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1.
Nat Commun ; 12(1): 1165, 2021 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-33608555

RESUMO

Animals endemic to deep-sea hydrothermal vents often form obligatory symbioses with bacteria, maintained by intricate host-symbiont interactions. Most genomic studies on holobionts have not investigated both sides to similar depths. Here, we report dual symbiosis in the peltospirid snail Gigantopelta aegis with two gammaproteobacterial endosymbionts: a sulfur oxidiser and a methane oxidiser. We assemble high-quality genomes for all three parties, including a chromosome-level host genome. Hologenomic analyses reveal mutualism with nutritional complementarity and metabolic co-dependency, highly versatile in transporting and using chemical energy. Gigantopelta aegis likely remodels its immune system to facilitate dual symbiosis. Comparisons with Chrysomallon squamiferum, a confamilial snail with a single sulfur-oxidising gammaproteobacterial endosymbiont, show that their sulfur-oxidising endosymbionts are phylogenetically distant. This is consistent with previous findings that they evolved endosymbiosis convergently. Notably, the two sulfur-oxidisers share the same capabilities in biosynthesising nutrients lacking in the host genomes, potentially a key criterion in symbiont selection.


Assuntos
Bactérias/genética , Fontes Hidrotermais/microbiologia , Caramujos/genética , Caramujos/microbiologia , Simbiose/genética , Animais , Bactérias/metabolismo , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Expressão Gênica , Genoma Bacteriano , Genômica , Filogenia , Caramujos/metabolismo , Enxofre/metabolismo , Simbiose/fisiologia , Transcriptoma
2.
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
3.
PLoS One ; 15(8): e0234839, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32853201

RESUMO

Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.


Assuntos
Gammaproteobacteria/genética , Sedimentos Geológicos/microbiologia , Regiões Árticas , Proteínas de Bactérias/genética , Estuários , Gammaproteobacteria/classificação , Gammaproteobacteria/metabolismo , Genoma Bacteriano , Proteínas de Choque Térmico/genética , Metagenoma , Filogenia , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Svalbard , Transcriptoma
4.
Nat Commun ; 11(1): 3602, 2020 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-32681114

RESUMO

Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members. We identify 83 PTUs in the order Enterobacterales, 28 of them corresponding to previously described archetypes. Furthermore, we develop an automated algorithm for PTU identification, and validate its performance using stochastic blockmodeling. The algorithm reveals a total of 276 PTUs in the bacterial domain. Each PTU exhibits a characteristic host distribution, organized into a six-grade scale (I-VI), ranging from plasmids restricted to a single host species (grade I) to plasmids able to colonize species from different phyla (grade VI). More than 60% of the plasmids in the global map are in groups with host ranges beyond the species barrier.


Assuntos
Gammaproteobacteria/genética , Transferência Genética Horizontal , Plasmídeos/genética , Algoritmos , Gammaproteobacteria/classificação , Genômica , Filogenia
5.
Chemosphere ; 258: 127271, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32535444

RESUMO

Water and soil contamination by industrial wastes is a global concern. Biological treatment of industrial wastewater using bioreactors allows the removal of organic matter and nutrients and enables either reuse or safe discharge. Wastewater bioremediation depends in part on the microbial communities present in the bioreactor. To ascertain which communities may play a role in the remediation process, the present study investigates the microbial community structure and diversity of microorganisms found in a full-scale membrane bioreactor (MBR) for industrial wastewater treatment. The study was carried out using high-throughput data observations following a failure (crash) of the MBR and during the extended recovery of the process. Results revealed a positive correlation between the MBR's ability to remove organic matter and its microbial community richness. The significant changes in relative microbial abundance between crash and recovery periods of the MBR revealed the important role of specific bacterial genera in wastewater treatment processes. A whole-genome metagenomics based comparison showed a clear difference in microbial makeup between two functional periods of MBR activity. The crash period was characterized by abundance in bacteria belonging to Achromobacter, Acinetobacter, Halomonas, Pseudomonas and an uncultured MBAE14. The recovery period on the other hand was characterized by Aquamicrobium and by Wenzhouxiangella marina. Our study also revealed some interesting functional pathways characterizing the microbial communities from the two periods of bioreactor function, such as Nitrate and Sulfate reduction pathways. These differences indicate the connection between the bacterial diversity of the MBR and its efficiency to remove TOC.


