scholarly journals Evidence for Interspecies Gene Transfer in the Evolution of 2,4-Dichlorophenoxyacetic Acid Degraders

1998 ◽  
Vol 64 (10) ◽  
pp. 4089-4092 ◽  
Author(s):  
Catherine McGowan ◽  
Roberta Fulthorpe ◽  
Alice Wright ◽  
J. M. Tiedje
Keyword(s):  
Gene Transfer ◽  
Burkholderia Cepacia ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Dichlorophenoxyacetic Acid ◽  
Rdna Genes ◽  
Degrading Bacteria ◽  
Pcr Products ◽  
2,4 Dichlorophenoxyacetic Acid ◽  
Small Subunit Ribosomal Dna

ABSTRACT Small-subunit ribosomal DNA (SSU rDNA) from 20 phenotypically distinct strains of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria was partially sequenced, yielding 18 unique strains belonging to members of the alpha, beta, and gamma subgroups of the classProteobacteria. To understand the origin of 2,4-D degradation in this diverse collection, the first gene in the 2,4-D pathway, tfdA, was sequenced. The sequences fell into three unique classes found in various members of the beta and gamma subgroups of Proteobacteria. None of the α-Proteobacteria yieldedtfdA PCR products. A comparison of the dendrogram of thetfdA genes with that of the SSU rDNA genes demonstrated incongruency in phylogenies, and hence 2,4-D degradation must have originated from gene transfer between species. Only those strains withtfdA sequences highly similar to the tfdAsequence of strain JMP134 (tfdA class I) transferred all the 2,4-D genes and conferred the 2,4-D degradation phenotype to aBurkholderia cepacia recipient.

scholarly journals Novel 2,4-Dichlorophenoxyacetic Acid Degradation Genes from Oligotrophic Bradyrhizobium sp. Strain HW13 Isolated from a Pristine Environment

2002 ◽  
Vol 184 (2) ◽  
pp. 509-518 ◽  
Author(s):  
Wataru Kitagawa ◽  
Sachiko Takami ◽  
Keisuke Miyauchi ◽  
Eiji Masai ◽  
Yoichi Kamagata ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Burkholderia Cepacia ◽  
Ralstonia Eutropha ◽  
Rhodococcus Erythropolis ◽  
Amino Acid Sequences ◽  
Dichlorophenoxyacetic Acid ◽  
Phenol Derivatives ◽  
Degrading Bacteria ◽  
2,4 Dichlorophenoxyacetic Acid

ABSTRACT The tfd genes of Ralstonia eutropha JMP134 are the only well-characterized set of genes responsible for 2,4-dichlorophenoxyacetic acid (2,4-D) degradation among 2,4-D-degrading bacteria. A new family of 2,4-D degradation genes, cadRABKC, was cloned and characterized from Bradyrhizobium sp. strain HW13, a strain that was isolated from a buried Hawaiian soil that has never experienced anthropogenic chemicals. The cadR gene was inferred to encode an AraC/XylS type of transcriptional regulator from its deduced amino acid sequence. The cadABC genes were predicted to encode 2,4-D oxygenase subunits from their deduced amino acid sequences that showed 46, 44, and 37% identities with the TftA and TftB subunits of 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) oxygenase of Burkholderia cepacia AC1100 and with a putative ferredoxin, ThcC, of Rhodococcus erythropolis NI86/21, respectively. They are thoroughly different from the 2,4-D dioxygenase gene, tfdA, of R. eutropha JMP134. The cadK gene was presumed to encode a 2,4-D transport protein from its deduced amino acid sequence that showed 60% identity with the 2,4-D transporter, TfdK, of strain JMP134. Sinorhizobium meliloti Rm1021 cells containing cadRABKC transformed several phenoxyacetic acids, including 2,4-D and 2,4,5-T, to corresponding phenol derivatives. Frameshift mutations indicated that each of the cadRABC genes was essential for 2,4-D conversion in strain Rm1021 but that cadK was not. Five 2,4-D degraders, including Bradyrhizobium and Sphingomonas strains, were found to have cadA gene homologs, suggesting that these 2,4-D degraders share 2,4-D degradation genes similar to those of strain HW13 cadABC.

scholarly journals Flexible Community Structure Correlates with Stable Community Function in Methanogenic Bioreactor Communities Perturbed by Glucose

2000 ◽  
Vol 66 (9) ◽  
pp. 4058-4067 ◽  
Author(s):  
Ana S. Fernandez ◽  
Syed A. Hashsham ◽  
Sherry L. Dollhopf ◽  
Lutgarde Raskin ◽  
Olga Glagoleva ◽  
...  
Keyword(s):  
Community Structure ◽  
Relative Abundance ◽  
Restriction Analysis ◽  
Companion Paper ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Ssu Rrna ◽  
Rdna Genes ◽  
Community Function ◽  
Fermentative Bacteria

