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1.
Appl Microbiol Biotechnol ; 104(5): 2067-2077, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31932896

RESUMO

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


Assuntos
Proteínas de Bactérias/metabolismo , Compostos de Epóxi/química , Compostos de Epóxi/metabolismo , Hidrolases/metabolismo , Alphaproteobacteria/enzimologia , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/isolamento & purificação , Biocatálise , Hidrolases/química , Hidrolases/genética , Hidrolases/isolamento & purificação , Cinética , Modelos Moleculares , Mutação , Engenharia de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Estereoisomerismo , Especificidade por Substrato
2.
J Microbiol ; 57(11): 976-981, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31555990

RESUMO

A novel, Gram-stain-negative marine bacterium, designated GH2-6T, was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) collected in Gangwha Island, the Republic of Korea. The cells of the organism were strictly aerobic, oxidase- and catalase-positive, non-flagellated rods. Growth occurred at 20-45°C, pH 5-10, and 0.5-9 (w/v) NaCl. The requirement of Na+ for growth (0.5-3%) was observed. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid and a glycolipid. The predominant fatty acids were C18:1ω7c, C18:0, C16:0, C19:0 cyclo ω8c, C18:1ω7c 11-methyl and summed feature 2 (C14:0 3-OH and/or C16:1 iso I). The genome size was 4.45 Mb and the G+C content of the genomic DNA was 61.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GH2-6T belonged to genus Martelella and formed a tight cluster with M. radicis BM5-7T and M. endophytica YC6887T. Levels of 16S rRNA gene sequence similarity between the novel isolate and members of the genus were 99.3-95.5%, but strain GH2-6T possessed an extended loop (49 nucleotides in length) between positions 187 and 213 of the 16S rRNA gene sequence (E. coli numbering). DDH values in vitro between the novel isolate and the closest relatives were 23.2±12.8-46.3±5.2%. On the basis of polyphasic data presented in this study, the type strain GH2-6T (= KACC 19403T = KCTC 62125T = NBRC 113212T) represents a novel species of the genus Martelella for which the name Martelella lutilitoris sp. nov. is proposed.


Assuntos
Alphaproteobacteria/classificação , Alphaproteobacteria/isolamento & purificação , Sedimentos Geológicos/microbiologia , Filogenia , Rizosfera , Água do Mar/microbiologia , Alphaproteobacteria/genética , Alphaproteobacteria/fisiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Escherichia coli/genética , Ácidos Graxos/química , Glicolipídeos/química , Ilhas , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Plantas Tolerantes a Sal , Análise de Sequência de DNA , Ubiquinona/química
3.
Elife ; 82019 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-31478833

RESUMO

Members of the SAR11 order Pelagibacterales dominate the surface oceans. Their extensive diversity challenges emerging operational boundaries defined for microbial 'species' and complicates efforts of population genetics to study their evolution. Here, we employed single-amino acid variants (SAAVs) to investigate ecological and evolutionary forces that maintain the genomic heterogeneity within ubiquitous SAR11 populations we accessed through metagenomic read recruitment using a single isolate genome. Integrating amino acid and protein biochemistry with metagenomics revealed that systematic purifying selection against deleterious variants governs non-synonymous variation among very closely related populations of SAR11. SAAVs partitioned metagenomes into two main groups matching large-scale oceanic current temperatures, and six finer proteotypes that connect distant oceanic regions. These findings suggest that environmentally-mediated selection plays a critical role in the journey of cosmopolitan surface ocean microbial populations, and the idea 'everything is everywhere but the environment selects' has credence even at the finest resolutions.