Assuntos
Reatores Biológicos/microbiologia , Microbiota/efeitos dos fármacos , Águas Residuárias , Purificação da Água/métodos , Biodegradação Ambiental , Gammaproteobacteria/efeitos dos fármacos , Gammaproteobacteria/genética , Resíduos Industriais/análise , Membranas Artificiais , Metagenômica , Microbiota/genética , Esgotos/microbiologia , Águas Residuárias/química , Águas Residuárias/microbiologia
6.
Sci Rep ; 10(1): 8497, 2020 05 22.
Artigo em Inglês | MEDLINE | ID: mdl-32444702

RESUMO

For the last decades, forensic microbiology became an emerging complementary tool in criminalistics. Although the insect-microbe interactions regarding pathogen transmission were extensively studied, only scarce information is available on bacterial transfer from necrophagous insects to host tissues. Our data provides the first report on the occurrence of Wohlfahrtiimonas chitiniclastica and Ignatzschineria indica in Lucilia illustris Meigen, 1826 (Diptera: Calliphoridae), and the quantitative dynamics of the two bacterial species along the insect life-stages and transfer to beef and pork host tissues using qPCR gyrase b specific primers. The content of both bacterial species increased along the insect life stages. W. chitiniclastica was detected in all developmental stages independent of the feeding substrate. I. indica was measurable with 102 gene copies ng-1 DNA threshold starting from the third instar larvae when feeding on beef, and from the egg stage with a 102× higher representation when using the pork substrate. The transfer of bacterial species to both tissues occurred after 3 colonization days except for I. indica that was visible in beef liver only during day 5. Considering the utilization of pork tissues as human analogues, these quantitative microbial dynamics data provides first insect-specific bacterial candidates as potential colonization biomarkers in forensic investigations.


Assuntos
Proteínas de Bactérias/genética , Biomarcadores/análise , DNA Girase/genética , DNA Bacteriano/análise , Dípteros/microbiologia , Gammaproteobacteria/isolamento & purificação , Animais , Bovinos , DNA Bacteriano/genética , Dípteros/crescimento & desenvolvimento , Dípteros/metabolismo , Ciências Forenses , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo
7.
Sci Rep ; 10(1): 8679, 2020 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-32457360

RESUMO

Cyanobacteria are ubiquitous organisms with a relevant contribution to primary production in all range of habitats. Cyanobacteria are well known for their part in worldwide occurrence of aquatic blooms while producing a myriad of natural compounds, some with toxic potential, but others of high economical impact, as geosmin. We performed an environmental survey of cyanobacterial soil colonies to identify interesting metabolic pathways and adaptation strategies used by these microorganisms and isolated, sequenced and assembled the genome of a cyanobacterium that displayed a distinctive earthy/musty smell, typical of geosmin, confirmed by GC-MS analysis of the culture's volatile extract. Morphological studies pointed to a new Oscillatoriales soil ecotype confirmed by phylogenetic analysis, which we named Microcoleus asticus sp. nov. Our studies of geosmin gene presence in Bacteria, revealed a scattered distribution among Cyanobacteria, Actinobacteria, Delta and Gammaproteobacteria, covering different niches. Careful analysis of the bacterial geosmin gene and gene tree suggests an ancient bacterial origin of the gene, that was probably successively lost in different time frames. The high sequence similarities in the cyanobacterial geosmin gene amidst freshwater and soil strains, reinforce the idea of an evolutionary history of geosmin, that is intimately connected to niche adaptation.


