Morphological and Genetic Evidence that the Cyanobacterium Lyngbya wollei (Farlow ex Gomont) Speziale and Dyck Encompasses at Least Two Species

ABSTRACT Dense blooms of the cyanobacterium Lyngbya wollei are increasingly responsible for declining water quality and habitat degradation in numerous springs, rivers, and reservoirs. This research represents the first molecular phylogenetic analysis of L. wollei in comparison with the traditional morphological characterization of this species. Specimens were collected from several springs in Florida and a reservoir in North Carolina. Segments of the small-subunit (SSU) rRNA and nifH genes were PCR amplified, cloned, and sequenced. The phylogenetic analysis of the SSU rRNA gene revealed sequences that fell into three distinct subclusters, each with >97% sequence similarity. These were designated operational taxonomic unit 1 (OTU1), OTU2, and OTU3. Similarly, the nifH sequences fell into three distinct subclusters named S1, S2, and S3. When either bulk samples or individual filaments were analyzed, we recovered OTU1 with S1, OTU2 with S2, and OTU3 with S3. The coherence between the three SSU rRNA gene and nifH subclusters was consistent with genetically distinct strains or species. Cells associated with subclusters OTU3 and S3 were significantly wider and longer than those associated with other subclusters. The combined molecular and morphological data indicate that the species commonly identified as L. wollei in the literature represents two or possibly more species. Springs containing OTU3 and S3 demonstrated lower ion concentrations than other collection sites. Geographical locations of Lyngbya subclusters did not correlate with residual dissolved inorganic nitrogen or phosphorus concentrations. This study emphasizes the need to complement traditional identification with molecular characterization to more definitively detect and characterize harmful cyanobacterial species or strains.

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Phylogenetic analysis of freshwater fish trypanosomes from Europe using ssu rRNA gene sequences and random amplification of polymorphic DNA

Parasitology ◽

10.1017/s0031182004006778 ◽

2004 ◽

Vol 130 (4) ◽

pp. 405-412 ◽

Cited By ~ 19

Author(s):

W. C. GIBSON ◽

J. LOM ◽

H. PECKOVÁ ◽

V. R. FERRIS ◽

P. B. HAMILTON

Keyword(s):

Phylogenetic Analysis ◽

Freshwater Fish ◽

Genetic Relationships ◽

Small Subunit ◽

Rrna Genes ◽

Rrna Gene ◽

Ssu Rrna ◽

Gene Sequences ◽

Ssu Rrna Gene ◽

Random Amplification

The taxonomy and phylogenetic relationships of fish trypanosomes are uncertain. A collection of 22 cloned trypanosome isolates from 14 species of European freshwater fish and 1 species of African freshwater fish were examined by molecular phylogenetic analysis. The small subunit ribosomal RNA (ssu rRNA) genes of 8 clones were sequenced and compared with ssu rRNA gene sequences from a wider selection of vertebrate trypanosome isolates by phylogenetic analysis. All trypanosomes from freshwater fish fell in a single clade, subdivided into 3 groups. This clade sits within a larger, robust clade containing trypanosomes from marine fish and various amphibious vertebrates. All 22 trypanosome clones were analysed by random amplification of polymorphic DNA. The resulting dendrogram shows 3 groups, which are congruent with the groups identified in the ssu rRNA gene phylogeny. Two of the groups contain the majority of trypanosome isolates and within-group variation is slight. These groups do not separate purported trypanosome species distinguished by morphology or host origin, and thus these criteria do not appear to be reliable guides to genetic relationships among fish trypanosomes. However, we suggest that the 2 groups themselves may represent different species of fish trypanosomes. The polymorphic DNA markers we have identified will facilitate future comparisons of the biology of these 2 groups of fish trypanosomes.

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Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria

10.1101/258137 ◽

2018 ◽

Cited By ~ 8

Author(s):

Jeffrey S. McLean ◽

Batbileg Bor ◽

Thao T. To ◽

Quanhui Liu ◽

Kristopher A. Kerns ◽

...

Keyword(s):

