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1.
mBio ; 12(1)2021 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-33402535

RESUMO

Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.IMPORTANCE Our study reveals the ecogenomic traits of microorganisms participating in the cellulose economy of soil. We identified three major categories of participants in this economy: (i) independent primary degraders, (ii) interdependent primary degraders, and (iii) secondary consumers (mutualists, opportunists, and parasites). Trade-offs between independent primary degraders, whose adaptations favor antagonism and competitive exclusion, and interdependent and secondary degraders, whose adaptations favor complex interspecies interactions, are expected to affect the fate of microbially processed carbon in soil. Our findings provide useful insights into the ecological relationships that govern one of the planet's most abundant resources of organic carbon. Furthermore, we demonstrate a novel gradient-resolved approach for stable isotope probing, which provides a cultivation-independent, genome-centric perspective into soil microbial processes.


Assuntos
Agricultura , Celulose/metabolismo , Metagenoma , Microbiologia do Solo , Solo/química , Actinobacteria/genética , Actinobacteria/metabolismo , Actinomycetales/genética , Actinomycetales/metabolismo , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Biomassa , Caulobacteraceae/genética , Caulobacteraceae/metabolismo , Celulose/química , Chaetomium/genética , Chaetomium/metabolismo , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Metagenômica , Filogenia , Proteobactérias/genética , Proteobactérias/metabolismo , RNA Ribossômico 16S/genética , Simbiose
2.
Nucleic Acids Res ; 49(3): 1550-1566, 2021 02 22.
Artigo em Inglês | MEDLINE | ID: mdl-33503266

RESUMO

Regulatory nascent peptides participate in the regulation of cellular functions by the mechanisms involving regulated translation arrest. A class of them in bacteria, called monitoring substrates, feedback-regulates the expression of a specific component of protein localization machinery. Three monitoring substrates, SecM, MifM and VemP have previously been identified. Here, we attempt at identifying additional arrest peptides in bacteria. Our bioinformatic searches over more than 400 bacterial genomic sequences for proteins that have the common characteristic features shared by the known monitoring substrates and subsequent in vitro and in vivo characterization of the highlighted sequences allowed the identification of three arrest peptides termed ApcA, ApdA and ApdP. ApcA and ApdA homologs are conserved among a subset of actinobacteria, whereas ApdP has homologs in a subset of α-proteobacteria. We demonstrate that these arrest peptides, in their ribosome-tethered nascent states, inhibit peptidyl transfer. The elongation arrest occurs at a specific codon near the 3' end of the coding region, in a manner depending on the amino acid sequence of the nascent chain. Interestingly, the arrest sequences of ApcA, ApdA and ApdP share a sequence R-A-P-G/P that is essential for the elongation arrest.


Assuntos
Elongação Traducional da Cadeia Peptídica , Peptídeos/química , Actinobacteria/genética , Alphaproteobacteria/genética , Códon , Biologia Computacional , Mutação , Fases de Leitura Aberta , Peptídeos/genética , Biossíntese de Proteínas , Ribossomos
3.
Nat Commun ; 11(1): 5598, 2020 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-33154364

RESUMO

Pimelic acid, a seven carbon α,ω-dicarboxylic acid (heptanedioic acid), is known to provide seven of the ten biotin carbon atoms including all those of the valeryl side chain. Distinct pimelate synthesis pathways were recently elucidated in Escherichia coli and Bacillus subtilis where fatty acid synthesis plus dedicated biotin enzymes produce the pimelate moiety. In contrast, the α-proteobacteria which include important plant and mammalian pathogens plus plant symbionts, lack all of the known pimelate synthesis genes and instead encode bioZ genes. Here we report a pathway in which BioZ proteins catalyze a 3-ketoacyl-acyl carrier protein (ACP) synthase III-like reaction to produce pimeloyl-ACP with five of the seven pimelate carbon atoms being derived from glutaryl-CoA, an intermediate in lysine degradation. Agrobacterium tumefaciens strains either deleted for bioZ or which encode a BioZ active site mutant are biotin auxotrophs, as are strains defective in CaiB which catalyzes glutaryl-CoA synthesis from glutarate and succinyl-CoA.


