scholarly journals Isolation and characterization of a novel bacterial strain from a Tris-Acetate-Phosphate agar medium plate of the green micro-alga Chlamydomonas reinhardtii that can utilize common environmental pollutants as a carbon source

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 656 ◽  
Author(s):  
Mautusi Mitra ◽  
Kevin Manoap-Anh-Khoa Nguyen ◽  
Taylor Wayland Box ◽  
Jesse Scott Gilpin ◽  
Seth Ryan Hamby ◽  
...  
Keyword(s):  
Carbon Source ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Chlamydomonas Reinhardtii ◽  
Bacterial Strain ◽  
Sole Carbon Source ◽  
Agar Medium ◽  
Environmental Pollutants ◽  
Rrna Gene ◽  
Motor Oil

Background: Chlamydomonas reinhardtii, a green micro-alga can be grown at the lab heterotrophically or photo-heterotrophically in Tris-Phosphate-Acetate (TAP) medium which contains acetate as the sole carbon source. When grown in TAP medium, Chlamydomonas can utilize the exogenous acetate in the medium for gluconeogenesis using the glyoxylate cycle, which is also present in many bacteria and higher plants. A novel bacterial strain, LMJ, was isolated from a contaminated TAP medium plate of Chlamydomonas. We present our work on the isolation and physiological and biochemical characterizations of LMJ. Methods: Several microbiological tests were conducted to characterize LMJ, including its sensitivity to four antibiotics. We amplified and sequenced partially the 16S rRNA gene of LMJ. We tested if LMJ can utilize cyclic alkanes, aromatic hydrocarbons, poly-hydroxyalkanoates, and fresh and combusted car motor oil as the sole carbon source on Tris-Phosphate (TP) agar medium plates for growth. Results: LMJ is a gram-negative rod, oxidase-positive, mesophilic, non-enteric, pigmented, salt-sensitive bacterium. LMJ can ferment glucose, is starch hydrolysis-negative, and is very sensitive to penicillin and chloramphenicol. Preliminary spectrophotometric analyses indicate LMJ produces pyomelanin. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of LMJ showed that it matched to that of an uncultured bacterium clone LIB091_C05_1243. The nearest genus relative of LMJ is an Acidovorax sp. strain. LMJ was able to use alkane hydrocarbons, fresh and combusted car motor oil, poly-hydroxybutyrate, phenanthrene, naphthalene, benzoic acid and phenyl acetate as the sole carbon source for growth on TP-agar medium plates. Conclusions: LMJ has 99.14% sequence identity with the Acidovorax sp. strain A16OP12 whose genome has not been sequenced yet. LMJ’s ability to use chemicals that are common environmental pollutants makes it a promising candidate for further investigation for its use in bioremediation and, provides us with an incentive to sequence its genome.

scholarly journals Isolation and characterization of a novel Sphingobium yanoikuyae strain variant that uses biohazardous saturated hydrocarbons and aromatic compounds as sole carbon sources

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 767
Author(s):  
Mautusi Mitra ◽  
Kevin Manoap-Anh-Khoa Nguyen ◽  
Taylor Wayland Box ◽  
Jesse Scott Gilpin ◽  
Seth Ryan Hamby ◽  
...  
Keyword(s):  
Carbon Source ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Aromatic Compounds ◽  
Agar Medium ◽  
Carbon Sources ◽  
Future Research ◽  
Rrna Gene ◽  
Saturated Hydrocarbons ◽  
Isolation And Characterization

Background: Green micro-alga, Chlamydomonas reinhardtii (a Chlorophyte), can be cultured in the laboratory heterotrophically or photo-heterotrophically in Tris-Phosphate-Acetate (TAP) medium, which contains acetate as the carbon source. Chlamydomonas can convert acetate in the TAP medium to glucose via the glyoxylate cycle, a pathway present in many microbes and higher plants. A novel bacterial strain, CC4533, was isolated from a contaminated TAP agar medium culture plate of a Chlamydomonas wild type strain. In this article, we present our research on the isolation, and biochemical and molecular characterizations of CC4533. Methods: We conducted several microbiological tests and spectrophotometric analyses to biochemically characterize CC4533. The 16S rRNA gene of CC4533 was partially sequenced for taxonomic identification. We monitored the growth of CC4533 on Tris-Phosphate (TP) agar medium (lacks a carbon source) containing different sugars, aromatic compounds and saturated hydrocarbons, to see if CC4533 can use these chemicals as the sole source of carbon. Results: CC4533 is a Gram-negative, non-enteric yellow pigmented, aerobic, mesophilic bacillus. It is alpha-hemolytic and oxidase-positive. CC4533 can ferment glucose, sucrose and lactose, is starch hydrolysis-negative, resistant to penicillin, polymyxin B and chloramphenicol. CC4533 is sensitive to neomycin. Preliminary spectrophotometric analyses indicate that CC4533 produces b-carotenes. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of CC4533 show 99.55% DNA sequence identity to that of Sphingobium yanoikuyae strain PR86 and S. yanoikuyae strain NRB095. CC4533 can use cyclo-chloroalkanes, saturated hydrocarbons present in car motor oil, polyhydroxyalkanoate, and mono- and poly-cyclic aromatic compounds, as sole carbon sources for growth. Conclusions: Taxonomically, CC4533 is very closely related to the alpha-proteobacterium S. yanoikuyae, whose genome has been sequenced. Future research is needed to probe the potential of CC4533 for environmental bioremediation. Whole genome sequencing of CC4533 will confirm if it is a novel strain of S. yanoikuyae or a new Sphingobium species.

