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1.
Artigo em Inglês | MEDLINE | ID: mdl-38240641

RESUMO

A Gram-stain-negative, catalase-positive and oxidase-positive, nonmotile, aerobic, light yellow, spherical-shaped bacterial strain with no flagella, designated strain YIM 152171T, was isolated from sediment of the South China Sea. Colonies were smooth and convex, light yellow and circular, and 1.0-1.5×1.0-1.5 µm in cell diameter after 7 days of incubation at 28°C on YIM38 media supplemented with sea salt. Colonies could grow at 20-45°C (optimum 28-35°C) and pH 6.0-11.0 (optimum, pH 7.0-9.0), and they could proliferate in the salinity range of 0-6.0 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C18 : 1 ω7c 11-methyl, C16 : 0, C16 : 1 ω11c, C16 : 1 ω5c, C17 : 1 ω6c and C18 : 1 ω5c. The respiratory quinone was ubiquinone 10, and the polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified aminolipid. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain YIM 152171T within the order Rhodospirillales in a distinct lineage that also included the genus Geminicoccus. The 16S rRNA gene sequence similarities of YIM 152171T to those of Arboricoccus pini, Geminicoccus roseus and Constrictibacter antarcticus were 92.17, 89.25 and 88.91 %, respectively. The assembled draft genome of strain YIM 152171T had 136 contigs with an N50 value of 134704 nt, a total length of 3 001 346 bp and a G+C content of 70.27 mol%. The phylogenetic, phenotypic and chemotaxonomic data showed that strain YIM 152171T (=MCCC 1K08488T=KCTC 92884T) represents a type of novel species and genus for which we propose the name Marinimicrococcus gen. nov., sp. nov.


Assuntos
Ácidos Graxos , Rhodospirillales , Ácidos Graxos/química , Filogenia , RNA Ribossômico 16S/genética , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Análise de Sequência de DNA , Sedimentos Geológicos/microbiologia , Fosfolipídeos/química , China
2.
J Dairy Sci ; 104(10): 10609-10627, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34253372

RESUMO

Accurately profiling and characterizing factors shaping raw milk microbiota would provide practical information for detecting microbial contamination and unusual changes in milk. The current work was an observational study aiming to profile the microbiota of raw milk collected across wide geographic regions in China in different seasons and to investigate the contribution of geographical, seasonal, and environmental factors in shaping the raw milk microbiota. A total of 355 raw cow milk samples from healthy Holsteins and 41 environmental samples (farm soil and surface of milking room floor) were collected from 5 dairy farms in 5 Chinese provinces (namely, Daqing in Heilongjiang province, Jiaozuo in Henan province, Qingyuan in Guangdong province, Suqian in Jiangsu province, and Yinchuan in Ningxia Hui Autonomous Region) in January, May, and September 2018. The microbial communities in raw milk and farm environmental samples were determined using the PacBio small-molecule real-time circular consensus sequencing, which generated high-fidelity microbiota profiles based on full-length 16S rRNA genes; such technology was advantageous in producing accurate species-level information. Our results showed that both seasonality and sampling region were significant factors influencing the milk microbiota; however, the raw milk microbiota was highly diverse according to seasonality, and sampling region was the less determining factor. The wide variation in raw milk microbial communities between samples made it difficult to define a representative species-level core milk microbiota. Nevertheless, 3 most universal milk-associated species were identified: Lactococcus lactis, Enhydrobacter aerosaccus, and Acinetobacter lwoffii, which were consistently detected in 99%, 95%, and 94% of all analyzed milk samples, respectively (n = 355). The top taxa accounting for the overall seasonal microbiota variation were Bacillus (Bacillus cereus, Bacillus flexus, Bacillus safensis), Lactococcus (Lactococcus lactis, Lactococcus piscium, Lactococcus raffinolactis), Lactobacillus (Lactobacillus helveticus, Lactobacillus delbrueckii), Lactiplantibacillus plantarum, Streptococcus agalactiae, Enhydrobacter aerosaccus, Pseudomonas fragi, and Psychrobacter cibarius. Unlike the milk microbiota, the environmental microbiota did not exhibit obvious pattern of seasonal or geographic variation. However, this study was limited by the relatively low number and types of environmental samples, making it statistically not meaningful to perform further correlation analysis between the milk and environmental microbiota. Nevertheless, this study generated novel information on raw milk microbiota across wide geographic regions of China and found that seasonality was more significant in shaping the raw milk microbiota compared with geographic origin.


