Journal of Microbiology

Journal Articles

UACG: Up‑to‑Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction: Seong-In Na , Michael James Bailey , Mauricio Chalita , Jae Hyoung Cho , Jongsik Chun; J. Microbiol. 2023;61(7):683-692. Published online August 11, 2023; DOI: https://doi.org/10.1007/s12275-023-00064-2

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In the post-genomic era, phylogenomics is a powerful and routinely-used tool to discover evolutionary relationships between microorganisms. Inferring phylogenomic trees by concatenating core gene sequences into a supermatrix is the standard
method
. The previously released up-to-date bacterial core gene (UBCG) tool provides a pipeline to infer phylogenomic trees using single-copy core genes for the Bacteria domain. In this study, we established up-to-date archaeal core gene (UACG), comprising 128 genes suitable for inferring archaeal phylogenomic trees. To test the gene set, we selected the Haloarcula genus and scrutinized its phylogeny. The phylogeny inferred using the UACG tool was consistent with the orthoANIu dendrogram, whereas the 16S rRNA gene phylogeny showed high intragenomic heterogeneity resulting in phylogenetic discrepancies. The software tool using the UACG set is available at https:// www. ezbio cloud. net/ tools/ uacg.

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Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Raúl Riesco, Martha E. Trujillo
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

The hyperthermophilic α-amylase from Thermococcus sp. HJ21 does not require exogenous calcium for thermostability because of high-binding affinity to calcium: Huaixu Cheng , Zhidan Luo , Mingsheng Lu , Song Gao , Shujun Wang; J. Microbiol. 2017;55(5):379-387. Published online March 1, 2017; DOI: https://doi.org/10.1007/s12275-017-6416-5

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Abstract

The hyperthermophilic α-amylase from Thermococcus sp. HJ21 does not require exogenous calcium ions for thermo-stability, and is a promising alternative to commercially avail-able α-amylases to increase the efficiency of industrial pro-cesses like the liquefaction of starch. We analyzed the amino acid sequence of this α-amylase by sequence alignments and structural modeling, and found that this α-amylase closely resembles the α-amylase from Pyrococcus woesei. The gene of this α-amylase was cloned in Escherichia coli and the re-combinant α-amylase was overexpressed and purified with a combined renaturation-purification procedure. We con-firmed thermostability and exogenous calcium ion indepen-dency of the recombinant α-amylase and further investigated the mechanism of the independency using biochemical ap-proaches. The results suggested that the α-amylase has a high calcium ion binding affinity that traps a calcium ion that would not dissociate at high temperatures, providing a direct expla-nation as to why the addition of calcium ions is not required for thermostability. Understanding of the mechanism offers a strong base on which to further engineer properties of this α-amylase for better potential applications in industrial pro-cesses.

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Enhanced Thermostability of Geobacillus stearothermophilus α-Amylase by Rational Design of Disulfide Bond and Application in Corn Starch Liquefaction and Bread Quality Improvement
Mengyu Zhu, Wenxin Zhai, Runfei Song, Lin Lin, Wei Wei, Dongzhi Wei
Journal of Agricultural and Food Chemistry.2023; 71(48): 18928. CrossRef
Structural and functional adaptation in extremophilic microbial α-amylases
Aziz Ahmad, Rahamtullah, Rajesh Mishra
Biophysical Reviews.2022; 14(2): 499. CrossRef
Biochemical characterization of an α-fucosidase PsaFuc from the GH29 family
Xiaohua Liu, Xin Geng, Weizhi Liu, Qianqian Lyu
Process Biochemistry.2022; 122: 258. CrossRef
Amylases from thermophilic bacteria: structure and function relationship
Bhavtosh A. Kikani, Satya P. Singh
Critical Reviews in Biotechnology.2022; 42(3): 325. CrossRef
Biochemical and synergistic properties of a novel alpha‐amylase from Chinese nong‐flavor Daqu
Lanchai Chen, Zhuolin Yi, Yang Fang, Yanling Jin, Kaize He, Yao Xiao, Dong Zhao, Huibo Luo, Hui He, Qun Sun, Hai Zhao
Microbial Cell Factories.2021;[Epub] CrossRef
Recombinant expression of insoluble enzymes in Escherichia coli: a systematic review of experimental design and its manufacturing implications
Suraj Mital, Graham Christie, Duygu Dikicioglu
Microbial Cell Factories.2021;[Epub] CrossRef
A new GH13 subfamily represented by the α-amylase from the halophilic archaeon Haloarcula hispanica
Štefan Janeček, Barbora Zámocká
Extremophiles.2020; 24(2): 207. CrossRef
Contribution of domain B to the catalytic properties of a Flavobacteriaceae α-amylase
Huijia Yin, Lina Zhang, Zhou Yang, Shannan Li, Xinyu Nie, Yan Wang, Chunyu Yang
Process Biochemistry.2018; 70: 104. CrossRef
Functional and cooperative stabilization of a two-metal (Ca, Zn) center in α-amylase derived from Flavobacteriaceae species
Huijia Yin, Zhou Yang, Xinyu Nie, Shannan Li, Xuyang Sun, Chao Gao, Zenghang Wang, Guangming Zhou, Ping Xu, Chunyu Yang
Scientific Reports.2017;[Epub] CrossRef

