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 Mucilaginibacter polysacchareus sp. nov., an exopolysaccharide-producing bacterial species isolated from the rhizoplane of the herb Angelica sinensis

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 632-637 ◽  
Author(s):  
Song-Ih Han ◽  
Hyo-Jin Lee ◽  
Hae-Ran Lee ◽  
Ki-Kwang Kim ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Bacterial Species ◽  
Angelica Sinensis ◽  
Rrna Gene ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three exopolysaccharide-producing bacteria, designated strains DRP28T, DRP29 and DRP31, were isolated from the rhizoplane of Angelica sinensis from the Geumsan, Republic of Korea. Cells were straight rods, Gram reaction-negative, aerobic, non-motile, and catalase- and oxidase- positive. Flexirubin-type pigments were absent. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities to strains of recognized species of the genus Mucilaginibacter were 93.8–97.4 %. The major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The strains contained MK-7 as the major isoprenoid quinone. Strains DRP28T, DRP29 and DRP31 formed a single, distinct genomospecies with DNA G+C contents of 41.9–42.7 mol% and DNA hybridization values of 82.6–86.8 %; the strains exhibited DNA–DNA hybridization values of only 20.4–41.3 % with related species of the genus Mucilaginibacter. On the basis of evidence presented in this study, strains DRP28T, DRP29 and DRP31 were considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter polysacchareus sp. nov. is proposed. The type strain is DRP28T ( = KACC 15075T  = NBRC 107757T).

scholarly journals Mesorhizobium robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia

2010 ◽  
Vol 60 (11) ◽  
pp. 2552-2556 ◽  
Author(s):  
Ping Fa Zhou ◽  
Wei Min Chen ◽  
Ge Hong Wei
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Robinia Pseudoacacia ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Previously, five rhizobial strains isolated from root nodules of Robinia pseudoacacia were assigned to the same genospecies on the basis of identical 16S rRNA gene sequences and phylogenetic analyses of the nodA, nodC and nifH genes, in which the five isolates formed a well-supported group that excluded other sequences found in public databases. In this study, the 16S rRNA gene sequence similarities between the isolates and Mesorhizobium mediterraneum UPM-Ca36T and Mesorhizobium temperatum SDW018T were 99.5 and 99.6 %, respectively. The five isolates were also different from defined Mesorhizobium species using ERIC fingerprint profiles and they formed a novel Mesorhizobium lineage in phylogenetic analyses of recA and atpD gene sequences. DNA–DNA relatedness values between the representative strain, CCNWYC 115T, and type strains of defined Mesorhizobium species were found to be lower than 47.5 %. These results indicated that the isolates represented a novel genomic species. Therefore, a novel species, Mesorhizobium robiniae sp. nov., is proposed, with type strain CCNWYC 115T (=ACCC 14543T =HAMBI 3082T). Strain CCNWYC 115T can form effective nodules only on its original host.

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 Flavobacterium nitrogenifigens sp. nov., isolated from switchgrass (Panicum virgatum)

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2803-2809 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Jia Xu ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Panicum Virgatum ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A yellow, nitrogen-fixing bacterial strain, NXU-44T, isolated from the rhizosphere of switchgrass (Panicum virgatum) in Auburn, Alabama, USA, was studied to determine its taxonomic position. Cells of the isolate were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Flavobacterium with highest sequence similarities to the type strains of Flavobacterium ginsenosidimutans (97.9 %), Flavobacterium phragmitis (97.6 %) and Flavobacterium anhuiense (97.5 %). The 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were below 97.5 %. The fatty acid profile of strain NXU-44T consisted of the major fatty acids iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c and iso-C17 : 0 3-OH. The major compounds in the polar lipid profile were phosphatidylethanolamine, phosphatidylserine, one aminolipid and two polar lipids. The quinone system was composed exclusively of menaquinone MK-6. The polyamine pattern contained the major compound sym-homospermidine and only minor amounts of other polyamines. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. These data and the differential biochemical and chemotaxonomic properties show that strain NXU-44T represents a novel species of the genus Flavobacterium for which the name Flavobacterium nitrogenifigens sp. nov. is proposed. The type strain is NXU-44T ( = LMG 28694T = CIP 110894T).

