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1.
Microbes Environ ; 35(1)2020.
Artigo em Inglês | MEDLINE | ID: mdl-31969532

RESUMO

The pmoA gene, encoding particulate methane monooxygenase in methanotrophs, and nirS and nirK genes, encoding bacterial nitrite reductases, were examined in the root and rhizosphere sediment of three common emergent macrophytes (Phragmites australis, Typha angustifolia, and Scirpus triqueter) and unvegetated sediment from eutrophic Wuliangsuhai Lake in China. Sequencing analyses indicated that 334 out of 351 cloned pmoA sequences were phylogenetically the most closely related to type I methanotrophs (Gammaproteobacteria), and Methylomonas denitrificans-like organisms accounted for 44.4% of the total community. In addition, 244 out of 250 cloned nirS gene sequences belonged to type I methanotrophs, and 31.2% of nirS genes were the most closely related to paddy rice soil clone SP-2-12 in Methylomonas of the total community. Three genera of type I methanotrophs, Methylomonas, Methylobacter, and Methylovulum, were common in both pmoA and nirS clone libraries in each sample. A quantitative PCR (qPCR) analysis demonstrated that the copy numbers of the nirS and nirK genes were significantly higher in rhizosphere sediments than in unvegetated sediments in P. australis and T. angustifolia plants. In the same sample, the nirS gene copy number was significantly higher than that of nirK. Furthermore, type I methanotrophs were localized in the root tissues according to catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Thus, nirS-carrying type I methanotrophs were enriched in macrophyte root and rhizosphere sediment and are expected to play important roles in carbon/nitrogen cycles in a eutrophic wetland.


Assuntos
Eutrofização , Gammaproteobacteria/genética , Genes Bacterianos/genética , Magnoliopsida/microbiologia , Microbiologia do Solo , Áreas Alagadas , Proteínas de Bactérias/genética , China , Gammaproteobacteria/classificação , Gammaproteobacteria/metabolismo , Dosagem de Genes , Lagos/microbiologia , Metano/metabolismo , Nitrito Redutases/genética , Oxigenases/genética , Raízes de Plantas/microbiologia , Rizosfera
2.
Mol Plant Microbe Interact ; 33(2): 296-307, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31851880

RESUMO

Dickeya dadantii is a plant-pathogenic bacterium that causes soft-rot in a wide range of plants. Although we have previously demonstrated that cyclic bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), a bacterial secondary messenger, plays a central role in virulence regulation in D. dadantii, the upstream signals that modulate c-di-GMP remain enigmatic. Using a genome-wide transposon mutagenesis approach of a Δhfq mutant strain that has high c-di-GMP and reduced motility, we uncovered transposon mutants that recovered the c-di-GMP-mediated repression on swimming motility. A number of these mutants harbored transposon insertions in genes encoding tricarboxylic acid (TCA) cycle enzymes. Two of these TCA transposon mutants were studied further by generating chromosomal deletions of the fumA gene (encoding fumarase) and the sdhCDAB operon (encoding succinate dehydrogenase). Disruption of the TCA cycle in these deletion mutants resulted in reduced intracellular c-di-GMP and enhanced production of pectate lyases (Pels), a major plant cell wall-degrading enzyme (PCWDE) known to be transcriptionally repressed by c-di-GMP. Consistent with this result, addition of TCA cycle intermediates such as citrate also resulted in increased c-di-GMP levels and decreased production of Pels. Additionally, we found that a diguanylate cyclase GcpA was solely responsible for the observed citrate-mediated modulation of c-di-GMP. Finally, we demonstrated that addition of citrate induced not only an overproduction of GcpA protein but also a concomitant repression of the c-di-GMP-degrading phosphodiesterase EGcpB which, together, resulted in an increase in the intracellular concentration of c-di-GMP. In summary, our report demonstrates that bacterial respiration and respiration metabolites serve as signals for the regulation of c-di-GMP signaling.


Assuntos
Proteínas de Bactérias , GMP Cíclico/análogos & derivados , Gammaproteobacteria , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Parede Celular/microbiologia , GMP Cíclico/genética , GMP Cíclico/metabolismo , Gammaproteobacteria/enzimologia , Gammaproteobacteria/genética , Regulação Bacteriana da Expressão Gênica/genética , Mutação
3.
ISME J ; 14(1): 178-188, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31611653

RESUMO

SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world's oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.