Cr(VI) removal from aqueous solution by thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1 in the presence of single and multiple heavy metals: Han Li , Shaobin Huang , Yongqing Zhang; J. Microbiol. 2016;54(9):602-610. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-5295-5

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Abstract

Cr(VI) pollution is increasing continuously as a result of ongoing industrialization. In this study, we investigated the thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1, isolated from the biofilm of a biotrickling filter used in nitrogen oxides (NOX) removal, with respect to its ability to remove Cr(VI) from an aqueous solution. TAD1 was capable of reducing Cr(VI) from an initial concentration of 10 mg/L to non-detectable levels over a pH range of 7–9 and at a temperature range of 30–50°C. TAD1 simultaneously removed both Cr(VI) and NO3 −-N at 50°C, when the pH was 7 and the initial Cr(VI) concentration was 15 mg/L. The reduction of Cr(VI) to Cr(III) correlated with the growth metabolic activity of TAD1. The presence of other heavy metals (Cu, Zn, and Ni) inhibited the ability of TAD1 to remove Cr(VI). The metals each individually inhibited Cr(VI) removal, and the extent of inhibition increased in a cooperative manner in the presence of a combination of the metals. The addition of biodegradable cellulose acetate microspheres (an adsorption material) weakened the toxicity of the heavy metals; in their presence, the Cr(VI) removal efficiency returned to a high level. The feasibility and applicability of simultaneous nitrate removal and Cr(VI) reduction by strain TAD1 is promising, and may be an effective biological method for the clean-up of wastewater.

