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1.
BMC Infect Dis ; 20(1): 687, 2020 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-32948147

RESUMO

BACKGROUND: Vogesella species are common aquatic, Gram-negative rod-shaped bacteria, originally described in 1997. Vogesella perlucida was first isolated from spring water in 2008. Furthermore, bacterial pathogenicity of Vogesella perlucida has never been reported. Here, we report the first case of rare Vogesella perlucida-induced bacteremia in an advanced-age patient with many basic diseases and history of dexamethasone abuse. CASE PRESENTATION: A 71-year-old female was admitted with inflamed upper and lower limbs, rubefaction, pain and fever (about 40 °C). She had been injured in a fall at a vegetable market and then touched river snails with her injury hands. A few days later, soft tissue infection of the patient developed and worsened. Non-pigmented colonies were isolated from blood cultures of the patient. Initially, Vogesella perlucida was wrongly identified as Sphingomonas paucimobilis by Vitek-2 system with GN card. Besides, we failed to obtain an acceptable identification by the MALDI-TOF analysis. Finally, the isolated strain was identified as Vogesella perlucida by 16S rRNA gene sequences. In addition, the patient recovered well after a continuous treatment of levofloxacin for 12 days. CONCLUSION: Traditional microbiological testing system may be inadequate in the diagnosis of rare pathogenic bacteria. Applications of molecular diagnostics techniques have great advantages in clinical microbiology laboratory. By using 16S rRNA gene sequence analysis, we report the the first case of rare Vogesella perlucida-induced bacteremia.


Assuntos
Bacteriemia/microbiologia , Betaproteobacteria/patogenicidade , Infecções dos Tecidos Moles/microbiologia , Idoso , Antibacterianos/uso terapêutico , Bacteriemia/tratamento farmacológico , Técnicas de Tipagem Bacteriana , Betaproteobacteria/classificação , Betaproteobacteria/genética , Betaproteobacteria/isolamento & purificação , Feminino , Humanos , Levofloxacino/uso terapêutico , RNA Ribossômico 16S/genética , Infecções dos Tecidos Moles/tratamento farmacológico , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Vancomicina/uso terapêutico
2.
Nat Commun ; 11(1): 3906, 2020 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-32764563

RESUMO

Enzymatic hydroxylation of unactivated primary carbons is generally associated with the use of molecular oxygen as co-substrate for monooxygenases. However, in anaerobic cholesterol-degrading bacteria such as Sterolibacterium denitrificans the primary carbon of the isoprenoid side chain is oxidised to a carboxylate in the absence of oxygen. Here, we identify an enzymatic reaction sequence comprising two molybdenum-dependent hydroxylases and one ATP-dependent dehydratase that accomplish the hydroxylation of unactivated primary C26 methyl group of cholesterol with water: (i) hydroxylation of C25 to a tertiary alcohol, (ii) ATP-dependent dehydration to an alkene via a phosphorylated intermediate, (iii) hydroxylation of C26 to an allylic alcohol that is subsequently oxidised to the carboxylate. The three-step enzymatic reaction cascade divides the high activation energy barrier of primary C-H bond cleavage into three biologically feasible steps. This finding expands our knowledge of biological C-H activations beyond canonical oxygenase-dependent reactions.


Assuntos
Trifosfato de Adenosina/metabolismo , Betaproteobacteria/metabolismo , Anaerobiose , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Betaproteobacteria/genética , Carbono/química , Colestadienóis/química , Colestadienóis/metabolismo , Colesterol/química , Colesterol/metabolismo , Genes Bacterianos , Hidroliases/genética , Hidroliases/metabolismo , Hidroxilação , Oxigenases de Função Mista/genética , Oxigenases de Função Mista/metabolismo , Modelos Biológicos , Oxirredução , Filogenia , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Água/metabolismo
3.
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
4.
Sci Rep ; 10(1): 3883, 2020 03 03.
Artigo em Inglês | MEDLINE | ID: mdl-32127605