Assuntos
Gammaproteobacteria/classificação , Ecótipo , Gammaproteobacteria/genética , Genes Bacterianos , Metagenoma , Oceanos e Mares , Filogeografia
4.
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
5.
Pol J Microbiol ; 68(4): 417-427, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31880886

RESUMO

Colistin is a member of cationic polypeptide antibiotics known as polymyxins. It is widely used in animal husbandry, plant cultivation, animal and human medicine and is increasingly used as one of the last available treatment options for patients with severe infections with carbapenem-resistant Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant (MDR) bacteria, the resistance to this antibiotic ought to be monitored. Bacterial resistance to colistin may be encoded on transposable genetic elements (e.g. plasmids with the mcr genes). Thus far, nine variants of the mcr gene, mcr-1 - mcr-9, have been identified. Chromosomal resistance to colistin is associated with the modification of lipopolysaccharide (LPS). Various methods, from classical microbiology to molecular biology methods, are used to detect the colistin-resistant bacterial strains and to identify resistance mechanisms. The broth dilution method is recommended for susceptibility testing of bacteria to colistin.Colistin is a member of cationic polypeptide antibiotics known as polymyxins. It is widely used in animal husbandry, plant cultivation, animal and human medicine and is increasingly used as one of the last available treatment options for patients with severe infections with carbapenem-resistant Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant (MDR) bacteria, the resistance to this antibiotic ought to be monitored. Bacterial resistance to colistin may be encoded on transposable genetic elements (e.g. plasmids with the mcr genes). Thus far, nine variants of the mcr gene, mcr-1 ­ mcr-9, have been identified. Chromosomal resistance to colistin is associated with the modification of lipopolysaccharide (LPS). Various methods, from classical microbiology to molecular biology methods, are used to detect the colistin-resistant bacterial strains and to identify resistance mechanisms. The broth dilution method is recommended for susceptibility testing of bacteria to colistin.


Assuntos
Antibacterianos/farmacologia , Infecções Bacterianas/microbiologia , Colistina/farmacologia , Farmacorresistência Bacteriana , Gammaproteobacteria/efeitos dos fármacos , Animais , Infecções Bacterianas/tratamento farmacológico , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Humanos
6.
Genome Biol Evol ; 11(12): 3510-3522, 2019 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-31725149

RESUMO

Heritable symbionts are common in terrestrial arthropods and often provide beneficial services to hosts. Unlike obligate, nutritional symbionts that largely persist under strict host control within specialized host cells, heritable facultative symbionts exhibit large variation in within-host lifestyles and services rendered with many retaining the capacity to transition among roles. One enigmatic symbiont, Candidatus Fukatsuia symbiotica, frequently infects aphids with reported roles ranging from pathogen, defensive symbiont, mutualism exploiter, and nutritional co-obligate symbiont. Here, we used an in vitro culture-assisted protocol to sequence the genome of a facultative strain of Fukatsuia from pea aphids (Acyrthosiphon pisum). Phylogenetic and genomic comparisons indicate that Fukatsuia is an aerobic heterotroph, which together with Regiella insecticola and Hamiltonella defensa form a clade of heritable facultative symbionts within the Yersiniaceae (Enterobacteriales). These three heritable facultative symbionts largely share overlapping inventories of genes associated with housekeeping functions, metabolism, and nutrient acquisition, while varying in complements of mobile DNA. One unusual feature of Fukatsuia is its strong tendency to occur as a coinfection with H. defensa. However, the overall similarity of gene inventories among aphid heritable facultative symbionts suggests that metabolic complementarity is not the basis for coinfection, unless playing out on a H. defensa strain-specific basis. We also compared the pea aphid Fukatsuia with a strain from the aphid Cinara confinis (Lachninae) where it is reported to have transitioned to co-obligate status to support decaying Buchnera function. Overall, the two genomes are very similar with no clear genomic signatures consistent with such a transition, which suggests co-obligate status in C. confinis was a recent event.


