Bergey's Manual Research Articles

CHITINASE AND CHITINOLYTIC MICROORGANISM : ISOLATION, CHARACTERIZATION AND POTENTIAL

Chitinase is enzyme that hydrolyzes chitin, a polimer of b-1,4-N-Acetilglucosamine which is the most abundant natural resource after cellulose. Chitinolytic microorganism can be found in environment like soil and water that contain chitin, or in extreme environment which is known as thermofilic microorganism. Chitinolytic microorganism is identified by recognizing the morphological and physiological properties based on Bergey's Manual of Systematic Bacteriology. The sequence data of the 16S rRNA genes is determinated in the GeneBank nucleotide sequence database. Chitinase activity can be qualitatively determined from the clearance zone around the colony formed in agar medium containing colloidal chitin. Chitinase can be utilized as biocontrol agent and derivate chitin as the result of chitinase degradation which can be used in the fieltd of health, food, industry and waste management Keywords: Biocontrol, chitin, chitinase, chitinolytic microorganism

The Pseudomonas Story

The <i>Pseudomonas</i> Story

Incidence and Severity of Crown Gall Disease of Cherry, Apple and Apricot Plants Caused by Agrobacterium tumefaciens in Nagar Valley of Gilgit-Baltistan, Pakistan

The crown gall is a world wide tumor forming disease of the plants and are a major problem for plant nursery industries. This disease is caused by pathogenic species of soil borne bacteria Agrobacterium and cause great economic loss in fruit plants. From July to November in 2008 an extensive survey was conducted in five villages (Chalt, Skindarabad, Gulmit, Askurdas and Nagarkhas) of the Nagar valley of Gilgit- Baltistan randomly by walking in a zigzag pattern and examined the plants for typical curly top symptoms to determine the incidence and severity of crown gall on cherry, apple and apricot plants. A total of 6100 cherry, 6900 apple and 8000 apricot plants were inspected and the mean incidence of crown gall on cherry plants was found to be 5360 (87.87%), apple plants 6069 (87.96%) and in apricot plants 00 (00.00%). In cherry plants, the severity of the disease observed varied from 33.80-40% in mild, 20-34.49% in moderate and 27.85-40% in severe. While in the apple plants it varied from 36.81-42.5% in mild, 29.14-34.49% in moderate and 27-30.31% in severity. There was no infestation of crown gall in apricot plants. A total of 35 samples (15 soil samples; 1 from each orchard of each village and 20 tumor samples; 2 from each orchard of cherry and apple infected plants) from each inspected village were cultured on modified selective medium (3- Ketolactose agar). The growth of Agrobacterium tumefaciens was identified on the basis of colon y characteristics and biochemical tests based on Bergey's Manual of determinative Bacteriology. A 100 % infestation of A. tumefaciens was observed from both the plant and soil samples except for the soil sample cultures from the apricot orchard. All the 30 A. tumefaciens strains isolated from the soil specimens and infected cherry and apple plant tumors were tested against six different antibiotics by disc diffusion method. All the strains were resistant against Lincomycin, Amoxycillin, Ampincillin and Cloxacillin while Cephradine, Tetracycline and Dioxycycline, showed intermediate sensitivity.

