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1.
Bioresour Technol ; 346: 126669, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-34995779

RESUMO

Sulfur-based autotrophic denitrification (SAD) and pyrite-based autotrophic denitrification (PAD) are important technologies that address nitrate pollution, but high sulfate production and low denitrification efficiency, respectively, limit their application in engineering. A bio-denitrification reactor with sulfur and pyrite as filler materials was studied to remove NO3--N from nitrate contaminated water. At an influent NO3--N concentration of 50 mg/L, NO3--N removal efficiency of the sulfur/pyrite-based bioreactor was 99.2%, producing less NH4+-N and SO42- than the sulfur-based bioreactor, even after long-term operation. Denitrification performance was significantly related to environmental variable, especially dissolved oxygen. Proteobacteria and Epsilonbacteraeota were the predominant phyla in the sulfur/pyrite-based bioreactor, and fewer dissimilatory nitrate reductions to ammonia process-related bacteria were enriched compared to those in the sulfur-based bioreactor. Sulfur-pyrite bio-denitrification provides an efficient alternative method for treatment of nitrate contaminated water.


Assuntos
Compostos de Amônio , Epsilonproteobacteria , Processos Autotróficos , Reatores Biológicos , Desnitrificação , Ferro , Nitratos , Sulfatos , Sulfetos , Enxofre , Água
2.
Mol Microbiol ; 117(1): 215-233, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34818434

RESUMO

Bacterial small RNAs (sRNAs) are widespread post-transcriptional regulators that control bacterial stress responses and virulence. Nevertheless, little is known about how they arise and evolve. Homologs can be difficult to identify beyond the strain level using sequence-based approaches, and similar functionalities can arise by convergent evolution. Here, we found that the virulence-associated CJnc190 sRNA of the foodborne pathogen Campylobacter jejuni resembles the RepG sRNA from the gastric pathogen Helicobacter pylori. However, while both sRNAs bind G-rich sites in their target mRNAs using a C/U-rich loop, they largely differ in their biogenesis. RepG is transcribed from a stand-alone gene and does not require processing, whereas CJnc190 is transcribed from two promoters as precursors that are processed by RNase III and also has a cis-encoded antagonist, CJnc180. By comparing CJnc190 homologs in diverse Campylobacter species, we show that RNase III-dependent processing of CJnc190 appears to be a conserved feature even outside of C. jejuni. We also demonstrate the CJnc180 antisense partner is expressed in C. coli, yet here might be derived from the 3'UTR (untranslated region) of an upstream flagella-related gene. Our analysis of G-tract targeting sRNAs in Epsilonproteobacteria demonstrates that similar sRNAs can have markedly different biogenesis pathways.


Assuntos
Infecções por Campylobacter/microbiologia , Campylobacter jejuni/genética , Epsilonproteobacteria/genética , Infecções por Helicobacter/microbiologia , Helicobacter pylori/genética , Pequeno RNA não Traduzido/genética , Regiões 3' não Traduzidas/genética , Campylobacter jejuni/patogenicidade , Epsilonproteobacteria/patogenicidade , Flagelos/genética , Helicobacter pylori/patogenicidade , Regiões Promotoras Genéticas/genética , RNA Bacteriano/genética , RNA Mensageiro/genética , Ribonuclease III/genética , Virulência
3.
Nucleic Acids Res ; 49(9): 5249-5264, 2021 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-33893809

RESUMO

Ribonucleases are central players in post-transcriptional regulation, a major level of gene expression regulation in all cells. Here, we characterized the 3'-5' exoribonuclease RNase R from the bacterial pathogen Helicobacter pylori. The 'prototypical' Escherichia coli RNase R displays both exoribonuclease and helicase activities, but whether this latter RNA unwinding function is a general feature of bacterial RNase R had not been addressed. We observed that H. pylori HpRNase R protein does not carry the domains responsible for helicase activity and accordingly the purified protein is unable to degrade in vitro RNA molecules with secondary structures. The lack of RNase R helicase domains is widespread among the Campylobacterota, which include Helicobacter and Campylobacter genera, and this loss occurred gradually during their evolution. An in vivo interaction between HpRNase R and RhpA, the sole DEAD-box RNA helicase of H. pylori was discovered. Purified RhpA facilitates the degradation of double stranded RNA by HpRNase R, showing that this complex is functional. HpRNase R has a minor role in 5S rRNA maturation and few targets in H. pylori, all included in the RhpA regulon. We concluded that during evolution, HpRNase R has co-opted the RhpA helicase to compensate for its lack of helicase activity.