Assuntos
Afídeos/fisiologia , Gammaproteobacteria/fisiologia , Animais , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/patogenicidade , Genoma Bacteriano , Simbiose
7.
Nat Commun ; 10(1): 4853, 2019 10 24.
Artigo em Inglês | MEDLINE | ID: mdl-31649262

RESUMO

Few secreted proteins involved in plant infection common to necrotrophic bacteria, fungi and oomycetes have been identified except for plant cell wall-degrading enzymes. Here we study a family of iron-binding proteins that is present in Gram-negative and Gram-positive bacteria, fungi, oomycetes and some animals. Homolog proteins in the phytopathogenic bacterium Dickeya dadantii (IbpS) and the fungal necrotroph Botrytis cinerea (BcIbp) are involved in plant infection. IbpS is secreted, can bind iron and copper, and protects the bacteria against H2O2-induced death. Its 1.7 Å crystal structure reveals a classical Venus Fly trap fold that forms dimers in solution and in the crystal. We propose that secreted Ibp proteins binds exogenous metals and thus limit intracellular metal accumulation and ROS formation in the microorganisms.


Assuntos
Arabidopsis/metabolismo , Cobre/metabolismo , Proteínas de Ligação ao Ferro/metabolismo , Ferro/metabolismo , Doenças das Plantas/microbiologia , Espécies Reativas de Oxigênio/metabolismo , Anti-Infecciosos Locais/farmacologia , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Botrytis/genética , Botrytis/metabolismo , Proteínas de Transporte/metabolismo , Defensinas/genética , Dimerização , Gammaproteobacteria/efeitos dos fármacos , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Peróxido de Hidrogênio/farmacologia , Proteínas de Ligação ao Ferro/genética , Doenças das Plantas/genética , Sideróforos/genética , Sideróforos/metabolismo
8.
Microbes Environ ; 34(4): 402-412, 2019 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-31631078

RESUMO

Thiocyanate (SCN-) is harmful to a wide range of organisms, and its removal is essential for environmental protection. A neutrophilic halophile capable of thiocyanate degradation, Thiohalobacter sp. strain FOKN1, was highly enriched (relative abundance; 98.4%) from activated sludge collected from a bioreactor receiving thiocyanate-rich wastewater. The enrichment culture degraded 3.38 mM thiocyanate within 140 h, with maximum activity at pH 8.8, 37°C, and 0.18 M sodium chloride. Thiocyanate degradation was inhibited by 30 mg L-1 phenol, but not by thiosulfate. Microbial thiocyanate degradation is catalyzed by thiocyanate dehydrogenase, while limited information is currently available on the molecular mechanisms underlying thiocyanate degradation by the thiocyanate dehydrogenase of neutrophilic halophiles. Therefore, (meta)genomic and proteomic analyses of enrichment cultures were performed to elucidate the whole genome sequence and proteome of Thiohalobacter sp. strain FOKN1. The 3.23-Mb circular Thiohalobacter sp. strain FOKN1 genome was elucidated using a PacBio RSII sequencer, and the expression of 914 proteins was identified by tandem mass spectrometry. The Thiohalobacter sp. strain FOKN1 genome had a gene encoding thiocyanate dehydrogenase, which was abundant in the proteome, suggesting that thiocyanate is degraded by thiocyanate dehydrogenase to sulfur and cyanate. The sulfur formed may be oxidized to sulfate by the sequential oxidation reactions of dissimilatory sulfite reductase, adenosine-5'-phosphosulfate reductase, and dissimilatory ATP sulfurylase. Although the Thiohalobacter sp. strain FOKN1 genome carried a gene encoding cyanate lyase, its protein expression was not detectable. The present study advances the understanding of the molecular mechanisms underlying thiocyanate degradation by the thiocyanate dehydrogenase of neutrophilic halophiles.