Assuntos
3-Oxoacil-(Proteína de Transporte de Acila) Sintase/metabolismo , Alphaproteobacteria/metabolismo , Biotina/metabolismo , Lisina/metabolismo , 3-Oxoacil-(Proteína de Transporte de Acila) Sintase/genética , Proteína de Transporte de Acila/metabolismo , Acil Coenzima A/metabolismo , Adipatos/metabolismo , Alphaproteobacteria/enzimologia , Alphaproteobacteria/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Vias Biossintéticas , Coenzima A-Transferases/genética , Coenzima A-Transferases/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Genes Bacterianos , Glutaratos/metabolismo , Mutação , Ácidos Pimélicos/metabolismo
4.
Arch Microbiol ; 202(10): 2655-2661, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32715322

RESUMO

A Gram stain-negative, aerobic, non-motile, short, rod-shaped bacterial strain CAU 1482T was isolated from coal mine wastewater in Hongcheon, Korea. It grew well at 30 °C, pH 8.5, 2% NaCl (w/v). 16S rRNA-based phylogeny indicated that CAU 1482T forms a distinct lineage within Aureimonas with high similarity to Aureimonas frigidaquae CW5T (98.2%), Aureimonas altamirensis S21BT (98.0%), and Aureimonas glaciei B5-2T (96.3%). The predominant cellular fatty acids were C18:1 2-OH, C16:0, C18:1 ω7c, and/or C18:1 ω6c (summed feature 8), with Q-10 as the major isoprenoid quinone. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified aminolipids, and three unidentified lipids. The 3.9-Mb genome included 8 contigs and 3599 protein-coding genes with a 56.7 mol% G + C content. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CAU 1482T and closely related strains of A. frigidaquae CW5T and A. altamirensis S21BT were 72.2‒72.4% and 18.7‒18.8%, respectively. These phenotypic, chemotaxonomic, and phylogenetic data support CAU 1482T as a novel Aureimonas species, for which the name Aureimonas fodinaquatilis sp. nov. is proposed. The type strain is CAU 1482T (= KCTC 62995T = NBRC 113692T).


Assuntos
Alphaproteobacteria/classificação , Filogenia , Águas Residuárias/microbiologia , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Composição de Bases , Carvão Mineral , Ácidos Graxos/análise , Genoma Bacteriano/genética , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Especificidade da Espécie
5.
Arch Microbiol ; 202(9): 2591-2597, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32607725

RESUMO

To date, the genus Parvularcula consists of 6 species and no potential application of this genus was reported. Current study presents the genome sequence of Parvularcula flava strain NH6-79 T and its cellulolytic enzyme analysis. The assembled draft genome of strain NH6-79 T consists of 9 contigs and 7 scaffolds with 3.68 Mbp in size and GC content of 59.87%. From a total of 3,465 genes predicted, 96 of them are annotated as glycoside hydrolases (GHs). Within these GHs, 20 encoded genes are related to cellulosic biomass degradation, including 12 endoglucanases (5 GH10, 4 GH5, and 3 GH51), 2 exoglucanases (GH9) and 6 ß-glucosidases (GH3). In addition, highest relative enzyme activities (endoglucanase, exoglucanase, and ß-glucosidase) were observed at 27th hour when the strain was cultured in the carboxymethyl cellulose/Avicel®-containing medium for 45 h. The combination of genome analysis with experimental studies indicated the ability of strain NH6-79 T to produce extracellular endoglucanase, exoglucanase, and ß-glucosidase. These findings suggest the potential of Parvularcula flava strain NH6-79 T in cellulose-containing biomass degradation and that the strain could be used in cellulosic biorefining process.


