scholarly journals The Effect of Spring Water Geochemistry on Copper Proteins in Tengchong Hot Springs, China

2020 ◽  
Vol 86 (13) ◽  
Author(s):  
Shreya Srivastava ◽  
Hailiang Dong ◽  
Brandon R. Briggs
Keyword(s):  
High Temperature ◽  
Binding Proteins ◽  
Hot Springs ◽  
Hot Spring ◽  
Metagenomic Data ◽  
Copper Proteins ◽  
Ph Gradients ◽  
Quinol Oxidase ◽  
Binding Domains ◽  
Wide Range

ABSTRACT Copper (Cu) is an essential trace metal cofactor for a variety of proteins; however, excess Cu is toxic to most organisms. Cu homeostasis is maintained by a complex machinery of Cu binding proteins that control the uptake, transport, sequestration, and efflux of Cu ions. Despite the importance of Cu binding proteins in electron transfer, substrate oxidation, superoxide dismutation, and denitrification, little information exists about microbial Cu utilization in extreme environments, where the geochemical conditions may affect Cu bioavailability. Using metagenomic data from 9 hot springs in Tengchong, China, which range in temperature from 42°C to 96°C and in pH from 2.3 to 9, the effects of pH, temperature, and spring geochemistry on the distribution of Cu binding domains of proteins and oxidoreductases were studied. Dissolved Cu and Cu binding domains were detected across all temperature and pH gradients. Cu binding domains of cytochrome c oxidase subunits, heavy-metal-associated domains, and nitrous oxide reductase were detected at all sites. DoxB, a quinol oxidase, and other quinol oxidase subunits were the dominant Cu binding oxidoreductase subunits present at low-pH and high-temperature sites, whereas cbb3-type cytochrome c oxidase subunits were dominant at high-pH and high-temperature sites. Additionally, aa3-type cytochrome c oxidase was more prominent than cbb3-type cytochrome c oxidase under circumneutral-pH conditions. This suggests that the type of cytochrome c oxidase pathway and the Cu proteins employed by microbes to carry out important functions such as energy acquisition and efflux of excess Cu are affected by the physicochemical conditions of the springs. IMPORTANCE Copper is present in a variety of proteins and is required to carry out essential functions by all organisms. However, in hot spring environments, copper availability may be limited due to the high temperatures and the wide range in pH. The significance of our research is in relating the physicochemical environment to the distribution of copper proteins across hot spring environments, which provides increased understanding of primary functions and adaptions in these environments.

scholarly journals Carbon Source Preference in Chemosynthetic Hot Spring Communities

2015 ◽  
Vol 81 (11) ◽  
pp. 3834-3847 ◽  
Author(s):  
Matthew R. Urschel ◽  
Michael D. Kubo ◽  
Tori M. Hoehler ◽  
John W. Peters ◽  
Eric S. Boyd
Keyword(s):  
High Temperature ◽  
National Park ◽  
Hot Springs ◽  
Dissolved Inorganic Carbon ◽  
Hot Spring ◽  
Affinity Constant ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Short Term ◽  
Acetate Assimilation

ABSTRACTRates of dissolved inorganic carbon (DIC), formate, and acetate mineralization and/or assimilation were determined in 13 high-temperature (>73°C) hot springs in Yellowstone National Park (YNP), Wyoming, in order to evaluate the relative importance of these substrates in supporting microbial metabolism. While 9 of the hot spring communities exhibited rates of DIC assimilation that were greater than those of formate and acetate assimilation, 2 exhibited rates of formate and/or acetate assimilation that exceeded those of DIC assimilation. Overall rates of DIC, formate, and acetate mineralization and assimilation were positively correlated with spring pH but showed little correlation with temperature. Communities sampled from hot springs with similar geochemistries generally exhibited similar rates of substrate transformation, as well as similar community compositions, as revealed by 16S rRNA gene-tagged sequencing. Amendment of microcosms with small (micromolar) amounts of formate suppressed DIC assimilation in short-term (<45-min) incubations, despite the presence of native DIC concentrations that exceeded those of added formate by 2 to 3 orders of magnitude. The concentration of added formate required to suppress DIC assimilation was similar to the affinity constant (Km) for formate transformation, as determined by community kinetic assays. These results suggest that dominant chemoautotrophs in high-temperature communities are facultatively autotrophic or mixotrophic, are adapted to fluctuating nutrient availabilities, and are capable of taking advantage of energy-rich organic substrates when they become available.