Assuntos
Proteínas de Bactérias/metabolismo , Cianobactérias/genética , Naftóis/metabolismo , Actinobacteria/genética , Actinobacteria/metabolismo , Proteínas de Bactérias/classificação , Proteínas de Bactérias/genética , Cianobactérias/química , Cianobactérias/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Cromatografia Gasosa-Espectrometria de Massas , Genoma Bacteriano , Família Multigênica , Naftóis/análise , Naftóis/isolamento & purificação , Filogenia , Extração em Fase Sólida , Terpenos/análise
8.
Sci Rep ; 10(1): 6727, 2020 04 21.
Artigo em Inglês | MEDLINE | ID: mdl-32317695

RESUMO

The biology of bacterial cells is, in general, based on information encoded on circular chromosomes. Regulation of chromosome replication is an essential process that mostly takes place at the origin of replication (oriC), a locus unique per chromosome. Identification of high numbers of oriC is a prerequisite for systematic studies that could lead to insights into oriC functioning as well as the identification of novel drug targets for antibiotic development. Current methods for identifying oriC sequences rely on chromosome-wide nucleotide disparities and are therefore limited to fully sequenced genomes, leaving a large number of genomic fragments unstudied. Here, we present gammaBOriS (Gammaproteobacterial oriC Searcher), which identifies oriC sequences on gammaproteobacterial chromosomal fragments. It does so by employing motif-based machine learning methods. Using gammaBOriS, we created BOriS DB, which currently contains 25,827 gammaproteobacterial oriC sequences from 1,217 species, thus making it the largest available database for oriC sequences to date. Furthermore, we present gammaBOriTax, a machine-learning based approach for taxonomic classification of oriC sequences, which was trained on the sequences in BOriS DB. Finally, we extracted the motifs relevant for identification and classification decisions of the models. Our results suggest that machine learning sequence classification approaches can offer great support in functional motif identification.


Assuntos
Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Aprendizado de Máquina , Motivos de Nucleotídeos/genética , Origem de Replicação/genética , Software , Sequência de Bases , Sequência Consenso/genética , Modelos Genéticos , Filogenia
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.
Sci Rep ; 10(1): 2988, 2020 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-32076066

RESUMO

Crohn's disease causes chronic inflammation in the gastrointestinal tract and its pathogenesis remains unclear. In the intestine of Crohn's disease patients, CD14+CD11+CD163low macrophages contribute to inflammation through the induction of Th17 cells and production of inflammatory cytokines; the CD14+CD11c+163high fraction is anti-inflammatory through the production of IL-10 in normal cases. In this report, the 16S rRNA gene amplicon sequencing method was used to identify bacteria that are specifically present in intestinal CD14+CD11c+ macrophages of Crohn's disease patients. Bacteria present in intestinal CD14+CD11c+ macrophages and mucus of Crohn's disease patients were separated into different clusters in principal coordinates analysis. There was a statistically significant increase in the relative composition of CD14+CD11c+ macrophages from mucus in two phyla (Proteobacteria [p = 0.01] and Actinobacteria [p = 0.02]) and two families (Moraxellaceae [p < 0.001] and Pseudomonadaceae [p = 0.01]). In addition, OTU-1: Acinetobacter and OTU-8: Pseudomonadaceae tended to concentrate in the CD14+CD11c+CD163low subset, whereas OTU-10: Proteus, OTU-15: Collinsella tended to concentrate more in the CD14+CD11c+CD163high subset than the other subset and mucus.


Assuntos
Doença de Crohn/microbiologia , Gammaproteobacteria/isolamento & purificação , Íleo/microbiologia , Mucosa Intestinal/microbiologia , Macrófagos/microbiologia , Adulto , Idoso , Doença de Crohn/imunologia , Doença de Crohn/patologia , Doença de Crohn/cirurgia , DNA Bacteriano/isolamento & purificação , Feminino , Gammaproteobacteria/genética , Gammaproteobacteria/imunologia , Humanos , Íleo/citologia , Íleo/imunologia , Íleo/patologia , Mucosa Intestinal/citologia , Mucosa Intestinal/imunologia , Mucosa Intestinal/patologia , Receptores de Lipopolissacarídeos/metabolismo , Macrófagos/imunologia , Macrófagos/metabolismo , Masculino , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Adulto Jovem
11.
Arch Microbiol ; 202(5): 1069-1076, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32020244