Assuntos
Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Substituição de Aminoácidos , Variação Genética , Filogeografia , Água do Mar/microbiologia , Proteínas de Bactérias/genética , Metagenômica , Mutação de Sentido Incorreto , Seleção Genética
4.
Nat Commun ; 10(1): 3290, 2019 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-31337764

RESUMO

Chromosome segregation typically occurs after replication has finished in eukaryotes but during replication in bacteria. Here, we show that the alphaproteobacterium Hyphomonas neptunium, which proliferates by bud formation at the tip of a stalk-like cellular extension, segregates its chromosomes in a unique two-step process. First, the two sister origin regions are targeted to opposite poles of the mother cell, driven by the ParABS partitioning system. Subsequently, once the bulk of chromosomal DNA has been replicated and the bud exceeds a certain threshold size, the cell initiates a second segregation step during which it transfers the stalk-proximal origin region through the stalk into the nascent bud compartment. Thus, while chromosome replication and segregation usually proceed concurrently in bacteria, the two processes are largely uncoupled in H. neptunium, reminiscent of eukaryotic mitosis. These results indicate that stalked budding bacteria have evolved specific mechanisms to adjust chromosome segregation to their unusual life cycle.


Assuntos
Alphaproteobacteria/genética , Segregação de Cromossomos , Alphaproteobacteria/citologia , Divisão Celular , Cromossomos Bacterianos/química , Cromossomos Bacterianos/metabolismo , Replicação do DNA
5.
ISME J ; 13(10): 2536-2550, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31227817

RESUMO

Unlike biologically available nitrogen and phosphorus, which are often at limiting concentrations in surface seawater, sulfur in the form of sulfate is plentiful and not considered to constrain marine microbial activity. Nonetheless, in a model system in which a marine bacterium obtains all of its carbon from co-cultured phytoplankton, bacterial gene expression suggests that at least seven dissolved organic sulfur (DOS) metabolites support bacterial heterotrophy. These labile exometabolites of marine dinoflagellates and diatoms include taurine, N-acetyltaurine, isethionate, choline-O-sulfate, cysteate, 2,3-dihydroxypropane-1-sulfonate (DHPS), and dimethylsulfoniopropionate (DMSP). Leveraging from the compounds identified in this model system, we assessed the role of sulfur metabolites in the ocean carbon cycle by mining the Tara Oceans dataset for diagnostic genes. In the 1.4 million bacterial genome equivalents surveyed, estimates of the frequency of genomes harboring the capability for DOS metabolite utilization ranged broadly, from only 1 out of every 190 genomes (for the C2 sulfonate isethionate) to 1 out of every 5 (for the sulfonium compound DMSP). Bacteria able to participate in DOS transformations are dominated by Alphaproteobacteria in the surface ocean, but by SAR324, Acidimicrobiia, and Gammaproteobacteria at mesopelagic depths, where the capability for utilization occurs in higher frequency than in surface bacteria for more than half the sulfur metabolites. The discovery of an abundant and diverse suite of marine bacteria with the genetic capacity for DOS transformation argues for an important role for sulfur metabolites in the pelagic ocean carbon cycle.


Assuntos
Bactérias/metabolismo , Carbono/metabolismo , Fitoplâncton/metabolismo , Enxofre/metabolismo , Alphaproteobacteria/genética , Bactérias/genética , Bactérias/isolamento & purificação , Ciclo do Carbono , Diatomáceas/metabolismo , Processos Heterotróficos , Oceanos e Mares , Fitoplâncton/genética , Fitoplâncton/isolamento & purificação , Água do Mar/microbiologia
7.
J Microbiol ; 57(8): 676-687, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31201724

RESUMO

Strain IMCC1322 was isolated from a surface water sample from the East Sea of Korea. Based on 16S rRNA analysis, IMCC1322 was found to belong to the OCS28 sub-clade of SAR116. The cells appeared as short vibrioids in logarithmic-phase culture, and elongated spirals during incubation with mitomycin or in aged culture. Growth characteristics of strain IMCC1322 were further evaluated based on genomic information; proteorhodopsin (PR), carbon monoxide dehydrogenase, and dimethylsulfoniopropionate (DMSP)-utilizing enzymes. IMCC1322 PR was characterized as a functional retinylidene protein that acts as a light-driven proton pump in the cytoplasmic membrane. However, the PR-dependent phototrophic potential of strain IMCC1322 was only observed under CO-inhibited and nutrient-limited culture conditions. A DMSP-enhanced growth response was observed in addition to cultures grown on C1 compounds like methanol, formate, and methane sulfonate. Strain IMCC1322 cultivation analysis revealed biogeochemical processes characteristic of the SAR116 group, a dominant member of the microbial community in euphotic regions of the ocean. The polyphasic taxonomy of strain IMCC1322 is given as Candidatus Puniceispirillum marinum, and was confirmed by chemotaxonomic tests, in addition to 16S rRNA phylogeny and cultivation analyses.