Assuntos
RNA Helicases DEAD-box/metabolismo , Exorribonucleases/metabolismo , Helicobacter pylori/enzimologia , Motivos de Aminoácidos , Epsilonproteobacteria/enzimologia , Exorribonucleases/química , RNA de Cadeia Dupla/metabolismo , RNA Ribossômico 5S/metabolismo
4.
Syst Appl Microbiol ; 44(1): 126170, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33340909

RESUMO

A novel thermophilic bacterium, strain SSM-sur55T, was isolated from a chimney structure at the Urashima site on the Southern Mariana Trough in the Pacific Ocean. Growth was observed at temperatures between 25 and 60°C (optimum, 55°C; 180min doubling time), at pH values between 5.3 and 7.2 (optimum, pH 5.9) and in the presence of between 1.6 and 5.6% (w/v) NaCl (optimum, 3.2%). The isolate used molecular hydrogen as its sole energy source, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and elemental sulfur as its sole sulfur source. Thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur was utilized as its sole electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SSM-sur55T belonged to the genus Hydrogenimonas of the class "Campylobacteria", and its closest relative was Hydrogenimonas thermophila EP1-55-1%T (94.9%). On the basis of the phylogenetic, physiological and molecular characteristics, strain SSM-sur55T represents a novel species within the genus Hydrogenimonas, for which the name Hydrogenimonas urashimensis sp. nov. is proposed, with the type strain SSM-sur55T (JCM 19825=KCTC 15926).


Assuntos
Epsilonproteobacteria/classificação , Fontes Hidrotermais/microbiologia , Filogenia , Compostos de Amônio , Dióxido de Carbono , Epsilonproteobacteria/isolamento & purificação , Hidrogênio , Oceano Pacífico , RNA Ribossômico 16S/genética , Enxofre
5.
PLoS One ; 15(12): e0241366, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33301463

RESUMO

A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4-3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class "Campylobacteria", but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that "Nitratiruptor labii" should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within "Campylobacteria" are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species.


Assuntos
Epsilonproteobacteria/classificação , Fontes Hidrotermais/microbiologia , DNA Bacteriano/genética , Epsilonproteobacteria/genética , Epsilonproteobacteria/metabolismo , Genoma Bacteriano , Hidrogênio/metabolismo , Oxirredução , Oceano Pacífico , Filogenia , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Especificidade da Espécie , Terminologia como Assunto
6.
PLoS One ; 15(11): e0241784, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33206681

RESUMO

In recent years, methylene blue (MB) has attracted considerable interest as a potential drug for the treatment of methemoglobinemia and neurodegenerative diseases. MB is active against microorganisms from various taxonomic groups. However, no studies have yet been conducted on the effect of MB on the intestinal microbiome of model animals. The aim of this work was to study the effect of different concentrations of MB on the mouse gut microbiome and its relationship with the cognitive abilities of mice. We showed that a low MB concentration (15 mg/kg/day) did not cause significant changes in the microbiome composition. The Bacteroidetes/Firmicutes ratio decreased relative to the control on the 2nd and 3rd weeks. A slight decrease in the levels Actinobacteria was detected on the 3rd week of the experiment. Changes in the content of Delta, Gamma, and Epsilonproteobacteria have been also observed. We did not find significant alterations in the composition of intestinal microbiome, which could be an indication of the development of dysbiosis or other gut dysfunction. At the same time, a high concentration of MB (50 mg/kg/day) led to pronounced changes, primarily an increase in the levels of Delta, Gamma and Epsilonproteobacteria. Over 4 weeks of therapy, the treatment with high MB concentration has led to an increase in the median content of Proteobacteria to 7.49% vs. 1.61% in the control group. Finally, we found that MB at a concentration of 15 mg/kg/day improved the cognitive abilities of mice, while negative correlation between the content of Deferribacteres and cognitive parameters was revealed. Our data expand the understanding of the relationship between MB, cognitive abilities, and gut microbiome in respect to the antibacterial properties of MB.