RESUMO

Rhodocyclales is an abundant bacterial order in wastewater treatment systems and putatively plays key roles in multiple functions. Its phylogenomics, prevalence of denitrifying genes in sub-lineages and distribution in wastewater treatment plants (WWTPs) worldwide have not been well characterized. In the present study, we collected 78 Rhodocyclales genomes, including 17 from type strains, non-type strains and genome bins contributed by this study. Phylogenomics indicated that the order could be divided into five family-level lineages. With only a few exceptions (mostly in Rhodocyclaceae), nirS-containing genomes in this order usually contained the downstream genes of norB and nosZ. Multicopy of denitrifying genes occurred frequently and events of within-order horizontal transfer of denitrifying genes were phylogenetically deduced. The distribution of Rhodocyclaceae, Zoogloeaceae and Azonexaceae in global WWTPs were significantly governed by temperature, mixed liquor suspended solids, etc. Metagenomic survey showed that the order generally ranked at the top or second for different denitrifying genes in wastewater treatment systems. Our results provided comprehensive genomic insights into the phylogeny and features of denitrifying genes of Rhodocyclales. Its contribution to the denitrifying gene pool in WWTPs was proved.


Assuntos
Betaproteobacteria/isolamento & purificação , Filogenia , Eliminação de Resíduos Líquidos , Águas Residuárias/microbiologia , Betaproteobacteria/genética , Desnitrificação , Transferência Genética Horizontal , RNA Ribossômico 16S/genética , Temperatura
5.
Ecotoxicol Environ Saf ; 191: 110161, 2020 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-31954219

RESUMO

Denitrification and nitrification processes are the two prominent pathways of nitrogen (N) transformation in composting matrix. This study explored the dynamics of denitrifying and nitrifying bacteria at different composting stages of cow manure and corn straw using functional gene sequencing at DNA and cDNA levels. Corresponding agreement among OTUs, NMDS, mental test and network analyses revealed that functional bacteria community compositions and responses to physicochemical factors were different at DNA and cDNA levels. Specifically, some OTUs were detected at the DNA level but were not observed at cDNA level, differences were also found in the distribution patterns of nitrifying and denitrifying bacteria communities at both levels. Furthermore, co-occurrence network analysis indicated that Pseudomonas, Paracoccus and Nitrosomonas were identified as the keystone OTUs at the DNA level, while Paracoccus, Agrobacterium and Nitrosospira were keystone OTUs at the cDNA level. Mantel test revealed that TN, C/N and moisture content significantly influenced both the denitrifying bacteria and ammonia-oxidizing bacteria (AOB) communities at the DNA level. NO3--N, NH4+-N, TN, C/N, and moisture content only registered significant correlation with the nosZ-type denitrifiers and ammonia-oxidizing bacteria (AOB) communities at the cDNA level. Structural equation model (SEM) showed that TN, NH4+-N, and pH were direct and significantly influenced the gene abundance of denitrifying bacteria. Howbeit, TN, NH4+-N, and NO3--N had significant direct effects on amoA gene abundance.


Assuntos
Betaproteobacteria/isolamento & purificação , Compostagem , DNA Bacteriano/genética , DNA Complementar/genética , Esterco/microbiologia , Amônia/metabolismo , Animais , Betaproteobacteria/genética , Betaproteobacteria/metabolismo , Bovinos , China , Desnitrificação , Feminino , Microbiota/genética , Nitrificação , Nitrogênio/metabolismo , Oxirredução
6.
Curr Microbiol ; 77(3): 500-508, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31893298

RESUMO

A novel polyhydroxyalkanoate (PHA)-producing bacterium, Jeongeupia sp. USM3 (JCM 19920) was isolated from the limestone soil at Gua Tempurung, Perak, Malaysia. This is the first report on the complete genome sequence for the genus Jeongeupia. This genome consists of a circular chromosome with a size of 3,788,814 bp and contains 3557 genes. Two PHA synthase (phaC) genes encoding for the key enzyme in the polymerization of PHA monomers and other PHA-associated genes were identified from the genome. Phylogenetic analysis of the PhaC protein sequences has revealed that both PhaC1 and PhaC2 of Jeongeupia sp. USM3 are categorized as Class I PHA synthases with 56% similarity to each other. Both of the PHA synthase genes of this isolate were cloned and heterologously expressed in a PHA mutant strain Cupriavidus necator PHB-4. The ability of the transformants to accumulate PHA showed that both PhaC1 and PhaC2 were functional.


