Strains.

J Eukaryot Microbiol. 2015 Aug 20;

Authors: Park JS, Simpson AG

Abstract
An unusual heterolobosean amoeba, isolate LO, was isolated recently from a sample with a salinity of ~4‰, from Lake Turkana in East Africa. 18S rDNA phylogenies confirm that isolate LO branches among halophilic amoeboflagellates assigned to Pharyngomonas. We examined the ultrastructure of the amoeba and cyst stages of isolate LO, as well as the amoebae and cysts of Pharyngomonas kirbyi (isolates AS12B and SD1A). The amoebae of all three isolates lacked discrete dictyosomes and had discoidal/flattened mitochondrial cristae, but the mitochondria were not enrobed by rough endoplasmic reticulum. The cysts of all three isolates showed a thick, bipartite cyst wall, and lacked cyst pores. The cysts of isolate LO were distinct in that the ectocyst was very loose-fitting, and could contain ‘crypts’. No flagellate form of isolate LO has been observed to date, and a salinity-for-growth experiment showed that isolate LO can grow at 15‰ to 100‰ salinity, indicating that it is halotolerant. By contrast, other studied Pharyngomonas isolates are amoeboflagellates and true halophiles. Therefore, we propose isolate LO as a new species, Pharyngomonas turkanaensis n. sp. It is possible that P. turkanaensis descended from halophilic ancestors, and represents a secondary reestablishment of a physiology adapted for moderate salinity. This article is protected by copyright. All rights reserved.

PMID: 26291784 [PubMed – as supplied by publisher]

Frailty and the Microbiome.

Interdiscip Top Gerontol Geriatr. 2015;41:54-65

Authors: Meehan CJ, Langille MG, Beiko RG

Abstract
From the moment of birth, the human body plays host to a rich diversity of microbes. Body sites such as the skin, the gut and the mouth support communities of microorganisms (collectively known as the microbiome) that are both numerous and diverse. As our understanding of the microbiome advances, it is evident that these microbial populations participate in a multitude of symbiotic associations with us. The disruption of these associations can lead to a range of diseases beyond mere pathogenesis as microbial nutrition, signaling, and immune defense break down. It is known that changes in microbial composition occur as the human host ages and that diet and living conditions influence the microbiome of older individuals. However, the link between the microbiome and frailty is as yet mostly unexplored. Although the microbiome is likely to influence health factors that contribute to frailty, further work is needed to determine whether overall microbial signatures of frailty exist and, if so, what the diagnostic and therapeutic utility of these signatures might be. © 2015 S. Karger AG, Basel.

PMID: 26301979 [PubMed – in process]

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Marine Isolates of Trimastix marina Form a Plesiomorphic Deep-branching Lineage within Preaxostyla, Separate from Other Known Trimastigids (Paratrimastix n. gen.).

Protist. 2015 Jul 22;166(4):468-491

Authors: Zhang Q, Táborský P, Silberman JD, Pánek T, Čepička I, Simpson AG

Abstract
Trimastigids are free-living, anaerobic protists that are closely related to the symbiotic oxymonads, forming together the taxon Preaxostyla (Excavata: Metamonada). We isolated fourteen new strains morphologically corresponding to two species assigned to Trimastix (until now the only genus of trimastigids), Trimastix marina and Trimastix pyriformis. Unexpectedly, marine strains of Trimastix marina branch separately from freshwater strains of this morphospecies in SSU rRNA gene trees, and instead form the sister group of all other Preaxostyla. This position is confirmed by three-gene phylogenies. Ultrastructural examination of a marine isolate of Trimastix marina demonstrates a combination of trimastigid-like features (e.g. preaxostyle-like I fibre) and ancestral characters (e.g. absence of thickened flagellar vane margins), consistent with inclusion of marine T. marina within Preaxostyla, but also supporting its distinctiveness from ‘freshwater T. marina’ and its deep-branching position within Preaxostyla. Since these results indicate paraphyly of Trimastix as currently understood, we transfer the other better-studied trimastigids to Paratrimastix n. gen. and Paratrimastigidae n. fam. The freshwater form previously identified as T. marina is described as Paratrimastix eleionoma n. sp., and Trimastix pyriformis becomes Paratrimastix pyriformis n. comb. Because of its phylogenetic position, ‘true’ Trimastix is potentially important for understanding the evolution of mitochondrion-related organelles in metamonads.