Assuntos
Alphaproteobacteria/enzimologia , Alphaproteobacteria/genética , Genoma Bacteriano/genética , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Composição de Bases , Biomassa , Celulase/genética , Celulase/metabolismo , Celulose/metabolismo , beta-Glucosidase/genética , beta-Glucosidase/metabolismo
6.
Nat Ecol Evol ; 4(9): 1213-1219, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32661403

RESUMO

Though it is well accepted that mitochondria originated from an alphaproteobacteria-like ancestor, the phylogenetic relationship of the mitochondrial endosymbiont to extant Alphaproteobacteria is yet unresolved. The focus of much debate is whether the affinity between mitochondria and fast-evolving alphaproteobacterial lineages reflects true homology or artefacts. Approaches such as site exclusion have been claimed to mitigate compositional heterogeneity between taxa, but this comes at the cost of information loss, and the reliability of such methods is so far unproven. Here we demonstrate that site-exclusion methods produce erratic phylogenetic estimates of mitochondrial origin. Thus, previous phylogenetic hypotheses on the origin of mitochondria based on pretreated datasets should be re-evaluated. We applied alternative strategies to reduce phylogenetic noise by systematic taxon sampling while keeping site substitution information intact. Cross-validation based on a series of trees placed mitochondria robustly within Alphaproteobacteria, sharing an ancient common ancestor with Rickettsiales and currently unclassified marine lineages.


Assuntos
Alphaproteobacteria , Alphaproteobacteria/genética , Mitocôndrias/genética , Filogenia , Reprodutibilidade dos Testes
7.
Arch Microbiol ; 202(7): 1939-1944, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32451593

RESUMO

One motile strain designated, YIM DR1026T was isolated from the roots of Psammosilene tunicoides collected from Gejiu, Yunnan province, China. The cells of strain YIM DR1026T were Gram-negative and short-rod shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM DR1026T was a member of the genus Aureimonas and closely related to Aureimonas rubiginis (96.7%). DNA-DNA relatedness values between strain YIM 1026T and Aureimonas rubiginis BCRC 80440T was 38.2 ± 1.5%. The ANI value between YIM DR1026T and other Aureimonas members were below the cut-off level (95-96%) recommended as the average nucleotide identity (ANI) criterion for interspecies identity. Strain YIM DR1026T grew at 4-30 °C (optimum 28 °C), pH 4.0-9.0 (optimum pH 6.0-7.0) and tolerated NaCl (w/v) up to 1% (optimum 0%). Q-10 was sole the respiratory ubiquinone present in YIM DR1026T. Polar lipids of strain YIM DR1026T were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, sulfoquinovosyldiacylglycerol, unidentified aminolipid and unidentified polar lipid. The genomic G + C content was 64.6 mol%. The major fatty acids were C18:1ω7c, C16:0 and summed feature 3 (C16:1ω7c/C16:1ω6c). Based on phenotypic, phylogenetic, chemotaxonomic and genome comparison, strain YIM DR1026T represents a novel species of the genus Aureimonas, for which the name Aureimonas psammosilene sp. nov. is proposed. The type strain is YIM DR1026T (= KCTC 42691T = NBRC 112412T).


Assuntos
Alphaproteobacteria/classificação , Caryophyllaceae/microbiologia , Filogenia , Raízes de Plantas/microbiologia , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/análise , Fosfolipídeos/análise , RNA Ribossômico 16S/genética , Especificidade da Espécie
8.
PLoS Genet ; 16(4): e1008724, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32324740

RESUMO

The Alphaproteobacteria show a remarkable diversity of cell cycle-dependent developmental patterns, which are governed by the conserved CtrA pathway. Its central component CtrA is a DNA-binding response regulator that is controlled by a complex two-component signaling network, mediating distinct transcriptional programs in the two offspring. The CtrA pathway has been studied intensively and was shown to consist of an upstream part that reads out the developmental state of the cell and a downstream part that integrates the upstream signals and mediates CtrA phosphorylation. However, the role of this circuitry in bacterial diversification remains incompletely understood. We have therefore investigated CtrA regulation in the morphologically complex stalked budding alphaproteobacterium Hyphomonas neptunium. Compared to relatives dividing by binary fission, H. neptunium shows distinct changes in the role and regulation of various pathway components. Most notably, the response regulator DivK, which normally links the upstream and downstream parts of the CtrA pathway, is dispensable, while downstream components such as the pseudokinase DivL, the histidine kinase CckA, the phosphotransferase ChpT and CtrA are essential. Moreover, CckA is compartmentalized to the nascent bud without forming distinct polar complexes and CtrA is not regulated at the level of protein abundance. We show that the downstream pathway controls critical functions such as replication initiation, cell division and motility. Quantification of the signal flow through different nodes of the regulatory cascade revealed that the CtrA pathway is a leaky pipeline and must involve thus-far unidentified factors. Collectively, the quantitative system-level analysis of CtrA regulation in H. neptunium points to a considerable evolutionary plasticity of cell cycle regulation in alphaproteobacteria and leads to hypotheses that may also hold in well-established model organisms such as Caulobacter crescentus.