RESUMO

An aerobic bacterium, designated strain Dysh456T, was isolated from a crude oil-contaminated soil. Cells of strain Dysh456T were rod-shaped, motile, and Gram-stain-negative. Strain Dysh456T grew at 13-48 °C and pH 4.3-7.9. Major cellular fatty acids were iso-C15:0 (42.5%), iso-C17:0 (15.3%) and summed feature 9 (iso-C17:1 ω9c/C16:0 10-methyl [13.7%]). Major respiratory quinone was ubiquinone-8. The genome of strain Dysh456T consists of a single circular chromosome of 2,874,969 bp in length with G + C content of 68.3%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain Dysh456T belongs to the family Rhodanobacteraceae, but none of the existing genera can accommodate this novel isolate. On the basis of physiological, chemotaxonomic, and genomic properties, strain Dysh456T (= NBRC 112897T = DSM 105662T) is proposed as the type strain representing a novel species of novel genus, for which the name Aerosticca soli gen. nov., sp. nov. is proposed.


Assuntos
Petróleo/microbiologia , Xanthomonadaceae/classificação , Xanthomonadaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases/genética , DNA Bacteriano/genética , Ácidos Graxos/química , Gammaproteobacteria/genética , Fosfolipídeos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo , Microbiologia do Solo , Ubiquinona/análise , Xanthomonadaceae/genética
12.
ISME J ; 14(5): 1290-1303, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32055028

RESUMO

Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral sulfur cycle by metabolizing dimethylsulfoniopropionate (DMSP) into dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) draft genomes of strains of the recently added species Endozoicomonas acroporae (Acr-14T, Acr-1, and Acr-5) isolated from the coral Acropora sp. and performed a comparative genomic analysis on the genus Endozoicomonas. We identified DMSP CoA-transferase/lyase-a dddD gene homolog in all sequenced genomes of E. acroporae strains-and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as a carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.


Assuntos
Antozoários/microbiologia , Gammaproteobacteria/metabolismo , Compostos de Sulfônio/metabolismo , Animais , Bactérias/genética , Liases de Carbono-Enxofre , Gammaproteobacteria/genética , Genômica , Sulfetos , Enxofre/metabolismo
13.
Arch Microbiol ; 202(4): 905-920, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-31897537

RESUMO

The development of drug-resistant bacteria and the necessity for unique antimicrobial agents, directed to the search of new habitats to screen the production of anti-infective substances. Culture-dependent studies of heterotrophic bacteria from the intertidal macroalgae thriving along the Southern coast of India resulted in the isolation of 148 strains, which were assayed for antibacterial activities against wide spectrum of pathogens including drug-resistant pathogens, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE). Two of the most active strains with a zone of inhibition ≥ 30 mm on spot over lawn assay, belonging to the phyla Firmicutes and Gamma-proteobacteria, isolated from a  Rhodophycean marine macroalga, Hypnea valentiae, were selected for bioprospecting studies. They were further characterized as Shewanella algae MTCC 12715 and Bacillus amyloliquefaciens MTCC 12716, based on integrated phenotypic and genotypic analysis. The bacterial extracts exhibited significant antibacterial activities against MRSA and VRE with minimum inhibitory concentrations of 6.25-12.5 µg/mL. Time kill kinetic profiles of these bacteria revealed rapid bactericidal activity against both MRSA and E. coli, showing a ≥ 3log10 decline in viable cell count compared to the initial. In BacLight™ live/dead staining technique, the propidium iodide uptake results appropriately attributed that the components in the B. amyloliquefaciens extract might compromise the integrity of the cytoplasmic membrane of the pathogenic bacteria. Type-1 pks gene (MH157093) of S. algae and hybrid nrps/pks gene (MH157092) of B. amyloliquefaciens could be amplified. Antibacterial activity study combined with the results of amplified genes coding for polyketide synthase and nonribosomal peptide synthetase showed that these marine symbiotic bacteria had a promising broad-spectrum activity, and therefore, could be used against the emerging dilemma of antibiotic-resistant bacterial infections.