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Hexavalent Chromium Pollution and its Sustainable Management through Bioremediation
Anushka Paul, Sudeshna Dey, Deo Karan Ram, Alok Prasad Das
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Adsorption of Hg2+/Cr6+ by metal-binding proteins heterologously expressed in Escherichia coli
Shuting Hu, Zixiang Wei, Teng Liu, Xinyu Zuo, Xiaoqiang Jia
BMC Biotechnology.2024;[Epub] CrossRef
Growth-dependent cr(VI) reduction by Alteromonas sp. ORB2 under haloalkaline conditions: toxicity, removal mechanism and effect of heavy metals
G. Kiran Kumar Reddy, K. Kavibharathi, Anuroop Singh, Y. V. Nancharaiah
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Hexavalent Cr, Its Toxicity and Removal Strategy: Revealing PGPB Potential in Its Remediation
Akanksha Gupta, Anubhuti Singh, Virendra Kumar Mishra
Water, Air, & Soil Pollution.2023;[Epub] CrossRef
Chromium Toxicity in Plants: Signaling, Mitigation, and Future Perspectives
Sajad Ali, Rakeeb A. Mir, Anshika Tyagi, Nazia Manzar, Abhijeet Shankar Kashyap, Muntazir Mushtaq, Aamir Raina, Suvin Park, Sandhya Sharma, Zahoor A. Mir, Showkat A. Lone, Ajaz A. Bhat, Uqab Baba, Henda Mahmoudi, Hanhong Bae
Plants.2023; 12(7): 1502. CrossRef
A comprehensive review on chromium (Cr) contamination and Cr(VI)-resistant extremophiles in diverse extreme environments
Zeeshanur Rahman, Lebin Thomas, Siva P. K. Chetri, Shrey Bodhankar, Vikas Kumar, Ravi Naidu
Environmental Science and Pollution Research.2023; 30(21): 59163. CrossRef
Health hazards of hexavalent chromium (Cr (VI)) and its microbial reduction
Pooja Sharma, Surendra Pratap Singh, Sheetal Kishor Parakh, Yen Wah Tong
Bioengineered.2022; 13(3): 4923. CrossRef
Reduced graphene oxide supported nanoscale zero-valent iron (nZVI/rGO) for in-situ remediation of Cr(VI)/nitrate-polluted aquifer
Xinyang Liu, Wanting Liu, Zifang Chi
Journal of Water Process Engineering.2022; 49: 103188. CrossRef
Simultaneous denitrification and hexavalent chromium removal by a newly isolated Stenotrophomonas maltophilia strain W26 under aerobic conditions
Qiang An, Shu-man Deng, Bin Zhao, Zheng Li, Jia Xu, Jia-Li Song
Environmental Chemistry.2021; 18(1): 20. CrossRef
Leucobacter coleopterorum sp. nov., Leucobacter insecticola sp. nov., and Leucobacter viscericola sp. nov., isolated from the intestine of the diving beetles, Cybister brevis and Cybister lewisianus, and emended description of the genus Leucobacter
Dong-Wook Hyun, Hojun Sung, Pil Soo Kim, Ji-Hyun Yun, Jin-Woo Bae
Journal of Microbiology.2021; 59(4): 360. CrossRef
Bioremediation of Chromium by Microorganisms and Its Mechanisms Related to Functional Groups
Abate Ayele, Yakob Godebo Godeto, Yifeng Zhang
Journal of Chemistry.2021; 2021: 1. CrossRef
Iron oxide minerals promote simultaneous bio-reduction of Cr(VI) and nitrate: Implications for understanding natural attenuation
Yutian Hu, Tong Liu, Nan Chen, Chuanping Feng
Science of The Total Environment.2021; 786: 147396. CrossRef
Cr(VI) reductase activity locates in the cytoplasm of Aeribacillus pallidus BK1, a novel Cr(VI)-reducing thermophile isolated from Tengchong geothermal region, China
Yan Ma, Hui Zhong, Zhiguo He
Chemical Engineering Journal.2019; 371: 524. CrossRef

Research Support, Non-U.S. Gov'ts

Characterization, Gene Cloning, and Heterologous Expression of β-Mannanase from a Thermophilic Bacillus subtilis: Pijug Summpunn , Suttidarak Chaijan , Duangnate Isarangkul , Suthep Wiyakrutta , Vithaya Meevootisom; J. Microbiol. 2011;49(1):86-93. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0357-1

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Abstract

Bacillus subtilis BCC41051 producing a thermostable β-mannanase was isolated from soybean meal-enriched soil and was unexpectedly found to be thermophilic in nature. The extracellular β-mannanase (ManA) produced was hydrophilic, as it was not precipitated even with ammonium sulfate at 80% saturation. The estimated molecular weight of ManA was 38.0 kDa by SDS-PAGE with a pI value of 5.3. Optimal pH and temperature for mannan-hydrolyzing activity was 7.0 and 60°C, respectively. The enzyme was stable over a pH range of 5.0-11.5, and at temperatures of up to 60°C for 30 min, with more than 80% of its activity retained. ManA was strongly inhibited by Hg2+ (1 mM), but was sensitive to other divalent ions to a lesser degree. The gene of ManA encoded a protein of 362 amino acid residues, with the first 26 residues identified as a signal peptide. High expression of recombinant ManA was achieved in both Escherichia coli BL21 (DE3) (415.18 U/ml) and B. megaterium UNcat (359 U/ml).