Assuntos
Microbiota , Leite , Acinetobacter , Animais , Bacillus , Bovinos , Feminino , Microbiologia de Alimentos , Lactococcus , Psychrobacter , RNA Ribossômico 16S/genética , Rhodospirillales
3.
Int J Syst Evol Microbiol ; 70(3): 2132-2136, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32027305

RESUMO

A Gram-stain-negative bacterium, designated strain PF-30T, was isolated from floodwater of a paddy field in South Korea. Strain PF-30T was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25-40 °C (optimum, 28 °C), at pH 5.0-9.0 (optimum pH 7.0) and at salinities of 0.5-3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30T belongs to the genus Elioraea, showing highest sequence similarity to Elioraea tepidiphila TU-7T (97.1%) and less than 91.3 % similarity with other members of the family Acetobacteraceae. The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain PF-30T and E. tepidiphila TU-7T yielded an ANI value of 75.1 % and DNA-DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C18 : 0 and C18 : 1 ω7c. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30T was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30T represents a novel species of the genus Elioraea, for which the name Elioraea rosea sp. nov. is proposed. The type strain is PF-30T (=KACC 19985T=NBRC 113984T).


Assuntos
Filogenia , Rhodospirillales/classificação , Microbiologia da Água , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Oryza , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Rhodospirillales/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
4.
Nat Chem Biol ; 15(9): 900-906, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31383974

RESUMO

Despite the potential of biotechnological processes for one-carbon (C1) bioconversion, efficient biocatalysts required for their implementation are yet to be developed. To address intrinsic limitations of native C1 biocatalysts, here we report that 2-hydroxyacyl CoA lyase (HACL), an enzyme involved in mammalian α-oxidation, catalyzes the ligation of carbonyl-containing molecules of different chain lengths with formyl-coenzyme A (CoA) to produce C1-elongated 2-hydroxyacyl-CoAs. We discovered and characterized a prokaryotic variant of HACL and identified critical residues for this newfound activity, including those supporting the hypothesized thiamine pyrophosphate-dependent acyloin condensation mechanism. The use of formyl-CoA as a C1 donor provides kinetic advantages and enables C1 bioconversion to multi-carbon products, demonstrated here by engineering an Escherichia coli whole-cell biotransformation system for the synthesis of glycolate and 2-hydroxyisobutyrate from formaldehyde and formaldehyde plus acetone, respectively. Our work establishes a new approach for C1 bioconversion and the potential for HACL-based pathways to support synthetic methylotrophy.


Assuntos
Enoil-CoA Hidratase/metabolismo , Álcoois Graxos/metabolismo , Rhodospirillales/enzimologia , Enoil-CoA Hidratase/classificação , Enoil-CoA Hidratase/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Álcoois Graxos/química , Regulação Bacteriana da Expressão Gênica , Regulação Enzimológica da Expressão Gênica , Variação Genética , Humanos , Engenharia Metabólica , Modelos Moleculares , Mutagênese Sítio-Dirigida , Filogenia , Conformação Proteica
5.
Extremophiles ; 21(6): 1091-1100, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-29027017