Assuntos
Bactérias/efeitos dos fármacos , Firmicutes/química , Gammaproteobacteria/química , Alga Marinha/microbiologia , Antibacterianos/isolamento & purificação , Antibacterianos/farmacologia , Bacillus amyloliquefaciens/enzimologia , Bacillus amyloliquefaciens/genética , Descoberta de Drogas , Escherichia coli/efeitos dos fármacos , Firmicutes/enzimologia , Firmicutes/genética , Gammaproteobacteria/enzimologia , Gammaproteobacteria/genética , Índia , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Peptídeo Sintases/genética , Policetídeo Sintases/genética , Estudos Prospectivos , Enterococos Resistentes à Vancomicina/efeitos dos fármacos
14.
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
15.
J Microbiol ; 58(2): 92-98, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31993984

RESUMO

A Gram-stain-negative strictly aerobic, short-rod-shaped, and non-motile bacterial strain designated HSLHS9T was isolated from surface seawater collected from the South China Sea. Strain HSLHS9T could grow at 15-41°C (optimum 28°C), at pH 5.0-9.0 (optimum 6.0-7.0), and in 0-7% (w/v) NaCl (optimum 2-3%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HSLHS9T shared high identities with the closely related Parahaliea aestuarii S2-26T (98.6%) and Parahaliea mediterranea 7SM29T (97.8%) and formed a distinct lineage within the genus Parahaliea. Wholegenome sequencing of strain HSLHS9T revealed the size of 4.8 Mbp and DNA G + C content of 61.8 mol%. Strain HSLHS9T shared the digital DNA-DNA hybridization values of 22.4% and 23.0%, and the average nucleotide identities of 79.7% and 79.9%, respectively, with the two type strains above. The predominant cellular fatty acids of the strain were summed feature 8 (C18:1ω6c and/or C18:1ω7c), summed feature 3 (C16:1ω7c and/or C16:1ω6c), C17:1ω8c, and C16:0. The sole isoprenoid quinone was identified as Q-8. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminolipid, and two glycolipids. Based on taxonomic data obtained in this study, it is suggested that strain HSLHS9T represents a novel species of the genus Parahaliea, for which the name Parahaliea maris sp. nov. is proposed. The type strain is HSLHS9T (= MCCC 1A06717T = KCTC 52307T). An emended description of the genus Parahaliea is also provided.


Assuntos
Gammaproteobacteria/classificação , Gammaproteobacteria/isolamento & purificação , Água do Mar/microbiologia , Classificação , DNA Bacteriano/genética , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , Filogenia , RNA Ribossômico 16S
16.
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
17.
J Appl Microbiol ; 128(6): 1703-1719, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31950553

RESUMO

AIMS: Dickeya species are high consequence plant pathogenic bacteria; associated with potato disease outbreaks and subsequent economic losses worldwide. Early, accurate and reliable detection of Dickeya spp. is needed to prevent establishment and further dissemination of this pathogen. Therefore, a multiplex TaqMan qPCR was developed for sensitive detection of Dickeya spp. and specifically, Dickeya dianthicola. METHODS AND RESULTS: A signature genomic region for the genus Dickeya (mglA/mglC) and unique genomic region for D. dianthicola (alcohol dehydrogenase) were identified using a whole genome-based comparative genomics approach. The developed multiplex TaqMan qPCR was validated using extensive inclusivity and exclusivity panels, and naturally/artificially infected samples to confirm broad range detection capability and specificity. Both sensitivity and spiked assays showed a detection limit of 10 fg DNA. CONCLUSION: The developed multiplex assay is sensitive and reliable to detect Dickeya spp. and D. dianthicola with no false positives or false negatives. It was able to detect mixed infection from naturally and artificially infected plant materials. SIGNIFICANCE AND IMPACT OF THE STUDY: The developed assay will serve as a practical tool for screening of propagative material, monitoring the presence and distribution, and quantification of target pathogens in a breeding programme. The assay also has applications in routine diagnostics, biosecurity and microbial forensics.