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A thermostable and acidophilic mannanase from Bacillus mojavensis: its sustainable production using spent coffee grounds, characterization, and application in grape juice processing
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Effects of Signal Peptide and Chaperone Co-Expression on Heterologous Protein Production in Escherichia coli
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Enhanced extracellular β‐mannanase production by overexpressing PrsA lipoprotein in Bacillus subtilis and optimizing culture conditions
Liyu Xu, Yongyong Zhang, Yuehan Dong, Gang Qin, Xiao Zhao, Yanyan Shen
Journal of Basic Microbiology.2022; 62(7): 815. CrossRef
Expression, Characterization and Structure Analysis of a New GH26 Endo-β-1, 4-Mannanase (Man26E) from Enterobacter aerogenes B19
Huijing Liu, Jie Liu, Tangbing Cui
Applied Sciences.2020; 10(21): 7584. CrossRef
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Martina Aulitto, Salvatore Fusco, Danila Limauro, Gabriella Fiorentino, Simonetta Bartolucci, Patrizia Contursi
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Cheng Zhou, Yanfen Xue, Yanhe Ma
Microbial Cell Factories.2018;[Epub] CrossRef
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Nur Fazrin Husna Abdul Aziz, Sahar Abbasiliasi, Hui Suan Ng, Pongsathon Phapugrangkul, Mohamad Hafizi Abu Bakar, Yew Joon Tam, Joo Shun Tan
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Li Li, Lan Mu, Xiaojuan Wang, Jingfeng Yu, Ruiping Hu, Zhen Li
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Weeranuch Seesom, Polphet Thongket, Tomohiro Yamamoto, Shigeo Takenaka, Tatsuji Sakamoto, Wasana Sukhumsirichart
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Characterization of Hyperthermostable Fructose-1,6-Bisphosphatase from Thermococcus onnurineus NA1: Yeol Gyun Lee , Sung Gyun Kang , Jung-Hyun Lee , Seung Il Kim , Young-Ho Chung; J. Microbiol. 2010;48(6):803-807. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0377-2

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Abstract: To understand the physiological functions of thermostable fructose-1,6-bisphosphatase (TNA1-Fbp) from Thermococcus onnurineus NA1, its recombinant enzyme was overexpressed in Escherichia coli, purified, and the enzymatic properties were characterized. The enzyme showed maximal activity for fructose-1,6- bisphosphate at 95°C and pH 8.0 with a half-life (t1/2) of about 8 h. TNA1-Fbp had broad substrate specificities for fructose-1,6-bisphosphate and its analogues including fructose-1-phosphate, glucose-1-phosphate, and phosphoenolpyruvate. In addition, its enzyme activity was increased five-fold by addition of 1 mM Mg2+, while Li+ did not enhance enzymatic activity. TNA1-Fbp activity was inhibited by ATP, ADP, and phosphoenolpyruvate, but AMP up to 100 mM did not have any effect. TNA1-Fbp is currently defined as a class V fructose-1,6-bisphosphatase (FBPase) because it is very similar to FBPase of Thermococcus kodakaraensis KOD1 based on sequence homology. However, this enzyme shows a different range of substrate specificities. These results suggest that TNA1-Fbp can establish new criterion for class V FBPases.

Production, Partial Characterization, and Immobilization in Alginate Beads of an Alkaline Protease from a New Thermophilic Fungus Myceliophthora sp.: Letícia Maria Zanphorlin , Fernanda Dell Antonio Facchini , Filipe Vasconcelos , Rafaella Costa Bonugli-Santos , André Rodrigues , Lara Durães Sette , Eleni Gomes , Gustavo Orlando Bonilla-Rodriguez; J. Microbiol. 2010;48(3):331-336. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9269-8

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Abstract: Thermophilic fungi produce thermostable enzymes which have a number of applications, mainly in biotechnological processes. In this work, we describe the characterization of a protease produced in solidstate (SSF) and submerged (SmF) fermentations by a newly isolated thermophilic fungus identified as a putative new species in the genus Myceliophthora. Enzyme-production rate was evaluated for both fermentation processes, and in SSF, using a medium composed of a mixture of wheat bran and casein, the proteolytic output was 4.5-fold larger than that obtained in SmF. Additionally, the peak of proteolytic activity was obtained after 3 days for SSF whereas for SmF it was after 4 days. The crude enzyme obtained by both SSF and SmF displayed similar optimum temperature at 50°C, but the optimum pH shifted from 7 (SmF) to 9 (SSF). The alkaline protease produced through solid-state fermentation (SSF), was immobilized on beads of calcium alginate, allowing comparative analyses of free and immobilized proteases to be carried out. It was observed that both optimum temperature and thermal stability of the immobilized enzyme were higher than for the free enzyme. Moreover, the immobilized enzyme showed considerable stability for up to 7 reuses.