Assuntos
Azul de Metileno/farmacologia , Animais , Bacteroidetes/genética , Bacteroidetes/metabolismo , Cognição/efeitos dos fármacos , Cognição/fisiologia , Epsilonproteobacteria/genética , Epsilonproteobacteria/metabolismo , Microbioma Gastrointestinal/efeitos dos fármacos , Microbioma Gastrointestinal/genética , Sequenciamento de Nucleotídeos em Larga Escala , Aprendizagem em Labirinto , Camundongos , Camundongos Endogâmicos C57BL , Proteobactérias/genética , Proteobactérias/metabolismo
7.
Pediatr Infect Dis J ; 39(12): 1081-1087, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32947600

RESUMO

BACKGROUND: The prevalence of extended-spectrum beta-lactamase producing Εnterobacteriaceae (ESBL-PE) is increasing globally. ESBL-PE are an important cause of urinary tract infections (UTIs) in children. We aimed to characterize the clinical presentation, treatment and outcomes of childhood UTI caused by ESBL-PE in Europe. METHODS: Multicenter retrospective cohort study. Children 0 to 18 years of age with fever, positive urinalysis and positive urine culture for an ESBL-PE uropathogen, seen in a participating hospital from January 2016 to July 2017, were included. MAIN OUTCOME MEASURES: Primary outcome measure: day of defervescence was compared between (1) initial microbiologically effective treatment (IET) versus initial microbiologically ineffective treatment (IIT) and (2) single initial antibiotic treatment versus combined initial antibiotic treatment. SECONDARY OUTCOME MEASURES: Clinical and microbiologic failure of initial treatment. RESULTS: We included 142 children from 14 hospitals in 8 countries. Sixty-one children had IET and 77 IIT. There was no statistical difference in time to defervescence for effective/ineffective groups (P = 0.722) and single/combination therapy groups (P = 0.574). Two of 59 (3.4%) and 4/66 (6.1%) patients exhibited clinical failure during treatment (P = 0.683) when receiving IET or IIT, respectively. Eight of 51 (15.7%) receiving IET and 6/58 (10.3%) receiving IIT patients (P = 0.568) had recurring symptoms/signs suggestive of a UTI. Recurrence of a UTI occurred 15.5 days (interquartile range, 9.0-19.0) after the end of treatment. CONCLUSIONS: Time to defervescence and clinical failure did not differ between IET/IIT groups. Non-carbapenem beta-lactam antibiotics may be used for the empiric treatment of ESBL febrile UTIs, until susceptibility testing results become available.


Assuntos
Infecções Bacterianas , Epsilonproteobacteria , Infecções Urinárias , Adolescente , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Infecções Bacterianas/tratamento farmacológico , Infecções Bacterianas/epidemiologia , Infecções Bacterianas/microbiologia , Criança , Pré-Escolar , Farmacorresistência Bacteriana , Epsilonproteobacteria/efeitos dos fármacos , Epsilonproteobacteria/enzimologia , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Pielonefrite , Estudos Retrospectivos , Resultado do Tratamento , Infecções Urinárias/tratamento farmacológico , Infecções Urinárias/epidemiologia , Infecções Urinárias/microbiologia , beta-Lactamases/metabolismo
8.
Syst Appl Microbiol ; 43(5): 126108, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32847783