Assuntos
Gammaproteobacteria/isolamento & purificação , Doenças das Plantas/microbiologia , Gammaproteobacteria/genética , Genoma Bacteriano/genética , Genômica , Limite de Detecção , Reação em Cadeia da Polimerase Multiplex , Solanum tuberosum/microbiologia , Especificidade da Espécie
18.
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
19.
Antonie Van Leeuwenhoek ; 113(4): 449-458, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31701358

RESUMO

A Gram-stain negative, rod-shaped, aerobic, oxidase-positive and catalase-weakly positive bacterial strain with polar or subpolar flagellum, designated RZ04T, was isolated from an intertidal sand sample collected from a coastal area of the Yellow Sea, China. The organism was observed to grow optimally at 25 °C and pH 6.5-7.0 with 2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RZ04T was closely related to Colwellia asteriadis (similarity 96.9%) and Litorilituus sediminis (similarity 96.8%), and 94.4-96.4% sequence similarities to other type strains of species of the genera belonged to the family Colwelliaceae. The dominant fatty acids of strain RZ04T were determined to be C17:1ω8c, C15:1ω8c, C16:0 and summed feature 3 (C16:1ω6c and/or C16:1ω7c), and the predominant isoprenoid quinone was determined to be quinone 8 (Q-8). Phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid and four unidentified lipids were determined to be the major constituents of the polar lipids. The genome of strain RZ04T is 4.14 Mbp with a G + C content of 37.4 mol%. A total of 3631 genes are predicted, with 3531 protein-coding genes, 75 RNA genes and 25 pseudogenes. Based on phenotypic, genotypic and phylogenetic analysis, strain RZ04T is considered to represent a novel species in the genus Litorilituus, for which the name Litorilituus lipolyticus is proposed. The type strain is RZ04T (= MCCC 1K03616T = KCTC 62835T). An emended description of Colwellia asteriadis is also provided.


Assuntos
Alteromonadaceae/classificação , Gammaproteobacteria/classificação , Gammaproteobacteria/isolamento & purificação , Alteromonadaceae/genética , China , DNA Bacteriano/genética , Gammaproteobacteria/genética , Genótipo , Humanos , Oceanos e Mares , Filogenia , Areia , Especificidade da Espécie
20.
Environ Microbiol ; 22(1): 397-412, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31709681

RESUMO

Reef-building corals form associations with a huge diversity of microorganisms, which are essential for the survival and well-being of their host. While the acquisition patterns of Symbiodiniaceae microalgal endosymbionts are strongly linked to the coral's reproductive strategy, few studies have investigated the transmission mode of bacteria, especially in brooding species. Here, we relied on 16S rRNA gene and Internal Transcribed Spacer 2 marker metabarcoding in conjunction with fluorescence in situ hybridisation microscopy to describe the onset of microbial associations in the common brooding coral Pocillopora acuta. We analysed the bacterial and Symbiodiniaceae community composition in five adult colonies, their larvae, and 4-day old recruits. Larvae and recruits inherited Symbiodiniaceae, as well as a small number of bacterial strains, from their parents. Rhodobacteraceae and Endozoicomonas were among the most abundant taxa that were likely maternally transmitted to the offspring. The presence of bacterial aggregates in newly released larvae was observed with confocal microscopy, confirming the occurrence of vertical transmission of bacteria in P. acuta. We concluded that host factors, as well as the environmental bacterial pool influenced the microbiome of P. acuta.


Assuntos
Antozoários/microbiologia , Recifes de Corais , Dinoflagelados/classificação , Gammaproteobacteria/classificação , Rhodobacteraceae/classificação , Animais , Dinoflagelados/genética , Dinoflagelados/isolamento & purificação , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Microbiota , RNA Ribossômico 16S/genética , Rhodobacteraceae/genética , Rhodobacteraceae/isolamento & purificação
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