RESUMO

The acidophilic, Fe(III)-reducing heterotrophic bacteria Acidocella aromatica PFBCT and Acidiphilium cryptum SJH were utilized to produce palladium (Pd) bionanoparticles via a simple 1-step microbiological reaction. Monosaccharide (or intracellular NADH)-dependent reactions lead to visualization of intra/extra-cellular enzymatic Pd(0) nucleation. Formic acid-dependent reactions proceeded via the first slow Pd(0) nucleation phase and the following autocatalytic Pd(II) reduction phase regardless of the presence or viability of the cells. However, use of active cells (with full enzymatic and membrane protein activities) at low formic acid concentration (5 mM) was critical to allow sufficient time for Pd(II) biosorption and the following enzymatic Pd(0) nucleation, which consequently enabled production of fine, dense and well-dispersed Pd(0) bionanoparticles. Differences of the resultant Pd(0) nanoparticles in size, density and localization between the two bacteria under each condition tested suggested different activity and location of enzymes and membrane "Pd(II) trafficking" proteins responsible for Pd(0) nucleation. Despite the inhibitory effect of leaching lixiviant and dissolved metal ions, Pd(0) bionanoparticles were effectively formed by active Ac. aromatica cells from both acidic synthetic Pd(II) solutions and from the actual spent catalyst leachates at equivalent 18-19 nm median size with comparable catalytic activity.


Assuntos
Nanopartículas Metálicas/microbiologia , Paládio/química , Rhodospirillales/metabolismo , Formiatos/química , Microbiologia Industrial/métodos , Nanopartículas Metálicas/química , Oxirredução , Poluentes Químicos da Água/química
6.
Int J Syst Evol Microbiol ; 67(6): 2031-2035, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28632116

RESUMO

A novel strain designated 11G32T was isolated from an agricultural soil cultivated with Chinese cabbage in Korea. The cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. The strain grew at 15-28 °C (optimum, 20 °C), pH 5.0-7.0 (optimum, pH 5.0-6.0) and without NaCl. Phylogenetically, the strain was found to be closely related to members of the genus Reyranella and showed 16S rRNA gene sequence similarities of 97.18, 96.76 and 95.99 % with Reyranella graminifolii Wo-34T, Reyranella massiliensis 521T and Reyranella soli KIS14-15T, respectively. The major fatty acids were C19 : 0 cyclo ω8c, C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and 11-methyl C18 : 1ω7c. The predominant ubiquinone was Q-10. The polar lipids profile revealed the presence of phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, unidentified aminolipids, unidentified phospholipids and unidentified lipids. On the basis of data presented, strain 11G32T is considered to represent a novel species of the genus Reyranella, for which the name Reyranella terrae sp. nov. is proposed. The type strain is 11G32T (=KACC 18486T=NBRC 111476T).


Assuntos
Agricultura , Filogenia , Rhodospirillales/classificação , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , Brassica , Produtos Agrícolas , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Rhodospirillales/genética , Rhodospirillales/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/química
7.
Extremophiles ; 21(3): 573-580, 2017 May.
Artigo em Inglês | MEDLINE | ID: mdl-28321614

RESUMO

This is the first study of the highest elevation cyanobacteria-dominated microbial mat yet described. The desiccated mat was sampled in 2010 from an ephemeral rock pool at 5500 m above sea level in the Cordillera Vilcanota of southern Perú. After being frozen for 6 years at -20 °C in the lab, pieces of the mat were sequenced to fully characterize both the 16 and 18S microbial communities and experiments were conducted to determine if organisms in the mat could revive and become active under the extreme freeze-thaw conditions that these mats experience in the field. Sequencing revealed an unexpectedly diverse, multi-trophic microbial community with 16S OTU richness comparable to similar, seasonally desiccated mats from the Dry Valleys of Antarctica and low elevation sites in the Atacama Desert region. The bacterial community of the mat was dominated by phototrophs in the Cyanobacteria (Nostoc) and the Rhodospirillales, whereas the eukaryotic community was dominated by predators such as bdelloid rotifers (Philodinidae). Microcosm experiments showed that bdelloid rotifers in the mat were able to come out of dormancy and actively forage even under realistic field conditions (diurnal temperature fluctuations of -12 °C at night to + 27 °C during the day), and after being frozen for 6 years. Our results broaden our understanding of the diversity of life in periodically desiccated, high-elevation habitats and demonstrate that extreme freeze-thaw cycles per se are not a major factor limiting the development of at least some members of these unique microbial mat systems.