Assuntos
Alphaproteobacteria/genética , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Redes Reguladoras de Genes , Fatores de Transcrição/genética , Alphaproteobacteria/metabolismo , Proteínas de Bactérias/metabolismo , Divisão Celular , Movimento Celular , Replicação do DNA , Evolução Molecular , Fatores de Transcrição/metabolismo
9.
Sci Rep ; 10(1): 6746, 2020 04 21.
Artigo em Inglês | MEDLINE | ID: mdl-32317769

RESUMO

With the increase in iron/steel production, the higher volume of by-products (slag) generated necessitates its efficient recycling. Because the Linz-Donawitz (LD) slag is rich in silicon (Si) and other fertilizer components, we aim to evaluate the impact of the LD slag amendment on soil quality (by measuring soil physicochemical and biological properties), plant nutrient uptake, and strengthens correlations between nutrient uptake and soil bacterial communities. We used 16 S rRNA illumine sequencing to study soil bacterial community and APIZYM assay to study soil enzymes involved in C, N, and P cycling. The LD slag was applied at 2 Mg ha-1 to Japonica and Indica rice cultivated under flooded conditions. The LD slag amendment significantly improved soil pH, plant photosynthesis, soil nutrient availability, and the crop yield, irrespective of cultivars. It significantly increased N, P, and Si uptake of rice straw. The slag amendment enhanced soil microbial biomass, soil enzyme activities and enriched certain bacterial taxa featuring copiotrophic lifestyles and having the potential role for ecosystem services provided to the benefit of the plant. The study evidenced that the short-term LD slag amendment in rice cropping systems is useful to improve soil physicochemical and biological status, and the crop yield.


Assuntos
Fertilizantes/análise , Consórcios Microbianos/efeitos dos fármacos , Oryza/efeitos dos fármacos , Fotossíntese/efeitos dos fármacos , Resíduos/análise , Actinobacteria/classificação , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Betaproteobacteria/classificação , Betaproteobacteria/genética , Betaproteobacteria/isolamento & purificação , Ciclo do Carbono/fisiologia , Deltaproteobacteria/classificação , Deltaproteobacteria/genética , Deltaproteobacteria/isolamento & purificação , Firmicutes/classificação , Firmicutes/genética , Firmicutes/isolamento & purificação , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Humanos , Concentração de Íons de Hidrogênio , Ferro/metabolismo , Ferro/farmacologia , Metalurgia/métodos , Consórcios Microbianos/fisiologia , Ciclo do Nitrogênio/fisiologia , Oryza/microbiologia , Oryza/fisiologia , Fósforo/fisiologia , Fotossíntese/fisiologia , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/microbiologia , Raízes de Plantas/fisiologia , RNA Ribossômico 16S/genética , Silício/metabolismo , Silício/farmacologia , Solo/química , Microbiologia do Solo , Aço/química
10.
PLoS One ; 15(4): e0231839, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32310978

