scholarly journals Expanding the Known Diversity and Environmental Distribution of an Uncultured Phylogenetic Division of Bacteria

2000 ◽  
Vol 66 (4) ◽  
pp. 1617-1621 ◽  
Author(s):  
Michael A. Dojka ◽  
J. Kirk Harris ◽  
Norman R. Pace
Keyword(s):  
Sequence Difference ◽  
Environmental Distribution ◽  
Contaminated Aquifer ◽  
Phylogenetic Methods ◽  
Bacterial Division ◽  
Culture Independent ◽  
Molecular Phylogenetic ◽  
Candidate Division ◽  
Phylogenetic Divergence ◽  
Do So

ABSTRACT Culture-independent molecular phylogenetic methods were used to explore the breadth of diversity and environmental distribution of members of the division-level “candidate” phylogenetic group WS6, recently discovered in a contaminated aquifer and with no cultivated representatives. A broad diversity of WS6-affiliated sequences were cloned from 7 of 12 environments investigated: mainly from anaerobic sediment environments. The number of sequences representing the WS6 candidate division was increased from 3 to 60 in this study. The extent of phylogenetic divergence (sequence difference) in this candidate division was found to be among the largest of any known bacterial division. This indicates that organisms representing the WS6 phylogenetic division offer a broad diversity of undiscovered biochemical and metabolic novelty. These results provide a framework for the further study of these evidently important kinds of organisms and tools, the sequences, with which to do so.

scholarly journals Phylogenomic analysis of echinoderm class relationships supports Asterozoa

2014 ◽  
Vol 281 (1786) ◽  
pp. 20140479 ◽  
Author(s):  
Maximilian J. Telford ◽  
Christopher J. Lowe ◽  
Christopher B. Cameron ◽  
Olga Ortega-Martinez ◽  
Jochanan Aronowicz ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Sea Urchins ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Phylogenomic Analysis ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
Complete Dataset ◽  
Type Larva ◽  
Molecular Phylogenetic

While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used ‘phylogenetic signal dissection’ to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.

scholarly journals Heat as a Proxy to Image Dynamic Processes with 4D Electrical Resistivity Tomography

Geosciences ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 414 ◽  
Author(s):  
Robert ◽  
Paulus ◽  
Bolly ◽  
Koo Seen Lin ◽  
Hermans
Keyword(s):  
Electrical Resistivity ◽  
Groundwater Flow ◽  
Electrical Resistivity Tomography ◽  
Time Lapse ◽  
Dynamic Processes ◽  
Geophysical Monitoring ◽  
Resistivity Tomography ◽  
Contaminated Aquifer ◽  
Geophysical Measurements ◽  
Do So

Since salt cannot always be used as a geophysical tracer (because it may pollute the aquifer with the mass that is necessary to induce a geophysical contrast), and since in many contaminated aquifer salts (e.g., chloride) already constitute the main contaminants, another geophysical tracer is needed to force a contrast in the subsurface that can be detected from surface geophysical measurements. In this context, we used heat as a proxy to image and monitor groundwater flow and solute transport in a shallow alluvial aquifer (< 10 m deep) with the help of electrical resistivity tomography (ERT). The goal of our study is to demonstrate the feasibility of such methodology in the context of the validation of the efficiency of a hydraulic barrier that confines a chloride contamination to its source. To do so, we combined a heat tracer push/pull test with time-lapse 3D ERT and classical hydrogeological measurements in wells and piezometers. Our results show that heat can be an excellent salt substitution tracer for geophysical monitoring studies, both qualitatively and semi-quantitatively. Our methodology, based on 3D surface ERT, allows to visually prove that a hydraulic barrier works efficiently and could be used as an assessment of such installations.

scholarly journals New Perspective on Uncultured Bacterial Phylogenetic Division OP11

2004 ◽  
Vol 70 (2) ◽  
pp. 845-849 ◽  
Author(s):  
J. Kirk Harris ◽  
Scott T. Kelley ◽  
Norman R. Pace
Keyword(s):  
Environmental Samples ◽  
Rrna Gene ◽  
Molecular Signatures ◽  
Diverse Group ◽  
Environmental Distribution ◽  
Molecular Analyses ◽  
Partial Sequencing ◽  
Candidate Division ◽  
New Perspective ◽  
Pcr Techniques

ABSTRACT Organisms belonging to the OP11 candidate phylogenetic division of Bacteria have been detected only in rRNA-based sequence surveys of environmental samples. Preliminary studies indicated that such organisms represented by the sequences are abundant and widespread in nature and highly diverse phylogenetically. In order to document more thoroughly the phylogenetic breadth and environmental distribution of this diverse group of organisms, we conducted further molecular analyses on environmental DNAs. Using PCR techniques and primers directed toward each of the five described subdivisions of OP11, we surveyed 17 environmental DNAs and analyzed rRNA gene sequences in 27 clonal libraries from 14 environments. Ninety-nine new and unique sequences were determined completely, and approximately 200 additional clones were subjected to partial sequencing. Extensive phylogenetic comparisons of the new sequences to those representing other bacterial divisions further resolved the phylogeny of the bacterial candidate division OP11 and identified two new candidate bacterial divisions, OP11-derived 1 (OD1) and Sulphur River 1 (SR1). The widespread environmental distribution of representatives of the bacterial divisions OD1, OP11, and SR1 suggests potentially conspicuous biogeochemical roles for these organisms in their respective environments. The information on environmental distribution offers clues for attempts to culture landmark representatives of these novel bacterial divisions, and the sequences are specific molecular signatures that provide for their identification in other contexts.