Assuntos
Biodiversidade , Cianobactérias/isolamento & purificação , Camada de Gelo/microbiologia , Rhodospirillales/isolamento & purificação , Rotíferos/isolamento & purificação , Altitude , Animais , Cianobactérias/genética , Dessecação , Ambientes Extremos , Congelamento , Peru , RNA Ribossômico 16S/genética , RNA Ribossômico 18S/genética , Rhodospirillales/genética , Rotíferos/genética
8.
Appl Microbiol Biotechnol ; 100(10): 4395-411, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-26754813

RESUMO

Solid-state acetic acid fermentation (AAF), a natural or semi-controlled fermentation process driven by reproducible microbial communities, is an important technique to produce traditional Chinese cereal vinegars. Highly complex microbial communities and metabolites are involved in traditional Chinese solid-state AAF, but the association between microbiota and metabolites during this process are still poorly understood. In this study, we performed amplicon 16S rRNA gene sequencing on the Illumina MiSeq platform, PCR-denaturing gradient gel electrophoresis, and metabolite analysis to trace the bacterial dynamics and metabolite changes under AAF process. A succession of bacterial assemblages was observed during the AAF process. Lactobacillales dominated all the stages. However, Acetobacter species in Rhodospirillales were considerably accelerated during AAF until the end of fermentation. Quantitative PCR results indicated that the biomass of total bacteria showed a "system microbe self-domestication" process in the first 3 days, and then peaked at the seventh day before gradually decreasing until the end of AAF. Moreover, a total of 88 metabolites, including 8 organic acids, 16 free amino acids, and 66 aroma compounds were detected during AAF. Principal component analysis and cluster analyses revealed the high correlation between the dynamics of bacterial community and metabolites.


Assuntos
Ácido Acético/química , Fermentação , Microbiologia de Alimentos , Acetobacter/metabolismo , Aminoácidos/análise , Fenômenos Químicos , Fragmentação do DNA , DNA Bacteriano/isolamento & purificação , Eletroforese em Gel de Gradiente Desnaturante , Grão Comestível/química , Grão Comestível/microbiologia , Lactobacillales/metabolismo , Odorantes/análise , Reação em Cadeia da Polimerase , Análise de Componente Principal , RNA Ribossômico 16S/isolamento & purificação , Rhodospirillales/metabolismo , Análise de Sequência
9.
PLoS One ; 10(7): e0132062, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26161539

RESUMO

The objectives of this study were to uncover Salix purpurea-microbe xenobiotic degradation systems that could be harnessed in rhizoremediation, and to identify microorganisms that are likely involved in these partnerships. To do so, we tested S. purpurea's ability to stimulate the expression of 10 marker microbial oxygenase genes in a soil contaminated with hydrocarbons. In what appeared to be a detoxification rhizosphere effect, transcripts encoding for alkane 1-monooxygenases, cytochrome P450 monooxygenases, laccase/polyphenol oxidases, and biphenyl 2,3-dioxygenase small subunits were significantly more abundant in the vicinity of the plant's roots than in bulk soil. This gene expression induction is consistent with willows' known rhizoremediation capabilities, and suggests the existence of S. purpurea-microbe systems that target many organic contaminants of interest (i.e. C4-C16 alkanes, fluoranthene, anthracene, benzo(a)pyrene, biphenyl, polychlorinated biphenyls). An enhanced expression of the 4 genes was also observed within the bacterial orders Actinomycetales, Rhodospirillales, Burkholderiales, Alteromonadales, Solirubrobacterales, Caulobacterales, and Rhizobiales, which suggest that members of these taxa are active participants in the exposed partnerships. Although the expression of the other 6 marker genes did not appear to be stimulated by the plant at the community level, signs of additional systems that rest on their expression by members of the orders Solirubrobacterales, Sphingomonadales, Actinomycetales, and Sphingobacteriales were observed. Our study presents the first transcriptomics-based identification of microbes whose xenobiotic degradation activity in soil appears stimulated by a plant. It paints a portrait that contrasts with the current views on these consortia's composition, and opens the door for the development of laboratory test models geared towards the identification of root exudate characteristics that limit the efficiency of current willow-based rhizoremediation applications.