토양으로부터 분리한 Bacillus licheniformis KJ 9의 특성

고품질의 발효퇴비를 생산할 목적으로 자연계로부터 효소활성이 높고 식물병원성 균주에 대한 항균활성이 우수한 미생물을 순수분리 하여 배양학적 특성을 검토하였다. 부엽토 등으로부터 CMCase, protease 및 chitinase 활성이 높고 식물병원성 균주에 대하여 항균활성이 우수한 KJ-9균주를 분리한 다음 형태학적 및 생화학적 특성을 검토하고 Bergey's Mannual of Systematic Bacteriology의 방법과 ATB (Automated Identification) computer system (Bio Merieux, France)을 이용한 API 50 CHL Carbohydrate Test Kit(Bio Merieux, France)를 통하여 동정한 결과 Bacillus licheniformis로 밝혀졌다. B. licheniformis KJ-9의 최적배지 성분을 검토한 결과 탄소원은 1.5% soluble starch, 질소원은 0.5% yeast extract, 무기염은 0.05% <TEX>$MgSO_4{\cdot}7H_2O$</TEX> 이었으며, 배지의 초기 pH는 7.0, 배양온도는 <TEX>$50^{\circ}C$</TEX> 그리고 진탕속도는 180 rpm으로 밝혀졌다. 최적배양 조건으로 B. licheniformis KJ-9를 배양하였을 때 36~60 hr째의 배양액은 잿빛 곰팡이병을 유발하는 Botrytis cinerea, 잎마름병의 원인균인 Corynespora cassicola, 시들음병을 유발하는 Fusarium oxysporum, 잘록병의 원인균인 Rhizocfonia solani의 식물병원성 미생물 균사생장을 효과적으로 억제하였다. In order to produce high-quality fermenting composts, a microorganism was isolated from the natural world. The bacterium has not only in high enzyme activities but also had good antimicrobial activities against phytopathogenic microorganisms. Its cultivating characteristics were then investigated. Bacterium KJ-9, which contains high CMCase, protease and chitinase activities and excellent antimicrobial activities against phytopathogenic microorganisms, was separated from leaf mold and identified as Bacillus licheniformis by two methods: Bergey's Manual of Systematic Bacteriology and API 50 CHL Carbohydrate Test Kit (Bio Merieux, France) using an ATB (Automated Identification) computer system (Bio Merieux, France). Optimal medium for cultivation of B. licheniformis was 2% soluble starch as a carbon source, 0.5% yeast extract as a nitrogen source and 0.05% <TEX>$MgSO_4{\cdot}7H_2O$</TEX>. Optimal growth conditions of pH, temperature and shake speed were pH 7.0, <TEX>$50^{\circ}C$</TEX> and 180 rpm, respectively. Culture broth of B. licheniformis KJ-9 cultured for 36~60 hr was effective in fungicidal activities against plant pathogens including Botrytis cinerea, Corynespora cassicola, Fusarium oxysporum, and Rhizoctonia solani.

HETEROGENEITY OF THE CYANOBACTERIAL GENUS SYNECHOCYSTIS AND DESCRIPTION OF A NEW GENUS, GEMINOCYSTIS(1).

The study and revision of the unicellular cyanobacterial genus Synechocystis was based on the type species S. aquatilis Sauv. and strain PCC 6803, a reference strain for this species. Uniformity in rRNA gene sequence, morphology, and ultrastructure was observed in all available Synechocystis strains, with the exception of the strain PCC 6308, which has been considered by some to be a model strain for Synechocystis. This strain differs substantially from the typical Synechocystis cluster according to both molecular (<90% of similarity, differences in 16S-23S rRNA internal transcribed spacer [ITS] secondary structure) and phenotypic criteria (different ultrastructure of cells). This strain is herein classified into the new genus Geminocystis gen. nov., as a sister taxon to the genus Cyanobacterium. Geminocystis differs from Cyanobacterium by genetic position (<94.4% of similarity) and more importantly by its different type of cell division. Because strain PCC 6308 was designated as a reference strain of the Synechocystis cluster 1 in Bergey's Manual, the members of this genetic cluster have to be revised and reclassified into Geminocystis gen. nov. Only the members of the Synechocystis cluster 2 allied with PCC 6803 correspond both genetically and phenotypically to the type species of the genus Synechocystis (S. aquatilis).

IDENTIFICATION OF CELLULOLYTIC BACTERIA ISOLATED FROM THE TERMITE COPTOTERMES CURVIGNATHUS (HOLMGREN)