scholarly journals Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4508-4513 ◽  
Author(s):  
Ji-Quan Sun ◽  
Min Liu ◽  
Xin-Ying Wang ◽  
Lian Xu ◽  
Xiao-Lei Wu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Northern China ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Genotypic Characteristics ◽  
The 16S Rrna Gene ◽  
Sequence Similarities ◽  
Suaeda Corniculata

A Gram-stain-negative, non-motile, non-spore-forming bacterium, designated T47T, was isolated from saline soil of the Suaeda corniculata rhizosphere, located on the bank of Wuliangsuhai Lake, Inner Mongolia, northern China. Strain T47T could grow at 10–40 °C (with 30 °C the optimal temperature), pH 6.0–8.0 (optimal pH 6.0) and in the presence of 0–6.0 % (w/v) NaCl [optimal 0–1.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain T47T formed a stable clade with Sphingobacterium composti 4M24T, Sphingobacterium bambusae IBFC2009T, Sphingobacterium paludis S37T and Sphingobacterium wenxiniae LQY-18T, with the 16S rRNA gene sequence similarities ranging from 91.9–95.4 %. Its major cellular fatty acids contained iso-C15 : 0 (39.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c, 23.0 %), C16 : 0 (12.8 %) and iso-C17 : 0 3-OH (9.9 %). MK7 was the major menaquinone. The G+C content of the genomic DNA was 45.5 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain T47T represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium suaedae sp. nov. is proposed. The type strain is T47T ( = CGMCC 1.15277T = KCTC 42662T).

Chryseobacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems

2010 ◽  
Vol 60 (8) ◽  
pp. 1765-1769 ◽  
Author(s):  
Peter Kämpfer ◽  
A. B. Arun ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen ◽  
K. R. Sridhar ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Closely Related Species ◽  
The 16S Rrna Gene ◽  
Sequence Similarities ◽  
Chryseobacterium Gleum

A bacterial strain (CC-VM-7T), isolated from the faeces of the pill millipede Arthrosphaera magna Attems collected in India, was studied to determine its taxonomic allocation. Cells stained Gram-negative and were rod-shaped. Comparative analyses of the 16S rRNA gene sequence of the strain with those of the most closely related species clearly suggested allocation to the genus Chryseobacterium, with the highest sequence similarities of 99.2 % to Chryseobacterium gleum CCUG 14555T, 98.6 % to Chryseobacterium indologenes CCUG 14556T and 98.4 % to Chryseobacterium aquifrigidense KCTC 12894T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 98 %. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1 ω9c. DNA–DNA hybridization resulted in relatedness values of only 29.6 % (reciprocal 31.3 %) to Chryseobacterium gleum CCUG 14555T, 41.2 % (reciprocal 38.8 %) to C. indologenes CCUG 14556T and 35.4 % (reciprocal 38.5 %) to C. aquifrigidense KCTC 12894T. DNA–DNA relatedness, biochemical and chemotaxonomic properties clearly show that strain CC-VM-7T represents a novel species, for which the name Chryseobacterium arthrosphaerae sp. nov. is proposed. The type strain is CC-VM-7T (=CCUG 57618T =CCM 7645T).

scholarly journals Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences

2010 ◽  
Vol 60 (12) ◽  
pp. 2697-2704 ◽  
Author(s):  
Byoung Jun Kim ◽  
Hee-Youn Kim ◽  
Yeo-Jun Yun ◽  
Bum-Joon Kim ◽  
Yoon-Hoh Kook
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rna Polymerase ◽  
Gene Sequence ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Partial RNA polymerase β-subunit gene (rpoB) sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus Bifidobacterium. The sequences were compared with those of the partial hsp60 (604 bp) and 16S rRNA genes (1475 or 1495 bp). The rpoB gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the hsp60 sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The Bifidobacterium catenulatum–Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum subsp. pseudolongum–Bifidobacterium pseudolongum subsp. globosum and Bifidobacterium gallinarum–Bifidobacterium pullorum–Bifidobacterium saeculare groups were more clearly differentiated in the partial rpoB and hsp60 gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined rpoB gene sequences are suitable molecular markers for the differentiation of species of the genus Bifidobacterium and support various other molecular tools used to determine the relationships among species of this genus.