Assuntos
Poluição por Petróleo/análise , Salix/fisiologia , Poluentes do Solo/análise , Actinomycetales/enzimologia , Actinomycetales/genética , Alteromonadaceae/enzimologia , Alteromonadaceae/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biodegradação Ambiental , Burkholderiaceae/enzimologia , Burkholderiaceae/genética , Caulobacteraceae/enzimologia , Caulobacteraceae/genética , Citocromo P-450 CYP4A/genética , Citocromo P-450 CYP4A/metabolismo , Sistema Enzimático do Citocromo P-450/genética , Sistema Enzimático do Citocromo P-450/metabolismo , Regulação Bacteriana da Expressão Gênica , Genes Bacterianos , Proteínas Ferro-Enxofre/genética , Proteínas Ferro-Enxofre/metabolismo , Lacase/genética , Lacase/metabolismo , Redes e Vias Metabólicas , Oxigenases/genética , Oxigenases/metabolismo , Rhizobiaceae/enzimologia , Rhizobiaceae/genética , Rhodospirillales/enzimologia , Rhodospirillales/genética , Xenobióticos
10.
mBio ; 5(4): e01157-14, 2014 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-25028422

RESUMO

Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon ((12)C) or stable-isotope-labeled ((13)C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the (13)C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. Importance: The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential.


Assuntos
Marcação por Isótopo/métodos , Metagenômica/métodos , Microbiologia do Solo , Actinomycetales/classificação , Actinomycetales/genética , Caulobacteraceae/efeitos dos fármacos , Caulobacteraceae/genética , Dados de Sequência Molecular , Rhodospirillales/classificação , Rhodospirillales/genética
11.
PLoS Comput Biol ; 10(2): e1003454, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24586126

RESUMO

Molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer (HGT) and bias from convergence in macromolecular compositions. Extensive variation in size, structure and base composition of alphaproteobacterial genomes has complicated their phylogenomics, sparking controversy over the origins and closest relatives of the SAR11 strains. SAR11 are highly abundant, cosmopolitan aquatic Alphaproteobacteria with streamlined, A+T-biased genomes. A dominant view holds that SAR11 are monophyletic and related to both Rickettsiales and the ancestor of mitochondria. Other studies dispute this, finding evidence of a polyphyletic origin of SAR11 with most strains distantly related to Rickettsiales. Although careful evolutionary modeling can reduce bias and noise in phylogenomic inference, entirely different approaches may be useful to extract robust phylogenetic signals from genomes. Here we develop simple phyloclassifiers from bioinformatically derived tRNA Class-Informative Features (CIFs), features predicted to target tRNAs for specific interactions within the tRNA interaction network. Our tRNA CIF-based model robustly and accurately classifies alphaproteobacterial genomes into one of seven undisputed monophyletic orders or families, despite great variability in tRNA gene complement sizes and base compositions. Our model robustly rejects monophyly of SAR11, classifying all but one strain as Rhizobiales with strong statistical support. Yet remarkably, conventional phylogenetic analysis of tRNAs classifies all SAR11 strains identically as Rickettsiales. We attribute this discrepancy to convergence of SAR11 and Rickettsiales tRNA base compositions. Thus, tRNA CIFs appear more robust to compositional convergence than tRNA sequences generally. Our results suggest that tRNA-CIF-based phyloclassification is robust to HGT of components of the tRNA interaction network, such as aminoacyl-tRNA synthetases. We explain why tRNAs are especially advantageous for prediction of traits governing macromolecular interactions from genomic data, and why such traits may be advantageous in the search for robust signals to address difficult problems in classification and phylogeny.


