ABSTRACT Microbiologists have been using agar growth medium for over 120 years. It revolutionized microbiology in the 1890s when microbiologists were seeking effective methods to isolate microorganisms, which led successful cultivation of microorganisms as single clones. But there has a disparity between total cell counts and cultivable on plates, often referred “great plate count anomaly,” that long phenomenon still remains unsolved. Here, we report common practice employed prepare hidden...

Symbiosis has significantly contributed to organismal adaptation and diversification. For establishment maintenance of such host-symbiont associations, host organisms must have evolved mechanisms for selective incorporation, accommodation, their specific microbial partners. Here we report the discovery a previously unrecognized type animal organ symbiont sorting. In bean bug Riptortus pedestris, posterior midgut is morphologically differentiated harboring symbiotic bacteria beneficial...

p-Nitrophenol (4-NP) is recognized as an environmental contaminant; it used primarily for manufacturing medicines and pesticides. To date, several 4-NP-degrading bacteria have been isolated; however, the genetic information remains very limited. In this study, a novel 4-NP degradation gene cluster from gram-positive bacterium, Rhodococcus opacus SAO101, was identified characterized. The deduced amino acid sequences of npcB, npcA, npcC showed identity with phenol 2-hydroxylase component B...

ABSTRACT The tfd genes of Ralstonia eutropha JMP134 are the only well-characterized set responsible for 2,4-dichlorophenoxyacetic acid (2,4-D) degradation among 2,4-D-degrading bacteria. A new family 2,4-D genes, cadRABKC , was cloned and characterized from Bradyrhizobium sp. strain HW13, a that isolated buried Hawaiian soil has never experienced anthropogenic chemicals. cadR gene inferred to encode an AraC/XylS type transcriptional regulator its deduced amino sequence. cadABC were predicted...

Most microorganisms living in the environment have yet to be cultured, owing at least part their slow and poor propagation properties susceptibility oxidative stress. Our previous studies demonstrated that a simple modification preparation of agar media, i.e., autoclaving phosphate separately (termed "PS" medium), can greatly improve culturability by mitigating stress compared with use "PT" medium (autoclaving together). Here, we attempted isolate phylogenetically novel bacteria combining PS...

ABSTRACT Benzoate catabolism is thought to play a key role in aerobic bacterial degradation of biphenyl and polychlorinated biphenyls (PCBs). catabolic genes were cloned from PCB degrader, Rhodococcus sp. strain RHA1, by using PCR amplification temporal temperature gradient electrophoresis separation. A nucleotide sequence determination revealed that the deduced amino acid sequences encoded RHA1 benzoate genes, benABCDK , exhibit 33 65% identity with those Acinetobacter ADP1. The gene...

To establish a host-bacterium symbiotic association, number of factors involved in symbiosis must operate coordinated manner. In insects, bacterial for have been poorly characterized at the molecular and biochemical levels, since many symbionts not yet cultured or are as genetically intractable. Recently, association between stinkbug, Riptortus pedestris, its beneficial gut bacterium, Burkholderia sp., has emerged promising experimental model system, providing opportunities to study insect...

Abstract Aurachin RE is a prenylated quinoline antibiotic that was first isolated from the genus Rhodococcus . It shows potent antibacterial activity against variety of Gram‐positive bacteria. Here we have identified minimal biosynthesis gene cluster for aurachin in erythropolis JCM 6824 by using random transposon mutagenesis and heterologous production. The ( rau ) consists genes encoding cytochrome P450 rauA ), prenyltransferase, polyketide synthase, farnesyl pyrophosphate as well others...

Abstract Interest in the interaction of microorganisms with cesium ions (Cs + ) has arisen, especially terms their potent ability for radiocesium bioaccumulation and important roles biogeochemical cycling. Although high concentrations Cs display toxic effects on microorganisms, there have been only limited reports -tolerant microorganisms. Here we report enrichment isolation from soil microbiota. Microbial community analysis revealed that bacteria within phylum Bacteroidetes , Flavobacterium...

To address the multiplicity of aromatic ring hydroxylation dioxygenases, we used PCR amplification and denaturing gradient gel electrophoresis (DGGE). The amplified DNA fragments separated into five bands, A to E. Southern hybridization analysis RHA1 total using probes for each band showed that C originated from a couple homologous genes. nucleotide sequences bands A, C, E would be parts new dioxygenase genes in RHA1. That B agreed with bphA1 gene, which was characterized previously. D did...