scholarly journals 16S rRNA Phylogenetic Investigation of the Candidate Division “Korarchaeota”

2006 ◽  
Vol 72 (7) ◽  
pp. 5077-5082 ◽  
Author(s):  
Thomas A. Auchtung ◽  
Cristina D. Takacs-Vesbach ◽  
Colleen M. Cavanaugh
Keyword(s):  
16S Rrna ◽  
Hot Springs ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Environmental Distribution ◽  
Candidate Division ◽  
High Level ◽  
The 16S Rrna Gene

ABSTRACT The environmental distribution and phylogeny of “Korarchaeota,” a proposed ancient archaeal division, was investigated by using the 16S rRNA gene framework. Korarchaeota-specific primers were designed based on previously published sequences and used to screen a variety of environments. Korarchaeota 16S rRNA genes were amplified exclusively from high temperature Yellowstone National Park hot springs and a 9°N East Pacific Rise deep-sea hydrothermal vent. Phylogenetic analyses of these and all available sequences suggest that Korarchaeota exhibit a high level of endemicity.

scholarly journals Cryptic fungal species unmasked

2012 ◽  
Vol 33 (1) ◽  
pp. 36 ◽  
Author(s):  
Roger G Shivas ◽  
Lei Cai
Keyword(s):  
Host Range ◽  
Cryptic Species ◽  
Geographic Distribution ◽  
Dna Sequences ◽  
Fungal Species ◽  
Phylogenetic Methods ◽  
Molecular Phylogenetic

The word cryptic is derived from the Greek adjective krupt�s which means hidden. Morphologically indistinguishable species that have been revealed by molecular phylogenetic methods, and 37ultimately only recognised by their DNA sequences, are referred to as cryptic species. The importance of cryptic species for plant pathologists is that they may have significant differences in the severity of diseases they cause, host range and geographic distribution. It is these differences that are of concern to many biosecurity agencies, particularly in Australia.

scholarly journals Discordant Phylogenomic Placement of Hydnoraceae and Lactoridaceae Within Piperales Using Data From All Three Genomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Matthias Jost ◽  
Marie-Stéphanie Samain ◽  
Isabel Marques ◽  
Sean W. Graham ◽  
Stefan Wanke
Keyword(s):  
Phylogenetic Relationships ◽  
Online Survey ◽  
Taxon Sampling ◽  
Angiosperm Phylogeny ◽  
Phylogenetic Placement ◽  
Genus Level ◽  
Phylogenetic Methods ◽  
Molecular Phylogenetic ◽  
Phylogenetic Hypotheses ◽  
Using Data

Phylogenetic relationships within the magnoliid order Piperales have been studied extensively, yet the relationships of the monotypic family Lactoridaceae and the holoparasitic Hydnoraceae to the remainder of the order remain a matter of debate. Since the first confident molecular phylogenetic placement of Hydnoraceae among Piperales, different studies have recovered various contradictory topologies. Most phylogenetic hypotheses were inferred using only a few loci and have had incomplete taxon sampling at the genus level. Based on these results and an online survey of taxonomic opinion, the Angiosperm Phylogeny Group lumped both Hydnoraceae and Lactoridaceae in Aristolochiaceae; however, the latter family continues to have unclear relationships to the aforementioned taxa. Here we present extensive phylogenomic tree reconstructions based on up to 137 loci from all three subcellular genomes for all genera of Piperales. We infer relationships based on a variety of phylogenetic methods, explore instances of phylogenomic discordance between the subcellular genomes, and test alternative topologies. Consistent with these phylogenomic results and a consideration of the principles of phylogenetic classification, we propose to exclude Hydnoraceae and Lactoridaceae from the broad circumscription of Aristolochiaceae, and instead favor recognition of four monophyletic and morphologically well circumscribed families in the perianth-bearing Piperales: Aristolochiaceae, Asaraceae, Hydnoraceae, and Lactoridaceae, with a total of six families in the order.

scholarly journals Detecting and visualising the impact of heterogeneous evolutionary processes on phylogenetic estimates

2019 ◽  
Author(s):  
Lars S Jermiin ◽  
David R Lovell ◽  
Bernhard Misof ◽  
Peter G Foster ◽  
John Robinson
Keyword(s):  
Sequence Data ◽  
Evolutionary Processes ◽  
Model Based ◽  
Phylogenetic Methods ◽  
Phylogenetic Data ◽  
Molecular Phylogenetic ◽  
The Impact