Assuntos
Alphaproteobacteria , RNA Ribossômico 16S/genética , Rodopsinas Microbianas , Água do Mar/microbiologia , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/crescimento & desenvolvimento , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana/métodos , DNA Bacteriano/genética , República da Coreia , Rodopsinas Microbianas/química , Rodopsinas Microbianas/metabolismo , Compostos de Sulfônio/metabolismo , Sequenciamento Completo do Genoma/métodos
8.
Curr Microbiol ; 76(9): 988-994, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31172271

RESUMO

Qipengyuania sediminis CGMCC 1.12928T, a family member of Erythrobacteraceae, the class of Alphaproteobacteria, was isolated from a borehole sediment sample collected from Qiangtang Basin in Qinghai-Tibetan Plateau, the largest permafrost in China. Understanding bacterial molecular feature may shed light on the ecological strategy in the extreme environment. Here we describe the complete genome sequence and annotation of strain CGMCC 1.12928T, including the complete genome sequence and annotation. The genome of strain CGMCC 1.12928T consist of a single-circular chromosome, comprises 2,416,000 bp with an average G + C content of 66.7 mol%, and contains 2414 genes; including 2367 CDSs, 44 tRNA genes, as well as one operon of 16S-23S-5S rRNA genes. Genomic properties indicated that strain CGMCC 1.12928T has a relatively smaller genome size and higher G + C content within the family Erythrobacteraceae. In addition, genomic analysis revealed its genome contains multiple function genes responsible for nitrogen, sulfur and phosphorus cycles and explained the cold adaption mechanism. Thus, this strain plays an active role in the biogeochemical cycle in cold niche. The whole-genome of this isolate will widen our understanding of the ecological role of the genus Qipengyuania in permafrost.


Assuntos
Alphaproteobacteria/isolamento & purificação , Genoma Bacteriano , Sedimentos Geológicos/microbiologia , Adaptação Fisiológica , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/fisiologia , Composição de Bases , China , Temperatura Baixa , DNA Bacteriano , Óperon , Pergelissolo/microbiologia , Filogenia , Sequenciamento Completo do Genoma
9.
J Microbiol ; 57(8): 655-660, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31187415

RESUMO

A Gram-negative, aerobic, short-rod-shaped, motile (with a terminal flagellum), non-spore-forming bacterium, designated strain 85T, was isolated from a surface-sterilized bark of Sonneratia caseolaris collected from Qinzhou in Guangxi, China and was analyzed using a polyphasic approach to determine its taxonomic position. Strain 85T grew optimally in the presence of 1-2% (w/v) NaCl at 30°C and pH 6.0-7.0. Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 85T belonged to the genus Fulvimarina and shared the highest 16S rRNA gene sequence similarity with Fulvimarina pelagi HTCC2506T (96.16%). The cell-wall peptidoglycan contained meso-diaminopimelic acid and ubiquinone Q-10 was the predominant respiratory lipoquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified amino lipid, three unidentified phospholipids and six unidentified lipids. The major fatty acid was C18:1ω7c. The DNA G+C content of strain 85T was 65.4 mol%, and the average nucleotide identity and estimated DDH values between strain 85T and the type strain of Fulvimarina pelagi HTCC2506T were 77.3% and 21.7%, respectively. Based on the phylogenetic, phenotypic, and chemotaxonomic analyses, strain 85T should be considered as a novel species of the genus Fulvimarina with the proposed name Fulvimarina endophytica sp. nov., and its type strain is 85T (= KCTC 62717T = CGMCC 1.13665T).