ABSTRACT The aim of the present research was to isolate and identify cellulolytic bacteria from the gut of the local termite Coptotermes curvignathus (Holmgren) present in the vicinity of the University of Putra Malaysia. The isolates were cultured in a medium containing carboxymethyl‐cellulose and cellobiose. The bacterial species were tentatively identified by using the Biolog reader as well as the Bergey's manual and later confirmed by 16S rRNA sequence homology. The species were all novel strains and identified as Bacillus cereus strain Razmin A, Enterobacter aerogenes strain Razmin B, Enterobacter cloacae strain Razmin C, Chryseobacterium kwangyangense strain Cb and Acinetobacter strain Raminalimon. Biolog reader was not able to identify one of the bacterial species in which it was identified as C. kwangyangense strain Cb by 16S rRNA sequence homology. The GenBank NCBI/EMBL accession numbers for the bacterial strains are EU294508, EU305608, EU305609, EU169201 and EU332791 for B. cereus Razmin A, E. aerogenes strain Razmin B, E. cloacae strain Razmin C, C. kwangyangense strain Cb and Acinetobacter strain Raminalimon, respectively.PRACTICAL APPLICATIONSThe experiment describes the isolation and identification of cellulolytic bacteria from termites, using Biolog reader and polymerase chain reaction technique. Termites are common insects in tropical regions and thrive on wood and cellulolytic materials. Hence, the bacteria isolated may be useful in the degradation of cellulosic materials to increase their digestibility and possibly production of metabolites and enzymes.

「Bergey's Manual of Systematic Bacteriology第1版」に記載された分類とその後の分類の異同―グラム陽性菌

「Bergey's Manual of Systematic Bacteriology第1版」に記載された分類とその後の分類の異同―グラム陽性菌

Biodegradability and degrading microbes of low‐density polyethylene

AbstractWe have isolated and identified three types of low‐density polyethylene (LDPE) degrading microbes, for the first time, from soil which was sampled from the field. It has been studied that thermooxidized or UV irradiation LDPE are degraded when incubated with mold (Volke‐sepulveda et al., J Appl Polym Sci 2002, 83, 305; Yamada‐Onodera et al., Polym Degrad Stab 2001, 72, 323); however, there was no article so far reporting the isolation of these particular microbes from the environment. Here, the mechanism of biodegradation of LDPE by the three microbes is described. We used LDPE film, which was buried in soil and biodegraded, and the surrounding soil, located at Nogi Town, Tochigi Prefecture, Japan as the sources of sample for this study. The sample was added to a liquid medium, together with powder of a photodegraded, antioxidant‐free LDPE film, as the sole source of carbon. After enriched cultivation, three strains of microbes were separated from the medium. They were classified on the basis of LDPE degrading capabilities, confirmed by OH generation and degradation traces. Using “Bergey's Manual of Determinative Bacteriology,” the genera of the microbes were identified as Bacillus circulans, Bacillus brevies, and Bacillus sphaericus, which belong among the Natto bacteria, common in soil. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009

Identification of Mycobacterium species using reversed-phase high performance liquid chromatographic analysis of mycolic acid

A method for the identification of Mycobacterium species using reversed-phase high performance liquid chromatography (RP-HPLC) was developed. The fingerprints library was constructed on the basis of RP-HPLC chromatograms of the mycolic acids derivatives from 49 Mycobacterium species cultures. Two inoculation loops of Mycobacterium, for fast growth with one week incubation or for slow growth with three weeks incubation, were saponified for 1 h and stocked at 4 degrees C. The mycolic acids from each culture of Mycobacterium species were acidified, extracted, derivatized, and analyzed by the RP-HPLC method. On the basis of the HPLC patterns of relative retention time and relative peak height, the identifications of Mycobacterium species were performed. This established method has a good precision of retention times with the relative standard deviations (RSDs) ranging from 0.13% to 1.07%. The mycolic acids fingerprints library of HPLC patterns was set up, including 49 species that were recorded in "Bergey's Manual of Systematic Bacteriology". Three patterns were observed from the chromatographic behaviors of mycolic acids derivatives, including single peak-cluster, double peak-clusters, triple and multiple peak-clusters. Forty-one species were successfully identified according to the different relative retention times of the peaks and the relative peak heights. The established method can identify Mycobacterium species with rapidity and high reliability.

