CultivatedBeggiatoaspp. define the phylogenetic root of morphologically diverse, noncultured, vacuolate sulfur bacteria

2006 ◽  
Vol 52 (6) ◽  
pp. 591-598 ◽  
Author(s):  
Azeem Ahmad ◽  
Karen M Kalanetra ◽  
Douglas C Nelson
Keyword(s):  
16S Rdna ◽  
Pure Culture ◽  
Natural Populations ◽  
Taxonomic Revision ◽  
Sulfur Cycle ◽  
Ssu Rrna ◽  
Sulfur Bacteria ◽  
Colorless Sulfur Bacteria ◽  
Superficial Similarity ◽  
Rrna Sequences

Within the last 10 years, numerous SSU rRNA sequences have been collected from natural populations of conspicuous, vacuolate, colorless sulfur bacteria, which form a phylogenetically cohesive cluster (large-vacuolate sulfur bacteria clade) in the γ-Proteobacteria. Currently, this clade is composed of four named or de facto genera: all known Thioploca and Thiomargarita strains, all vacuolate Beggiatoa strains, and several strains of vacuolate, attached filaments, which bear a superficial similarity to Thiothrix. Some of these vacuolate bacteria accumulate nitrate for respiratory purposes. This clade encompasses the largest known prokaryotic cells (Thiomargarita namibiensis) and several strains that are important in the global marine sulfur cycle. Here, we report additional sequences from five pure culture strains of Beggiatoa spp., including the only two cultured marine strains (nonvacuolate), which firmly establish the root of this vacuolate clade. Each of several diverse metabolic motifs, including obligate and facultative chemolithoautotrophy, probable mixotrophy, and seemingly strict organoheterotrophy, is represented in at least one of the nonvacuolate strains that root the vacuolate clade. Because the genus designation Beggiatoa is interspersed throughout the vacuolate clade along with other recognized or de facto genera, the need for taxonomic revision is clear.Key words: vacuolate, sulfur bacteria, Beggiatoa, 16S rDNA, phylogeny.

The Basal Position of Scaly Green Flagellates among the Green Algae (Chlorophyta) is Revealed by Analyses of Nuclear-Encoded SSU rRNA Sequences

Protist ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 367-380 ◽  
Author(s):  
Takeshi Nakayama ◽  
Birger Marin ◽  
Harald D. Kranz ◽  
Barbara Surek ◽  
Volker A.R. Huss ◽  
...  
Keyword(s):  
Green Algae ◽  
Ssu Rrna ◽  
Basal Position ◽  
Rrna Sequences

scholarly journals Expansion of ability of denitrification within the filamentous colorless sulfur bacteria of the genusThiothrix

2014 ◽  
Vol 358 (1) ◽  
pp. 72-80 ◽  
Author(s):  
Ivan V. Trubitsyn ◽  
Elena V. Belousova ◽  
Maria N. Tutukina ◽  
Alexander Y. Merkel ◽  
Galina A. Dubinina ◽  
...  
Keyword(s):  
Sulfur Bacteria ◽  
Colorless Sulfur Bacteria

Human intestinal spirochetosis diagnosed with colonoscopy and analysis of partial 16S rDNA sequences of involved spirochetes

2001 ◽  
Vol 2 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Wolfgang Kraatz ◽  
Ulf Thunberg ◽  
Bertil Pettersson ◽  
Claes Fellström
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rdna Sequences ◽  
Intestinal Spirochetosis ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Human Intestinal Spirochetosis ◽  
Type Strains ◽  
Rrna Sequences

AbstractDNA was extracted from colonic biopsies of 33 patients with and three without evidence of intestinal spirochetosis (IS) in the large bowel. The biopsies were subjected to PCR. A pair of primers, generating a 207 bp fragment, were designed to detect specifically the 16S rDNA gene ofBrachyspira. PCR products of the expected size were obtained from 33 samples with histologic evidence of IS. The PCR amplicons were used for sequencing. The sequences obtained were aligned to the corresponding 16S rRNA sequences of five type strains ofBrachyspira. The sequences of 23 PCR products were 99–100% identical with the correspond-ingB.aalborgitype strain sequence. Two cases showed 99–100% sequence similarity with the type strain ofB.pilosicoliP43/6/78. Six cases could not be referred to any of the known species ofBrachyspira. Two PCR products gave incomplete sequences.

scholarly journals In Situ Detection, Isolation, and Physiological Properties of a Thin Filamentous Microorganism Abundant in Methanogenic Granular Sludges: a Novel Isolate Affiliated with a Clone Cluster, the Green Non-Sulfur Bacteria, Subdivision I

2001 ◽  
Vol 67 (12) ◽  
pp. 5740-5749 ◽  
Author(s):  
Yuji Sekiguchi ◽  
Hiroki Takahashi ◽  
Yoichi Kamagata ◽  
Akiyoshi Ohashi ◽  
Hideki Harada
Keyword(s):  
16S Rdna ◽  
Yeast Extract ◽  
Sea Urchins ◽  
Granular Sludge ◽  
Limited Range ◽  
Strictly Anaerobic ◽  
Sulfur Bacteria ◽  
Filamentous Microorganisms ◽  
Methanothermobacter Thermautotrophicus