Peptoniphilus methioninivorax sp. nov., a Gram-positive anaerobic coccus isolated from retail ground beef

2011 ◽  
Vol 61 (8) ◽  
pp. 1962-1967 ◽  
Author(s):  
Alejandro P. Rooney ◽  
James L. Swezey ◽  
Rüdiger Pukall ◽  
Peter Schumann ◽  
Stefan Spring
Keyword(s):  
Carbon Source ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sole Carbon Source ◽  
Sequence Similarity ◽  
Ground Beef ◽  
Source Analysis ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Gram Positive

Strain NRRL B-23883T was isolated from retail ground beef as part of a study on the genetic diversity of Clostridium perfringens. The strain was found to be a strictly anaerobic, Gram-positive coccus that was able to utilize peptone as a sole carbon source. Analysis of the 16S rRNA gene sequence revealed that the strain was closely related to species within the genera Peptoniphilus and Anaerosphaera, but it was substantially different from the closest recognized species by nearly 10 % sequence divergence. The strain was also found to be closely related (>99 % sequence similarity) to an uncultured bacterial strain that was sequenced from a 16S rRNA gene clone library constructed to characterize the bacterial community of faeces from a captive spotted hyena. Strain NRRL B-23883T shared the peptidoglycan type A4β, l-Orn–d-Glu with members of the genus Peptoniphilus. Further phenotypic analysis revealed that strain NRRL B-23883T was able to utilize glycyl l-methionine as a sole carbon source, in contrast to other species of the genus Peptoniphilus. Therefore, it is proposed that the isolate represents a novel species, Peptoniphilus methioninivorax sp. nov.; the type strain is NRRL B-23883T ( = DSM 22461T).

scholarly journals Algoriphagus faecimaris sp. nov., isolated from coastal sediment

2011 ◽  
Vol 61 (12) ◽  
pp. 2856-2860 ◽  
Author(s):  
Yongxia Li ◽  
Shulin Yan ◽  
Qian Yang ◽  
Zizhong Qi ◽  
Xiao-Hua Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Agar Medium ◽  
Sequence Similarity ◽  
Coastal Sediment ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Marine Agar

A Gram-negative, non-motile, non-sporulating bacterial strain, designated LYX05T, was isolated from coastal sediment of Qingdao, China, on the coast of the Yellow Sea. Strain LYX05T was aerobic and heterotrophic. The strain grew optimally at 37 °C and pH 7.5 and in the presence of 2 % (w/v) NaCl. Colonies were 1–2 mm in diameter, circular, reddish orange and shiny with entire edges on marine agar medium. Cells were rods (0.3–0.5 µm wide and 0.8–1.6 µm long). The dominant fatty acids were iso-C15 : 0 (40.82 %) and C16 : 0 (10.45 %). The DNA G+C content was 42.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LYX05T was phylogenetically related to the members of the genus Algoriphagus and the closest relative was Algoriphagus hitonicola 7-UAHT (95.8 % 16S rRNA gene sequence similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain LYX05T was considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus faecimaris sp. nov. is proposed. The type strain is LYX05T ( = JCM 16561T  = DSM 23095T  = LMG 25474T).

scholarly journals Tumebacillus luteolus sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4107-4112 ◽  
Author(s):  
Jihee Her ◽  
Sathiyaraj Srinivasan ◽  
Sang-Seob Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Agar Medium ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Two strains of Gram-stain-positive, aerobic, spore-forming and rod-shaped bacteria, designated U13T and U14, were isolated from soil of the Ukraine. Comparative analysis of the 16S rRNA gene sequences indicated that these strains belong to the genus Tumebacillus, with the highest 16S rRNA gene sequence similarity with Tumebacillus ginsengisoli Gsoil 1105T (95.48 % and 95.49 %, respectively). Strains U13T and U14 had iso-C15 : 0 and summed features 1 and 4 as the main fatty acids, and were able to grow at pH ranging from pH 5.0 to 9.0 (optimum pH 6.0–7.0), temperatures ranging from 25 to 42 °C (optimum 28–37 °C) and with 0–1 % (w/v) NaCl (optimum 0 %, w/v) on R2A agar medium. Chemotaxonomic data revealed that the cell-wall peptidoglycan type of the two strains was type A1γ (meso-diaminopimelic acid). On the basis of the evidence from this study, strains U13T and U14 represent a novel species of the genus Tumebacillus, for which the name Tumebacillus luteolus sp. nov. is proposed. The type strain is U13T ( = KEMB 7305-100T = JCM 19866T) and a second strain is U14 ( = KEMB 7305-101 = JCM 19867).

scholarly journals Penapisan Bakteri Penghambat Fusarium yang Diisolasi dari Cairan Kantung Semar (Nepenthes sp.)