Assuntos
Gammaproteobacteria/metabolismo , Genoma Bacteriano/genética , Esgotos/microbiologia , Tiocianatos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Reatores Biológicos/microbiologia , DNA Bacteriano/genética , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Redes e Vias Metabólicas , Filogenia , Proteoma/metabolismo , RNA Ribossômico 16S/genética , Esgotos/química , Tiocianatos/análise
9.
J Med Microbiol ; 68(11): 1604-1606, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31513006

RESUMO

The increase in carbapenemase-producing Enterobacterales (CPE), including metallo-ß-lactamase (MBL) producers, is a severe global health concern. Thus, highly sensitive and specific methods for detecting MBL producers are needed. In this study, we tested the detectability of MBL-producing Enterobacterales against three types of MBL inhibitors (sodium mercaptoacetate, SMA; ethylenediaminetetraacetic acid, EDTA; and dipicolinic acid, DPA) used in combination with a modified carbapenem inactivation method (mCIM). These inhibitor-combination mCIMs were tested against 129 CPE (IMP, 93; NDM, 11; KPC, 13; NMC, 1; OXA-48, 11) and 75 non-CPE. For evaluation of MBL inhibitors, we used two concentrations for each of the three inhibitors: DPA (200 and 300 mg l- 1), EDTA (5 and 10 mM), and SMA (1500 and 3000 mg l- 1). The overall sensitivities of SMA, EDTA and DPA were 97.1-99.0 %, 81.7-99.0 % and 88.5-96.2 %, respectively. Moreover, each method showed high specificity (99.0-100 %). Although inhibitor-combination mCIMs were highly sensitive and specific for the detection of MBL producers, we found that sensitivity was dependent on the concentration of inhibitors.


Assuntos
Antibacterianos/farmacologia , Infecções Bacterianas/microbiologia , Carbapenêmicos/farmacologia , Gammaproteobacteria/efeitos dos fármacos , Inibidores de beta-Lactamases/farmacologia , beta-Lactamases/metabolismo , Gammaproteobacteria/enzimologia , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Humanos , Testes de Sensibilidade Microbiana , Penicilinas/farmacologia , beta-Lactamases/genética
10.
Appl Microbiol Biotechnol ; 103(19): 8229-8239, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31485689

RESUMO

The utilization of rubber (poly (cis-1,4-isoprene)) by rubber-degrading bacteria depends on the synthesis of rubber oxygenases that cleave the polymer extracellularly to low molecular weight products that can be taken up and used as a carbon source. All so far described Gram-negative rubber-degrading species use two related ≈ 70 kDa rubber oxygenases (RoxA and RoxB) for the primary attack of rubber while all described Gram-positive rubber-degrading strains use RoxA/RoxB-unrelated latex-clearing proteins (Lcps, ≈ 40 kDa) as rubber oxygenase(s). In this study, we identified an lcp orthologue in a Gram-negative species (Solimonas fluminis). We cloned and heterologously expressed the lcp gene of S. fluminis HR-BB, purified the corresponding Lcp protein (LcpHR-BB) from recombinant Escherichia coli, and biochemically characterised the LcpHR-BB activity. LcpHR-BB cleaved polyisoprene to a mixture of C20 and higher oligoisoprenoids at a specific activity of 1.5 U/mg. Furthermore, spectroscopic investigation identified LcpHR-BB as a b-haem-containing protein with an oxidised, fivefold coordinated (open) haem centre. To the best of our knowledge, this is the first report that Gram-negative bacteria can have an active rubber oxygenase of the Lcp type.


Assuntos
Proteínas de Bactérias/metabolismo , Gammaproteobacteria/enzimologia , Látex/metabolismo , Oxigenases/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/isolamento & purificação , Biotransformação , Clonagem Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Gammaproteobacteria/genética , Expressão Gênica , Oxigenases/genética , Oxigenases/isolamento & purificação , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo
11.
Biotechnol Lett ; 41(10): 1187-1200, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31418101