PMID: 26312987 [PubMed – as supplied by publisher]

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Multilevel selection theory and the evolutionary functions of transposable elements.
Genome Biol Evol. 2015 Aug 6;
Authors: Brunet TD, Doolittle WF
Abstract
One of several issues at …

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Diversity of Heterotrophic Protists from Extremely Hypersaline Habitats.

Protist. 2015 Jun 18;166(4):422-437

Authors: Park JS, Simpson AG

Abstract
Heterotrophic protists (protozoa) are a diverse but understudied component of the biota of extremely hypersaline environments, with few data on molecular diversity within halophile ‘species’, and almost nothing known of their biogeographic distribution. We have garnered SSU rRNA gene sequences for several clades of halophilic protozoa from enrichments from waters of >12.5% salinity from Australia, North America, and Europe (6 geographic sites, 25 distinct samples). The small stramenopile Halocafeteria was found at all sites, but phylogenies did not show clear geographic clustering. The ciliate Trimyema was recorded from 6 non-European samples. Phylogenies confirmed a monophyletic halophilic Trimyema group that included possible south-eastern Australian, Western Australian and North American clusters. Several halophilic Heterolobosea were detected, demonstrating that Pleurostomum contains at least three relatively distinct clades, and increasing known continental ranges for Tulamoeba peronaphora and Euplaesiobystra hypersalinica. The unclassified flagellate Palustrimonas, found in one Australian sample, proves to be a novel deep-branching alveolate. These results are consistent with a global distribution of halophilic protozoa groups (∼morphospecies), but the Trimyema case suggests that is worth testing whether larger forms exhibit biogeographic phylogenetic substructure. The molecular detection/characterization of halophilic protozoa is still far from complete at the clade level, let alone the ‘species level’.

PMID: 26202993 [PubMed – as supplied by publisher]

Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.

BMC Genomics. 2015;16:526

Authors: Wong DH, Beiko RG

Abstract
BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced Biological Phosphorus Removal (EBPR) have been used to treat wastewater in the last 50 years and may provide insights into adaptation to an engineered environment. We introduce two different types of analysis to identify LGT in EBPR sewage communities, based on identifying assembled sequences with more than one strong taxonomic match, and on unusual phylogenetic patterns. We applied these methods to investigate the role of LGT in six energy-related metabolic pathways.
RESULTS: The analyses identified overlapping but non-identical sets of transferred enzymes. All of these were homologous with sequences from known mobile genetic elements, and many were also in close proximity to transposases and integrases in the EBPR data set. The taxonomic method had higher sensitivity than the phylogenetic method, identifying more potential LGTs. Both analyses identified the putative transfer of five enzymes within an Australian community, two in a Danish community, and none in a US-derived culture.
CONCLUSIONS: Our methods were able to identify sequences with unusual phylogenetic or compositional properties as candidate LGT events. The association of these candidates with known mobile elements supports the hypothesis of transfer. The results of our analysis strongly suggest that LGT has influenced the development of functionally important energy-related pathways in EBPR systems, but transfers may be unique to each community due to different operating conditions or taxonomic composition.

PMID: 26173980 [PubMed – in process]

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Dual Organellar Targeting of Aminoacyl-tRNA Synthetases in Diatoms and Cryptophytes.
Genome Biol Evol. 2015;7(6):1728-42
Authors: Gile GH, Moog D, Slamovits CH, Maier UG, Archibald JM
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Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase.
Mol Phylogenet Evol. 2015 May 27;91:12-16
Authors: Gawryluk RM, Eme L, Roger A…