Assuntos
Alphaproteobacteria/classificação , Endófitos/classificação , Lythraceae/microbiologia , Casca de Planta/microbiologia , Alphaproteobacteria/genética , Alphaproteobacteria/crescimento & desenvolvimento , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana/métodos , Composição de Bases , China , DNA Bacteriano/genética , Endófitos/genética , Endófitos/crescimento & desenvolvimento , Endófitos/isolamento & purificação , RNA Ribossômico 16S/genética , Sequenciamento Completo do Genoma/métodos
10.
Syst Appl Microbiol ; 42(4): 495-505, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31085022

RESUMO

The ubiquitous alpha-proteobacteria of the order "Candidatus Pelagibacterales" (SAR11) are highly abundant in aquatic environments, and among them, members of the monophyletic lineage LD12 (also known as SAR11 clade IIIb) are specifically found in lacustrine ecosystems. Clade IIIb bacteria are some of the most prominent members of freshwater environments, but little is known about their biology due to the lack of genome representatives. Only recently, the first non-marine isolate was cultured and described as "Candidatus Fonsibacter ubiquis". Here, we expand the collection of freshwater IIIb representatives and describe a new IIIb species of the genus "Ca. Fonsibacter". Specifically, we assembled a collection of 67 freshwater metagenomic datasets from the interconnected lakes of the Chattahoochee River basin (GA, USA) and obtained nearly complete metagenome-assembled genomes (MAGs) representing 5 distinct IIIb subclades, roughly equivalent to species based on genomic standards, including the previously described "Ca. F. ubiquis". Genomic comparisons between members of the IIIb species revealed high similarity in gene content. However, when comparing their abundance profiles in the Chattahoochee basin and various aquatic environments, differences in temporal and spatial distributions among the distinct species were observed implying niche differentiation might be underlying the coexistence of the highly functionally similar representatives. The name Ca. Fonsibacter lacus sp. nov. is proposed for the most abundant and widespread species in the Chattahoochee River basin and various freshwater ecosystems.


Assuntos
Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Água Doce/microbiologia , Metagenoma/genética , Filogenia , Proteínas de Bactérias/genética , DNA Bacteriano/genética , Genes Essenciais/genética , Variação Genética , Genômica , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sudeste dos Estados Unidos , Especificidade da Espécie
11.
Antonie Van Leeuwenhoek ; 112(10): 1457-1463, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31089913

RESUMO

A Gram-negative, aerobic, short rodshaped, asporogenous bacterium, designated CBS5Q-3T, was isolated from a surface-sterilised root of Ficus microcarpa Linn. f. collected from Guangxi, China and investigated by a polyphasic approach to determine its taxonomic position. Strain CBS5Q-3T was found to grow optimally with 2% (w/v) NaCl at 30 °C, pH 7.0-8.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBS5Q-3T is closely related to species of genus Jiella and shares high 16S rRNA gene sequence similarity of 98.1% with Jiella aquimaris JCM 30119T. The average nucleotide identity and in silico DNA-DNA hybridization values between strain CBS5Q-3T and J. aquimaris JCM 30119T were 82.8% and 26.0%, respectively. The DNA G + C content of strain CBS5Q-3T was determined to be 66.5 mol %. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid and ubiquinone Q-10 identified as the respiratory lipoquinone. The polar lipids were found to be comprised of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and three unidentified aminolipids, while the major fatty acids were identified as C18:1ω7c and cyclo-C19:0ω8c. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain CBS5Q-3T can be concluded to represent a novel species of the genus Jiella, for which the name Jiella endophytica sp. nov. is proposed. The type strain is CBS5Q-3T (= JCM 33167T = CGMCC 1.13863T).


Assuntos
Alphaproteobacteria/classificação , Alphaproteobacteria/isolamento & purificação , Ficus/microbiologia , Aerobiose , Alphaproteobacteria/genética , Alphaproteobacteria/fisiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , China , Análise por Conglomerados , Citosol/química , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácido Diaminopimélico/análise , Endófitos/classificação , Endófitos/genética , Endófitos/isolamento & purificação , Endófitos/fisiologia , Ácidos Graxos/análise , Hibridização de Ácido Nucleico , Peptidoglicano/análise , Fosfolipídeos/análise , Filogenia , Pigmentos Biológicos , Raízes de Plantas/microbiologia , Quinonas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Cloreto de Sódio/metabolismo , Temperatura Ambiente
12.
Appl Biochem Biotechnol ; 189(1): 144-159, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-30957194