ABSTRACT We previously showed that very thin filamentous bacteria affiliated with the division green non-sulfur bacteria were abundant in the outermost layer of thermophilic methanogenic sludge granules fed with sucrose and several low-molecular-weight fatty acids (Y. Sekiguchi, Y. Kamagata, K. Nakamura, A. Ohashi, H. Harada, Appl. Environ. Microbiol. 65:1280–1288, 1999). Further 16S ribosomal DNA (rDNA) cloning-based analysis revealed that the microbes were classified within a unique clade, green non-sulfur bacteria (GNSB) subdivision I, which contains a number of 16S rDNA clone sequences from various environmental samples but no cultured representatives. To investigate their function in the community and physiological traits, we attempted to isolate the yet-to-be-cultured microbes from the original granular sludge. The first attempt at isolation from the granules was, however, not successful. In the other thermophilic reactor that had been treating fried soybean curd-manufacturing wastewater, we found filamentous microorganisms to outgrow, resulting in the formation of projection-like structures on the surface of granules, making the granules look like sea urchins. 16S rDNA-cloning analysis combined with fluorescent in situ hybridization revealed that the projections were comprised of the uncultured filamentous cells affiliated with the GNSB subdivision I and Methanothermobacter-like cells and the very ends of the projections were comprised solely of the filamentous cells. By using the tip of the projection as the inoculum for primary enrichment, a thermophilic, strictly anaerobic, filamentous bacterium, designated strain UNI-1, was successfully isolated with a medium supplemented with sucrose and yeast extract. The strain was a very slow growing bacterium which is capable of utilizing only a limited range of carbohydrates in the presence of yeast extract and produced hydrogen from these substrates. The growth was found to be significantly stimulated when the strain was cocultured with a hydrogen-utilizing methanogen, Methanothermobacter thermautotrophicus, suggesting that the strain is a sugar-fermenting bacterium, the growth of which is dependent on hydrogen consumers in the granules.

The taxonomy and phylogeny of the genus Cylindrospermopsis (Cyanobacterium) evaluated by adding five new records from China

Phytotaxa ◽  
2017 ◽  
Vol 316 (3) ◽  
pp. 224 ◽  
Author(s):  
XIAO-CHUANG LI ◽  
SHOU-LIANG HUO ◽  
FANG-FANG CAI ◽  
YI-MING YANG ◽  
BEI-DOU XI ◽  
...  
Keyword(s):  
16S Rrna ◽  
New Records ◽  
Natural Populations ◽  
Taxonomic Revision ◽  
Species Level ◽  
Freshwater Bodies ◽  
Genetic Characters

The diversity of the genus Cylindrospermopsis was underestimated, and the species in majority were described from natural populations, and not evaluated genetically except for the widely reported C. raciborskii. In the study, five new records (C. catemaco, C. philippinensis, C. taverae, C. africana and C. helicoidea) were herein described from Chinese freshwater bodies. By isolating their unialgal cultures, they were taxonomically evaluated based on phenotypic and genetic characters (16S rRNA, ITS-L, cpcBA-IGS and rpoC1). New insights into the Cylindrospermopsis taxonomy were obtained that different species within the genus could not be fully distinguished. The present result suggested that morphospecies based taxonomy within cyanobacterial genera will still be used, waiting for further verification and taxonomic revision at species level based on the modern approaches.

scholarly journals Novel Eukaryotic Lineages Inferred from Small-Subunit rRNA Analyses of Oxygen-Depleted Marine Environments

2003 ◽  
Vol 69 (5) ◽  
pp. 2657-2663 ◽  
Author(s):  
Thorsten Stoeck ◽  
Slava Epstein
Keyword(s):  
Salt Marsh ◽  
Phylogenetic Tree ◽  
Sequence Similarity ◽  
Small Subunit ◽  
Cape Cod ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Related Sequence ◽  
Diverse Communities ◽  
Rrna Sequences

ABSTRACT Microeukaryotes in oxygen-depleted environments are among the most diverse, as well as the least studied, organisms. We conducted a cultivation-independent, small-subunit (SSU) rRNA-based survey of microeukaryotes in suboxic waters and anoxic sediments in the great Sippewisset salt marsh, Cape Cod, Mass. We generated two clone libraries and analyzed approximately 300 clones, which contained a large diversity of microeukaryotic SSU rRNA signatures. Only a few of these signatures were closely related (sequence similarity of >97%) to the sequences reported earlier. The bulk of our sequences represented deep novel branches within green algae, fungi, cercozoa, stramenopiles, alveolates, euglenozoa and unclassified flagellates. In addition, a significant number of detected rRNA sequences exhibited no affiliation to known organisms and sequences and thus represent novel lineages of the highest taxonomical order, most of them branching off the base of the global phylogenetic tree. This suggests that oxygen-depleted environments harbor diverse communities of novel organisms, which may provide an interesting window into the early evolution of eukaryotes.

scholarly journals The Plot Thickens: Haploid and Triploid-Like Thalli, Hybridization, and Biased Mating Type Ratios in Letharia

2021 ◽  
Vol 2 ◽  
Author(s):  
Sandra Lorena Ament-Velásquez ◽  
Veera Tuovinen ◽  
Linnea Bergström ◽  
Toby Spribille ◽  
Dan Vanderpool ◽  
...  
Keyword(s):  
Mating Type ◽  
Pure Culture ◽  
Natural Populations ◽  
Common Belief ◽  
Genetic Studies ◽  
Type Locus ◽  
Genomic Study ◽  
The Common ◽  
Mat Locus

The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we infer the genome organization and reproduction in Letharia by analyzing genomic data from a pure culture and from thalli, and performing a PCR survey of the MAT locus in natural populations. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations.

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