2020 ◽  
Vol 25 (4) ◽  
pp. 627-635
Author(s):  
Siti Meliah ◽  
Annisa Wahyu Hardiyanti ◽  
Ni’ma Haida ◽  
Gita Azizah Putri ◽  
Erny Qurotul Ainy
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Agar Medium ◽  
Cultivated Plants ◽  
Rrna Gene ◽  
Malt Extract ◽  
Bacterial Isolates ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Fusarium Sp

The genus Fusarium sp. is a pathogenic fungal for many cultivated plants. The bacteria isolated from monkey cup (Nepenthes sp.) fluid possess the ability to produce hydrolytic enzyme, such as chitinase which can be utilized to inhibit the growth of mycelia of pathogenic fungi. The aims of this study are to isolate bacteria from monkey cup liquid, to test their abilities to produce protease, chitinase, and cellulase, as well as their abilities to inhibit Fusarium. The bacteria were isolated using serial dilution method on Reasoner’s 2A agar medium. Enzymatic activities of bacterial isolates were determined by inoculating them on tested medium supplemented with casein protein, chitin, and cellulose, whereas their antifungal activities were assayed using a direct confrontation method between tested bacterial isolates and pathogenic fungal on Malt Extract Agar medium. Molecular identification of bacteria with antifungal activity was performed by analyzing the 16S rRNA gene sequences. Isolation process of bacteria from monkey cup fluid resulted in 99 bacterial isolates with the ability to produce either protease, chitinase, and/or cellulose enzymes. A total of 37 bacterial isolates were capable of producing at least two hydrolytic enzymes. Antifungal assay of those bacteria showed that as many as 25 isolates have the ability to inhibit the growth of Fusarium sp. Based on the analysis of 16S rRNA gene sequences revealed that those isolates were closely related to three Burkholderia species, namely B. arboris, B. contaminans, and B. rijonensis. Keywords: antifungal, Burkholderia, chitinase, cellulaseN, epenthes, protease

scholarly journals Cellulolytic enzyme-producing thermophilic Actinobacteria isolated from the soil of Cisolok Geysers, West Java, Indonesia

2019 ◽  
Vol 20 (11) ◽  
Author(s):  
PUTRI PRATIWI SETYANINGSIH ◽  
FITRIA NINGSIH ◽  
MAZYTHA KINANTI RACHMANIA ◽  
WINDA AYU SYAFITRI ◽  
DHIAN CHITRA AYU FITRIA SARI ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Agar Medium ◽  
Cellulose Hydrolysis ◽  
Cellulolytic Enzyme ◽  
Rrna Gene ◽  
Cellulolytic Activity ◽  
West Java ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Abstract. Setyaningsih PP, Ningsih F, Rachmania MK, Syafitri WA, Sari DCAF, Yabe S, Yokota A, Oetari A, Sjamsuridzal W. 2019. Cellulolytic enzyme-producing thermophilic Actinobacteria isolated from the soil of Cisolok Geysers, West Java, Indonesia. Biodiversitas 20: 3134-3141. This study investigated 17 thermophilic Actinobacteria isolated from the soil of geysers in the Cisolok geothermal area, West Java, as potential producers of cellulase. Screening for cellulase was performed on minimal (Mm) agar medium with and without the addition of 1% (w/v) carboxymethylcellulose (CMC) and microcrystalline cellulose (MCC), then incubated at 45, 50, 55 and 60°C for up to 7 days. Formation of clear zones around colonies indicated cellulose hydrolysis. The results showed that 15, 14, 4, and 3 isolates showed cellulolytic activity on CMC agar medium at 45, 50, 55, and 60°C, respectively, after 7 days of incubation. Three potential isolates showed cellulolytic activity on MCC agar medium after being incubated for 7 days at 45°C. Molecular identification based on the 16S rRNA gene was performed for three isolates with positive cellulolytic activity at 60°C. The results showed that the three isolates are closely related to Actinomadura keratinilytica WCC-2265T with 99.93-100% sequence similarities. A phylogenetic tree based on 16S rRNA gene sequences confirmed that the three isolates were clustered together with Actinomadura keratinilytica WCC-2265T with 100% bootstrap value. The tree also showed that cellulase producers and non-cellulase producers in Thermomonosporaceae are grouped into different clades.

scholarly journals Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga.

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 533
Author(s):  
Mautusi Mitra ◽  
Kevin Manoap-Anh-Khoa Nguyen ◽  
Taylor Wayland Box ◽  
Taylor Lynne Berry ◽  
Megumi Fujita
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Chlamydomonas Reinhardtii ◽  
Metal Tolerance ◽  
Heavy Metal Tolerance ◽  
Rrna Gene ◽  
Isolation And Characterization ◽  
Bacterial Cell Membrane

Background: Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.

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