RESUMO

High temperature and high ethanol concentrations obviously affect vinegar fermentation. The thermotolerant and ethanol-resistant strains are expected to become one of the technologies for effective vinegar fermentation. This study aimed to further improve thermotolerant Komagataeibacter oboediens MSKU 3 through thermal and ethanol adaptations for acetic acid fermentation. The MSKU 3 strain was independently cultured by a repetitive cultivation in gradually increasing temperature from 37 to 39 °C for thermal adaptation, while adaptation to ethanol was carried out from concentrations of 3 to 5.5% (v/v) at 37 °C. Acetic acid fermentation revealed that the thermo-adapted T4 strain could produce 2.82% acidity with 3% ethanol at 39 °C, whereas the ethanol-adapted E3 strain could produce 3.54% acidity with 5.5% ethanol at 37 °C, in contrast to the parental strain, MSKU 3, in which no fermentation occurs at either 39 °C or 5.5% ethanol. Furthermore, genome mapping analysis of T4 and E3 strains against the genome of parental strain MSKU 3 revealed several mutated genes that are associated with thermotolerance or ethanol adaptation. The occurrence of these adaptation-associated mutations during adaptive evolution was also analyzed. Therefore, adapted strains T4 and E3 revealed the potential of Komagataeibacter oboediens strain improvement to further enhance vinegar fermentation with high ethanol concentration at high temperature.


Assuntos
Ácido Acético/administração & dosagem , Alphaproteobacteria/metabolismo , Etanol/administração & dosagem , Fermentação , Temperatura Alta , Alphaproteobacteria/genética , Alphaproteobacteria/crescimento & desenvolvimento , Genoma Bacteriano , Técnicas In Vitro
13.
J Agric Food Chem ; 67(15): 4193-4199, 2019 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-30864436

RESUMO

We previously isolated a monocrotophos-degrading strain Starkeya sp. YW6, which could also degrade propham. Here, we show that strain YW6 metabolizes propham via a pathway in which propham is initially hydrolyzed to aniline and then converted to catechol, which is then oxidized via an ortho-cleavage pathway. The novel amidase gene mmH was cloned from strain YW6 and expressed in Escherichia coli BL21(DE3). MmH, which exhibits aryl acylamidase activity, was purified for enzymatic analysis. Bioinformatic analysis confirmed that MmH belongs to the amidase signature (AS) enzyme family and shares 26-50% identity with several AS family members. MmH (molecular mass of 53 kDa) was most active at 40 °C and pH 8.0 and showed high activity toward propham, with Kcat and Km values of 33.4 s-1 and 16.9 µM, respectively. These characteristics make MmH suitable for novel amide biosynthesis and environmental remediation.


Assuntos
Alphaproteobacteria/metabolismo , Amidoidrolases/química , Amidoidrolases/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Fenilcarbamatos/metabolismo , Alphaproteobacteria/química , Alphaproteobacteria/enzimologia , Alphaproteobacteria/genética , Amidoidrolases/metabolismo , Proteínas de Bactérias/metabolismo , Biodegradação Ambiental , Clonagem Molecular , Cinética , Peso Molecular , Especificidade por Substrato
14.
Biotechnol Lett ; 41(4-5): 591-604, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30895484

RESUMO

OBJECTIVE: We aimed to characterize a novel SGNH (Ser-Gly-Asn-His) family hydrolase from the annotated genome of marine bacteria with new features. RESULTS: A novel esterase Ali5 from Altererythrobacter ishigakiensis has been identified and classified into SGNH family. Ali5 presented a novel GNSL (Gly-Asn-Ser-Leu(X)) motif that differs from the classic GDSL (Gly-Asp-Ser-Leu(X)) motif of SGNH family. The enzyme has esterase and thioesterase activity and exhibited apparent temperature and pH optima of 40 °C and pH 7.5 (in phosphate buffer), respectively. Ali5 was found to be halotolerant and thermostable, and exhibited strong resistance to several organic solvents and metal ions. The residue Tyr196 has a great influence on the catalytic activity, which was proved by site-directed mutagenesis and subsequent kinetic characterization. CONCLUSION: The esterase Ali5 with esterase and thioesterase activities, salt and metal ions resistance and unique structural features was identified, which holds promise for research on the SGNH family of hydrolases.