RESUMO

OBJECTIVES: Bifunctional alginate lyase can efficiently saccharify alginate biomass and prepare functional oligosaccharides of alginate. RESULTS: A new BP-2 strain that produces alginate lyase was screened and identified from rotted Sargassum. A new alginate lyase, Alg17B, belonging to the polysaccharide lyase family 17, was isolated and purified from BP-2 fermentation broth by freeze-drying, dialysis, and ion exchange chromatography. The enzymatic properties of the purified lyase were investigated. The molecular weight of Alg17B was approximately 77 kDa, its optimum reaction temperature was 40-45 °C, and its optimum reaction pH was 7.5-8.0. The enzyme was relatively stable at pH 7.0-8.0, with a temperature range of 25-35 °C, and the specific activity of the purified enzyme reached 4036 U/mg. A low Na+ concentration stimulated Alg17B enzyme activity, but Ca2+, Zn2+, and other metal ions inhibited it. Substrate specificity analysis, thin-layer chromatography, and mass spectrometry showed that Alg17B is an alginate lyase that catalyses the hydrolysis of sodium alginate, polymannuronic acid (polyM) and polyguluronic acid to produce monosaccharides and low molecular weight oligosaccharides. Alg17B is also bifunctional, exhibiting both endolytic and exolytic activities toward alginate, and has a wide substrate utilization range with a preference for polyM. CONCLUSIONS: Alg17B can be used to saccharify the main carbohydrate, alginate, in the ethanolic production of brown algae fuel as well as in preparing and researching oligosaccharides.


Assuntos
Organismos Aquáticos/enzimologia , Gammaproteobacteria/enzimologia , Polissacarídeo-Liase/isolamento & purificação , Polissacarídeo-Liase/metabolismo , Sargassum/microbiologia , Alginatos/metabolismo , Ácido Algínico/metabolismo , Organismos Aquáticos/classificação , Organismos Aquáticos/genética , Organismos Aquáticos/isolamento & purificação , Ativadores de Enzimas/análise , Inibidores Enzimáticos/análise , Estabilidade Enzimática , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Concentração de Íons de Hidrogênio , Hidrólise , Peso Molecular , Monossacarídeos/metabolismo , Oligossacarídeos/metabolismo , Polissacarídeo-Liase/química , Polissacarídeo-Liase/genética , Polissacarídeos Bacterianos/metabolismo , Especificidade por Substrato , Temperatura Ambiente
12.
PLoS One ; 14(6): e0218868, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31233546

RESUMO

Destructive maceration, a wide host range, and longevity in non-plant substrates has established Dickeya dianthicola (blackleg of potato) as a significant threat to potato industries worldwide. To protect these businesses, a specific and sensitive point-of-care D. dianthicola detection tool is necessary. We have developed a loop-mediated isothermal amplification (LAMP) assay for specific, sensitive, and rapid detection of D. dianthicola, which can be streamlined for point-of-care use. The developed LAMP assay targets a unique gene, alcohol dehydrogenase, of D. dianthicola. Assay specificity was assessed using strains present in inclusivity (16 D. dianthicola strains) and exclusivity panels (56 closely related, potato pathogenic, and other bacterial strains). Amplification with strains of inclusivity panel occurred, and cross-reactivity with non-target DNA was not observed. The limit of detection (LOD) was 10 CFU/ml when dilutions were made before isolating the genomic DNA; however, LOD was determined as 1 pg using 10-fold serially diluted D. dianthicola genomic DNA. Similar LOD of 1 pg was observed when serially diluted target genomic DNA was mixed with host genomic DNA. LOD (1 pg) was also calculated with 10-fold serially diluted synthetic DNA fragments containing primer target sites. Naturally and artificially inoculated plant samples were used for field adaptability tests with the field-deployable Optigene Plant Material Lysis Kit and a heat block (65°C); the results were obtained within 20 minutes. Despite the lack of method precision, no false positives or false negatives were observed. Therefore, with prepared reactions and a steady heat source, this assay can be used for rapid point-of-care detection, which is imperative for quarantine, eradication, disease management, and border protection.


Assuntos
Álcool Desidrogenase/genética , Gammaproteobacteria/genética , Técnicas de Amplificação de Ácido Nucleico/métodos , Solanum tuberosum/microbiologia , Gammaproteobacteria/isolamento & purificação , Limite de Detecção , Doenças das Plantas/microbiologia , Proteínas de Plantas/genética , Sensibilidade e Especificidade , Fatores de Tempo
13.
Mar Pollut Bull ; 142: 135-144, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31232286

RESUMO

This study investigated the microbial structure in the surface seawater from five coastal sites around Xiamen Island, China, over four seasons to evaluate seasonal environmental fluctuations impact on them. This subtropical island is characterized by long, hot, humid summers, and short, mild, dry winters. All sites were dominated by Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes; microbial community composition was similar across four seasons. However, larger proportions of Gammaproteobacteria and Bacillus were observed during the summer than during any other season. The high ratio of Bacillus, Bacteroidetes, and Clostridia richness to Alphaproteobacteria richness in the summer, suggested that the sites we tested were heavily affected by waste water to other seasons. Correlation-based network analyses among the bacterial species and environmental variables indicated important connections between physiochemical variables and specific taxonomic groups. Collectively, our results suggested that seasonal shifts and wastewater pollution together shape the structures of the microbial communities around Xiamen Island.