RESUMO

Magnetotactic bacteria (MTB) are prokaryotes that sense the geomagnetic field lines to geolocate and navigate in aquatic sediments. They are polyphyletically distributed in several bacterial divisions but are mainly represented in the Proteobacteria. In this phylum, magnetotactic Deltaproteobacteria represent the most ancestral class of MTB. Like all MTB, they synthesize membrane-enclosed magnetic nanoparticles, called magnetosomes, for magnetic sensing. Magnetosome biogenesis is a complex process involving a specific set of genes that are conserved across MTB. Two of the most conserved genes are mamB and mamM, that encode for the magnetosome-associated proteins and are homologous to the cation diffusion facilitator (CDF) protein family. In magnetotactic Alphaproteobacteria MTB species, MamB and MamM proteins have been well characterized and play a central role in iron-transport required for biomineralization. However, their structural conservation and their role in more ancestral groups of MTB like the Deltaproteobacteria have not been established. Here we studied magnetite cluster MamB and MamM cytosolic C-terminal domain (CTD) structures from a phylogenetically distant magnetotactic Deltaproteobacteria species represented by BW-1 strain, which has the unique ability to biomineralize magnetite and greigite. We characterized them in solution, analyzed their crystal structures and compared them to those characterized in Alphaproteobacteria MTB species. We showed that despite the high phylogenetic distance, MamBBW-1 and MamMBW-1 CTDs share high structural similarity with known CDF-CTDs and will probably share a common function with the Alphaproteobacteria MamB and MamM.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas de Transporte/metabolismo , Cátions/metabolismo , Magnetossomos/metabolismo , Proteobactérias/metabolismo , Alphaproteobacteria/química , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Biomineralização , Proteínas de Transporte/química , Proteínas de Transporte/genética , Sequência Conservada , Deltaproteobacteria/química , Deltaproteobacteria/genética , Deltaproteobacteria/metabolismo , Transporte de Íons , Magnetossomos/química , Magnetossomos/genética , Modelos Moleculares , Filogenia , Conformação Proteica , Proteobactérias/química , Proteobactérias/genética , Alinhamento de Sequência
11.
FEMS Microbiol Lett ; 367(5)2020 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-32166327

RESUMO

Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.


Assuntos
Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Imidazóis/química , Metano/metabolismo , Oligopeptídeos/química , Oligopeptídeos/genética , Cobre/metabolismo , Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Oxirredução , Processamento de Proteína Pós-Traducional
12.
Appl Microbiol Biotechnol ; 104(5): 2067-2077, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31932896

RESUMO

Halohydrin dehalogenases (HHDHs) have attracted much attention due to their ability to synthesize enantiomerically enriched epoxides and ß-haloalcohols. However, most of the HHDHs exhibit low enantioselectivity. Here, a HHDH from the alphaproteobacteria isolate 46_93_T64 (AbHHDH), which shows only poor enantioselectivity in the catalytic resolution of rac-PGE (E = 9.9), has been subjected to protein engineering to enhance its enantioselectivity. Eight mutants (R89K, R89Y, V137I, P178A, N179Q, N179L, F187L, F187A) showed better enantioselectivity than the wild type. The best single mutant N179L (E = 93.0) showed a remarkable 9.4-fold increase in the enantioselectivity. Then, the single mutations were combined to produce the double, triple, quadruple, and quintuple mutants. Among the combinational mutants, the best variant (R89Y/N179L) showed an increased E value of up to 48. The E values of the variants N179L and R89Y/N179L for other epoxides 2-7 were 12.2 to > 200, which showed great improvement compared to 1.2 to 10.5 for the wild type. Using the variant N179L, enantiopure (R)-PGE with > 99% ee could be readily prepared, affording a high yield and a high concentration.


Assuntos
Proteínas de Bactérias/metabolismo , Compostos de Epóxi/química , Compostos de Epóxi/metabolismo , Hidrolases/metabolismo , Alphaproteobacteria/enzimologia , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/isolamento & purificação , Biocatálise , Hidrolases/química , Hidrolases/genética , Hidrolases/isolamento & purificação , Cinética , Modelos Moleculares , Mutação , Engenharia de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Estereoisomerismo , Especificidade por Substrato
13.
Antonie Van Leeuwenhoek ; 113(5): 707-717, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-31950303

RESUMO

Here we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2456 to 2728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaproteobacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.