Assuntos
Alphaproteobacteria/enzimologia , Motivos de Aminoácidos , Tioléster Hidrolases/genética , Tioléster Hidrolases/metabolismo , Alphaproteobacteria/genética , Cátions/metabolismo , Biologia Computacional , Análise Mutacional de DNA , Inibidores Enzimáticos/metabolismo , Estabilidade Enzimática , Concentração de Íons de Hidrogênio , Metais/metabolismo , Mutagênese Sítio-Dirigida , Solventes/metabolismo , Temperatura Ambiente , Tioléster Hidrolases/química , Tioléster Hidrolases/classificação
15.
ISME J ; 13(6): 1506-1519, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30742057

RESUMO

Prochlorococcus and SAR11 are among the smallest and most abundant organisms on Earth. With a combined global population of about 2.7 × 1028 cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro. Here we describe co-cultures of Prochlorococcus and SAR11 isolates representing both high- and low-light adapted clades. We examined: (1) the influence of Prochlorococcus on the growth of SAR11 and vice-versa, (2) whether Prochlorococcus can meet specific nutrient requirements of SAR11, and (3) how co-culture dynamics vary when Prochlorococcus is grown with SAR11 compared with sympatric copiotrophic bacteria. SAR11 grew 15-70% faster in co-culture with Prochlorococcus, while the growth of the latter was unaffected. When Prochlorococcus populations entered stationary phase, this commensal relationship rapidly became amensal, as SAR11 abundances decreased dramatically. In parallel experiments with copiotrophic bacteria; however, the heterotrophic partner increased in abundance as Prochlorococcus densities leveled off. The presence of Prochlorococcus was able to meet SAR11's central requirement for organic carbon, but not reduced sulfur. Prochlorococcus strain MIT9313, but not MED4, could meet the unique glycine requirement of SAR11, which could be due to the production and release of glycine betaine by MIT9313, as supported by comparative genomic evidence. Our findings also suggest, but do not confirm, that Prochlorococcus MIT9313 may compete with SAR11 for the uptake of 3-dimethylsulfoniopropionate (DMSP). To give our results an ecological context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes. At many locations, more than half of the identifiable genome equivalents in the euphotic zone belonged to Prochlorococcus and SAR11 - highlighting the biogeochemical potential of these two groups.


Assuntos
Alphaproteobacteria/crescimento & desenvolvimento , Prochlorococcus/crescimento & desenvolvimento , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Técnicas de Cocultura , Processos Heterotróficos , Prochlorococcus/genética , Prochlorococcus/metabolismo , Água do Mar/microbiologia , Compostos de Sulfônio/metabolismo
16.
Antonie Van Leeuwenhoek ; 112(6): 919-925, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30631983

RESUMO

A Gram-stain negative, aerobic, coccus-shaped bacterium, designated strain M2BS9Y-3-1T, was isolated from a surface-sterilized leaf of Rhizophora stylosa. It grew in the pH range 5.0-9.0 (optimum, 7.0) and at temperatures between 20 and 37 °C (optimum, 30 °C). Growth was possible at concentrations of 1-10% (w/v) NaCl (optimum, 2%). The phylogenetic trees based on 16S rRNA gene sequences indicated that strain M2BS9Y-3-1T clustered together with Notoacmeibacter marinus XMTR2A4T (98.44% similarity) and separated from other species of the family Notoacmeibacteraceae. The average nucleotide identity and in silico DNA-DNA hybridization values between strain M2BS9Y-3-1T and N. marinus XMTR2A4T were 76.8%, 19.8%, respectively. The G+C content of the genomic DNA was 60.0 mol%. The cell wall peptidoglycan contained meso-diaminobutyric acid and ubiquinone Q-10 was the respiratory lipoquinone. The major fatty acid was C18:1ω7c. The lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, an unidentified aminophospholipid and three unidentified lipids. The results of taxonomic analysis suggested that strain M2BS9Y-3-1T represents a novel species of the genus Notoacmeibacter for which the name Notoacmeibacter ruber sp. nov. is proposed. The type strain is M2BS9Y-3-1T (KCTC 62838T = CGMCC 1.13746T).