scholarly journals Distinct microbial composition and functions in an underground high-temperature hot spring at different depths

2019 ◽  
Author(s):  
Shijie Bai ◽  
Xiaotong Peng
Keyword(s):  
High Temperature ◽  
Microbial Communities ◽  
Hot Springs ◽  
Hot Spring ◽  
Hydrogen Oxidation ◽  
Archaeal Community ◽  
Limited Area ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Different Depths

Abstract. The microbial diversity and functions of three high-temperature neutral hot springs water samples at different depths (0 m, 19 m and 58 m) were investigated based on 16S rRNA gene sequencing and a functional gene array (GeoChip 5.0). The results revealed that the bacterial communities were distinct at different depths in the hot springs. Additionally, in response to the depths, bacterial/archaeal community compositions exhibited shifts over the depth profiles. Aquificae, Alpha-proteobacteria, and Deinococcus-Thermus were the dominating phyla at 0 m, 19 m, and 58 m, respectively. Hydrogenobacter, Sphingobium, and Thermus were the most abundant genera at 0 m, 19 m, and 58 m, respectively. The phylum Thaumarchaeota was the most abundant member of the archaeal community in the samples at different hot spring depths. Functional results of the microbial communities indicated that microbial metabolic functions were mainly related to sulfur, nitrogen cycling, and hydrogen oxidation. In summary, our results demonstrated that distinct microbial communities and functions were found at different depths of hot springs in a very limited area. These findings will provide new insights into the deep-subsurface biosphere associated with terrestrial hot springs.

scholarly journals INTERPRETATION OF ALTERATION MINERALS AROUND THE OMA-HARUKU HOT SPRINGS, CENTRAL OF MOLUCCAS

2019 ◽  
Vol 2 (2) ◽  
pp. 090-096
Author(s):  
Helda Andayany ◽  
Josephus Ronny Kelibulin
Keyword(s):  
Particle Size ◽  
High Temperature ◽  
Hot Springs ◽  
Hot Spring ◽  
Geothermal Field ◽  
Petrographic Analysis ◽  
Rock Samples ◽  
Spring Area ◽  
Alteration Minerals ◽  
Xrd Method

Petrographic analysis to rock samples located at Oma-Haruku hot springs was dominated by mudstone. Another alteration mineral types of the rocks in this area are quartz, aragonite/calcite and feldspar minerals. Petrographic analysis was supported by the XRD method. The method indicated that the alteration minerals content was generally dominated by the presence of aragonite/calcite with particle size of 0.05 - 2 mm, the abundance of 55% and the spread evenly. Based on such presence of aragonite/calcite, one can interpret that the origin rock was carbonate. Alteration minerals which were generally dominated by mudstone indicate that the type of hot spring area in Oma-Haruku is a type of high-temperature reservoir, namely > 175 oC. Therefore, the area is  potentially as geothermal field in Central of Moluccas.

scholarly journals Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

2017 ◽  
Author(s):  
Feiqiao Brian Yu ◽  
Paul C. Blainey ◽  
Frederik Schulz ◽  
Tanja Woyke ◽  
Mark A. Horowitz ◽  
...  
Keyword(s):  
Single Cell ◽  
Statistical Power ◽  
Ad Hoc ◽  
Hot Spring ◽  
Genomic Structure ◽  
Metagenomic Data ◽  
Rigorous Approach ◽  
Environmental Selection ◽  
Wide Range ◽  
Genome Level

AbstractMetagenomics and single-cell genomics have enabled the discovery of many new genomes from previously unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and in many respects represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes from complex samples. In addition, by generating 96 sub-samples from each environmental sample, this method maintains high throughput, reduces sample complexity, and preserves single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes larger than 0.5 Mbps. These genomes represent novel lineages at different taxonomic levels, including three deeply branching lineages. Functional analysis revealed that these organisms utilize diverse pathways for energy metabolism. The resolution of this mini-metagenomic method enabled accurate quantification of genome abundance, even for genomes less than 1% in relative abundance. Our analyses also revealed a wide range of genome level single nucleotide polymorphism (SNP) distributions with nonsynonymous to synonymous ratio indicative of low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomic make it a powerful tool to dissect the genomic structure microbial communities while effectively preserving the fundamental unit of biology, the single cell.