Oral Cavity ◽

De Novo ◽

Gc Content ◽

Single Copy ◽

Small Subunit ◽

Rrna Gene ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Human Oral Cavity

ABSTRACTRecently, we discovered that a member of the Saccharibacteria/TM7 phylum (strain TM7x) isolated from the human oral cavity, has an ultra-small cell size (200-300nm), a highly reduced genome (705 Kbp) with limited de novo biosynthetic capabilities, and a very novel lifestyle as an obligate epibiont on the surface of another bacterium 1. There has been considerable interest in uncultivated phyla, particularly those that are now classified as the proposed candidate phyla radiation (CPR) reported to include 35 or more phyla and are estimated to make up nearly 15% of the domain Bacteria. Most members of the larger CPR group share genomic properties with Saccharibacteria including reduced genomes (<1Mbp) and lack of biosynthetic capabilities, yet to date, strain TM7x represents the only member of the CPR that has been cultivated and is one of only three CPR routinely detected in the human body. Through small subunit ribosomal RNA (SSU rRNA) gene surveys, members of the Saccharibacteria phylum are reported in many environments as well as within a diversity of host species and have been shown to increase dramatically in human oral and gut diseases. With a single copy of the 16S rRNA gene resolved on a few limited genomes, their absolute abundance is most often underestimated and their potential role in disease pathogenesis is therefore underappreciated. Despite being an obligate parasite dependent on other bacteria, six groups (G1-G6) are recognized using SSU rRNA gene phylogeny in the oral cavity alone. At present, only genomes from the G1 group, which includes related and remarkably syntenic environmental and human oral associated representatives1, have been uncovered to date. In this study we systematically captured the spectrum of known diversity in this phylum by reconstructing completely novel Class level genomes belonging to groups G3, G6 and G5 through cultivation enrichment and/or metagenomic binning from humans and mammalian rumen. Additional genomes for representatives of G1 were also obtained from modern oral plaque and ancient dental calculus. Comparative analysis revealed remarkable divergence in the host-associated members across this phylum. Within the human oral cavity alone, variation in as much as 70% of the genes from nearest oral clade (AAI 50%) as well as wide GC content variation is evident in these newly captured divergent members (G3, G5 and G6) with no environmental relatives. Comparative analyses suggest independent episodes of transmission of these TM7 groups into humans and convergent evolution of several key functions during adaptation within hosts. In addition, we provide evidence from in vivo collected samples that each of these major groups are ultra-small in size and are found attached to larger cells.

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Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004936 ◽

2021 ◽

Vol 71 (8) ◽

Author(s):

Ran Li ◽

Wenbao Zhuang ◽

Congcong Wang ◽

Hamed El-Serehy ◽

Saleh A. Al-Farraj ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Small Subunit ◽

The Yellow Sea ◽

Rrna Gene ◽

Ssu Rrna ◽

Gene Trees ◽

Ssu Rrna Gene ◽

Anaerobic Ciliate ◽

Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

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New Intranuclear Symbiotic Bacteria from Macronucleus of Paramecium putrinum—“Candidatus Gortzia Yakutica”

Diversity ◽

10.3390/d12050198 ◽

2020 ◽

Vol 12 (5) ◽

pp. 198 ◽

Cited By ~ 2

Author(s):

Alexandra Y. Beliavskaia ◽

Alexander V. Predeus ◽

Sofya K. Garushyants ◽

Maria D. Logacheva ◽

Jun Gong ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Life Cycle ◽

Host Species ◽

Novel Species ◽

Symbiotic Bacteria ◽

Rrna Gene ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Obligate Intracellular

Holospora-like bacteria (HLB) are obligate intracellular Alphaproteobacteria, inhabiting nuclei of Paramecium and other ciliates such as “Candidatus Hafkinia” is in Frontonia. The HLB clade is comprised of four genera, Holospora, Preeria, “Candidatus Gortzia”, and “Candidatus Hafkinia”. These bacteria have a peculiar life cycle with two morphological forms and some degree of specificity to the host species and the type of nucleus they inhabit. Here we describe a novel species of HLB—“Candidatus Gortzia yakutica” sp. nov.—a symbiont from the macronucleus of Paramecium putrinum, the first described HLB for this Paramecium species. The new endosymbiont shows morphological similarities with other HLB. The phylogenetic analysis of the SSU rRNA gene places it into the “Candidatus Gortzia” clade.

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Telonema antarcticum sp. nov., a common marine phagotrophic flagellate

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63652-0 ◽

2005 ◽

Vol 55 (6) ◽

pp. 2595-2604 ◽

Cited By ~ 26

Author(s):

Dag Klaveness ◽

Kamran Shalchian-Tabrizi ◽

Helge Abildhauge Thomsen ◽

Wenche Eikrem ◽

Kjetill S. Jakobsen

Keyword(s):

Molecular Phylogeny ◽

Small Subunit ◽

Food Vacuole ◽

Rrna Gene ◽

Ssu Rrna ◽

Small Subunit Rrna ◽

Ssu Rrna Gene ◽

Structural Identity ◽

Food Particles ◽

Ssu Rrna Gene Sequence

Telonema is a widely distributed group of phagotrophic flagellates with two known members. In this study, the structural identity and molecular phylogeny of Telonema antarcticum was investigated and a valid description is proposed. Molecular phylogeny was studied using small-subunit rRNA (SSU rRNA) gene sequences. The pear-shaped cell had two subequal flagella that emerged laterally on the truncated antapical tail. One flagellum had tripartite hairs. The cell was naked, but had subsurface vesicles containing angular paracrystalline bodies of an unknown nature. A unique complex cytoskeletal structure, the subcortical lamina, was found to be an important functional and taxonomic feature of the genus. Telonema has an antero-ventral depression where food particles are ingested and then transferred to a conspicuous anterior food vacuole. The molecular phylogeny inferred from the SSU rRNA gene sequence suggested that Telonema represents an isolated and deep branch among the tubulocristate protists.

