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

2012 ◽  
Vol 78 (11) ◽  
pp. 4051-4056 ◽  
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.

scholarly journals Microbes in High Arctic Snow and Implications for the Cold Biosphere

2011 ◽  
Vol 77 (10) ◽  
pp. 3234-3243 ◽  
Author(s):  
Tommy Harding ◽  
Anne D. Jungblut ◽  
Connie Lovejoy ◽  
Warwick F. Vincent
Keyword(s):  
Microbial Mats ◽  
High Arctic ◽  
Small Subunit ◽  
Transport Processes ◽  
The Arctic ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Content Type ◽  
Ssu Rrna Gene ◽  
Aerial Transport

ABSTRACTWe applied molecular, microscopic, and culture techniques to characterize the microbial communities in snow and air at remote sites in the Canadian High Arctic (Ward Hunt Island, Ellesmere Island, and Cornwallis Island, latitudes 74 to 83oN). Members of theBacteriaandEukaryawere prevalent in the snow, and their small subunit (SSU) rRNA gene signatures indicated strong local aerial transport within the region over the preceding 8 months of winter snowpack accumulation. Many of the operational taxonomic units (OTUs) were similar to previously reported SSU rRNA gene sequences from the Arctic Ocean, suggesting the importance of local aerial transport processes for marine microbiota. More than 47% of the cyanobacterial OTUs in the snow have been previously found in microbial mats in the region, indicating that this group was also substantially derived from local sources. Viable cyanobacteria isolated from the snow indicated free exchange between the snow and adjacent mat communities. Other sequences were most similar to those found outside the Canadian Arctic but were from snow, lake and sea ice, glaciers and permafrost, alpine regions, Antarctica, and other regions of the Arctic, supporting the concept of global distribution of microbial ecotypes throughout the cold biosphere.

scholarly journals Biodiversity and Emerging Biogeography of the Neutrophilic Iron-Oxidizing Zetaproteobacteria

2011 ◽  
Vol 77 (15) ◽  
pp. 5445-5457 ◽  
Author(s):  
Sean M. McAllister ◽  
Richard E. Davis ◽  
Joyce M. McBeth ◽  
Bradley M. Tebo ◽  
David Emerson ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Geographic Distance ◽  
Environmental Parameters ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Content Type ◽  
Ssu Rrna Gene ◽  
The Pacific ◽  
The Pacific Ocean

ABSTRACTMembers of the neutrophilic iron-oxidizing candidate classZetaproteobacteriahave predominantly been found at sites of microbially mediated iron oxidation in marine environments around the Pacific Ocean. Eighty-four full-length (>1,400-bp) and 48 partial-lengthZetaproteobacteriasmall-subunit (SSU) rRNA gene sequences from five novel clone libraries, one novelZetaproteobacteriaisolate, and the GenBank database were analyzed to assess the biodiversity of this burgeoning class of theProteobacteriaand to investigate its biogeography between three major sampling regions in the Pacific Ocean: Loihi Seamount, the Southern Mariana Trough, and the Tonga Arc. Sequences were grouped into operational taxonomic units (OTUs) on the basis of a 97% minimum similarity. Of the 28 OTUs detected, 13 were found to be endemic to one of the three main sampling regions and 2 were ubiquitous throughout the Pacific Ocean. Additionally, two deeply rooted OTUs that potentially dominate communities of iron oxidizers originating in the deep subsurface were identified. Spatial autocorrelation analysis and analysis of molecular variance (AMOVA) showed that geographic distance played a significant role in the distribution ofZetaproteobacteriabiodiversity, whereas environmental parameters, such as temperature, pH, or total Fe concentration, did not have a significant effect. These results, detected using the coarse resolution of the SSU rRNA gene, indicate that theZetaproteobacteriahave a strong biogeographic signal.

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

2018 ◽  
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.

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

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.

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

2005 ◽  
Vol 55 (6) ◽  
pp. 2595-2604 ◽  
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.

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

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
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.

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

2008 ◽  
Vol 74 (12) ◽  
pp. 3710-3717 ◽  
Author(s):  
Jennifer J. Joyner ◽  
R. Wayne Litaker ◽  
Hans W. Paerl
Keyword(s):  
Phylogenetic Analysis ◽  
Habitat Degradation ◽  
Sequence Similarity ◽  
Inorganic Nitrogen ◽  
Small Subunit ◽  
Morphological Data ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Lyngbya Wollei ◽  
Ssu Rrna Gene

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.

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

1999 ◽  
Vol 22 (1) ◽  
pp. 106-112 ◽  
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

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

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1179-1191 ◽  
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.

scholarly journals Trypanosoma melophagium from the sheep ked Melophagus ovinus on the island of St Kilda

Parasitology ◽  
2010 ◽  
Vol 137 (12) ◽  
pp. 1799-1804 ◽  
Author(s):  
W. GIBSON ◽  
J. G. PILKINGTON ◽  
J. M. PEMBERTON
Keyword(s):  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Spliced Leader ◽  
Melophagus Ovinus ◽  
Outer Hebrides ◽  
The Uk ◽  
Relationship Of

SUMMARYThe sheep ked has been largely eradicated in the UK but persists in the feral Soay sheep of St Kilda in the Outer Hebrides. Sheep keds transmit Trypanosoma melophagium, but parasitaemias are typically cryptic and this trypanosome has not been recorded in the St Kilda sheep. Trypanosomes were detected by PCR in preserved keds and were also found in gut smears from live keds; one infected gut was used to establish the trypanosome in vitro. Examination of the morphology of bloodstream forms from culture confirmed its identity as T. melophagium. Most keds were found to harbour the trypanosome, particularly those collected from lambs. DNA was extracted from preserved keds and from trypanosomes grown in vitro. Sequence analysis of the small subunit ribosomal RNA (SSU rRNA) gene and the spliced leader transcript showed the T. melophagium sequences to be very similar to those from T. theileri. A partial sequence of the ked SSU rRNA gene was also obtained. The close genetic relationship of T. melophagium and T. theileri suggests that T. melophagium represents a lineage of T. theileri that adapted to transmission by sheep keds and hence became a specific parasite of sheep.

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