scholarly journals Genomic Insights of “Candidatus Nitrosocaldaceae” Based on Nine New Metagenome-Assembled Genomes, Including “Candidatus Nitrosothermus” Gen Nov. and Two New Species of “Candidatus Nitrosocaldus”

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhen-Hao Luo ◽  
Manik Prabhu Narsing Rao ◽  
Hao Chen ◽  
Zheng-Shuang Hua ◽  
Qi Li ◽  
...  
Keyword(s):  
High Temperature ◽  
Stress Responses ◽  
Hot Springs ◽  
Ammonia Oxidation ◽  
Hot Spring ◽  
Thermal Adaptation ◽  
Amino Acid Identity ◽  
Phylogenomic Analysis ◽  
Adenosylmethionine Decarboxylase ◽  
Almost All

“Candidatus Nitrosocaldaceae” are globally distributed in neutral or slightly alkaline hot springs and geothermally heated soils. Despite their essential role in the nitrogen cycle in high-temperature ecosystems, they remain poorly understood because they have never been isolated in pure culture, and very few genomes are available. In the present study, a metagenomics approach was employed to obtain “Ca. Nitrosocaldaceae” metagenomic-assembled genomes (MAGs) from hot spring samples collected from India and China. Phylogenomic analysis placed these MAGs within “Ca. Nitrosocaldaceae.” Average nucleotide identity and average amino acid identity analysis suggested the new MAGs represent two novel species of “Candidatus Nitrosocaldus” and a novel genus, herein proposed as “Candidatus Nitrosothermus.” Key genes responsible for chemolithotrophic ammonia oxidation and a thaumarchaeal 3HP/4HB cycle were detected in all MAGs. Furthermore, genes coding for urea degradation were only present in “Ca. Nitrosocaldus,” while biosynthesis of the vitamins, biotin, cobalamin, and riboflavin were detected in almost all MAGs. Comparison of “Ca. Nitrosocaldales/Nitrosocaldaceae” with other AOA revealed 526 specific orthogroups. This included genes related to thermal adaptation (cyclic 2,3-diphosphoglycerate, and S-adenosylmethionine decarboxylase), indicating their importance for life at high temperature. In addition, these MAGs acquired genes from members from archaea (Crenarchaeota) and bacteria (Firmicutes), mainly involved in metabolism and stress responses, which might play a role to allow this group to adapt to thermal habitats.

scholarly journals The bldC Developmental Locus of Streptomyces coelicolor Encodes a Member of a Family of Small DNA-Binding Proteins Related to the DNA-Binding Domains of the MerR Family

2005 ◽  
Vol 187 (2) ◽  
pp. 716-728 ◽  
Author(s):  
Alison C. Hunt ◽  
Luis Servín-González ◽  
Gabriella H. Kelemen ◽  
Mark J. Buttner
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
Aerial Mycelium ◽  
Dna Binding Proteins ◽  
S1 Nuclease ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Wide Range

ABSTRACT The bldC locus, required for formation of aerial hyphae in Streptomyces coelicolor, was localized by map-based cloning to the overlap between cosmids D17 and D25 of a minimal ordered library. Subcloning and sequencing showed that bldC encodes a member of a previously unrecognized family of small (58- to 78-residue) DNA-binding proteins, related to the DNA-binding domains of the MerR family of transcriptional activators. BldC family members are found in a wide range of gram-positive and gram-negative bacteria. Constructed ΔbldC mutants were defective in differentiation and antibiotic production. They failed to form an aerial mycelium on minimal medium and showed severe delays in aerial mycelium formation on rich medium. In addition, they failed to produce the polyketide antibiotic actinorhodin, and bldC was shown to be required for normal and sustained transcription of the pathway-specific activator gene actII-orf4. Although ΔbldC mutants produced the tripyrrole antibiotic undecylprodigiosin, transcripts of the pathway-specific activator gene (redD) were reduced to almost undetectable levels after 48 h in the bldC mutant, in contrast to the bldC + parent strain in which redD transcription continued during aerial mycelium formation and sporulation. This suggests that bldC may be required for maintenance of redD transcription during differentiation. bldC is expressed from a single promoter. S1 nuclease protection assays and immunoblotting showed that bldC is constitutively expressed and that transcription of bldC does not depend on any of the other known bld genes. The bldC18 mutation that originally defined the locus causes a Y49C substitution that results in instability of the protein.