RESUMO

The proposal to restructure the genus Arcobacter into six distinct genera was critically examined using: comparative analyses of up to 80 Epsilonproteobacterial genome sequences (including 26 arcobacters); phylogenetic analyses of three housekeeping genes and also 342 core genes; and phenotypic criteria. Genome sequences were analysed with tools to calculate Percentage of Conserved Proteins, Average Amino-acid Identity, BLAST-based Average Nucleotide Identity, in silico DNA-DNA hybridisation values, genome-wide Average Nucleotide Identity, Alignment Fractions and G+C percentages. Genome analyses revealed the genus Arcobacter sensu lato to be relatively homogenous, and phylogenetic analyses clearly distinguished the group from other Epsilonproteobacteria. Genomic distinction of the genera proposed by Pérez-Cataluña et al. [2018] was not supported by any of the measures used and a subsequent risk of strain misidentification clearly identified. Similarly, phenotypic analyses supported the delineation of Arcobacter sensu lato but did not justify the position of the proposed novel genera. The present polyphasic taxonomic study strongly supports the continuance of the classification of "aerotolerant campylobacters" as Arcobacter and refutes the proposed genus-level subdivision of Pérez-Cataluña et al. [2018].


Assuntos
Arcobacter/classificação , Epsilonproteobacteria/classificação , Arcobacter/genética , Arcobacter/crescimento & desenvolvimento , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Técnicas de Tipagem Bacteriana , Sequência de Bases , DNA Bacteriano/genética , Epsilonproteobacteria/genética , Epsilonproteobacteria/crescimento & desenvolvimento , Genes Bacterianos , Genes de RNAr , Genoma Bacteriano , Genômica , Hibridização de Ácido Nucleico , Fenótipo , Filogenia , Proteoma , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
9.
N Biotechnol ; 57: 67-75, 2020 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-32360635

RESUMO

Anoxic biotrickling filters (BTFs) represent a technology with high H2S elimination capacity and removal efficiencies widely studied for biogas desulfurization. Three changes in the final electron acceptors were made using nitrate and nitrite during an operating period of 520 days. The stability and performance of the anoxic BTF were maintained when a significant perturbation was applied to the system that involved the progressive change of nitrate to nitrite and vice versa. Here the impact of electron acceptor changes on the microbial community was characterized by denaturing gel gradient electrophoresis (DGGE) and next generation sequencing (NGS). Both platforms revealed that the community underwent changes during the perturbations but was resilient because the removal capacity did not significantly change. Proteobacteria and Bacteroidetes were the main Phyla and Sulfurimonas and Thiobacillus the main nitrate-reducing sulfide-oxidizing bacteria (NR-SOB) genera involved in the biodesulfurization process.


Assuntos
Eletroforese em Gel de Gradiente Desnaturante , Elétrons , Filtração , Sequenciamento de Nucleotídeos em Larga Escala , Nitratos/química , Nitritos/química , Epsilonproteobacteria/química , Microbiota , Thiobacillus/química
10.
Nucleic Acids Res ; 48(6): 3343-3355, 2020 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-32016421

RESUMO

NrS-1 is the first known phage that can infect Epsilonproteobacteria, one of the predominant primary producers in the deep-sea hydrothermal vent ecosystems. NrS-1 polymerase is a multidomain enzyme and is one key component of the phage replisome. The N-terminal Prim/Pol and HBD domains are responsible for DNA polymerization and de novo primer synthesis activities of NrS-1 polymerase. However, the structure and function of the C-terminus (CTR) of NrS-1 polymerase are poorly understood. Here, we report two crystal structures, showing that NrS-1 CTR adopts one unique hexameric ring-shaped conformation. Although the central helicase domain of NrS-1 CTR shares structural similarity with the superfamily III helicases, the folds of the Head and Tail domains are completely novel. Via mutagenesis and in vitro biochemical analysis, we identified many residues important for the helicase and polymerization activities of NrS-1 polymerase. In addition to NrS-1 polymerase, our study may also help us identify and understand the functions of multidomain polymerases expressed by many NrS-1 related phages.


Assuntos
Bacteriófagos/enzimologia , Replicação do DNA/genética , DNA Polimerase Dirigida por DNA/ultraestrutura , Conformação Proteica , Sequência de Aminoácidos/genética , Bacteriófagos/genética , Bacteriófagos/ultraestrutura , Cristalografia por Raios X , DNA Polimerase Dirigida por DNA/química , Ecossistema , Epsilonproteobacteria/genética , Epsilonproteobacteria/virologia , Fontes Hidrotermais/química
11.
ISME J ; 14(1): 104-122, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31562384

RESUMO

Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.