Assuntos
Aciltransferases/metabolismo , Betaproteobacteria/enzimologia , Betaproteobacteria/genética , Genoma Bacteriano , Poli-Hidroxialcanoatos/biossíntese , Microbiologia do Solo , Aciltransferases/genética , Cupriavidus necator/genética , Malásia , Filogenia , Sequenciamento Completo do Genoma
7.
Res Microbiol ; 171(1): 37-43, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31606487

RESUMO

Amongst iron-oxidizing bacteria playing a key role in the natural attenuation of arsenic in acid mine drainages (AMDs), members of the Ferrovum genus were identified in mine effluent or water treatment plants, and were shown to dominate biogenic precipitates in field pilot experiments. In order to address the question of the in situ activity of the uncultivated Ferrovum sp. CARN8 strain in the Carnoulès AMD, we assembled its genome using metagenomic and metatranscriptomic sequences and we determined standardized expression values for protein-encoding genes. Our results showed that this microorganism was indeed metabolically active and allowed us to sketch out its metabolic activity in its natural environment. Expression of genes related to the respiratory chain and carbon fixation suggests aerobic energy production coupled to ferrous iron oxidation and chemolithoautotrophic growth. Notwithstanding the presence of nitrogenase genes in its genome, expression data also indicated that Ferrovum sp. CARN8 relied on ammonium import rather than nitrogen fixation. The expression of flagellum and chemotaxis genes hints that at least a proportion of this strain population was motile. Finally, apart from some genes related to metal resistance showing surprisingly low expression values, genes involved in stress response were well expressed as expected in AMDs.


Assuntos
Betaproteobacteria/genética , Esgotos/microbiologia , Compostos de Amônio/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Betaproteobacteria/classificação , Betaproteobacteria/isolamento & purificação , Betaproteobacteria/metabolismo , Regulação Bacteriana da Expressão Gênica , Metagenômica , Transcriptoma
8.
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
9.
ISME J ; 14(3): 714-726, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31796935

RESUMO

Copper-containing membrane monooxygenases (CuMMOs) are encoded by xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, or some short-chain alkanes and alkenes. In a metagenome constructed from an oilsands tailings pond we detected an xmoCABD gene cluster with <59% derived protein sequence identity to genes from known bacteria. Stable isotope probing experiments combined with a specific xmoA qPCR assay demonstrated that the bacteria possessing these genes were incapable of methane assimilation, but did grow on ethane and propane. Single-cell amplified genomes (SAGs) from propane-enriched samples were screened with the specific PCR assay to identify bacteria possessing the target gene cluster. Multiple SAGs of Betaproteobacteria belonging to the genera Rhodoferax and Polaromonas possessed homologues of the metagenomic xmoCABD gene cluster. Unexpectedly, each of these two genera also possessed other xmoCABD paralogs, representing two additional lineages in phylogenetic analyses. Metabolic reconstructions from SAGs predicted that neither bacterium encoded enzymes with the potential to support catabolic methane or ammonia oxidation, but that both were capable of higher n-alkane degradation. The involvement of the encoded CuMMOs in alkane oxidation was further suggested by reverse transcription PCR analyses, which detected elevated transcription of the xmoA genes upon enrichment of water samples with propane as the sole energy source. Enrichments, isotope incorporation studies, genome reconstructions, and gene expression studies therefore all agreed that the unknown xmoCABD operons did not encode methane or ammonia monooxygenases, but rather n-alkane monooxygenases. This study broadens the known diversity of CuMMOs and identifies these enzymes in non-nitrifying Betaproteobacteria.


Assuntos
Alcanos/metabolismo , Proteínas de Bactérias/metabolismo , Betaproteobacteria/enzimologia , Oxigenases de Função Mista/metabolismo , Amônia/metabolismo , Proteínas de Bactérias/genética , Betaproteobacteria/classificação , Betaproteobacteria/genética , Betaproteobacteria/metabolismo , Cobre/metabolismo , Metagenoma , Metano/metabolismo , Oxigenases de Função Mista/genética , Família Multigênica , Oxirredução , Oxirredutases/genética , Oxirredutases/metabolismo , Filogenia , Tanques/microbiologia
10.
Proc Natl Acad Sci U S A ; 117(3): 1395-1403, 2020 01 21.
Artigo em Inglês | MEDLINE | ID: mdl-31848239

