scholarly journals Nocturnal Production of Endospores in Natural Populations of Epulopiscium-Like Surgeonfish Symbionts

2005 ◽  
Vol 187 (21) ◽  
pp. 7460-7470 ◽  
Author(s):  
Joseph F. Flint ◽  
Dan Drzymalski ◽  
W. Linn Montgomery ◽  
Gordon Southam ◽  
Esther R. Angert
Keyword(s):  
Intestinal Tract ◽  
Dipicolinic Acid ◽  
Phylogenetic Analyses ◽  
Natural Populations ◽  
Rrna Gene ◽  
Gram Positive Bacteria ◽  
Close Relationship ◽  
Close Relatives ◽  
In Situ Hybridizations

ABSTRACT Prior studies have described a morphologically diverse group of intestinal microorganisms associated with surgeonfish. Despite their diversity of form, 16S rRNA gene surveys and fluorescent in situ hybridizations indicate that these bacteria are low-G+C gram-positive bacteria related to Epulopiscium spp. Many of these bacteria exhibit an unusual mode of reproduction, developing multiple offspring intracellularly. Previous reports have suggested that some Epulopiscium-like symbionts produce dormant or phase-bright intracellular offspring. Close relatives of Epulopiscium, such as Metabacterium polyspora and Clostridium lentocellum, are endospore-forming bacteria, which raises the possibility that the phase-bright offspring are endospores. Structural evidence and the presence of dipicolinic acid demonstrate that phase-bright offspring of Epulopiscium-like bacteria are true endospores. In addition, endospores are formed as part of the normal daily life cycle of these bacteria. In the populations studied, mature endospores were seen only at night and the majority of cells in a given population produced one or two endospores per mother cell. Phylogenetic analyses confirmed the close relationship between the endospore-forming surgeonfish symbionts characterized here and previously described Epulopiscium spp. The broad distribution of endospore formation among the Epulopiscium phylogenetic group raises the possibility that sporulation is a characteristic of the group. We speculate that spore formation in Epulopiscium-like symbionts may be important for dispersal and may also enhance survival in the changing conditions of the fish intestinal tract.

scholarly journals Phylogenetic Diversity, Abundance, and Axial Distribution of Bacteria in the Intestinal Tract of Two Soil-Feeding Termites (Cubitermes spp.)

2003 ◽  
Vol 69 (10) ◽  
pp. 6007-6017 ◽  
Author(s):  
Dirk Schmitt-Wagner ◽  
Michael W. Friedrich ◽  
Bianca Wagner ◽  
Andreas Brune
Keyword(s):  
Intestinal Tract ◽  
Companion Paper ◽  
Rrna Gene ◽  
Molecular Fingerprinting ◽  
Axial Distribution ◽  
Phylogenetic Groups ◽  
Clone Libraries ◽  
Gram Positive Bacteria ◽  
Good Agreement

ABSTRACT The hindgut of soil-feeding termites is highly compartmentalized and characterized by pronounced axial dynamics of the intestinal pH and microbial processes such as hydrogen production, methanogenesis, and reductive acetogenesis. Nothing is known about the bacterial diversity and the abundance or axial distribution of the major phylogenetic groups in the different gut compartments. In this study, we showed that the variety of physicochemical conditions is reflected in the diversity of the microbial communities in the different gut compartments of two Cubitermes species (Termitidae: Termitinae). 16S rRNA gene clones from the highly alkaline first proctodeal segment (P1) of Cubitermes orthognathus represented almost exclusively gram-positive bacteria with low G+C content (LGC bacteria). In the posterior gut segments, their proportion decreased progressively, and the clone libraries comprised a variety of phyla, including the Cytophaga-Flexibacter-Bacteroides group, various subgroups of Proteobacteria, and the spirochetes. Phylogenetic analysis revealed that many of the clones clustered with sequences from the guts of other termites, and some even formed clusters containing only clones from C. orthognathus. The abundance and axial distribution of major phylogenetic groups in the gut of Cubitermes ugandensis were determined by fluorescence in situ hybridization with group-specific oligonucleotide probes. While the results were generally in good agreement with those of the clonal analysis, direct counts with probes specific for the Planctomycetales revealed a severe underestimation of representatives of this phylum in the clone libraries. Results obtained with newly designed FISH probes directed against two clusters of LGC clones from C. orthognathus indicated that the clones were restricted to specific gut regions. A molecular fingerprinting analysis published in a companion paper (D. Schmitt-Wagner, M. W. Friedrich, B. Wagner, and A. Brune, Appl. Environ. Microbiol. 69:6018-6024, 2003) corroborated the presence of compartment-specific bacterial communities in the gut of different Cubitermes species.

scholarly journals Enterobacter arachidis sp. nov., a plant-growth-promoting diazotrophic bacterium isolated from rhizosphere soil of groundnut