Assuntos
Alphaproteobacteria/classificação , Alphaproteobacteria/genética , RNA Bacteriano/genética , RNA de Transferência/genética , Proteínas de Bactérias/genética , Biologia Computacional , Evolução Molecular , Redes Reguladoras de Genes , Transferência Genética Horizontal , Genoma Bacteriano , Modelos Genéticos , Filogenia , Rhodospirillales/classificação , Rhodospirillales/genética
12.
PLoS One ; 8(1): e53368, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23308202

RESUMO

There is a good deal of published evidence that indicates that all magnetosomes within a single cell of a magnetotactic bacterium are magnetically oriented in the same direction so that they form a single magnetic dipole believed to assist navigation of the cell to optimal environments for their growth and survival. Some cells of the cultured magnetotactic bacterium Magnetovibrio blakemorei strain MV-1 are known to have relatively wide gaps between groups of magnetosomes that do not seem to interfere with the larger, overall linear arrangement of the magnetosomes along the long axis of the cell. We determined the magnetic orientation of the magnetosomes in individual cells of this bacterium using Fe 2p X-ray magnetic circular dichroism (XMCD) spectra measured with scanning transmission X-ray microscopy (STXM). We observed a significant number of cases in which there are sub-chains in a single cell, with spatial gaps between them, in which one or more sub-chains are magnetically polarized opposite to other sub-chains in the same cell. These occur with an estimated frequency of 4.0±0.2%, based on a sample size of 150 cells. We propose possible explanations for these anomalous cases which shed insight into the mechanisms of chain formation and magnetic alignment.


Assuntos
Magnetismo , Magnetossomos/ultraestrutura , Rhodospirillales/ultraestrutura , Dicroísmo Circular , Campos Magnéticos , Magnetossomos/fisiologia , Microscopia Eletrônica de Transmissão , Movimento/fisiologia , Rhodospirillales/fisiologia
13.
J Bacteriol ; 194(20): 5698, 2012 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-23012280

RESUMO

Reyranella massiliensis is an Alphaproteobacterium member of the class Rhodospirillaceae, growing in amoebae. We sequenced the genome of type strain 521(T). It is composed of a 5,792,218-bp chromosome and encodes 5,675 protein-coding genes and 53 RNA genes, including 3 rRNA genes.


Assuntos
DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Rhodospirillales/genética , Análise de Sequência de DNA , Amoeba/microbiologia , Dados de Sequência Molecular , Rhodospirillales/isolamento & purificação
14.
PLoS One ; 7(4): e34709, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22509347

RESUMO

Bacteriocytes set the stage for some of the most intimate interactions between animal and bacterial cells. In all bacteriocyte possessing systems studied so far, de novo formation of bacteriocytes occurs only once in the host development, at the time of symbiosis establishment. Here, we present the free-living symbiotic flatworm Paracatenula galateia and its intracellular, sulfur-oxidizing bacteria as a system with previously undescribed strategies of bacteriocyte formation and bacterial symbiont transmission. Using thymidine analogue S-phase labeling and immunohistochemistry, we show that all somatic cells in adult worms - including bacteriocytes - originate exclusively from aposymbiotic stem cells (neoblasts). The continued bacteriocyte formation from aposymbiotic stem cells in adult animals represents a previously undescribed strategy of symbiosis maintenance and makes P. galateia a unique system to study bacteriocyte differentiation and development. We also provide morphological and immunohistochemical evidence that P. galateia reproduces by asexual fragmentation and regeneration (paratomy) and, thereby, vertically transmits numerous symbiont-containing bacteriocytes to its asexual progeny. Our data support the earlier reported hypothesis that the symbiont population is subjected to reduced bottleneck effects. This would justify both the codiversification between Paracatenula hosts and their Candidatus Riegeria symbionts, and the slow evolutionary rates observed for several symbiont genes.


Assuntos
Platelmintos/microbiologia , Platelmintos/fisiologia , Reprodução Assexuada/fisiologia , Rhodospirillales/fisiologia , Bactérias Redutoras de Enxofre/fisiologia , Simbiose/fisiologia , Animais , Evolução Biológica , Química Click , Mitose/fisiologia , Platelmintos/ultraestrutura , Fase S/fisiologia , Timidina
15.
Proc Natl Acad Sci U S A ; 108(29): 12078-83, 2011 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-21709249