A total of 15 Rhodococcus erythropolis strains were characterized as antibiotic producers and classified into three groups according to their spectrum growth compatibility (strains within a group did not inhibit each other's growth). Each the exhibited activity against taxonomically different breadth bacteria: Group I broad range Gram-positives; II, mainly genus some other III, particularly R. erythropolis. The compounds belonging Groups II partially purified from liquid culture media. It...

The emergence of multiple-antibiotic-resistance bacteria is increasing, which a particular concern on livestock farms. We previously isolated 1,347 antimicrobial-resistant (AMR) Escherichia coli strains from the feces beef cattle 14 Japanese In present study, genetic backgrounds and phylogenetic relationships 45 AMR isolates were characterized by chromosome phylotype, phenotype, genotype, plasmid type. These classified into five phylotypes, closely linked to farms they isolated, suggesting...

Codon optimization by synonymous substitution is widely used for recombinant protein expression. Recent studies have investigated sequence features codon based on large-scale expression analyses. However, these been limited to common host organisms such as Escherichia coli. Here, we develop a method Rhodococcus erythropolis, gram-positive GC-rich actinobacterium attracting attention an alternative organism. We evaluate the of 204 genes in R. erythropolis with same plasmid vector. The...

Although the bioavailability of rare earth elements (REEs, including scandium, yttrium, and 15 lanthanides) has not yet been examined in detail, methane-oxidizing bacteria (methanotrophs) were recently shown to harbor specific types methanol dehydrogenases (XoxF-MDHs) that contain lanthanides their active site, whereas well-characterized counterparts (MxaF-MDHs) Ca2+-dependent. However, lanthanide dependency methanotrophs demonstrated, except acidic environments which solubility is high. We...

Rhodococcus has been extensively studied for its excellent ability to degrade artificial chemicals and capability synthesize biosurfactants antibiotics. In recent years, studies have attempted use as a gene expression host. Various genetic tools, such plasmid vectors, transposon mutagenesis, disruption methods developed in Rhodococcus; however, no effective method reported performing large-size genome reduction. Therefore, the present study an plasmid-curing using levansucrase-encoding sacB...

It is well-known that most of environmental microorganisms do not form colonies on agar medium despite the commonly used solidified medium. We previously demonstrated negative effects H 2 O generation during preparation colony formation.

Functional variation of Rpf, a growth factor found exclusively in Actinobacteria, is differentiated by its source and amino acid sequences. Only purified Rpf proteins from three species have been studied so far. To seek new Rpfs for use future studies to understand their role the objective this study was identify rpf gene homologs Tomitella biformata AHU 1821(T), novel Actinobacteria isolated permafrost ice wedge. Amplification using degenerate primers targeting essential domain led...

The cytochrome P450 RauA from Rhodococcus erythropolis JCM 6824 catalyzes the hydroxylation of a nitrogen atom in quinolone ring aurachin, thereby conferring strong antibiotic activity on aurachin alkaloid. Here, we report crystal structure complex with its substrate, biosynthetic intermediate RE. Clear electron density showed that is oriented parallel to porphyrin plane heme cofactor, while farnesyl chain curls into U‐shape topology and buried inside solvent‐inaccessible hydrophobic...

Supplementation with conductive magnetite particles promoted methanogenic acetate degradation by microbial communities enriched from the production water of a high-temperature petroleum reservoir. A community analysis revealed that Petrothermobacter spp. (phylum Deferribacteres), known as thermophilic Fe(III) reducers, predominated in magnetite-supplemented enrichment, whereas other types such Thermincola and Thermotoga spp., were dominant under ferrihydrite-reducing conditions. These...

The quinoline antibiotics aurachins C, D, and L, a structurally simplified analog of aurachin C were synthesized from 1-(2-nitrophenyl)butane-1,3-dione via reductive cyclizations δ-nitro ketone intermediates, with zinc or iron as key steps. results antimicrobial tests indicate that the N-hydroxyquinolone nucleus mimics electron carrier in respiratory chain more strongly than N-oxide nucleus.

We previously demonstrated that a simple modification in the preparation of agar media, i.e., autoclaving phosphate and separately (termed "PS protocol"), improved culturability aerobic microorganisms by reducing generation reactive oxygen species. herein investigated effects PS protocol on cultivation anaerobic using sludge from wastewater treatment system as microbial source. The application increased colony numbers frequency phylogenetically novel isolates under aerobic, nitrate...

Resuscitation-promoting factor (Rpf) is a protein that has been found in number of different Actinobacteria species and shown to promote the growth active cells resuscitate dormant (non-dividing) cells. We previously reported biological activity an Rpf Tomitella biformata AHU 1821T, isolated from permafrost ice wedge. This excreted outside cell; however, few studies have investigated its contribution environmental samples or resuscitation bacteria other than original host. Therefore, aim...