Assuntos
Epsilonproteobacteria/metabolismo , Fotossíntese , Animais , Bivalves/microbiologia , Ciclo do Carbono , Ciclo do Ácido Cítrico , Epsilonproteobacteria/classificação , Epsilonproteobacteria/genética , Gammaproteobacteria/genética , Filogenia , Simbiose
12.
Sci Rep ; 9(1): 11692, 2019 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-31406214

RESUMO

Benthic foraminifera are known to play an important role in marine carbon and nitrogen cycles. Here, we report an enrichment of sulphur cycle -associated bacteria inside intertidal benthic foraminifera (Ammonia sp. (T6), Haynesina sp. (S16) and Elphidium sp. (S5)), using a metabarcoding approach targeting the 16S rRNA and aprA -genes. The most abundant intracellular bacterial groups included the genus Sulfurovum and the order Desulfobacterales. The bacterial 16S OTUs are likely to originate from the sediment bacterial communities, as the taxa found inside the foraminifera were also present in the sediment. The fact that 16S rRNA and aprA -gene derived intracellular bacterial OTUs were species-specific and significantly different from the ambient sediment community implies that bacterivory is an unlikely scenario, as benthic foraminifera are known to digest bacteria only randomly. Furthermore, these foraminiferal species are known to prefer other food sources than bacteria. The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host. Future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminiferal/endobiont contribution to the sulphur-cycle.


Assuntos
Deltaproteobacteria/genética , Epsilonproteobacteria/genética , Foraminíferos/microbiologia , Gammaproteobacteria/genética , Enxofre/metabolismo , Simbiose/fisiologia , Bacteroidaceae/classificação , Bacteroidaceae/genética , Bacteroidaceae/isolamento & purificação , Campylobacter/classificação , Campylobacter/genética , Campylobacter/isolamento & purificação , Código de Barras de DNA Taxonômico/métodos , DNA Bacteriano/genética , Deltaproteobacteria/classificação , Deltaproteobacteria/isolamento & purificação , Epsilonproteobacteria/classificação , Epsilonproteobacteria/isolamento & purificação , Foraminíferos/fisiologia , Gammaproteobacteria/classificação , Gammaproteobacteria/isolamento & purificação , Sedimentos Geológicos/química , Sedimentos Geológicos/microbiologia , Mar do Norte , Filogenia , Análise de Componente Principal , RNA Ribossômico 16S/genética , Água do Mar/química , Água do Mar/microbiologia , Serina Endopeptidases/genética , Enxofre/química
13.
J Biosci Bioeng ; 127(1): 45-51, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30082219

RESUMO

In the natural gas field located in central Japan, high concentrations of natural gases and iodide ions are dissolved in formation water and commercially produced in deep aquifers. In the iodine recovery process, the produced formation water is amended with sulfate, and this fluid is injected into gas-bearing aquifers, which may lead to infrastructure corrosion by hydrogen sulfide. In this study, we examined the microbial community in aquifers subjected to sulfate-containing fluid injection. Formation water samples were collected from production wells located at different distances from the injection wells. The chemical analysis showed that the injection fluid contained oxygen, nitrate, nitrite and sulfate, in contrast to the formation water, which had previously been shown to be depleted in these components. Sulfur isotopic analysis indicated that sulfate derived from the injection fluid was present in the sample collected from near the injection wells. Quantitative and sequencing analysis of dissimilatory sulfite reductase and 16S rRNA genes revealed that sulfate-reducing bacteria (SRB), sulfur-oxidizing bacteria, and anaerobic methanotrophic archaea (ANME) in the wells located near injection wells were more abundant than those in wells located far from the injection wells, suggesting that fluid injection stimulated these microorganisms through the addition of oxygen, nitrate, nitrite and sulfate to the methane-rich aquifers. The predominant taxa were assigned to the ANME-2 group, its sulfate-reducing partner SEEP-SRB1 cluster and sulfur-oxidizing Epsilonproteobacteria. These results provide important insights for future studies to support the development of natural gas and iodine resources in Japan.