scholarly journals Williamsia faeni sp. nov., an actinomycete isolated from a hay meadow

2010 ◽  
Vol 60 (11) ◽  
pp. 2548-2551 ◽  
Author(s):  
Amanda L. Jones ◽  
Gail D. Payne ◽  
Michael Goodfellow
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Tree ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phyletic Line ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

The taxonomic status of an actinomycete isolated from soil collected from a hay meadow was determined using a polyphasic approach. The strain, designated N1350T, had morphological and chemotaxonomic properties consistent with its classification in the genus Williamsia and formed a distinct phyletic line within the clade comprising the type strains of species of the genus Williamsia in the 16S rRNA gene tree. Strain N1350T shared highest 16S rRNA gene sequence similarities with Williamsia marianensis MT8T (98.1 %) and Williamsia muralis MA140-96T (98.3 %). However, strain N1350T was readily distinguished from the type strains of Williamsia species using a combination of phenotypic properties. On the basis of these data, strain N1350T is considered to represent a novel species of the genus Williamsia. The name proposed for this taxon is Williamsia faeni sp. nov., with the type strain N1350T (=DSM 45372T =NCIMB 14575T =NRRL B-24794T).

scholarly journals Draconibacterium sediminis sp. nov., isolated from river sediment

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2310-2314 ◽  
Author(s):  
Juan Du ◽  
Qiliang Lai ◽  
Yang Liu ◽  
Chunming Dong ◽  
Yanrong Xie ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A Gram-reaction-negative, facultatively anaerobic and rod-shaped bacterium, designated strain JN14CK-3T, was isolated from surface sediment of the Jiulong River of China and was characterized phenotypically and phylogenetically. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain JN14CK-3T belonged to the genus Draconibacterium, with the highest sequence similarity (98.3 %) to Draconibacterium orientale FH5T. By contrast, strain JN14CK-3T shared low 16S rRNA gene sequence similarities ( < 91.0 %) with other type strains. The sole respiratory quinone was MK-7.The polar lipids were phosphatidylethanolamine and several unidentified phospholipids and lipids. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, C17:0 2-OH, iso-C16:0 3-OH and iso-C17:0 3-OH. The G+C content of the genomic DNA was 40.9 mol%. The digital DNA–DNA hybridization value and average nucleotide identity (ANI) between strain JN14CK-3T and D. orientale FH5T were 34.2 ± 2.5 % and 87.1 %, respectively. The combined genotypic and phenotypic data showed that strain JN14CK-3T represents a novel species of the genus Draconibacterium, for which the name Draconibacterium sediminis sp. nov. is proposed, with the type strain JN14CK-3T ( = MCCC 1A00734T = KCTC 42152T).

scholarly journals Sporolactobacillus putidus sp. nov., an endospore-forming lactic acid bacterium isolated from spoiled orange juice

2010 ◽  
Vol 60 (7) ◽  
pp. 1499-1503 ◽  
Author(s):  
Rieko Fujita ◽  
Kaoru Mochida ◽  
Yuko Kato ◽  
Keiichi Goto
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Lactic Acid Bacterium ◽  
Orange Juice ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
B Subunit ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A Gram-positive, endospore-forming, lactic acid bacterium was isolated from spoiled orange juice. The organism, strain QC81-06T, grew microaerobically or anaerobically at 30–45 °C (optimum 35 °C) and pH 3.5–5.5 (optimum pH 4.5), and produced acid from various sugars. d-Lactic acid was produced. It contained menaquinone-7 as the major isoprenoid quinone. The G+C content of the genomic DNA was 47.5 mol%. The predominant cellular fatty acids of the strain were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Phylogenetic analyses based on the 16S rRNA gene and gyrB gene (DNA gyrase B subunit gene) revealed that strain QC81-06T clustered with Sporolactobacillus species but the strain was clearly distinct from other Sporolactobacillus species with significant bootstrap values. The levels of 16S rRNA gene and gyrB gene sequence similarities between strain QC81-06T and the other strains of the cluster were 96.0–97.0 % and 75.1–77.2 %, respectively. On the basis of these results, strain QC81-06T should be classified as a novel Sporolactobacillus species for which the name Sporolactobacillus putidus is proposed. The type strain is strain QC81-06T (=DSM 21265T=JCM 15325T).

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