Isolamento de coliformes, estafilococos e enterococos de leite cru provenientes de tanques de refrigeração por expansão comunitários: identificação, ação lipolítica e proteolítica

Isolation and identification of microorganisms in raw milk is interesting from the viewpoint of public health, since, depending on the species isolated, directed actions may be taken to improve milk quality. Milk deterioration is mainly the result of the growth of psychrotrophic microorganisms that produce heat-resistant lipases and proteases which are not denatured during pasteurization, conferring rancid and sour flavors, respectively. Thus, this work aimed at isolating and identifying the main genera of bacteria belonging to the Enterobacteriaceae family, oxidase-positive Gram-negative, Staphylococcus and Enterococcus genera, as well as determining lipase and protease activity in 16 rural farms in Boa Esperanca-MG, Brazil. The Gram-negative bacteria were isolated in Eosin Methylene Blue (EMB) and Hektoen Enteric agar media. Staphylococci were isolated in Baird-Parker agar and Enterococcus in KF agar. Colonies of interest were collected and submitted to Gram stain and to catalase and oxidase tests. Following these procedures, the isolates selected were identified using Bactray I, II and III; Api 20 Strep and tests suggested by Bergey's Manual of Determinative Bacteriology. Sorological identification of Enterococcus was carried out using Prolex. Milk from the 16 rural properties contained strains of fecal microorganisms, such as Escherichia coli and Enterococcus from the Lancefield D group. Oxidase-positive Gram-negative bacteria were identified in five farms. Staphylococcus was found in 10 farms. Milk collected from the farms investigated contained microorganisms that compromise its quality. All the microorganism groups tested showed lipase and protease activities.

「Bergey's Manual of Systematic Bacteriology第1版」に記載された分類とその後の分類の異同―グラム陰性菌

「Bergey's Manual of Systematic Bacteriology第1版」に記載された分類とその後の分類の異同―グラム陰性菌

International Society of Microbial Taxonomists

Bergey's Manual Trust is exploring interest among microbiologists in establishing an international society of microbial taxonomists. If you are interested in learning more about this or possibly becoming a charter member, please visit the Trust's Newsletter section (Volume 2, 2008 March and May issues) at our website www.bergeys.org and complete a survey from the May issue to provide input on this proposal.

Reprint of “Nucleic acid techniques in bacterial systematics and identification" [Int. J. Food Microbiol., 120 (2007) 225–236

Systematics and identification play central roles in any discipline of microbiology. The current prokaryotic taxonomic framework as proposed in Bergey's Manual of Systematic Bacteriology is mainly based on small subunit rRNA data. Alternative markers representing the conserved core of the prokaryotic genomes roughly support rRNA based phylogenetic inference. Consequently, many of the nucleic acid based techniques for identification target these molecules: i.e. comparative sequencing, specific probing, diagnostic PCR, and pattern techniques. For studies at species and lower taxonomic ranks, however, alternative less conserved targets have to be chosen. An overview of commonly used targets and methods for identification or differentiation is given below.

A myxobacterium strain Sorangium cellulosum AHB125 producing epothilone B and other anticancer substances

A myxobacterium strain AHB125 belonging to genus Sorangium cellulosum was isolated from Anhui area in China and identified with morphological analysis by electron microscopy and phase contrast microscope according to Bergey's manual of systematic bacteriology (8th Ed.). Its high-antitumor bioactivity metabolites was evaluated by bioassay-directed screening technique with B16 tumor cell line etc. Research results showed that it exhibited not only strong antitumor ability bioactivities and broad-spectrum antitumor abilities to B16, Bel7402, H446, SGC7901 cell lines, but also has selectivity and pertinence to B16 and SGC7901 cell lines. The compound was confirmed as epothilone B by HPLC and LC/MS analysis, compared to the epothilone B standard sample. Bioassay indicated that there were other high-bioactive substances in the metabolites.