Assuntos
Água Subterrânea/microbiologia , Fraturamento Hidráulico , Microbiota , Gás Natural/microbiologia , Campos de Petróleo e Gás/microbiologia , Sulfatos/química , Archaea/genética , Archaea/isolamento & purificação , Epsilonproteobacteria/genética , Epsilonproteobacteria/isolamento & purificação , Sedimentos Geológicos/microbiologia , Fraturamento Hidráulico/métodos , Japão , Metano/química , Microbiota/genética , Nitratos/metabolismo , Oxirredução , Filogenia , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genética , Enxofre/metabolismo , Bactérias Redutoras de Enxofre/genética , Bactérias Redutoras de Enxofre/isolamento & purificação
14.
ISME J ; 13(2): 482-493, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30291329

RESUMO

The central Baltic Sea is characterized by a pelagic redox zone exhibiting high dark CO2 fixation rates below the chemocline. These rates are mainly driven by chemolithoautotrophic and denitrifying Sulfurimonas GD17 subgroup cells which are motile and fast-reacting r-strategists. Baltic Sea redox zones are unstable and a measurable overlap of nitrate and reduced sulfur, essential for chemosynthesis, is often only available on small scales and short times due to local mixing events. This raises the question of how GD17 cells gain access to electron donors or acceptors over longer term periods and under substrate deficiency. One possible answer is that GD17 cells store high-energy-containing polyphosphate during favorable nutrient conditions to survive periods of nutrient starvation. We used scanning electron microscopy with energy-dispersive X-ray spectroscopy to investigate potential substrate enrichments in single GD17 cells collected from Baltic Sea redox zones. More specific substrate enrichment features were identified in experiments using Sulfurimonas gotlandica GD1T, a GD17 representative. Sulfurimonas cells accumulated polyphosphate both in situ and in vitro. Combined genome and culture-dependent analyses suggest that polyphosphate serves as an energy reservoir to maintain cellular integrity at unfavorable substrate conditions. This redox-independent energy supply would be a precondition for sustaining the r-strategy lifestyle of GD17 and may represent a newly identified survival strategy for chemolithoautotrophic prokaryotes occupying eutrophic redox zones.


Assuntos
Ecossistema , Epsilonproteobacteria/metabolismo , Polifosfatos/metabolismo , Água do Mar/microbiologia , Países Bálticos , Desnitrificação , Oxirredução , Água do Mar/química
15.
Int J Syst Evol Microbiol ; 68(7): 2183-2187, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29757127

RESUMO

A novel marine sulfur-oxidizing bacterium, designated strain eps51T, was isolated from a surface rock sample collected from the hydrothermal field of Suiyo Seamount on the Izu-Bonin Arc in the Western Pacific Ocean. This bacterium was Gram-staining-negative, non-motile and rod-shaped. Strain eps51T grew chemolithoautotrophically, by sulfur-oxidizing respiration with elemental sulfur and thiosulfate as electron donors and used only carbon dioxide as a carbon source. Oxygen and nitrate were used as its electron acceptors. The isolate grew optimally at 30 °C, at pH 7.0 and with 3 % NaCl. The predominant fatty acids were C16 : 1ω7c, C18 : 1ω7c and C16 : 0. The respiratory quinone was menaquinone-6 and the genomic DNA G+C content was 40.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence revealed that eps51T represented a member of the genus Sulfurovum and the closest relative was Sulfurovum aggregans (96.7 %). Based on its phylogenetic position along with its physiological and chemotaxonomic characteristics, the name Sulfurovum denitrificans sp. nov. is proposed, with the type strain eps51T (=NBRC 102602T=DSM 19611T).


