scholarly journals Genomic and Phenotypic Characterization of Chloracidobacterium Isolates Provides Evidence for Multiple Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Mohit Kumar Saini ◽  
Aswathy Sebastian ◽  
Yoshiki Shirotori ◽  
Nathan T. Soulier ◽  
Amaya M. Garcia Costas ◽  
...  
Keyword(s):  
Growth Medium ◽  
Microbial Mats ◽  
Hot Spring ◽  
Enrichment Culture ◽  
Green Sulfur Bacteria ◽  
Phenotypic Characterization ◽  
Comparative Genomic ◽  
Phenotypic Properties ◽  
New Family ◽  
Genomic Studies

Chloracidobacterium is the first and until now the sole genus in the phylum Acidobacteriota (formerly Acidobacteria) whose members perform chlorophyll-dependent phototrophy (i.e., chlorophototrophy). An axenic isolate of Chloracidobacterium thermophilum (strain BT) was previously obtained by using the inferred genome sequence from an enrichment culture and diel metatranscriptomic profiling analyses in situ to direct adjustments to the growth medium and incubation conditions, and thereby a defined growth medium for Chloracidobacterium thermophilum was developed. These advances allowed eight additional strains of Chloracidobacterium spp. to be isolated from microbial mat samples collected from Mushroom Spring, Yellowstone National Park, United States, at temperatures of 41, 52, and 60°C; an axenic strain was also isolated from Rupite hot spring in Bulgaria. All isolates are obligately photoheterotrophic, microaerophilic, non-motile, thermophilic, rod-shaped bacteria. Chloracidobacterium spp. synthesize multiple types of (bacterio-)chlorophylls and have type-1 reaction centers like those of green sulfur bacteria. Light harvesting is accomplished by the bacteriochlorophyll a-binding, Fenna-Matthews-Olson protein and chlorosomes containing bacteriochlorophyll c. Their genomes are approximately 3.7 Mbp in size and comprise two circular chromosomes with sizes of approximately 2.7 Mbp and 1.0 Mbp. Comparative genomic studies and phenotypic properties indicate that the nine isolates represent three species within the genus Chloracidobacterium. In addition to C. thermophilum, the microbial mats at Mushroom Spring contain a second species, tentatively named Chloracidobacterium aggregatum, which grows as aggregates in liquid cultures. The Bulgarian isolate, tentatively named Chloracidobacterium validum, will be proposed as the type species of the genus, Chloracidobacterium. Additionally, Chloracidobacterium will be proposed as the type genus of a new family, Chloracidobacteriaceae, within the order Blastocatellales, the class Blastocatellia, and the phylum Acidobacteriota.

scholarly journals Microscopic Examination of Distribution and Phenotypic Properties of Phylogenetically Diverse Chloroflexaceae-Related Bacteria in Hot Spring Microbial Mats

2002 ◽  
Vol 68 (9) ◽  
pp. 4593-4603 ◽  
Author(s):  
Ulrich Nübel ◽  
Mary M. Bateson ◽  
Verona Vandieken ◽  
Andrea Wieland ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Hot Spring ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Small Scale ◽  
Phenotypic Properties ◽  
In Situ Conditions ◽  
Type C ◽  
Microelectrode Measurements

ABSTRACT We investigated the diversity, distribution, and phenotypes of uncultivated Chloroflexaceae-related bacteria in photosynthetic microbial mats of an alkaline hot spring (Mushroom Spring, Yellowstone National Park). By applying a directed PCR approach, molecular cloning, and sequence analysis of 16S rRNA genes, an unexpectedly large phylogenetic diversity among these bacteria was detected. Oligonucleotide probes were designed to target 16S rRNAs from organisms affiliated with the genus Chloroflexus or with the type C cluster, a group of previously discovered Chloroflexaceae relatives of this mat community. The application of peroxidase-labeled probes in conjunction with tyramide signal amplification enabled the identification of these organisms within the microbial mats by fluorescence in situ hybridization (FISH) and the investigation of their morphology, abundance, and small-scale distribution. FISH was combined with oxygen microelectrode measurements, microscope spectrometry, and microautoradiography to examine their microenvironment, pigmentation, and carbon source usage. Abundant type C-related, filamentous bacteria were found to flourish within the cyanobacterium-dominated, highly oxygenated top layers and to predominate numerically in deeper orange-colored zones of the investigated microbial mats, correlating with the distribution of bacteriochlorophyll a. Chloroflexus sp. filaments were rare at 60°C but were more abundant at 70°C, where they were confined to the upper millimeter of the mat. Both type C organisms and Chloroflexus spp. were observed to assimilate radiolabeled acetate under in situ conditions.