Assuntos
Bactérias/genética , Água do Mar/microbiologia , China , Cianobactérias/genética , Estuários , Gammaproteobacteria/genética , Ilhas , Filogenia , Proteobactérias/genética , RNA Ribossômico 16S/genética , Estações do Ano , Águas Residuárias , Microbiologia da Água , Poluição da Água
14.
Chemosphere ; 233: 101-109, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31170581

RESUMO

The wide application of 6:2 fluorotelomer sulfonate (6:2 FTS) and its precursors results in their ubiquitous occurrence in the environment. This study investigated the biotransformation of 6:2 FTS using fresh slurries collected from constructed wetland under aerobic and anoxic conditions. Biotransformation rates of 6:2 FTS was extremely slow under both aerobic and anoxic conditions. The analysis of transformation products showed that less than 0.7 mol% of initial concentration of 6:2 FTS was biotransformed under anoxic conditions. Effects of 6:2 FTS on the shifts in microbial community in wetland slurry during aerobic and anoxic transformation were evaluated using 16S rRNA gene amplicon sequencing. Under aerobic conditions, 6:2 FTS altered the microbial community structure, in which Methylocaldum (Gamma-proteobacteria) became the predominant genus after being exposed to 6:2 FTS. This means that Methylocaldum appears to have higher tolerance to 6:2 FTS and seems to be potential 6:2 FTS-degrading bacteria. Under anoxic transformation, only the genus Methanomethylovorans (Euryarchaeota) was increased remarkably in wetland slurry exposed to 6:2 FTS.


Assuntos
Fluorcarbonetos/metabolismo , Consórcios Microbianos/fisiologia , Poluentes Químicos da Água/metabolismo , Áreas Alagadas , Aerobiose , Alcanossulfonatos/metabolismo , Bactérias/genética , Bactérias/metabolismo , Biodegradação Ambiental , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Consórcios Microbianos/genética , RNA Ribossômico 16S , Rizosfera , Eliminação de Resíduos Líquidos/métodos
15.
Emerg Infect Dis ; 25(6): 1169-1176, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31107235

RESUMO

In 2015, a mass die-off of ≈200,000 saiga antelopes in central Kazakhstan was caused by hemorrhagic septicemia attributable to the bacterium Pasteurella multocida serotype B. Previous analyses have indicated that environmental triggers associated with weather conditions, specifically air moisture and temperature in the region of the saiga antelope calving during the 10-day period running up to the event, were critical to the proliferation of latent bacteria and were comparable to conditions accompanying historically similar die-offs in the same areas. We investigated whether additional viral or bacterial pathogens could be detected in samples from affected animals using 3 different high-throughput sequencing approaches. We did not identify pathogens associated with commensal bacterial opportunisms in blood, kidney, or lung samples and thus concluded that P. multocida serotype B was the primary cause of the disease.


Assuntos
Doenças dos Animais/mortalidade , Antílopes , Doenças dos Animais/epidemiologia , Doenças dos Animais/história , Doenças dos Animais/microbiologia , Animais , Antílopes/microbiologia , Infecções Bacterianas/veterinária , Feminino , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Geografia Médica , História do Século XXI , Cazaquistão/epidemiologia , Masculino , Metagenômica , RNA Ribossômico 16S/genética
16.
Clin Microbiol Infect ; 25(9): 1158.e1-1158.e4, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31128286