ABSTRACT Methanogenic bioreactor communities were used as model ecosystems to evaluate the relationship between functional stability and community structure. Replicated methanogenic bioreactor communities with two different community structures were established. The effect of a substrate loading shock on population dynamics in each microbial community was examined by using morphological analysis, small-subunit (SSU) rRNA oligonucleotide probes, amplified ribosomal DNA (rDNA) restriction analysis (ARDRA), and partial sequencing of SSU rDNA clones. One set of replicated communities, designated the high-spirochete (HS) set, was characterized by good replicability, a high proportion of spiral and short thin rod morphotypes, a dominance of spirochete-related SSU rDNA genes, and a high percentage ofMethanosarcina-related SSU rRNA. The second set of communities, designated the low-spirochete (LS) set, was characterized by incomplete replicability, higher morphotype diversity dominated by cocci, a predominance of Streptococcus-related and deeply branching Spirochaetales-related SSU rDNA genes, and a high percentage of Methanosaeta-related SSU rRNA. In the HS communities, glucose perturbation caused a dramatic shift in the relative abundance of fermentative bacteria, with temporary displacement of spirochete-related ribotypes byEubacterium-related ribotypes, followed by a return to the preperturbation community structure. The LS communities were less perturbed, with Streptococcus-related organisms remaining prevalent after the glucose shock, although changes in the relative abundance of minor members were detected by morphotype analysis. A companion paper demonstrates that the more stable LS communities were less functionally stable than the HS communities (S. A. Hashsham, A. S. Fernandez, S. L. Dollhopf, F. B. Dazzo, R. F. Hickey, J. M. Tiedje, and C. S. Criddle, Appl. Environ. Microbiol. 66:4050–4057, 2000).

scholarly journals Are microbes fundamentally different than macroorganisms? Convergence and a possible case for neutral phenotypic evolution in testate amoeba (Amoebozoa: Arcellinida)

2015 ◽  
Vol 2 (12) ◽  
pp. 150414 ◽  
Author(s):  
Angela M. Oliverio ◽  
Daniel J. G. Lahr ◽  
Jessica Grant ◽  
Laura A. Katz
Keyword(s):  
Testate Amoebae ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Coi Gene ◽  
Testate Amoeba ◽  
Phenotypic Evolution ◽  
Gene Sequences ◽  
Small Subunit Ribosomal Dna ◽  
Mitochondrial Cytochrome Oxidase ◽  
Phenotypic Convergence

This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI), we demonstrate discordance between morphology and molecules for ‘core Nebela ’ species (Arcellinida; Amoebozoa). Prior work using just a single locus, ssu-rDNA, also supported the non-monophyly of the genera Hyalosphenia and Nebela as well as for several morphospecies within these genera. Here, we obtained COI gene sequences of 59 specimens from seven morphospecies and ssu-rDNA gene sequences of 50 specimens from six morphospecies of hyalosphenids. Our analyses corroborate the prior ssu-rDNA findings of morphological convergence in test (shell) morphologies, as COI and ssu-rDNA phylogenies are concordant. Further, the monophyly of morphospecies is rejected using approximately unbiased tests. Given that testate amoebae are used as bioindicators in both palaeoecological and contemporary studies of threatened ecosystems such as bogs and fens, understanding the discordance between morphology and genetics in the hyalosphenids is essential for interpretation of indicator species. Further, while convergence is normally considered the result of natural selection, it is possible that neutrality underlies phenotypic evolution in these microorganisms.

scholarly journals Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria.

1997 ◽  
Vol 63 (6) ◽  
pp. 2266-2272 ◽  
Author(s):  
Y Kamagata ◽  
R R Fulthorpe ◽  
K Tamura ◽  
H Takami ◽  
L J Forney ◽  
...  
Keyword(s):  
Dichlorophenoxyacetic Acid ◽  
Degrading Bacteria ◽  
2,4 Dichlorophenoxyacetic Acid

A 2,4-dichlorophenoxyacetic acid degradation plasmid pM7012 discloses distribution of an unclassified megaplasmid group across bacterial species

Microbiology ◽  
2014 ◽  
Vol 160 (3) ◽  
pp. 525-536 ◽  
Author(s):  
Yoriko Sakai ◽  
Naoto Ogawa ◽  
Yumi Shimomura ◽  
Takeshi Fujii
Keyword(s):  
Bacterial Species ◽  
The United States ◽  
Dichlorophenoxyacetic Acid ◽  
Trna Genes ◽  
Plasmid Maintenance ◽  
Type Iv ◽  
Degrading Bacterium ◽  
Degrading Bacteria ◽  
2,4 Dichlorophenoxyacetic Acid ◽  
High Level