scholarly journals Molecular identification of amylase-producing thermophilic bacteria isolated from Bukit Gadang Hot Spring, West Sumatra, Indonesia

2020 ◽  
Vol 21 (3) ◽  
Author(s):  
Aulia Ardhi ◽  
Arina Nadenggan Sidauruk ◽  
Nabella Suraya ◽  
Nova Wahyu Pratiwi ◽  
Usman Pato ◽  
...  
Keyword(s):  
High Temperature ◽  
Molecular Identification ◽  
Hot Springs ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Amylase Activity ◽  
Hydrolytic Enzymes ◽  
Molecular Technique ◽  
West Sumatra ◽  
Pharmaceutical Industries

Abstract. Ardhi A, Sidauruk AN, Suraya N, Pratiwi NW, Pato U, Saryono. 2020. Molecular identification of amylase-producing thermophilic bacteria isolated from Bukit Gadang Hot Spring, West Sumatra, Indonesia. Biodiversitas 21: 994-1000.  Amylase is one of the hydrolytic enzymes that is widely used in a wide number of industrial processes such as food, fermentation, textile, paper, detergent, and pharmaceutical industries. Amylase produced by thermophilic bacteria may be thermostable, which is very beneficial in several applications requiring high temperature, for example, the process of gelatinization, liquefaction, and saccharification are performed in high temperature involved in the starch processing. In this study, the amylase-producing ability of thermophilic bacteria isolated from Bukit Gadang hot spring, West Sumatra, Indonesia, was checked and followed by molecular identification. Thirteen isolates that were successfully isolated from the hot springs were microscopically and macroscopically characterized, biochemically tested, and determined their amylase enzyme activity both qualitatively and quantitatively. The isolate that performed the best amylase activity was identified using the molecular technique. The DNA sequencing was carried out in 16S rRNA and continued with BLAST search for species identification. The result of molecular identification showed that the isolate with the best amylase activity was identified as Bacillus licheniformis. The optimum amylase production  (231.33 U/ml)  and the best enzyme-specific activity  (101.79 U/mg) were obtained at the incubation time of 36 hours.

scholarly journals Short-Term Seismic Precursor Anomalies of Hydrogen Concentration in Luojishan Hot Spring Bubbling Gas, Eastern Tibetan Plateau

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiaocheng Zhou ◽  
Yucong Yan ◽  
Wenya Fang ◽  
Wanli Wang ◽  
Hongyu Shi ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Hydrogen Concentration ◽  
Hot Springs ◽  
Hot Spring ◽  
Isotope Ratios ◽  
Fault System ◽  
Eastern Tibetan Plateau ◽  
Short Term ◽  
Wide Range ◽  
Seismic Precursor

The gas compositions (He, H2, CO2, CH4, Ar and N2) and isotope ratios (3He/4He and δ13C) were yearly investigated from April 2010 to April 2019 at the Luojishan spring located in the proximity of the Zemuhe Fault, eastern Tibetan Plateau. The continuous automatic monitoring of hydrogen concentrations in Luojishan hot spring bubbling gas for the purpose of earthquake prediction requires the discrimination of seismic precursor anomalies. Helium isotope ratios (3He/4He) in the bubbling gas of hot springs varied from 0.05 to 0.18 Ra (Ra = 3He/4He = 1.39 × 10−6 in the air), with a maximum mantle-derived He up to 2.2% of the total He measured in the Luojishan hot spring (assuming R/Ra = 8.0 for mantle). This suggests that Zemuhe Fault might act as a conduit for crustal-derived fluid. N2 concentrations in the majority of the hot spring was ≥80 vol%, and δ13CCO2 values varied from −13.2 to −9.3‰ (vs.PDB). Hydrogen concentration time series display a complex temporal pattern reflecting a wide range of different physical processes. There were short-term (5–60 h) seismic precursor anomalies of hydrogen concentration before natural earthquake. The anthropogenically-induced earthquakes provoke only post-earthquake responses. The concentration of hydrogen in bubbling gas of the Luojishan hot spring is sensitive to increase of stress in the Xianshuihe-Xiaojiang fault system. Monitoring the hydrogen concentrations with automatic gas stations may be promising tool for unraveling earthquake mechanisms and for predicting earthquakes.