Assuntos
Alphaproteobacteria/isolamento & purificação , Endófitos/isolamento & purificação , Rhizophoraceae/microbiologia , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Endófitos/classificação , Endófitos/genética , Endófitos/metabolismo , Ácidos Graxos/química , Ácidos Graxos/metabolismo , Filogenia , Folhas de Planta/microbiologia , RNA Ribossômico 16S/genética
17.
Antonie Van Leeuwenhoek ; 112(6): 947-954, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30637538

RESUMO

A motile, rod-shaped and yellow coloured proteobacterium, designated strain SYSU D60017T, was isolated from a desert soil sample. The bacterium was found to be an obligately aerobic, mesophilic and neutrophilic chemo-heterotroph. Cells were observed to be Gram-stain negative, catalase positive and oxidase positive. The major cellular fatty acids were identified as C19:0ω8c cyclo and Summed Feature 8 (C18:1ω7c and/or C18:1ω6c). The main respiratory quinone identified was ubiquinone-10. The DNA G + C content was determined to be 63.8% based on draft genome sequence data. The polar lipids detected were identified as diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and five unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D60017T is a member of the order Rhizobiales, but forms a distinct phylogenetic lineage. The differences in the phenotypic characteristics from members of related genera and its distinct phylogenetic position suggested that the isolate SYSU D60017T represents a novel species of a novel genus within the order Rhizobiales, for which the name Flaviflagellibacter deserti gen. nov., sp. nov. is proposed. The type strain of the new taxon is SYSU D60017T (= CGMCC 1.16444T = NBRC 112958T).


Assuntos
Alphaproteobacteria/isolamento & purificação , Microbiologia do Solo , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Composição de Bases , DNA Bacteriano/genética , Clima Desértico , Ácidos Graxos/química , Ácidos Graxos/metabolismo , Filogenia , RNA Ribossômico 16S/genética
18.
ISME J ; 13(5): 1198-1208, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30643197

RESUMO

The Black Sea is the world's largest anoxic basin and a model system for studying processes across redox gradients. In between the oxic surface and the deeper sulfidic waters there is an unusually broad layer of 10-40 m, where neither oxygen nor sulfide are detectable. In this suboxic zone, dissolved phosphate profiles display a pronounced minimum at the upper and a maximum at the lower boundary, with a peak of particulate phosphorus in between, which was suggested to be caused by the sorption of phosphate on sinking particles of metal oxides. Here we show that bacterial polyphosphate inclusions within large magnetotactic bacteria related to the genus Magnetococcus contribute substantially to the observed phosphorus peak, as they contain 26-34% phosphorus compared to only 1-5% in metal-rich particles. Furthermore, we found increased gene expression for polyphosphate kinases by several groups of bacteria including Magnetococcaceae at the phosphate maximum, indicating active bacterial polyphosphate degradation. We propose that large magnetotactic bacteria shuttle up and down within the suboxic zone, scavenging phosphate at the upper and releasing it at the lower boundary. In contrast to a passive transport via metal oxides, this bacterial transport can quantitatively explain the observed phosphate profiles.


Assuntos
Alphaproteobacteria/metabolismo , Polifosfatos/metabolismo , Água do Mar/química , Água do Mar/microbiologia , Alphaproteobacteria/genética , Mar Negro , Fenômenos Magnéticos , Fosfatos/análise , Fósforo/análise , Fosfotransferases (Aceptor do Grupo Fosfato)/genética , Fosfotransferases (Aceptor do Grupo Fosfato)/metabolismo
19.
Sci Total Environ ; 657: 1543-1552, 2019 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-30677920