RESUMO

Steroid estrogens modulate physiology and development of vertebrates. Conversion of C19 androgens into C18 estrogens is thought to be an irreversible reaction. Here, we report a denitrifying Denitratisoma sp. strain DHT3 capable of catabolizing estrogens or androgens anaerobically. Strain DHT3 genome contains a polycistronic gene cluster, emtABCD, differentially transcribed under estrogen-fed conditions and predicted to encode a cobalamin-dependent methyltransferase system conserved among estrogen-utilizing anaerobes; an emtA-disrupted DHT3 derivative could catabolize androgens but not estrogens. These data, along with the observed androgen production in estrogen-fed strain DHT3 cultures, suggested the occurrence of a cobalamin-dependent estrogen methylation to form androgens. Consistently, the estrogen conversion into androgens in strain DHT3 cell extracts requires methylcobalamin and is inhibited by propyl iodide, a specific inhibitor of cobalamin-dependent enzymes. The identification of the cobalamin-dependent estrogen methylation thus represents an unprecedented metabolic link between cobalamin and steroid metabolism and suggests that retroconversion of estrogens into androgens occurs in the biosphere.


Assuntos
Androgênios/metabolismo , Proteínas de Bactérias/metabolismo , Betaproteobacteria/metabolismo , Estrogênios/metabolismo , Metiltransferases/metabolismo , Vitamina B 12/metabolismo , Proteínas de Bactérias/genética , Betaproteobacteria/enzimologia , Betaproteobacteria/genética , Metiltransferases/genética
11.
Appl Environ Microbiol ; 86(4)2020 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-31811031

RESUMO

Microorganisms in wastewater treatment plants (WWTPs) play a key role in the removal of pollutants from municipal and industrial wastewaters. A recent study estimated that activated sludge from global municipal WWTPs harbors 1 × 109 to 2 × 109 microbial species, the majority of which have not yet been cultivated, and 28 core taxa were identified as "most-wanted" ones (L. Wu, D. Ning, B. Zhang, Y. Li, et al., Nat Microbiol 4:1183-1195, 2019, https://doi.org/10.1038/s41564-019-0426-5). Cultivation and characterization of the "most-wanted" core bacteria are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the performance of WWTPs. In this study, we isolated a bacterial strain, designated SJ-1, that represents a novel cluster within Betaproteobacteria and corresponds to OTU_16 within the 28 core taxa in the "most-wanted" list. Strain SJ-1 was identified and nominated as Casimicrobium huifangae gen. nov., sp. nov., of a novel family, Casimicrobiaceae. C. huifangae is ubiquitously distributed and is metabolically versatile. In addition to mineralizing various carbon sources (including carbohydrates, aromatic compounds, and short-chain fatty acids), C. huifangae is capable of nitrate reduction and phosphorus accumulation. The population of C. huifangae accounted for more than 1% of the bacterial population of the activated sludge microbiome from the Qinghe WWTP, which showed seasonal dynamic changes. Cooccurrence analysis suggested that C. huifangae was an important module hub in the bacterial network of Qinghe WWTP.IMPORTANCE The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.


Assuntos
Betaproteobacteria/classificação , Betaproteobacteria/fisiologia , Esgotos/microbiologia , Betaproteobacteria/genética , Microbiota , Filogenia , RNA Bacteriano/análise , RNA Ribossômico 16S/análise
12.
Diagn Microbiol Infect Dis ; 96(2): 114948, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31787408

RESUMO

We characterized a strain of Laribacter hongkongensis isolated from the blood of a patient with fatal sepsis, who had alcoholic cirrhosis with ascites and portal hypertension. L. hongkongensis bacteremia is associated with underlying liver diseases (P < 0.001) and mortality (P < 0.05), whereas L. hongkongensis gastroenteritis is associated with recent travel history (P < 0.05).