Phylogenetic systematics of microorganisms inhabiting thermal environments

Thermal habitats harbor specialized communities of thermophilic microorganisms, primarily prokaryotes. This review considers modern systematics of prokaryotes and the place of thermophilic archaea and bacteria in it. Among the existing hierarchical classifications of prokaryotes, the bulk of attention is given to the one accepted in the current second edition of "Bergey's Manual of Systematic Bacteriology", which is primarily based on 16S rRNA phylogeny and phenotypic properties of the organisms. Analysis of the genomics data shows that they on the whole agree with the 16S rRNA-based system, although revealing the significance of the evolutionary role of lateral transfer, duplication, and loss of genes. According to the classification elaborated in the current edition of "Bergey's Manual", the prokaryotes currently culturable under laboratory conditions are distributed among 26 phyla, two of which belong to the domain Archaea and 24 to the domain Bacteria. Six phyla contain exclusively thermophiles, and eleven phyla contain thermophiles along with mesophiles, thermophiles being usually separated phylogenetically and representing high-level taxa (classes, orders). In light of the data on the topology of the 16S rRNA-based phylogenetic tree and some other data, this review discusses the probable hyperthermophilic nature of the universal common ancestor.

Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology

We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacteriologists' taxonomy--primarily the latest online Outline of the Bergey's Manual of Systematic Bacteriology. The CVTree phylogeny agrees very well with the Bergey's taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences.

Molecular Detection of Streptomyces griseus Isolated from Isfahan Soil

The aim of the present study was to detect Streptomyces griseus from Isfahan soil using biochemical, morphological and molecular techniques. Soil samples were collected from different regions (compost, 50 year old garden, river bed, clove, wheat farms and domestic yards) of Isfahan in two different seasons. One gram of each sample was serially diluted and cultivated in a primary isolation medium. Morphological shapes of colonies and vegetative hyphae were initially used to separate the grown bacteria of the samples. Various biochemical tests based on Bergey's manual of systemic bacteriology were performed to separate the Streptomyces from other related Genera. In order to further separate Streptomyces grisesus, Polymerase Chain Reaction (PCR) was used to detect the presence of aphE and strA genes in isolated colonies. Biochemical and morphological results, showed the presence of several species of Streptomyces in the collected samples. The expected band of 924 bp belonging to strA gene was observed in the positive control bacterial DNA (PTCC 1125). Several other bands were also observed in the positive control sample. From the total of 10 colonies that undergone molecular detection for the presents of strA gene, 6 colonies (W1, W3, W5, F4, F5, F26) showed only one band at 750 bp and four (W1, W3, F5, F26) showed an extra band of approximately 924 bp band as well. The expected band of 671 bp belonging to aphE gene was detected in positive control bacterial DNA (PTCC 1125). None of the soil samples, however, showed the presence of the aphE gene (data not shown).

Nucleic acid techniques in bacterial systematics and identification

Systematics and identification play central roles in any discipline of microbiology. The current prokaryotic taxonomic framework as proposed in Bergey's Manual of Systematic Bacteriology is mainly based on small subunit rRNA data. Alternative markers representing the conserved core of the prokaryotic genomes roughly support rRNA based phylogenetic inference. Consequently, many of the nucleic acid based techniques for identification target these molecules: i.e. comparative sequencing, specific probing, diagnostic PCR, and pattern techniques. For studies at species and lower taxonomic ranks, however, alternative less conserved targets have to be chosen. An overview of commonly used targets and methods for identification or differentiation is given below.

The genius of Roger Stanier

The genius of Roger Stanier

低密度ポリエチレン分解能を有する微生物の同定

Three types of low density polyethylene (LDPE)-degrading microbes were discovered, and unambiguous evidence for biodegradation of LDPE was presented. Pieces of LDPE film, buried and biodegraded, and their surrounding soil were used as the source of microbes. Powder of a photo-degraded and antioxidant-free LDPE film was added as the sole source of carbon in the liquid medium. From the medium that underwent enriched cultivation, three strains of microbes were separated. They were classified on the basis of LDPE-degrading capabilities, confirmed by -OH generation and degradation traces. Using “Bergey's Manual of Determinative Bacteriology”, the genuses of the microbes were identified as Bacillus circulans, Bacillus brevies, Bacillus sphaericus, which belong among the natto bacteria, common in soil. Their degrading ability was confirmed on LDPE film previously photo-degraded by outdoor exposure for six weeks. After three months of cultivation, we identified the existence of body marks on the film surface, which are characteristic of microbial biodegradation.