RESUMO

Next generation sequencing provides new insights into the diversity and ecophysiology of bacteria communities throughout wastewater treatment plants (WWTP), as well as the fate of pathogens in wastewater treatment system. In the present study, we investigated the bacterial communities and human-associated Bacteroidales (HF183) marker in two WWTPs in North America that utilize Bardenpho treatment processes. Although, most pathogens were eliminated during wastewater treatment, some pathogenic bacteria were still observed in final effluents. The HF183 genetic marker demonstrated significant reductions between influent and post-Bardenpho treated samples in each WWTP, which coincided with changes in bacteria relative abundances and community compositions. Consistent with previous studies, the major phyla in wastewater samples were predominantly comprised by Proteobacteria (with Gammaproteobacteria and Alphaproteobacteria among the top two classes), Actinobacteria, Bacteroidetes, and Firmicutes. Dominant genera were often members of Proteobacteria and Firmicutes, including several pathogens of public health concern, such as Pseudomonas, Serratia, Streptococcus, Mycobacterium and Arcobacter. Pearson correlations were calculated to observe the seasonal variation of relative abundances of gene sequences at different levels based on the monthly average temperature. These findings profile how changes in bacterial communities can function as a robust method for monitoring wastewater treatment quality and performance for public and environmental health purposes.


Assuntos
Águas Residuárias/microbiologia , Purificação da Água/normas , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Bacteroidaceae/genética , Bacteroidaceae/isolamento & purificação , Biodiversidade , Biomarcadores/análise , Gammaproteobacteria/classificação , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala , América do Norte , Proteobactérias/classificação , Proteobactérias/genética , Proteobactérias/isolamento & purificação
20.
Physiol Plant ; 166(3): 729-747, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30175853

RESUMO

The study was envisaged to assess the extent of normally uncultivable endophytic bacteria in field papaya plants and in vitro established cultures adopting cultivation vs molecular analysis and microscopy. Surface-sterilized axillary shoot-buds of papaya 'Arka Surya' revealed high bacterial diversity as per 16S rRNA metagene amplicon sequencing (6 phyla, 10 classes, 21 families) with an abundance of Pseudomonas (Gammaproteobacteria), which also formed a common contaminant for in vitro cultured field explants. Molecular analysis of seedling shoot-tip-derived healthy proliferating cultures of three genotypes ('Arka Surya', 'Arka Prabhath', 'Red Lady') with regular monthly subculturing also displayed high bacterial diversity (11-16 phyla, >25 classes, >50 families, >200 genera) about 12-18 months after initial establishment. 'Arka Surya' and 'Red Lady' cultures bore predominantly Actinobacteria (75-78%) while 'Arka Prabhath' showed largely Alphaproteobacteria corroborating the slowly activated Methylobacterium sp. Bright-field direct microscopy on tissue sections and tissue homogenate and epi-fluorescence microscopy employing bacterial DNA probe SYTO-9 revealed abundant intracellular bacteria embracing the next-generation sequencing elucidated high taxonomic diversity. Phylogenetic investigation of communities by reconstruction of unobserved states- PICRUSt- functional annotation suggested significant operational roles for the bacterial-biome. Metabolism, environmental information processing, and genetic information processing constituted major Kyoto Encyclopedia of Genes and Genomes KEGG attributes. Papaya stocks occasionally displayed bacterial growth on culture medium arising from the activation of originally uncultivable organisms to cultivation. The organisms included Bacillus (35%), Methylobacterium (15%), Pseudomonas (10%) and seven other genera (40%). This study reveals a hidden world of diverse and abundant conventionally uncultivable cellular-colonizing endophytic bacteria in field shoots and micropropagating papaya stocks with high genotypic similarity and silent participation in various plant processes/pathways.


Assuntos
Carica/microbiologia , Endófitos/fisiologia , Brotos de Planta/microbiologia , Alphaproteobacteria/genética , Alphaproteobacteria/fisiologia , Bacillus/genética , Bacillus/fisiologia , Endófitos/genética , Genótipo , Methylobacterium/genética , Methylobacterium/fisiologia , Filogenia , Brotos de Planta/genética , Pseudomonas/genética , Pseudomonas/fisiologia , RNA Ribossômico 16S/genética
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