scholarly journals Comparative genomic investigation of high-elevation adaptation in ectothermic snakes

2018 ◽  
Vol 115 (33) ◽  
pp. 8406-8411 ◽  
Author(s):  
Jia-Tang Li ◽  
Yue-Dong Gao ◽  
Liang Xie ◽  
Cao Deng ◽  
Peng Shi ◽  
...  
Keyword(s):  
De Novo ◽  
Hot Spring ◽  
High Elevation ◽  
Comparative Genomic ◽  
The Tibetan Plateau ◽  
Functional Assays ◽  
Damage Repair ◽  
Genomic Studies ◽  
Genetic Mechanisms ◽  
High Elevations

Several previous genomic studies have focused on adaptation to high elevations, but these investigations have been largely limited to endotherms. Snakes of the genus Thermophis are endemic to the Tibetan plateau and therefore present an opportunity to study high-elevation adaptations in ectotherms. Here, we report the de novo assembly of the genome of a Tibetan hot-spring snake (Thermophis baileyi) and then compare its genome to the genomes of the other two species of Thermophis, as well as to the genomes of two related species of snakes that occur at lower elevations. We identify 308 putative genes that appear to be under positive selection in Thermophis. We also identified genes with shared amino acid replacements in the high-elevation hot-spring snakes compared with snakes and lizards that live at low elevations, including the genes for proteins involved in DNA damage repair (FEN1) and response to hypoxia (EPAS1). Functional assays of the FEN1 alleles reveal that the Thermophis allele is more stable under UV radiation than is the ancestral allele found in low-elevation lizards and snakes. Functional assays of EPAS1 alleles suggest that the Thermophis protein has lower transactivation activity than the low-elevation forms. Our analysis identifies some convergent genetic mechanisms in high-elevation adaptation between endotherms (based on studies of mammals) and ectotherms (based on our studies of Thermophis).

scholarly journals Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria

2010 ◽  
Vol 60 (6) ◽  
pp. 1376-1382 ◽  
Author(s):  
Takao Iino ◽  
Koji Mori ◽  
Yoshihito Uchino ◽  
Tatsunori Nakagawa ◽  
Shigeaki Harayama ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Green Sulfur Bacteria ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Moderately Thermophilic ◽  
Sulfur Bacteria ◽  
Green Sulfur

A moderately thermophilic chemoheterotrophic bacterium, strain Mat9-16T, was isolated from microbial mats developed in hot spring water streams from Yumata, Nagano, Japan. Cells of strain Mat9-16T were strictly anaerobic, Gram-stain-negative, non-sporulating, non-motile and short to long rods (2.0–15.5 μm in length). Strain Mat9-16T grew fermentatively with optimum growth at 45 °C, pH 7.0–7.5 and 1 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene revealed that strain Mat9-16T was affiliated with an uncultivated lineage, and the nearest cultivated neighbours were green sulfur bacteria belonging to the class Chlorobea with 77–83 % sequence similarity. However, strain Mat9-16T could not grow phototrophically and did not possess light-harvesting structures, morphologically and genetically, such as the chlorosomes of green sulfur bacteria. On the basis of phenotypic features and phylogenetic position, a novel genus and species are proposed for strain Mat9-16T, to be named Ignavibacterium album gen. nov., sp. nov. (=NBRC 101810T =DSM 19864T). We also propose to place the cultivated bacterial lineage accommodating the sole representative Mat9-16T in a novel class, Ignavibacteria classis nov. In addition, we present a formal description of the phylum-level taxon ‘Chlorobi’ as Chlorobi phyl. nov.

scholarly journals High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata

2021 ◽  
Vol 22 (11) ◽  
pp. 5723
Author(s):  
Yuan-Yuan Xu ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Ren-Fang Zeng ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
Expression Patterns ◽  
High Density ◽  
Poncirus Trifoliata ◽  
Leaf Abscission ◽  
Comparative Genomic ◽  
Map Comparison ◽  
Genomic Studies

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

scholarly journals The Diversity and Evolution of Sex Chromosomes in Frogs

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 483
Author(s):  
Wen-Juan Ma ◽  
Paris Veltsos
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Comparative Genomic ◽  
Ancestral State ◽  
Heteromorphic Sex Chromosomes ◽  
Genomic Studies ◽  
Evolutionary Trajectories ◽  
Heterogametic Sex

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

Obligately phototrophic Chloroflexus: primary production in anaerobic hot spring microbial mats

1987 ◽  
Vol 147 (1) ◽  
pp. 80-87 ◽  
Author(s):  
S. J. Giovannoni ◽  
N. P. Revsbech ◽  
D. M. Ward ◽  
R. W. Castenholz
Keyword(s):  
Primary Production ◽  
Microbial Mats ◽  
Hot Spring

scholarly journals In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexusaggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat

2021 ◽  
Vol 9 (3) ◽  
pp. 652
Author(s):  
Shigeru Kawai ◽  
Joval N. Martinez ◽  
Mads Lichtenberg ◽  
Erik Trampe ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Environmental Conditions ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Photosynthetic Bacterium ◽  
Early Morning ◽  
Metabolic Flexibility

Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.

scholarly journals Identification of RD5-EncodedMycobacterium tuberculosisProteins As B-Cell Antigens Used for Serodiagnosis of Tuberculosis

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Miao-Miao Zhang ◽  
Jun-Wei Zhao ◽  
Zhan-Qiang Sun ◽  
Jun Liu ◽  
Xiao-Kui Guo ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Detection Sensitivity ◽  
Comparative Genomic ◽  
Healthy Controls ◽  
Specific Diagnosis ◽  
Pulmonary Tb ◽  
Genomic Studies ◽  
Immunodominant Antigens ◽  
Genomic Regions ◽  
Hiv Negative

Comparative genomic studies have identified severalMycobacterium tuberculosis-specific genomic regions of difference (RDs) which are absent in the vaccine strains ofMycobacterium bovisBCG and which may be useful in the specific diagnosis of tuberculosis (TB). In this study, all encoded proteins from DNA segment RD5 ofMycobacterium tuberculosis, that is, Rv3117–Rv3121, were recombined and evaluated by enzyme-linked immunosorbent assays for antibody reactivity with sera from HIV-negative pulmonary TB patients (n=60) and healthy controls (n=32). The results identified two immunodominant antigens, that is, Rv3117 and Rv3120, both of which revealed a statistically significant antigenic distinction between healthy controls and TB patients (P<0.05). In comparison with the well-known early-secreted antigen target 6 kDa (ESAT-6) (sensitivity 21.7%, specificity 90.6%), the higher detection sensitivity and higher specificity were achieved (Rv3117: sensitivity 25%, specificity 96.9%; Rv3120: sensitivity 31.7%, specificity 96.9%). Thus, the results highlight the immunosensitive and immunospecific nature of Rv3117 and Rv3120 and indicate promise for their use in the serodiagnosis of TB.

scholarly journals Changes in Quinone Profiles of Hot Spring Microbial Mats with a Thermal Gradient

1999 ◽  
Vol 65 (1) ◽  
pp. 198-205 ◽  
Author(s):  
Akira Hiraishi ◽  
Taichi Umezawa ◽  
Hiroyuki Yamamoto ◽  
Kenji Kato ◽  
Yonosuke Maki
Keyword(s):  
Thermal Gradient ◽  
Microbial Mats ◽  
Hot Springs ◽  
Hot Spring ◽  
Thermal Gradients ◽  
Cyanobacterial Mats ◽  
Dissimilarity Index ◽  
Quinone Profile ◽  
Bacterial Mats ◽  
Different Temperatures

ABSTRACT The respiratory and photosynthetic quinones of microbial mats which occurred in Japanese sulfide-containing neutral-pH hot springs at different temperatures were analyzed by spectrochromatography and mass spectrometry. All of the microbial mats that developed at high temperatures (temperatures above 68°C) were so-called sulfur-turf bacterial mats and produced methionaquinones (MTKs) as the major quinones. A 78°C hot spring sediment had a similar quinone profile.Chloroflexus-mixed mats occurred at temperatures of 61 to 65°C and contained menaquinone 10 (MK-10) as the major component together with significant amounts of either MTKs or plastoquinone 9 (PQ-9). The sunlight-exposed biomats growing at temperatures of 45 to 56°C were all cyanobacterial mats, in which the photosynthetic quinones (PQ-9 and phylloquinone) predominated and MK-10 was the next most abundant component in most cases. Ubiquinones (UQs) were not found or were detected in only small amounts in the biomats growing at temperatures of 50°C and above, whereas the majority of the quinones of a purple photosynthetic mat growing at 34°C were UQs. A numerical analysis of the quinone profiles was performed by using the following three parameters: dissimilarity index (D), microbial divergence index (MDq ), and bioenergetic divergence index (BDq ). A D matrix tree analysis showed that the hot spring mats consisting of the sulfur-turf bacteria, Chloroflexus spp., cyanobacteria, and purple phototrophic bacteria formed distinct clusters. Analyses ofMDq and BDq values indicated that the microbial diversity of hot spring mats decreased as the temperature of the environment increased. The changes in quinone profiles and physiological types of microbial mats in hot springs with thermal gradients are discussed from evolutionary viewpoints.

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