Assuntos
Bacteriemia/complicações , Bacteriemia/diagnóstico , Infecções Bacterianas/complicações , Infecções Bacterianas/diagnóstico , Betaproteobacteria , Hepatopatias/complicações , Hepatopatias/diagnóstico , Bacteriemia/microbiologia , Infecções Bacterianas/microbiologia , Betaproteobacteria/classificação , Betaproteobacteria/genética , Biomarcadores , Evolução Fatal , Humanos , Filogenia , RNA Bacteriano , RNA Ribossômico 16S , Índice de Gravidade de Doença , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
13.
Appl Microbiol Biotechnol ; 103(23-24): 9711-9722, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31705181

RESUMO

As the key organism for enhanced biological phosphorus removal, Accumulibacter has shown high intragenus diversity based on the phylogeny of polyphosphate kinase1 gene (ppk1) and many clade-specific features related to performance of wastewater treatment. However, the widely used molecular approaches are deficient or cost-inefficient in providing a comprehensive and quantitative population-level profile for Accumulibacter in complex community. In this study, we introduced a pipeline to analyze the population-level diversity and dynamics of Accumulibacter via high throughput sequencing (HTS) of ppk1 and 16S rRNA gene simultaneously. The HTS approach was assessed by testing primer coverage, performing sample replication, and comparing with a traditional clone library. Based on survey on full-scale activated sludge samples, unexpected high microdiversity in Accumulibacter and a tendency of exclusivity between two phylogenetic types were discovered. Moreover, the pipeline facilitated monitoring the population-level dynamics and co-occurrence pattern under various laboratory enriching conditions. The results revealed previously uncharacterized intraclade dynamics during enrichment, little effect of denitrifying process on the Accumulibacter diversity, and the niche adaption of Clade IIC on propionate as sole carbon source. Co-occurrence of Accumulibacter populations further partially supported the exclusivity of two types. A few bacterial taxa, including Cytophagaceae-, Prosthecobacter-, and Compteibacter-related taxa, showed co-occurrence with many Accumulibacter populations, suggesting their niche co-selection or potential metabolic interactions with Accumulibacter. The present pipeline is transplantable for studying microdiversity and niche differentiation of other functional microorganisms in complex microbial systems.


Assuntos
Betaproteobacteria/genética , Reatores Biológicos/microbiologia , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Fosfotransferases (Aceptor do Grupo Fosfato)/genética , Betaproteobacteria/enzimologia , Carbono/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Esgotos/microbiologia
14.
Crit Rev Microbiol ; 45(5-6): 649-667, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31686572

RESUMO

Betaproteobacteria include some of the most abundant and ubiquitous bacterial genera that can be found in drinking water, including mineral water. The combination of physiology and ecology traits place some Betaproteobacteria in the list of potential, yet sometimes neglected, opportunistic pathogens that can be transmitted by water or aqueous solutions. Indeed, some drinking water Betaproteobacteria with intrinsic and sometimes acquired antibiotic resistance, harbouring virulence factors and often found in biofilm structures, can persist after water disinfection and reach the consumer. This literature review summarises and discusses the current knowledge about the occurrence and implications of Betaproteobacteria in drinking water. Although the sparse knowledge on the ecology and physiology of Betaproteobacteria thriving in tap or bottled natural mineral/spring drinking water (DW) is an evidence of this review, it is demonstrated that DW holds a high diversity of Betaproteobacteria, whose presence may not be innocuous. Frequently belonging to genera also found in humans, DW Betaproteobacteria are ubiquitous in different habitats, have the potential to resist antibiotics either due to intrinsic or acquired mechanisms, and hold different virulence factors. The combination of these factors places DW Betaproteobacteria in the list of candidates of emerging opportunistic pathogens. Improved bacterial identification of clinical isolates associated with opportunistic infections and additional genomic and physiological studies may contribute to elucidate the potential impact of these bacteria.


Assuntos
Betaproteobacteria/isolamento & purificação , Água Potável/microbiologia , Betaproteobacteria/classificação , Betaproteobacteria/genética , Betaproteobacteria/fisiologia , Biofilmes , Humanos , Microbiologia da Água , Qualidade da Água
15.
Appl Microbiol Biotechnol ; 103(21-22): 9155-9168, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31641816