2010 ◽  
Vol 60 (7) ◽  
pp. 1559-1564 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Selvaraj Poonguzhali ◽  
Jung-Sook Lee ◽  
Venkatakrishnan Sivaraj Saravanan ◽  
Keun-Chul Lee ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Gene Sequence Analysis ◽  
Plant Growth Promoting ◽  
Taxonomic Approach ◽  
Close Relatives

A methylotrophic nitrogen-fixing bacterial strain, Ah-143T, isolated from the rhizosphere soil of field-grown groundnut was analysed by a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated strain Ah-143T to the family Enterobacteriaceae, with Enterobacter radicincitans and Enterobacter cowanii as the closest relatives. The strain is Gram-stain-negative, non-spore-forming, aerobic and motile, having straight rod-shaped cells with a DNA G+C content of approximately 53.2 mol%. The strain utilizes methanol as a carbon source and the mxaF gene was closely related to the mxaF gene of members of the genus Methylobacterium. The fatty acid profile consisted of C16 : 0, C17 : 0 cyclo, C18 : 1 ω7c, summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH) and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c) as the major components. DNA–DNA relatedness of strain Ah-143T with its close relatives was less than 20 %. On the basis of the phylogenetic analyses, DNA–DNA hybridization data, and unique physiological and biochemical characteristics, it is proposed that the strain represents a novel species of the genus Enterobacter and should be named Enterobacter arachidis sp. nov. The type strain is Ah-143T (=NCIMB 14469T =KCTC 22375T).

New cyanobacterium Nodosilinea svalbardensis sp. nov. (Prochlorotrichaceae, Synechococcales) isolated from alluvium in Mimer river valley of the Svalbard archipelago

Phytotaxa ◽  
2020 ◽  
Vol 442 (2) ◽  
pp. 61-79 ◽  
Author(s):  
DENIS DAVYDOV ◽  
SERGEI SHALYGIN ◽  
ANNA VILNET
Keyword(s):  
Phylogenetic Analyses ◽  
Natural Populations ◽  
Its Region ◽  
Total Evidence ◽  
Rrna Gene ◽  
New Taxon ◽  
Cyanobacterial Strain ◽  
Svalbard Archipelago ◽  
Molecular Approaches ◽  
The 16S Rrna Gene

A cyanobacterial strain isolated from the Svalbard archipelago was studied using morphological, ecological, and molecular approaches. The morphology of natural populations fit well the description of the Leptolyngbya s.l. however, in culture, they formed specific nodules that prevented affiliation to this genus. Further phylogenetic analyses including the 16S rRNA gene and 16S-23S ITS region revealed that the strain corresponds to the genus Nodosilinea. Based on this total evidence approach, we provide here a description of the new taxon Nodosilinea svalbardensis sp. nov.

scholarly journals SUP05 Dominates the Gammaproteobacterial Sulfur Oxidizer Assemblages in Pelagic Redoxclines of the Central Baltic and Black Seas

2013 ◽  
Vol 79 (8) ◽  
pp. 2767-2776 ◽  
Author(s):  
Sabine Glaubitz ◽  
Katrin Kießlich ◽  
Christian Meeske ◽  
Matthias Labrenz ◽  
Klaus Jürgens
Keyword(s):  
Baltic Sea ◽  
Phylogenetic Analyses ◽  
The Black Sea ◽  
Rrna Gene ◽  
Gene Transcript ◽  
Oligonucleotide Probes ◽  
Bisphosphate Carboxylase ◽  
Prokaryotic Abundance ◽  
Card Fish

ABSTRACTGammaproteobacterial sulfur oxidizers (GSOs), particularly SUP05-related sequences, have been found worldwide in numerous oxygen-deficient marine environments. However, knowledge regarding their abundance, distribution, and ecological role is scarce. In this study, on the basis of phylogenetic analyses of 16S rRNA gene sequences originating from a Baltic Sea pelagic redoxcline, thein situabundances of different GSO subgroups were quantified by CARD-FISH (catalyzed reporter fluorescencein situhybridization) with oligonucleotide probes developed specifically for this purpose. Additionally, ribulose bisphosphate carboxylase/oxygenase form II (cbbM) gene transcript clone libraries were used to detect potential active chemolithoautotrophic GSOs in the Baltic Sea. Taken together, the results obtained by these two approaches demonstrated the existence of two major phylogenetic subclusters embedded within the GSO, one of them affiliated with sequences of the previously described SUP05 subgroup. CARD-FISH analyses revealed that only SUP05 occurred in relatively high numbers, reaching 10 to 30% of the total prokaryotes around the oxic-anoxic interface, where oxygen and sulfide concentrations are minimal. The applicability of the oligonucleotide probes was confirmed with samples from the Black Sea redoxcline, in which the SUP05 subgroup accounted for 10 to 13% of the total prokaryotic abundance. ThecbbMtranscripts presumably originating from SUP05 cells support previous evidence for the chemolithoautotrophic activity of this phylogenetic group. Our findings on the vertical distribution and high abundance of SUP05 suggest that this group plays an important role in marine redoxcline biogeochemistry, probably as anaerobic or aerobic sulfur oxidizers.