Assuntos
Bactérias/isolamento & purificação , Sedimentos Geológicos/microbiologia , Metagenoma , Microbiota/genética , Água do Mar/microbiologia , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Biodiversidade , DNA Bacteriano/genética , Deltaproteobacteria/classificação , Deltaproteobacteria/genética , Deltaproteobacteria/isolamento & purificação , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Hidrocarbonetos/metabolismo , Metagenômica/métodos , RNA Ribossômico 16S/genética , Microbiologia da Água
14.
Curr Microbiol ; 77(5): 762-768, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-31919672

RESUMO

Emcibacter congregatus ZYLT was isolated from a sediment sample cultured in situ in a coast located in the East China Sea. The genome of E. congregatus ZYLT was sequenced and assembled into one single circular chromosome with the size of 4,189,011 bp and G+C content of 52.6%. Genomic annotation showed that E. congregatus ZYLT had an intact Type II-C CRISPR-Cas system consists of three cas genes (cas 9, cas 1, and cas 2), 34 direct repeat sequences with the length of 36 bp, and 33 spacers. The predicted Cas 9 protein was smaller than most of existing genome editing tools. This structure might have potential in developing new gene editing system and uncovering the regulatory mechanisms of CRISPR-Cas system. Besides, the comparison between E. congregatus ZYLT and its relative species living in neritic environments unraveled some common traits of the defective strategies of these bacteria to face inshore challenges including the motility, multidrug resistance, and universal efflux pumps.


Assuntos
Alphaproteobacteria/genética , Sistemas CRISPR-Cas/genética , Genoma Bacteriano , Organismos Aquáticos/genética , Composição de Bases , China , Edição de Genes , Genômica , Sedimentos Geológicos/microbiologia , Filogenia , Análise de Sequência de DNA
15.
Antonie Van Leeuwenhoek ; 113(4): 477-489, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31741189

RESUMO

This study of lichens in the subarctic zone of the northern hemisphere has resulted in the detection of new representatives of the order Rhizobiales. The16S rRNA gene sequence phylogeny placed the strains as a separate branch inside the Rhizobiales clade. Strain RmlP001T exhibits 91.85% similarity to Roseiarcus fermentans strain Pf56T and 91.76% to Beijerinckia doebereinerae strain LMG 2819T, whilst strain RmlP026T is closely related to B. doebereinerae strain LMG 2819T (91.85%) and Microvirga pakistanensis strain NCCP-1258T (91.39%). A whole-genome phylogeny of the strains confirmed their taxonomic positions. The cells of both strains were observed to be Gram-negative, motile rods that multiplied by binary fission. The cells were found to contain poly-ß-hydroxybutyrate and polyphosphate, to grow at pH 3.5-8.0 and 10-30 °C, and could not fix atmospheric nitrogen. Their major cellular fatty acid identified was C18:1ω7c (68-71%) and their DNA G + C contents determined to be 70.5-70.8%. Beta-carotene was identified as their major carotenoid pigment; Q-10 was the only ubiquinone detected. Strains RmlP001T and RmlP026T are distinguishable from related species by the presence of ß-carotene, the absence of C1 metabolism and the ability to grow in the presence of 3.5% NaCl. Based on their phylogenetic, phenotypic and chemotaxonomic features, we propose a novel genus Lichenibacterium and two novel species, Lichenibacterium ramalinae (the type species of the genus) and Lichenibacterium minor, to accommodate these bacteria within the family Lichenibacteriaceae fam. nov. of the order Rhizobiales. The L. ramalinae type strain is RmlP001T (= KCTC 72076T = VKM B-3263T) and the L. minor type strain is RmlP026T (= KCTC 72077T = VKM B-3277T).


Assuntos
Alphaproteobacteria/classificação , Alphaproteobacteria/isolamento & purificação , Líquens/microbiologia , beta Caroteno/biossíntese , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , DNA Bacteriano/genética , Genoma Bacteriano , Filogenia , Reação em Cadeia da Polimerase , RNA Bacteriano/genética , RNA Ribossômico 16S/genética , Especificidade da Espécie
16.
Environ Microbiol ; 22(1): 433-446, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31736217

RESUMO

The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI-B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI-C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.