RESUMO

Wastewater treatment plants (WWTPs) rely mainly on the microbial assemblages to contribute significantly for the removal of organic pollutants and nutrients. However, limited information is available on the ecological driving forces underlying the turnover of prokaryotic communities across wastewater treatment processes (i.e., from influents (IFs) and effluents (EFs)) within WWTPs. Here, we used a combination of the 16S rRNA gene amplicon sequencing and a quantitative ecological null model analysis to explore the ecological processes governing the turnover of the prokaryotic communities and the dominant taxonomic taxa across wastewater treatment processes of five full-scale WWTPs in China. Our results indicated that a significant variation in the composition of prokaryotic communities and the dominant taxa between IFs and EFs. The analysis of the environmental sources of indicator OTUs showed that a relatively lower abundance of the sludge/sewage and human guts associated OTUs in EFs than in IFs. Ecological null models revealed that among the ecological processes, deterministic processes were dominant in controlling the turnover of the overall communities from IFs to EFs, whereas the relative importance of deterministic processes varied among the dominant taxa (i.e., Bacteroidetes > Proteobacteria > Gammaproteobacteria > Firmicutes > Betaproteobacteria). However, the assembly of IF and EF communities was influenced mainly by the deterministic and stochastic processes, respectively. In addition, our results indicated that EF communities have a higher phylogenetic diversity than those of the IF communities, but the abundance of prokaryotic 16S rRNA genes was lower in EFs than in IFs. Overall, our study provides a novel insight of the assembly mechanisms underlying the turnover of prokaryotic communities during wastewater treatment processes.


Assuntos
Bacteroidetes/classificação , Betaproteobacteria/classificação , Firmicutes/classificação , Gammaproteobacteria/classificação , Águas Residuárias/microbiologia , Purificação da Água/métodos , Bacteroidetes/genética , Bacteroidetes/metabolismo , Betaproteobacteria/genética , Betaproteobacteria/metabolismo , China , Firmicutes/genética , Firmicutes/metabolismo , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , RNA Ribossômico 16S/genética , Águas Residuárias/química , Poluentes Químicos da Água/análise
16.
FEMS Microbiol Ecol ; 95(10)2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31504446

RESUMO

Waters draining from flooded and abandoned coal mines in the South Wales Coalfield (SWC) are substantial sources of pollution to the environment characterized by circumneutral pH and elevated dissolved iron concentrations (>1 mg L-1). The discharged Fe precipitates to form Fe(III) (oxyhydr)oxides which sustain microbial communities. However, while several studies have investigated the geochemistry of mine drainage in the SWC, less is known about the microbial ecology of the sites presenting a gap in our understanding of biogeochemical cycling and pollutant turnover. This study investigated the biogeochemistry of the Ynysarwed mine adit in the SWC. Samples were collected from nine locations within sediment at the mine entrance from the upper and lower layers three times over one year for geochemical and bacterial 16S rRNA gene sequence analysis. During winter, members of the Betaproteobacteria bloomed in relative abundance (>40%) including the microaerophilic Fe(II)-oxidizing genus Gallionella. A concomitant decrease in Chlorobi-associated bacteria occurred, although by summer the community composition resembled that observed in the previous autumn. Here, we provide the first insights into the microbial ecology and seasonal dynamics of bacterial communities of Fe(III)-rich deposits in the SWC and demonstrate that neutrophilic Fe(II)-oxidizing bacteria are important and dynamic members of these communities.


Assuntos
Betaproteobacteria/metabolismo , Chlorobi/metabolismo , Compostos Ferrosos/metabolismo , Sedimentos Geológicos/microbiologia , Ferro/metabolismo , Betaproteobacteria/classificação , Betaproteobacteria/genética , Betaproteobacteria/isolamento & purificação , Chlorobi/genética , Chlorobi/isolamento & purificação , Carvão Mineral/análise , Minas de Carvão , Poluição Ambiental , Oxirredução , RNA Ribossômico 16S/genética , Estações do Ano
17.
J Insect Physiol ; 118: 103931, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31442480