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phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

mSystems ◽

10.1128/msystems.00920-20 ◽

2020 ◽

Vol 5 (5) ◽

Cited By ~ 1

Author(s):

Harald R. Gruber-Vodicka ◽

Brandon K. B. Seah ◽

Elmar Pruesse

Keyword(s):

High Throughput ◽

Small Subunit ◽

General Purpose ◽

Reference Database ◽

Rrna Gene ◽

Ssu Rrna ◽

Small Subunit Rrna ◽

Ssu Rrna Gene ◽

Domains Of Life ◽

Environmental Microbes

ABSTRACT The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual. IMPORTANCE To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing.

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Phylogeny of Actinobacteria Small Subunit (SSU) rRNA Gene Clones Recovered From Marine Bacterioplankton

Systematic and Applied Microbiology ◽

10.1016/s0723-2020(99)80033-2 ◽

1999 ◽

Vol 22 (1) ◽

pp. 106-112 ◽

Cited By ~ 42

Author(s):

Michael S. Rappé ◽

Douglas A. Gordon ◽

Kevin L. Vergin ◽

Stephen J. Giovannoni

Keyword(s):

Small Subunit ◽

Rrna Gene ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Marine Bacterioplankton

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Taxonomy, morphology and molecular systematics of three oligotrich ciliates, including a description of Apostrombidium parakielum spec. nov. (Ciliophora, Oligotrichia)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.048314-0 ◽

2013 ◽

Vol 63 (Pt_3) ◽

pp. 1179-1191 ◽

Cited By ~ 14

Author(s):

Wen Song ◽

Jiamei Li ◽

Weiwei Liu ◽

Jiamei Jiang ◽

Khaled A. S. Al- Rasheid ◽

...

Keyword(s):

Sequence Data ◽

Novel Species ◽

Small Subunit ◽

Rrna Gene ◽

Ssu Rrna ◽

The Novel ◽

Small Subunit Rrna ◽

Ssu Rrna Gene ◽

Single Clade ◽

Ssu Rrna Gene Sequence

Three oligotrich ciliates, Apostrombidium parakielum spec. nov., Novistrombidium apsheronicum (Alekperov & Asadullayeva, 1997) Agatha, 2003 and Novistrombidium testaceum (Anigstein, 1914) Song & Bradbury, 1998 were collected from the coastal waters of China and their morphology and small-subunit rRNA (SSU rRNA) gene sequences were studied. The novel species can be recognized by the combination of its obconical body shape, 14–16 anterior and 6–8 ventral membranelles, somatic kinety in three parts and conspicuously long dorsal cilia. Based on the data obtained for this novel species, an improved diagnosis of the genus Apostrombidium is supplied. Descriptions of the population of N. apsheronicum and N. testaceum collected in this study are also provided and compared with the existing descriptions. In addition, the phylogenetic positions of these three species are inferred from their SSU rRNA gene sequence data. The results indicate that the genus Apostrombidium, the systematics of which has not previously been discussed using molecular information, clusters with Varistrombidium kielum and Omegastrombidium elegans, whereas N. testaceum and N. apsheronicum form a single clade.

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Community Structure Analysis of Methanogens Associated with Rumen Protozoa Reveals Bias in Universal Archaeal Primers

Applied and Environmental Microbiology ◽

10.1128/aem.07994-11 ◽

2012 ◽

Vol 78 (11) ◽

pp. 4051-4056 ◽

Cited By ~ 30

Author(s):

Lisa D. Tymensen ◽

Tim A. McAllister

Keyword(s):

Community Structure ◽

Species Composition ◽

Structure Analysis ◽

Small Subunit ◽

Rrna Gene ◽

Ssu Rrna ◽

Content Type ◽

Ssu Rrna Gene ◽

Rumen Protozoa ◽

Primer Sets

ABSTRACTThe diversity of protozoan-associated methanogens in cattle was investigated using five universal archaeal small-subunit (SSU) rRNA gene primer sets.Methanobrevibacterspp. and rumen cluster C (distantly related toThermoplasmaspp.) were predominant. Significant differences in species composition among libraries indicate that some primers used previously to characterize rumen methanogens exhibit biased amplification.

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