RESUMO

Harnessing chemosynthetic symbionts is a recurring evolutionary strategy. Eukaryotes from six phyla as well as one archaeon have acquired chemoautotrophic sulfur-oxidizing bacteria. In contrast to this broad host diversity, known bacterial partners apparently belong to two classes of bacteria--the Gamma- and Epsilonproteobacteria. Here, we characterize the intracellular endosymbionts of the mouthless catenulid flatworm genus Paracatenula as chemoautotrophic sulfur-oxidizing Alphaproteobacteria. The symbionts of Paracatenula galateia are provisionally classified as "Candidatus Riegeria galateiae" based on 16S ribosomal RNA sequencing confirmed by fluorescence in situ hybridization together with functional gene and sulfur metabolite evidence. 16S rRNA gene phylogenetic analysis shows that all 16 Paracatenula species examined harbor host species-specific intracellular Candidatus Riegeria bacteria that form a monophyletic group within the order Rhodospirillales. Comparing host and symbiont phylogenies reveals strict cocladogenesis and points to vertical transmission of the symbionts. Between 33% and 50% of the body volume of the various worm species is composed of bacterial symbionts, by far the highest proportion among all known endosymbiotic associations between bacteria and metazoans. This symbiosis, which likely originated more than 500 Mya during the early evolution of flatworms, is the oldest known animal-chemoautotrophic bacteria association. The distant phylogenetic position of the symbionts compared with other mutualistic or parasitic Alphaproteobacteria promises to illuminate the common genetic predispositions that have allowed several members of this class to successfully colonize eukaryote cells.


Assuntos
Evolução Biológica , Filogenia , Rhodospirillales/genética , Simbiose , Turbelários/microbiologia , Sequência de Aminoácidos , Animais , Sequência de Bases , Teorema de Bayes , Análise por Conglomerados , Primers do DNA/genética , Hibridização in Situ Fluorescente , Funções Verossimilhança , Microscopia Eletrônica de Varredura , Microscopia Eletrônica de Transmissão , Modelos Genéticos , Dados de Sequência Molecular , RNA Ribossômico 16S/genética , Rhodospirillales/ultraestrutura , Análise de Sequência de DNA , Especificidade da Espécie , Análise Espectral Raman , Turbelários/ultraestrutura
16.
PLoS One ; 6(5): e20388, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21629664

RESUMO

The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above.


Assuntos
Metagenoma/genética , Água do Mar/microbiologia , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Bacteroidetes/classificação , Bacteroidetes/genética , Citometria de Fluxo , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Dados de Sequência Molecular , Filogenia , RNA Ribossômico/genética , Rhodospirillales/classificação , Rhodospirillales/genética
17.
Int J Syst Evol Microbiol ; 61(Pt 9): 2151-2154, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-20889765

RESUMO

The analysis of three water samples from two cooling towers and one river allowed us to isolate three strains of a novel species of the class Alphaproteobacteria which is phylogenetically related to uncultured alphaproteobacteria. Based upon 16S rRNA gene sequence analysis and phenotypic characterization, we propose to name this novel species Reyranella massiliensis gen. nov., sp. nov., type strain 521(T) ( = CSUR P115(T)  = DSM 23428(T)). The most closely related cultivable micro-organism to this novel bacterium is a member of the genus Magnetospirillum.


Assuntos
Amoeba/microbiologia , Água Doce/microbiologia , Rhodospirillales/crescimento & desenvolvimento , Rhodospirillales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Dados de Sequência Molecular , Filogenia , RNA Ribossômico 16S/genética , Rhodospirillales/classificação , Rhodospirillales/genética , Análise de Sequência de DNA
18.
Water Res ; 41(9): 1885-96, 2007 May.
Artigo em Inglês | MEDLINE | ID: mdl-17368713