RESUMO

The Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Sternorrhyncha: Psylloidea: Liviidae) is an important pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria); the causative agents of an incurable citrus disease known as huanglongbing or greening disease. D. citri possesses a vertically transmitted intracellular symbiont, Candidatus Profftella armatura (Betaproteobacteria), which produces diaphorin; a polyketide that is toxic to various eukaryotic organisms. Our previous study demonstrated that the total amount and average concentration of diaphorin in adult D. citri, when homogeneous distribution is assumed within the insect, are sufficient to exert inhibitory effects on fungi and insects, including the Asian lady beetle Harmonia axyridis (Coleoptera: Coccinellidae); one of the major predators of D. citri. However, diaphorin may be localized to a limited body area within D. citri, and its concentration may change during development. In the present study, to better understand the physiological and ecological function of diaphorin, we assessed the distribution of diaphorin within the D. citri body and analyzed concentrations of diaphorin in various developmental stages. Expression of genes involved in diaphorin synthesis was also analyzed. The results demonstrated that diaphorin is distributed widely in the D. citri body, which appears to be a prerequisite for effective deterrence of natural enemies. The concentration of diaphorin was shown to change significantly during the development of D. citri. It was highest in mature adults, followed by embryos and teneral adults, and lowest in nymphs. The lowest concentrations of diaphorin observed in nymphs are still presumed to be effective in deterring invasive natural enemies, including parasites, parasitoids, and entomopathogenic fungi. Quantitative RT-PCR indicated that amounts of transcripts for diaphorin synthesis genes dipP and dipT were at a minimum in embryos, increased during the nymphal period, and reached a maximum level just after adult eclosion. The alteration pattern of the amounts of transcripts for diaphorin synthesis genes appeared to partially disagree with that of the concentration of diaphorin. The present study provides new insights into the function of diaphorin, which is essential for further investigations that aim to improve the efficacy of D. citri biological control.


Assuntos
Betaproteobacteria/metabolismo , Hemípteros/química , Hemípteros/microbiologia , Policetídeos/metabolismo , Animais , Betaproteobacteria/genética , Regulação Bacteriana da Expressão Gênica , Hemípteros/crescimento & desenvolvimento , Estágios do Ciclo de Vida , Simbiose
18.
Mol Biol Rep ; 46(5): 5309-5321, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31346912

RESUMO

A microbial community was enriched in the anoxic compartment of a pilot-scale bioreactor that was operated for 180 days, fed with sewage and designed for organic matter, nitrogen and sulfide removal by coupling anaerobic digestion, nitrification and mixotrophic denitrification. Denitrification occurred with endogenous electron donors, mainly sulfide and residual organic matter, coming from the anaerobic compartment. The microorganisms involved in denitrification with sulfide as electron donor were identified by DNA-stable isotope probing with [U-13C]-labelled CO2 and NaHCO3. Complete denitrification occurred every two days, and the applied NO3-/S2- ratio was 1.6. Bacteria belonging to the Sulfurimonas denitrificans was identified as a chemoautotrophic denitrifier, and those related to Georgfuchisa toluolica, Geothrix fermentans and Ferritrophicum radicicola were most probably associated with heterotrophic denitrification using endogenous cells and/or intermediate metabolites. This study showed that DNA-SIP was a suitable technique to identify the active microbiota involved in sulfide-driven denitrification in a complex environment, which may contribute to improve design and operation of bioreactors aiming for carbon-nitrogen-sulfur removal.


Assuntos
Reatores Biológicos/microbiologia , Desnitrificação/fisiologia , Sulfetos/metabolismo , Acidobacteria/genética , Bactérias/genética , Técnicas de Cultura Celular por Lotes/métodos , Betaproteobacteria/genética , Helicobacteraceae/genética , Marcação por Isótopo/métodos , Isótopos , Nitratos , Nitrogênio/metabolismo , Esgotos , Sulfetos/química
19.
Microbiome ; 7(1): 96, 2019 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-31238973

RESUMO

BACKGROUND: The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method. RESULTS: Here, we present a method to infer the hidden traits for the enrichment of not-yet-cultured populations. We demonstrate this method using Candidatus Accumulibacter. Our method constructs a whole picture of the carbon, electron, and energy flows in the not-yet-cultured populations from the genomic datasets. Then, it decodes the coordination across three flows from the transcriptional datasets. Based on it, our method diagnoses the status of the not-yet-cultured populations and provides strategy to optimize the enrichment systems. CONCLUSION: Our method could shed light to the exploration into the bacterial dark matter in the environments.


Assuntos
Betaproteobacteria/genética , Betaproteobacteria/isolamento & purificação , Genoma Bacteriano , Genômica/métodos , Betaproteobacteria/metabolismo , Perfilação da Expressão Gênica , Redes e Vias Metabólicas/genética , Filogenia
20.
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
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