Assuntos
Actinobacteria/isolamento & purificação , Alphaproteobacteria/isolamento & purificação , Archaea/isolamento & purificação , Chloroflexi/isolamento & purificação , Lagos/microbiologia , Microbiota/genética , Actinobacteria/classificação , Actinobacteria/genética , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Archaea/classificação , Archaea/genética , Chloroflexi/classificação , Chloroflexi/genética , Michigan , Filogenia , Plâncton/classificação , Plâncton/genética , RNA Ribossômico 16S/genética
17.
Environ Microbiol ; 22(1): 297-309, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31680440

RESUMO

Microbial communities in natural ecosystems are subject to strong ecological rules. The study of local communities along a regional metacommunity can reveal patterns of community assembly, and disentangle the underlying ecological processes. In particular, we seek drivers of community assembly at the regional scale using a large lacustrine dataset (>300 lakes) along the geographical, limnological and physico-chemical gradients in the Pyrenees. By using high throughput amplicon sequencing of the 16S rRNA gene, and inferring environmental sources of bacterial immigrants, we showed that surface aquatic bacterial assemblages were strongly influenced by terrestrial populations from soil, biofilms or sediments, and primarily selected by a pH-alkalinity gradient. Indeed, source proportions explained 27% of the community variation, and chemistry 15% of the total variation, half of it shared with the sources. Major taxonomic groups such as Verrucomicrobia, Actinobacteria and Bacteroidetes showed higher aquatic affinities than Parcubacteria, Gammaproteobacteria, Alphaproteobacteria or Betaproteobacteria, which may be recruited and selected through different hydrographic habitats. A regional fingerprint was observed with lower alpha diversity and higher beta diversity in the central Pyrenees than in both ends. We suggest an ecological succession process, likely influenced by complex interactions of environmental source dispersal and environmental filtering along the mountain range geography.


Assuntos
Organismos Aquáticos/classificação , Bactérias/classificação , Bactérias/isolamento & purificação , Lagos/microbiologia , Actinobacteria/classificação , Actinobacteria/genética , Actinobacteria/isolamento & purificação , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Organismos Aquáticos/genética , Organismos Aquáticos/isolamento & purificação , Bactérias/genética , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Betaproteobacteria/classificação , Betaproteobacteria/genética , Betaproteobacteria/isolamento & purificação , Biodiversidade , Ecossistema , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Microbiota , Plâncton/classificação , RNA Ribossômico 16S/genética , Espanha , Verrucomicrobia/classificação , Verrucomicrobia/genética , Verrucomicrobia/isolamento & purificação
18.
Arch Microbiol ; 202(4): 815-824, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-31844948

RESUMO

Kiloniella laminariae is a true marine bacterium and the first member of the family and order, the Kiloniellaceae and Kiloniellales. K. laminariae LD81T (= DSM 19542T) was isolated from the marine macroalga Saccharina latissima and is a mesophilic, typical marine chemoheterotrophic aerobic bacterium with antifungal activity. Phylogenetic analysis of 16S rRNA gene sequence revealed the similarity of K. laminariae LD81T not only with three validly described species of the genus Kiloniella, but also with undescribed isolates and clone sequences from marine samples in the range of 93.6-96.7%. We report on the analysis of the draft genome of this alphaproteobacterium and describe some selected features. The 4.4 Mb genome has a G + C content of 51.4%, contains 4213 coding sequences including 51 RNA genes as well as 4162 protein-coding genes, and is a part of the Genomic Encyclopaedia of Bacteria and Archaea (GEBA) project. The genome provides insights into a number of metabolic properties, such as carbon and sulfur metabolism, and indicates the potential for denitrification and the biosynthesis of secondary metabolites. Comparative genome analysis was performed with K. laminariae LD81T and the animal-associated species Kiloniella majae M56.1T from a spider crab, Kiloniella spongiae MEBiC09566T from a sponge as well as Kiloniella litopenai P1-1 from a white shrimp, which all inhabit quite different marine habitats. The analysis revealed that the K. laminariae LD81T contains 1397 unique genes, more than twice the amount of the other species. Unique among others is a mixed PKS/NRPS biosynthetic gene cluster with similarity to the biosynthetic gene cluster responsible for the production of syringomycin.