Assuntos
Epsilonproteobacteria/classificação , Filogenia , Água do Mar/microbiologia , Enxofre/metabolismo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Epsilonproteobacteria/genética , Epsilonproteobacteria/isolamento & purificação , Ácidos Graxos/química , Oxirredução , Oceano Pacífico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Bactérias Redutoras de Enxofre/classificação , Bactérias Redutoras de Enxofre/genética , Bactérias Redutoras de Enxofre/isolamento & purificação , Tiossulfatos/metabolismo , Vitamina K 2/análogos & derivados , Vitamina K 2/química
16.
Microbiome ; 6(1): 95, 2018 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-29793531

RESUMO

BACKGROUND: The early-life gut microbiota plays a critical role in host metabolism in later life. However, little is known about how the fatty acid profile of the maternal diet during gestation and lactation influences the development of the offspring gut microbiota and subsequent metabolic health outcomes. RESULTS: Here, using a unique transgenic model, we report that maternal endogenous n-3 polyunsaturated fatty acid (PUFA) production during gestation or lactation significantly reduces weight gain and markers of metabolic disruption in male murine offspring fed a high-fat diet. However, maternal fatty acid status appeared to have no significant effect on weight gain in female offspring. The metabolic phenotypes in male offspring appeared to be mediated by comprehensive restructuring of gut microbiota composition. Reduced maternal n-3 PUFA exposure led to significantly depleted Epsilonproteobacteria, Bacteroides, and Akkermansia and higher relative abundance of Clostridia. Interestingly, offspring metabolism and microbiota composition were more profoundly influenced by the maternal fatty acid profile during lactation than in utero. Furthermore, the maternal fatty acid profile appeared to have a long-lasting effect on offspring microbiota composition and function that persisted into adulthood after life-long high-fat diet feeding. CONCLUSIONS: Our data provide novel evidence that weight gain and metabolic dysfunction in adulthood is mediated by maternal fatty acid status through long-lasting restructuring of the gut microbiota. These results have important implications for understanding the interaction between modern Western diets, metabolic health, and the intestinal microbiome.


Assuntos
Dieta Hiperlipídica , Ácidos Graxos Ômega-3/metabolismo , Microbioma Gastrointestinal/fisiologia , Intestinos/microbiologia , Obesidade/patologia , Animais , Animais Recém-Nascidos/metabolismo , Animais Recém-Nascidos/microbiologia , Bacteroides/isolamento & purificação , Clostridiaceae/isolamento & purificação , Epsilonproteobacteria/isolamento & purificação , Ácidos Graxos Dessaturases/genética , Feminino , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Verrucomicrobia/isolamento & purificação , Aumento de Peso
17.
Antonie Van Leeuwenhoek ; 111(6): 841-858, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29423768

RESUMO

The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569-584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes. Here we report on the comparative analyses of the diversity and distribution patterns of Planctomycetes associated with metalliferous deposits from two diffuse-flow hydrothermal vent fields (Mariner and Vai Lili) from the Valu Fa Ridge in the Southwestern Pacific. Metabarcoding of 16S rRNA genes showed that the major prokaryotic phyla were Proteobacteria (51-73% of all 16S rRNA gene reads), Epsilonbacteraeota (0.5-19%), Bacteriodetes (5-17%), Planctomycetes (0.4-11%), Candidatus Latescibacteria (0-5%) and Marine Benthic Group E (Hydrothermarchaeota) (0-5%). The two different sampling sites differed considerably in overall community composition. The abundance of Planctomycetes also varied substantially between the samples and the sites, with the majority of the sequences affiliated with uncultivated members of the classes Planctomycetacia and Phycisphaerae, and other deep branching lineages. Seven different strains affiliated with the order Planctomycetales were isolated, mostly from the Vai Lili samples, where also the highest Planctomycetales diversity was seen. Most of the isolates were affiliated with the genera Gimesia, Rhodopirellula and Blastopirellula. One isolate was only distantly related to known cultured, but uncharacterized species within the Pir4 group. This study shows that the deep-sea Planctomycetes represent a very heterogeneous group with a high phylogenetic diversity and a substantial potential for novel organism discovery in these deep ocean environments.