Analysis of the complete nucleotide sequence of plasmid pM7012 from 2,4-dichlorophenoxyacetic-acid (2,4-D)-degrading bacterium Burkholderia sp. M701 revealed that the plasmid had 582 142 bp, with 541 putative protein-coding sequences and 39 putative tRNA genes for the transport of the standard 20 aa. pM7012 contains sequences homologous to the regions involved in conjugal transfer and plasmid maintenance found in plasmids byi_2p from Burkholderia sp. YI23 and pBVIE01 from Burkholderia sp. G4. No relaxase gene was found in any of these plasmids, although genes for a type IV secretion system and type IV coupling proteins were identified. Plasmids with no relaxase gene have been classified as non-mobile plasmids. However, nucleotide sequences with a high level of similarity to the genes for plasmid transfer, plasmid maintenance, 2,4-D degradation and arsenic resistance contained on pM7012 were also detected in eight other megaplasmids (~600 or 900 kb) found in seven Burkholderia strains and a strain of Cupriavidus, which were isolated as 2,4-D-degrading bacteria in Japan and the United States. These results suggested that the 2,4-D degradation megaplasmids related to pM7012 are mobile and distributed across various bacterial species worldwide, and that the plasmid group could be distinguished from known mobile plasmid groups.

scholarly journals First record of Nocturama (Batrachospermales, Rhodophyta) in South America, with the description of a new species N. novamundensis

Phytotaxa ◽  
2016 ◽  
Vol 278 (3) ◽  
pp. 273
Author(s):  
ORLANDO NECCHI JR ◽  
TIMOTHY J. ENTWISLE ◽  
CIRO C.Z. BRANCO ◽  
MONICA O. PAIANO
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Large Subunit ◽  
First Record ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Molecular Evidence ◽  
Southern Brazil ◽  
Small Subunit Ribosomal Dna ◽  
A New Species

Specimens from southeastern and southern Brazil previously identified as Sheathia arcuata (= Batrachospermum arcuatum) are shown to be members of the recently described genus Nocturama, previously known only from Australia and New Zealand. Morphological and molecular evidence support recognizing the Brazilian specimens as a new species, described here as Nocturama novamundensis, sp. nov. Comparison of DNA sequences of the plastid-encoded ribulose-1,5-bisphosphatecarboxylase–oxygenase large subunit (rbcL) and the nuclear small subunit ribosomal DNA (SSU rDNA) markers showed Nocturama as a well supported clade. The sequence divergences between the new and the type species were high (95-98bp, 7.4–7.6%) for rbcL and 19bp, 1.1% for SSU), and those within each species were extremely low (0-1 bp, 0-0.1%). The new species can be distinguished from N. antipodites in having curved primary fascicles composed of non-‘audouinelloid’ cells (compared to straight primary fascicles with audouinelloid—cylindrical—cells) and in being always dioecious (only rarely is N. antipodites dioecious).

Description of the pseudocryptic species Conticribra weissflogiopsis sp. nov. (Thalassiosirales, Bacillariophyta) isolated from brackish waters in Korea, based on its cingulum structure and molecular analysis

Phytotaxa ◽  
2014 ◽  
Vol 191 (1) ◽  
pp. 115 ◽  
Author(s):  
JOON SANG PARK ◽  
JIN HWAN LEE
Keyword(s):  
Morphological Evolution ◽  
Morphological Characters ◽  
Molecular Data ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Diatom Species ◽  
Brackish Waters ◽  
Valve Structure ◽  
Small Subunit Ribosomal Dna ◽  
Pseudocryptic Species

We describe the new fultoportulate diatom species, Conticribra weissflogiopsis, isolated from brackish waters in Korea, based on morphological characters and molecular data. The new species is characterized by having areolae venation with internal (semi-) continuous cribra, a flat valve face, a single marginal rimoportula replacing a marginal fultoportula, a subcentral ring of the valve face fultoportulae, and a dextral pattern of cingulum structure. The overall valve structure of C. weissflogiopsis resembles that of C. weissflogii; however, the cingulum structure differs between the two species—C. weissflogiopsis has a dextral offset of band opening in the cingulum, whereas C. weissflogii has a sinistral offset. Phylogenetic analysis of the nuclear small subunit ribosomal DNA (SSU rDNA) revealed that C. weissflogiopsis is located in the Conticribra clade. Further, the pairwise genetic distance based on the SSU rDNA and the internal transcribed spacer 2 (ITS2) indicated that C. weissflogiopsis is a distinct Conticribra species. On the basis of the morphology and molecular phylogeny, we expand the hypothesis regarding the morphological evolution of Conticribra species.

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