AbstractMost model-based molecular phylogenetic methods assume that the sequences diverged on a tree under homogeneous conditions. If evolution occurred under these conditions, then it is unlikely that the sequences would become compositionally heterogeneous. Conversely, if the sequences are compositionally heterogeneous, then it is unlikely that they have evolved under homogeneous conditions. We present methods to detect and analyse heterogeneous evolution in aligned sequence data and to examine—visually and numerically—its effect on phylogenetic estimates. The methods are implemented in three programs, allowing users to better examine under what conditions their phylogenetic data may have evolved.

scholarly journals Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the candidate division FBP

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7876
Author(s):  
Kazuki Kobayashi ◽  
Hideki Aoyagi
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rdna ◽  
Microbial Community Structure ◽  
Phylogenetic Analyses ◽  
Tree Bark ◽  
Molecular Phylogenetic ◽  
Candidate Division ◽  
Promising Source ◽  
Uncultured Microorganisms

Background The potential of unidentified microorganisms for academic and other applications is limitless. Plants have diverse microbial communities associated with their biomes. However, few studies have focused on the microbial community structure relevant to tree bark. Methods In this report, the microbial community structure of bark from the broad-leaved tree Acer palmatum was analyzed. Both a culture-independent approach using polymerase chain reaction (PCR) amplification and next generation sequencing, and bacterial isolation and sequence-based identification methods were used to explore the bark sample as a source of previously uncultured microorganisms. Molecular phylogenetic analyses based on PCR-amplified 16S rDNA sequences were performed. Results At the phylum level, Proteobacteria and Bacteroidetes were relatively abundant in the A. palmatum bark. In addition, microorganisms from the phyla Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Armatimonadetes, and candidate division FBP, which contain many uncultured microbial species, existed in the A. palmatum bark. Of the 30 genera present at relatively high abundance in the bark, some genera belonging to the phyla mentioned were detected. A total of 70 isolates could be isolated and cultured using the low-nutrient agar media DR2A and PE03. Strains belonging to the phylum Actinobacteria were isolated most frequently. In addition, the newly identified bacterial strain IAP-33, presumed to belong to Acidobacteria, was isolated on PE03 medium. Of the isolated bacteria, 44 strains demonstrated less than 97% 16S rDNA sequence-similarity with type strains. Molecular phylogenetic analysis of IAD-21 showed the lowest similarity (79%), and analyses suggested it belongs to candidate division FBP. Culture of the strain IAD-21 was deposited in Japan Collection of Microorganisms (JCM) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as JCM 32665 and DSM 108248, respectively. Discussion Our results suggest that a variety of uncultured microorganisms exist in A. palmatum bark. Microorganisms acquirable from the bark may prove valuable for academic pursuits, such as studying microbial ecology, and the bark might be a promising source of uncultured bacterial isolates.

scholarly journals Microbial Diversity in a Hydrocarbon- and Chlorinated-Solvent-Contaminated Aquifer Undergoing Intrinsic Bioremediation

1998 ◽  
Vol 64 (10) ◽  
pp. 3869-3877 ◽  
Author(s):  
Michael A. Dojka ◽  
Philip Hugenholtz ◽  
Sheridan K. Haack ◽  
Norman R. Pace
Keyword(s):  
Chlorinated Solvents ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Intrinsic Bioremediation ◽  
Sulfate Reducing ◽  
Aceticlastic Methanogenesis ◽  
Culture Independent ◽  
Molecular Phylogenetic ◽  
Sequence Types

ABSTRACT A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and chlorinated solvents undergoing intrinsic bioremediation. Samples were obtained from three redox zones: methanogenic, methanogenic-sulfate reducing, and iron or sulfate reducing. Small-subunit rRNA genes were amplified directly from aquifer material DNA by PCR with universally conserved or Bacteria- orArchaea-specific primers and were cloned. A total of 812 clones were screened by restriction fragment length polymorphisms (RFLP), approximately 50% of which were unique. All RFLP types that occurred more than once in the libraries, as well as many of the unique types, were sequenced. A total of 104 (94 bacterial and 10 archaeal) sequence types were determined. Of the 94 bacterial sequence types, 10 have no phylogenetic association with known taxonomic divisions and are phylogenetically grouped in six novel division level groups (candidate divisions WS1 to WS6); 21 belong to four recently described candidate divisions with no cultivated representatives (OP5, OP8, OP10, and OP11); and 63 are phylogenetically associated with 10 well-recognized divisions. The physiology of two particularly abundant sequence types obtained from the methanogenic zone could be inferred from their phylogenetic association with groups of microorganisms with a consistent phenotype. One of these sequence types is associated with the genus Syntrophus; Syntrophus spp. produce energy from the anaerobic oxidation of organic acids, with the production of acetate and hydrogen. The organism represented by the other sequence type is closely related to Methanosaetaspp., which are known to be capable of energy generation only through aceticlastic methanogenesis. We hypothesize, therefore, that the terminal step of hydrocarbon degradation in the methanogenic zone of the aquifer is aceticlastic methanogenesis and that the microorganisms represented by these two sequence types occur in syntrophic association.

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