scholarly journals Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

2008 ◽  
Vol 74 (17) ◽  
pp. 5422-5428 ◽  
Author(s):  
Mostafa S. Elshahed ◽  
Noha H. Youssef ◽  
Anne M. Spain ◽  
Cody Sheik ◽  
Fares Z. Najar ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Tall Grass ◽  
Data Set ◽  
Bacterial Phyla ◽  
Rare Biosphere ◽  
Soil Bacterial ◽  
Close Relatives ◽  
Taxonomic Groups

ABSTRACT Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

Small-subunit rRNA gene sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 1. Evidence for the Plocamiales ord.nov.

1994 ◽  
Vol 72 (9) ◽  
pp. 1250-1263 ◽  
Author(s):  
G. W. Saunders ◽  
G. T. Kraft
Keyword(s):  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Chain Reaction ◽  
Small Subunit Rrna Gene ◽  
New Information ◽  
The Family ◽  
Close Relationship ◽  
Polymerase Chain

Nucleotide sequences of the nuclear, small-subunit (SSU) ribosomal RNAs, as inferred from polymerase chain reaction (PCR)-amplified products, are presented for Areschougia congesta (Turner) J. Agardh (Solieriaceae), Dasyphloea insignis Montagne (Dumontiaceae), Sarcothalia crassifolia (C. Agardh) Edyvane & Womersley (Gigartinaceae), Nizymenia australis Sonder (Nizymeniaceae), Phacelocarpus peperocarpos (Poiret) Wynne, Ardré & Silva (Phacelocarpaceae), Plocamiocolax pulvinata Setchell, Plocamium angustum (J. Agardh) J.D. Hooker, Plocamium cartilagineum (Linnaeus) Dixon (Plocamiaceae), Rhodymenia linearis J. Agardh (Rhodymeniaceae), and Sphaerococcus coronopifolius Stackhouse (Sphaerococcaceae). Phylogenetic analyses of the SSU sequences between the Plocamiaceae and members of the Sphaerococcaceae, Phacelocarpaceae, and Nizymeniaceae, with which the Plocamiaceae has been associated historically, show SSU differences of between 87 and 105 nucleotides and do not indicate a close relationship. A review of anatomical knowledge of the Plocamiaceae and Pseudoanemoniaceae and new information on vegetative and tetrasporangial development in Plocamium and Plocamiocolax are presented to buttress a case for the Plocamiales ord.nov. Representatives of the Nizymeniaceae and Phacelocarpaceae differ from one another by only nine nucleotides, suggesting that these two taxa are very closely related and perhaps not distinct at the family rank. Key words: Gigartinales, PCR, phylogeny, Plocamiales ord.nov., Pseudoanemoniaceae, Rhodophyta, small-subunit rRNA, systematics.

scholarly journals Intestinal Integrity and Akkermansia muciniphila, a Mucin-Degrading Member of the Intestinal Microbiota Present in Infants, Adults, and the Elderly

2007 ◽  
Vol 73 (23) ◽  
pp. 7767-7770 ◽  
Author(s):  
M. Carmen Collado ◽  
Muriel Derrien ◽  
Erika Isolauri ◽  
Willem M. de Vos ◽  
Seppo Salminen
Keyword(s):  
Early Life ◽  
Intestinal Tract ◽  
The Elderly ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Akkermansia Muciniphila ◽  
Intestinal Integrity ◽  
The 16S Rrna Gene ◽  
Human Intestinal Tract

ABSTRACT Fluorescence in situ hybridization and real-time PCR analysis targeting the 16S rRNA gene of Akkermansia muciniphila were performed to determine its presence in the human intestinal tract. These techniques revealed that an A. muciniphila-like bacterium is a common member of the human intestinal tract and that its colonization starts in early life and develops within a year to a level close to that observed in adults (108 cells/g) but decreases (P < 0.05) in the elderly.

scholarly journals Phylogenetic Characterization and In Situ Detection of a Cytophaga-Flexibacter-Bacteroides Phylogroup Bacterium in Tuber borchii Vittad. Ectomycorrhizal Mycelium

2000 ◽  
Vol 66 (11) ◽  
pp. 5035-5042 ◽  
Author(s):  
Elena Barbieri ◽  
Lucia Potenza ◽  
Ismaela Rossi ◽  
Davide Sisti ◽  
Giovanna Giomaro ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Direct Sequencing ◽  
Phylogenetic Analyses ◽  
Mycorrhizal Fungus ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Tuber Borchii ◽  
In Situ Detection