RESUMO

The anaerobic uptake of acetate and propionate as single and dual carbon sources by the putative Defluviicoccus vanus related glycogen accumulating organisms (DvGAOs) is investigated. A high enrichment of DvGAOs, representing 95+/-3% of the bacterial community bound to the EUBMIX probes, was achieved in a lab-scale reactor operated under alternating anaerobic and aerobic conditions with acetate as the sole carbon source. The culture is able to take up both acetate and propionate under anaerobic conditions, and the metabolism in both cases is well described by the metabolic models previously proposed for GAOs and verified with experimental data obtained with other types of GAO cultures. In the simultaneous presence of acetate and propionate, DvGAOs take up these two carbon sources sequentially, with propionate uptake preceding acetate uptake. Through model-based analysis, we hypothesise that DvGAOs prefer propionate in order to maximise their production of polyhydroxyalkanoates (PHAs) with the same glycogen consumption, which would enhance their growth potential in the following aerobic period. Despite a low to negligible consumption of acetate in the presence of large amounts of propionate, the presence of acetate considerably stimulated the uptake of propionate with the rate increased by over 60% in comparison to the case where only propionate was present. This property enhances the competitive capability of DvGAOs in enhanced biological phosphorus removal (EBPR) wastewater treatment systems, given the fact that wastewater typically contains both acetate and propionate.


Assuntos
Acetatos/metabolismo , Reatores Biológicos , Glicogênio/metabolismo , Propionatos/metabolismo , Rhodospirillales/metabolismo , Eliminação de Resíduos Líquidos , Purificação da Água , Anaerobiose/fisiologia , Carbono/metabolismo , Glicólise , Esgotos/química , Esgotos/microbiologia , Fatores de Tempo
19.
Appl Environ Microbiol ; 71(7): 3928-34, 2005 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-16000806

RESUMO

Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.


Assuntos
Azospirillum/metabolismo , Ecossistema , Nitratos/metabolismo , Percloratos/metabolismo , Rhodospirillales/metabolismo , Compostos de Sódio/metabolismo , Microbiologia do Solo , Acetatos/metabolismo , Azospirillum/classificação , Azospirillum/genética , Azospirillum/isolamento & purificação , Meios de Cultura , DNA Bacteriano/análise , Humanos , Hidrogênio/metabolismo , Dados de Sequência Molecular , Oxirredução , RNA Ribossômico 16S/genética , Rhodospirillales/classificação , Rhodospirillales/genética , Rhodospirillales/isolamento & purificação , Análise de Sequência de DNA
20.
J Basic Microbiol ; 44(5): 360-73, 2004.
Artigo em Inglês | MEDLINE | ID: mdl-15378530

RESUMO

The gene mak1FN coding for maltokinase from Actinoplanes missouriensis is located in a cluster similar to glycogen metabolism clusters identified in Streptomyces coelicolor. Sequence comparisons demonstrate that mak1-related genes coding for homologous proteins are present in many bacterial genomes including taxonomic distantly related groups such as Rhodospirillales or green sulfur bacteria. More than 50% of the aligned sequences are longer than the mak1 gene from A. missouriensis, and the N-terminal portion of these putative maltokinases exhibit high sequence homologies with trehalose synthases. A more detailed sequence comparison indicates a relationship of maltokinases to aminoglycoside phospho-transferases and protein kinases. Transformation of S. lividans with plasmid vectors containing either the mak1 gene from A. missouriensis or the pep2 gene from S. coelicolor resulted in recombinant strains, which produced measurable amounts of maltokinase activity. The proteins Pep2 and Mak1 were over expressed with Streptomyces lividans 66 as a heterologous host and further characterized. The possible physiological function of maltokinases is discussed.


Assuntos
Micromonosporaceae/enzimologia , Fosfotransferases (Aceptor do Grupo Álcool)/genética , Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo , Streptomyces coelicolor/enzimologia , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Clonagem Molecular , Sequência Conservada , DNA Bacteriano/química , DNA Bacteriano/isolamento & purificação , Estabilidade Enzimática , Expressão Gênica , Genes Bacterianos , Glucosiltransferases/genética , Concentração de Íons de Hidrogênio , Canamicina Quinase/genética , Micromonosporaceae/genética , Dados de Sequência Molecular , Família Multigênica , Fosfotransferases (Aceptor do Grupo Álcool)/isolamento & purificação , Filogenia , Proteínas Quinases/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Rhodospirillales/genética , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência , Streptomyces coelicolor/genética , Streptomyces lividans/genética , Streptomyces lividans/metabolismo , Temperatura
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