scholarly journals Identical Penicillin-Binding Domains in Penicillin-Binding Proteins of Streptococcus pneumoniae Clinical Isolates with Different Levels of β-Lactam Resistance

2005 ◽  
Vol 49 (7) ◽  
pp. 2895-2902 ◽  
Author(s):  
Laurent Chesnel ◽  
Raphaël Carapito ◽  
Jacques Croizé ◽  
Otto Dideberg ◽  
Thierry Vernet ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Binding Proteins ◽  
Laboratory Strain ◽  
Clinical Isolates ◽  
Penicillin G ◽  
Resistance Level ◽  
Penicillin Binding Proteins ◽  
Binding Domains ◽  
Wide Range ◽  
Genes Encoding

ABSTRACT We have sequenced the penicillin-binding domains of the complete repertoire of penicillin-binding proteins and MurM from 22 clinical isolates of Streptococcus pneumoniae that span a wide range of β-lactam resistance levels. Evidence of mosaicism was found in the genes encoding PBP 1a, PBP 2b, PBP 2x, MurM, and, possibly, PBP 2a. Five isolates were found to have identical PBP and MurM sequences, even though the MICs for penicillin G ranged from 0.25 to 2.0 mg/liter. When the sequences encoding PBP 1a, PBP 2b, and PBP 2x from one of these isolates were used to transform laboratory strain R6, the resulting strain had a resistance level higher than that of the less resistant isolates carrying that PBP set but lower than that of the most resistant isolates carrying that PBP set. This result demonstrates that if the R6 strain is arbitrarily defined as the standard genotype, some wild genetic backgrounds can either increase or decrease the PBP-based resistance phenotype.

scholarly journals Meet me in the middle: median temperatures impact cyanobacteria and photoautotrophy in eruptive Yellowstone hot springs

2021 ◽  
Author(s):  
Trinity L. Hamilton ◽  
Jeff Havig
Keyword(s):  
High Temperature ◽  
Community Composition ◽  
Hot Springs ◽  
Hot Spring ◽  
Temperature Fluctuations ◽  
Model Systems ◽  
Large Temperature ◽  
Ecological Diversification ◽  
Outflow Channels

AbstractGeographic isolation can be a main driver of microbial evolution in hot springs while temperature plays a role on local scales. For example, cyanobacteria, particularly high temperature Synechococcus spp., have undergone ecological diversification along temperature gradients in hot spring outflow channels. While water flow, and thus temperature, is largely stable in many hot springs, flow can vary in geysing/eruptive hot springs resulting in large temperature fluctuations (sometimes more than 40°C). However, the role of large temperature fluctuations in driving diversification of cyanobacteria in eruptive hot springs has not been explored. Here, we examined phototroph community composition and potential photoautotrophic activity in two alkaline eruptive hot springs with similar geochemistry in the Lower Geyser Basin in Yellowstone National Park, WY. We observed distinct cyanobacterial amplicon sequencing variants (ASVs) consistent with allopatry and levels of light-dependent inorganic carbon uptake rates similar to other hot springs, despite large temperature fluctuations. Our data suggests median temperatures may drive phototroph fitness in eruptive hot springs while future studies are necessary to determine the evolutionary consequences of thriving under continuously fluctuating temperatures. We propose that large temperature swings in eruptive hot springs offer unique environments to examine the role of allopatry vs. physical and chemical characteristics of ecosystems in driving cyanobacteria evolution and add to the debate regarding the ecology of thermal adaptation and the potential for narrowing niche breadth with increasing temperature.ImportanceHot spring cyanobacteria have long been model systems for examining ecological diversification as well as characterizing microbial adaptation and evolution to extreme environments. These studies have reported cyanobacterial diversification in hot spring outflow channels that can be defined by distinct temperature ranges. Our study builds on these previous studies by examining cyanobacteria in geysing hot springs. Geysing hot springs result in outflow channel that experience regular and large temperature fluctuations. While community composition is similar between geysing and nongeysing hot spring outflow channels, our data suggests median, rather than high temperature, drive the fitness of cyanobacteria in geysing hot springs. We propose that large temperature swings may result in patterns of ecological diversification that are distinct from more stable outflows.

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