ABSTRACT Mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. In this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus Tuber borchii Vittad. Universal eubacterial primers specific for the 5′ and 3′ ends of the 16S rRNA gene (16S rDNA) were used for PCR amplification, direct sequencing, and phylogenetic analyses. The 16S rDNA was amplified directly from four pure cultures of T. borchii Vittad. mycelium. A nearly full-length sequence of the gene coding for the prokaryotic small-subunit rRNA was obtained from each T. borchii mycelium studied. The 16S rDNA sequences were almost identical (98 to 99% similarity), and phylogenetic analysis placed them in a single unique rRNA branch belonging to theCytophaga-Flexibacter-Bacteroides (CFB) phylogroup which had not been described previously. In situ detection of the CFB bacterium in the hyphal tissue of the fungus T. borchii was carried out by using 16S rRNA-targeted oligonucleotide probes for the eubacterial domain and the Cytophaga-Flexibacter phylum, as well as a probe specifically designed for the detection of this mycelium-associated bacterium. Fluorescent in situ hybridization showed that all three of the probes used bound to the mycelium tissue. This study provides the first direct visual evidence of a not-yet-cultured CFB bacterium associated with a mycorrhizal fungus of the genusTuber.

Characterization of halophilic bacteria from environmental samples from the brackish water of Pulicat Lake, India

Biologia ◽  
2011 ◽  
Vol 66 (5) ◽  
Author(s):  
Harmesh Sahay ◽  
Surendra Singh ◽  
Rajeev Kaushik ◽  
Anil Saxena ◽  
Dilip Arora
Keyword(s):  
16S Rdna ◽  
Brackish Water ◽  
Phylogenetic Analyses ◽  
Halophilic Bacteria ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Gram Positive Bacteria ◽  
Nutrient Agar Medium

AbstractCulture dependent phenotypic characterization and 16S rDNA based phylogenetic analyses were applied to study the aerobic halophilic bacterial population present in the Pulicat brackish-water Lake of India. Five different media were employed for isolation of bacteria. A total of 198 morphotypes were recovered, purified and screened for salt tolerance in nutrient agar medium amended with 5–25% NaCl. Based on 16S rDNA restriction fragment length polymorphism analysis with three restriction endonucleases, 51 isolates tolerant to 5% or more NaCl were grouped into 29 clusters. Phylogenetic analysis using 16S rRNA gene sequences revealed that 29 strains could further be allocated into two clades: 19 to Firmicutes and 10 to γ-Proteobacteria. Firmicutes included low G+C Gram-positive bacteria related to family Bacillaceae, which included five genera Bacillus, Virgibacillus, Rummelibacillus, Alkalibacillus and Halobacillus. Another genera included in Firmicutes was Salimicrobium halophilum. In the γ-Proteobacteria group, all the isolates belonged to one genus Halomonas, represented by six different species Halomonas salina, H. shengliensis, H. salifodinae, H. pacifica, H. aquamarina and H. halophila. Most of the isolates exhibited cellulase, xylanase, amylase and protease activities.

scholarly journals ‘Candidatus Midichloria mitochondrii’, an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle

2006 ◽  
Vol 56 (11) ◽  
pp. 2535-2540 ◽  
Author(s):  
Davide Sassera ◽  
Tiziana Beninati ◽  
Claudio Bandi ◽  
Edwin A. P. Bouman ◽  
Luciano Sacchi ◽  
...  
Keyword(s):  
Ixodes Ricinus ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Hard Tick ◽  
Intermembrane Space ◽  
16S Rrna Gene Sequences ◽  
Ovarian Cells ◽  
Midichloria Mitochondrii

An intracellular bacterium with the unique ability to enter mitochondria exists in the European vector of Lyme disease, the hard tick Ixodes ricinus. Previous phylogenetic analyses based on 16S rRNA gene sequences suggested that the bacterium formed a divergent lineage within the Rickettsiales (Alphaproteobacteria). Here, we present additional phylogenetic evidence, based on the gyrB gene sequence, that confirms the phylogenetic position of the bacterium. Based on these data, as well as electron microscopy (EM), in situ hybridization and other observations, we propose the name ‘Candidatus Midichloria mitochondrii’ for this bacterium. The symbiont appears to be ubiquitous in females of I. ricinus across the tick's distribution, while lower prevalence is observed in males (44 %). Based on EM and in situ hybridization studies, the presence of ‘Candidatus M. mitochondrii’ in females appears to be restricted to ovarian cells. The bacterium was found to be localized both in the cytoplasm and in the intermembrane space of the mitochondria of ovarian cells. ‘Candidatus M. mitochondrii’ is the first bacterium to be identified that resides within animal mitochondria.

Sign in / Sign up

Export Citation Format

Share Document