RESUMO

OBJECTIVES: We aimed to evaluate the effect of ampC derepression on the cefepime MIC in different species of Enterobacterales with chromosomally encoded inducible AmpC ß-lactamase. METHODS: We analysed a large number of wild-type/mutant pairs (n = 1030 in total). Cefepime MICs were determined by broth microdilution according to EUCAST recommendations. RESULTS: ampC derepression led to increases in MIC by up to 10 dilutions, and significant increases by > 2 MIC dilutions were common across species (744/1030 mutants (72.2%) in total). Interestingly, the frequency of cefepime S→I/S→R transitions varied considerably between species: 66.3% in Enterobacter cloacae complex (167/252 mutants), 1.1% in Klebsiella aerogenes (2/180 mutants), 18.1% in Citrobacter freundii complex (50/277 mutants), 36.4% in Hafnia alvei (59/162 mutants), 19.0% in Providencia rettgeri (4/21 mutants), 22.9% in Providencia stuartii (11/48 mutants), 12.3% in Serratia marcescens (7/57 mutants), 20.0% in Serratia liquefaciens (6/30 mutants) and 0% in Morganella morganii (0/3 mutants). CONCLUSIONS: Our data show that the cefepime MIC is often increased by ampC derepression. However, the risk of S→I/S→R transition is dependent on the species.


Assuntos
Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Cefepima/farmacologia , Cromossomos Bacterianos/genética , Gammaproteobacteria/efeitos dos fármacos , beta-Lactamases/genética , Gammaproteobacteria/classificação , Gammaproteobacteria/enzimologia , Gammaproteobacteria/genética , Humanos , Testes de Sensibilidade Microbiana , Mutação , Especificidade da Espécie , Resistência beta-Lactâmica/efeitos dos fármacos , Resistência beta-Lactâmica/genética
17.
Arch Microbiol ; 201(7): 951-967, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31025055

RESUMO

With the advent of new molecular tools, new taxa of sulphur-oxidising bacteria (SOB) in diverse environments are being discovered. However, there is a significant gap of knowledge about the ecology and diversity of SOB in thermal springs. Here, the species diversity and phylogenetic affiliations of SOB were investigated using 16S rRNA and functional gene marker, soxB in thermal springs of Thane district of Maharashtra, India. Most SOB detected by 16S rDNA sequences belong to different operational taxonomic units (OTU's): Firmicutes, α-, ß-, γ-Proteobacteria and Actinobacteria with the dominance of first class. However, the soxB gene clone library sequences had shown affiliation with the ß-, γ- and α-Proteobacteria. ß-Proteobacteria-related sequences were dominant, with 53.3% clones belonging to genus Hydrogenophaga. The thiosulphate oxidation assay carried out for different isolates having distinct identity showed the mean sulphate-sulphur production from 117.86 ± 0.50 to 218.82 ± 2.56 mg SO4-S l-1 after 9 days of incubation. Also, sulphur oxidation by the genus Nitratireductor, Caldimonas, Geobacillus, Paenibacillus, Brevibacillus, Tristrella and Chelatococcus has been reported for the first time that reveals ecological widening over which thiotrophs are distributed.


Assuntos
Bactérias/classificação , Bactérias/genética , Biodiversidade , Marcadores Genéticos/genética , Fontes Termais/microbiologia , RNA Ribossômico 16S/genética , Actinobacteria/genética , Betaproteobacteria/genética , DNA Bacteriano/genética , Gammaproteobacteria/genética , Índia , Oxirredução , Filogenia , Enxofre/metabolismo
18.
Nat Microbiol ; 4(7): 1149-1159, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30936484

RESUMO

Marine sponges often house small-molecule-producing symbionts extracellularly in their mesohyl, providing the host with a means of chemical defence against predation and microbial infection. Here, we report an intriguing case of chemically mediated symbiosis between the renieramycin-containing sponge Haliclona sp. and its herein discovered renieramycin-producing symbiont Candidatus Endohaliclona renieramycinifaciens. Remarkably, Ca. E. renieramycinifaciens has undergone extreme genome reduction where it has lost almost all necessary elements for free living while maintaining a complex, multi-copy plasmid-encoded biosynthetic gene cluster for renieramycin biosynthesis. In return, the sponge houses Ca. E. renieramycinifaciens in previously uncharacterized cellular reservoirs (chemobacteriocytes), where it can acquire nutrients from the host and avoid bacterial competition. This relationship is highly specific to a single clade of Haliclona sponges. Our study reveals intracellular symbionts as an understudied source for defence chemicals in the oldest-living metazoans and paves the way towards discovering similar systems in other marine sponges.