Assuntos
Alphaproteobacteria/genética , Organismos Aquáticos/genética , Genômica , Filogenia , Alphaproteobacteria/classificação , Animais , Organismos Aquáticos/classificação , Organismos Aquáticos/microbiologia , Proteínas de Bactérias/genética , Composição de Bases , Feófitas/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie
19.
Nat Commun ; 10(1): 5529, 2019 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-31827088

RESUMO

Phagocytosis is a key eukaryotic feature, conserved from unicellular protists to animals, that enabled eukaryotes to feed on other organisms. It could also be a driving force behind endosymbiosis, a process by which α-proteobacteria and cyanobacteria evolved into mitochondria and plastids, respectively. Here we describe a planctomycete bacterium, 'Candidatus Uab amorphum', which is able to engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism. Observations via light and electron microscopy suggest that this bacterium digests prey cells in specific compartments. With the possible exception of a gene encoding an actin-like protein, analysis of the 'Ca. Uab amorphum' genomic sequence does not reveal any genes homologous to eukaryotic phagocytosis genes, suggesting that cell engulfment in this microorganism is probably not homologous to eukaryotic phagocytosis. The discovery of this "phagotrophic" bacterium expands our understanding of the cellular complexity of prokaryotes, and may be relevant to the origin of eukaryotic cells.


Assuntos
Alphaproteobacteria/fisiologia , Fagocitose , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/ultraestrutura , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Evolução Biológica , Genoma Bacteriano , Filogenia
20.
Appl Environ Microbiol ; 85(24)2019 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-31585988

RESUMO

A number of anaerobic ciliates, unicellular eukaryotes, intracellularly possess methanogenic archaea and bacteria as symbiotic partners. Although this tripartite relationship is of interest in terms of the fact that each participant is from a different domain, the difficulty in culture and maintenance of those host species with symbiotic partners has disturbed both ecological and functional studies so far. In this study, we obtained a stable culture of a small anaerobic scuticociliate, strain GW7. By transmission electron microscopic observation and fluorescent in situ hybridization with domain-specific probes, we demonstrate that GW7 possesses both archaeal and bacterial endosymbionts in its cytoplasm. These endosymbionts are in dependently associated with hydrogenosomes, which are organelle producing hydrogen and ATP under anaerobic conditions. Clone library analyses targeting prokaryotic 16S rRNA genes, fluorescent in situ hybridization with endosymbiont-specific probes, and molecular phylogenetic analyses revealed the phylogenetic affiliations and intracellular localizations of these endosymbionts. The endosymbiotic archaeon is a methanogen belonging to the genus Methanoregula (order Methanomicrobiales); a member of this genus has previously been described as the endosymbiont of an anaerobic ciliate from the genus Metopus (class Armophorea), which is only distantly related to strain GW7 (class Oligohymenophorea). The endosymbiotic bacterium belongs to the family Holosporaceae of the class Alphaproteobacteria, which also comprises several endosymbionts of various aerobic ciliates. For this endosymbiotic bacterium, we propose a novel candidate genus and species, "Candidatus Hydrogenosomobacter endosymbioticus."IMPORTANCE Tripartite symbioses between anaerobic ciliated protists and their intracellular archaeal and bacterial symbionts are not uncommon, but most reports have been based mainly on microscopic observations. Deeper insights into the function, ecology, and evolution of these fascinating symbioses involving partners from all three domains of life have been hampered by the difficulties of culturing anaerobic ciliates in the laboratory and the frequent loss of their prokaryotic partners during long-term cultivation. In the present study, we report the isolation of an anaerobic scuticociliate, strain GW7, which has been stably maintained in our laboratory for more than 3 years without losing either of its endosymbionts. Unexpectedly, molecular characterization of the endosymbionts revealed that the bacterial partner of GW7 is phylogenetically related to intranuclear endosymbionts of aerobic ciliates. This strain will enable future genomic, transcriptomic, and proteomic analyses of the interactions in this tripartite symbiosis and a comparison with endosymbioses in aerobic ciliates.


Assuntos
Alphaproteobacteria/metabolismo , Anaerobiose/fisiologia , Cilióforos/microbiologia , Euryarchaeota/metabolismo , Holosporaceae/fisiologia , Organelas/microbiologia , Simbiose , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Meios de Cultura/química , Euryarchaeota/classificação , Euryarchaeota/genética , Holosporaceae/classificação , Holosporaceae/genética , Hibridização in Situ Fluorescente , Filogenia , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/isolamento & purificação , Análise de Sequência de DNA
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