Assuntos
Fontes Hidrotermais/microbiologia , Planctomycetales/genética , RNA Ribossômico 16S/genética , Epsilonproteobacteria/genética , Sedimentos Geológicos/microbiologia , Filogenia , Proteobactérias/genética , Água do Mar/microbiologia
18.
Microbiologyopen ; 7(4): e00586, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29423975

RESUMO

Chemoautotrophic bacteria belonging to the genus Sulfurimonas in the class Campylobacteria are widespread in many marine environments characterized by redox interfaces, yet little is known about their physiological adaptations to different environmental conditions. Here, we used liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) in a targeted metabolomics approach to study the adaptations of Sulfurimonas denitrificans to varying salt concentrations that are found in its natural habitat of tidal mudflats. Proline was identified as one of the most abundant internal metabolites and its concentration showed a strong positive correlation with ionic strength, suggesting that it acts as an important osmolyte in S. denitrificans. 2,3-dihydroxypropane-1-sulfonate was also positively correlated with ionic strength, indicating it might play a previously unrecognized role in osmoregulation. Furthermore, the detection of metabolites from the reductive tricarboxylic acid cycle at high internal concentrations reinforces the importance of this pathway for carbon fixation in Campylobacteria and as a hub for biosynthesis. As the first report of metabolomic data for an campylobacterial chemolithoautotroph, this study provides data that will be useful to understand the adaptations of Campylobacteria to their natural habitat at redox interfaces.


Assuntos
Epsilonproteobacteria/metabolismo , Prolina/metabolismo , Crescimento Quimioautotrófico , Cromatografia Líquida , Ecossistema , Epsilonproteobacteria/química , Epsilonproteobacteria/genética , Metabolômica , Oxirredução , Prolina/análise , Espectrometria de Massas em Tandem
19.
Microb Ecol ; 76(2): 387-403, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29354879

RESUMO

The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.


Assuntos
Sedimentos Geológicos/microbiologia , Fontes Hidrotermais/microbiologia , Metagenômica , Microbiota/fisiologia , Archaea/classificação , Archaea/genética , Archaea/metabolismo , Processos Autotróficos , Açores , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Biodiversidade , Carbono/metabolismo , Ciclo do Carbono , Crescimento Quimioautotrófico/fisiologia , Ciclo do Ácido Cítrico , Epsilonproteobacteria/metabolismo , Metagenoma/fisiologia , Metano/metabolismo , Nitrogênio/metabolismo , Oxirredução , Fotossíntese , Filogenia , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Enxofre/metabolismo
20.
FEBS J ; 284(23): 4017-4034, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-28977725

RESUMO

The uracil DNA glycosylase superfamily consists of at least six families with a diverse specificity toward DNA base damage. Family 1 uracil N-glycosylase (UNG) exhibits exclusive specificity on uracil-containing DNA. Here, we report a family 1 UNG homolog from Nitratifractor salsuginis with distinct biochemical features that differentiate it from conventional family 1 UNGs. Globally, the crystal structure of N. salsuginisUNG shows a few additional secondary structural elements. Biochemical and enzyme kinetic analysis, coupled with structural determination, molecular modeling, and molecular dynamics simulations, shows that N. salsuginisUNG contains a salt bridge network that plays an important role in DNA backbone interactions. Disruption of the amino acid residues involved in the salt bridges greatly impedes the enzymatic activity. A tyrosine residue in motif 1 (GQDPY) is one of the distinct sequence features setting family 1 UNG apart from other families. The crystal structure of Y81G mutant indicates that several subtle changes may account for its inactivity. Unlike the conventional family 1 UNG enzymes, N. salsuginisUNG is not inhibited by Ugi, a potent inhibitor specific for family 1 UNG. This study underscores the diversity of paths that a uracil DNA glycosylase may take to acquire its unique structural and biochemical properties during evolution. DATABASE: Structure data are available in the PDB under accession numbers 5X3G and 5X3H.


Assuntos
Proteínas de Bactérias/química , DNA/química , Epsilonproteobacteria/enzimologia , Uracila-DNA Glicosidase/química , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Cristalografia por Raios X , DNA/genética , DNA/metabolismo , Epsilonproteobacteria/genética , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Ligação Proteica , Domínios Proteicos , Homologia de Sequência de Aminoácidos , Uracila-DNA Glicosidase/genética , Uracila-DNA Glicosidase/metabolismo
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