Assuntos
Gammaproteobacteria/fisiologia , Haliclona/química , Haliclona/microbiologia , Simbiose , Tetra-Hidroisoquinolinas/metabolismo , Animais , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Tamanho do Genoma , Haliclona/citologia , Haliclona/genética , Especificidade de Hospedeiro , Metagenoma , Estrutura Molecular , Família Multigênica , Filogenia , Plasmídeos/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Simbiose/genética , Tetra-Hidroisoquinolinas/química
19.
Appl Microbiol Biotechnol ; 103(11): 4483-4497, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31011775

RESUMO

Several evolutionarily distinct, near full-length draft metagenome-resolved genomes (MRG), were assembled from sequences recovered from the International Space Station (ISS) environments. The retrieval of MRGs facilitated the exploration of a large collection of archived strains (~ 500 isolates) and assisted in isolating seven related strains. The whole genome sequences (WGS) of seven ISS strains exhibited 100% identity to the 4.85 × 106 bp of four MRGs. The "metagenome to phenome" approach led to the description of a novel bacterial genus from the ISS samples. The phylogenomics and traditional taxonomic approaches suggested that these seven ISS strains and four MRGs were not phylogenetically affiliated to any validly described genera of the family Erwiniaceae, but belong to a novel genus with the proposed name Kalamiella. Comparative genomic analyses of Kalamiella piersonii strains and MRGs showed genes associated with carbohydrate (348 genes), amino acid (384), RNA (59), and protein (214) metabolisms; membrane transport systems (108), pathways for biosynthesis of cofactors, vitamins, prosthetic groups, and pigments (179); as well as mechanisms for virulence, disease, and defense (50). Even though Kalamiella genome annotation and disc diffusion tests revealed multidrug resistance, the PathogenFinder algorithm predicted that K. piersonii strains are not human pathogens. This approach to isolating microbes allows for the characterization of functional pathways and their potential virulence properties that can directly affect human health. The isolation of novel strains from the ISS has broad applications in microbiology, not only because of concern for astronaut health but it might have a great potential for biotechnological relevance. The metagenome to phenome approach will help to improve our understanding of complex metabolic networks that control fundamental life processes under microgravity and in deep space.


Assuntos
Microbiologia Ambiental , Gammaproteobacteria/classificação , Gammaproteobacteria/isolamento & purificação , Filogenia , Astronave , Técnicas de Tipagem Bacteriana , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Humanos , Metagenômica , Sequenciamento Completo do Genoma
20.
ISME J ; 13(8): 2129-2134, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-30952995

RESUMO

Modeling crude-oil biodegradation in sediments remains a challenge due in part to the lack of appropriate model organisms. Here we report the metagenome-guided isolation of a novel organism that represents a phylogenetically narrow (>97% 16S rRNA gene identity) group of previously uncharacterized, crude-oil degraders. Analysis of available sequence data showed that these organisms are highly abundant in oiled sediments of coastal marine ecosystems across the world, often comprising ~30% of the total community, and virtually absent in pristine sediments or seawater. The isolate genome encodes functional nitrogen fixation and hydrocarbon degradation genes together with putative genes for biosurfactant production that apparently facilitate growth in the typically nitrogen-limited, oiled environment. Comparisons to available genomes revealed that this isolate represents a novel genus within the Gammaproteobacteria, for which we propose the provisional name "Candidatus Macondimonas diazotrophica" gen. nov., sp. nov. "Ca. M. diazotrophica" appears to play a key ecological role in the response to oil spills around the globe and could be a promising model organism for studying ecophysiological responses to oil spills.


Assuntos
Gammaproteobacteria/genética , Sedimentos Geológicos/microbiologia , Hidrocarbonetos/metabolismo , Metagenoma , Petróleo/metabolismo , Biodegradação Ambiental , DNA Bacteriano/genética , Ecossistema , Gammaproteobacteria/isolamento & purificação , Gammaproteobacteria/fisiologia , Sedimentos Geológicos/química , Fixação de Nitrogênio , Poluição por Petróleo , Filogenia , RNA Ribossômico 16S/genética , Água do Mar
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