Diversity of Thermophilic Fungi in Tengchong Rehai National Park Revealed by ITS Nucleotide Sequence Analyses: Wen-Zheng Pan , Xiao-Wei Huang , Kang-Bi Wei , Chun-Mei Zhang , Dong-Mei Yang , Jun-Mei Ding , Ke-Qin Zhang; J. Microbiol. 2010;48(2):146-152. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-9157-2

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Abstract: The geothermal sites near neutral and alkalescent thermal springs in Tengchong Rehai National Park were examined through cultivation-dependent approach to determine the diversity of thermophilic fungi in these environments. Here, we collected soils samples in this area, plated on agar media conducive for fungal growth, obtained pure cultures, and then employed the method of internal transcribed spacer (ITS) sequencing combined with morphological analysis for identification of thermophilic fungi to the species level. In total, 102 strains were isolated and identified as Rhizomucor miehei, Chaetomium sp., Talaromyces thermophilus, Talaromyces byssochlamydoides, Thermoascus aurantiacus Miehe var. levisporus, Thermomyces lanuginosus, Scytalidium thermophilum, Malbranchea flava, Myceliophthora sp. 1, Myceliophthora sp. 2, Myceliophthora sp. 3, and Coprinopsis sp. Two species, T. lanuginosus and S. thermophilum were the dominant species, representing 34.78% and 28.26% of the sample, respectively. Our results indicated a greater diversity of thermophilic fungi in neutral and alkaline geothermal sites than acidic sites around hot springs reported in previous studies. Most of our strains thrived at alkaline growth conditions.

Purification and Biochemical Properties of a Glucose-Stimulated β-D-Glucosidase Produced by Humicola grisea var. thermoidea Grown on Sugarcane Bagasse: Cesar Vanderlei Nascimento , Flávio Henrique Moreira Souza , Douglas Chodi Masui , Francisco Assis Leone , Rosane Marina Peralta , João Atílio Jorge , Rosa Prazeres Melo Furriel; J. Microbiol. 2010;48(1):53-62. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0159-x

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Abstract: The effect of several carbon sources on the production of mycelial-bound β-glucosidase by Humicola grisea var. thermoidea in submerged fermentation was investigated. Maximum production occurred when cellulose was present in the culture medium, but higher specific activities were achieved with cellobiose or sugarcane bagasse. Xylose or glucose (1%) in the reaction medium stimulated β-glucosidase activity by about 2-fold in crude extracts from mycelia grown in sugarcane bagasse. The enzyme was purified by ammonium sulfate precipitation, followed by Sephadex G-200 and DEAE-cellulose chromatography, showing a single band in PAGE and SDS-PAGE. The β-glucosidase had a carbohydrate content of 43% and showed apparent molecular masses of 57 and 60 kDa, as estimated by SDS-PAGE and gel filtration, respectively. The optimal pH and temperature were 6.0 and 50°C, respectively. The purified enzyme was thermostable up to 60 min in water at 55°C and showed half-lives of 7 and 14 min when incubated in the absence or presence of 50 mM glucose, respectively, at 60°C. The enzyme hydrolyzed p-nitrophenyl-β-D-glucopyranoside, p-nitrophenyl-β-galactopyranoside, p-nitrophenyl-β-D-fucopyranoside, p-nitrophenyl-β-D-xylopyranoside, o-nitrophenyl-β-Dgalactopyranoside, lactose, and cellobiose. The best synthetic and natural substrates were p-nitrophenyl-β-Dfucopyranoside and cellobiose, respectively. Purified enzyme activity was stimulated up to 2-fold by glucose or xylose at concentrations from 25 to 200 mM. The addition of purified or crude β-glucosidase to a reaction medium containing Trichoderma reesei cellulases increased the saccharification of sugarcane bagasse by about 50%. These findings suggest that H. grisea var. thermoidea β-glucosidase has a potential for biotechnological applications in the bioconversion of lignocellulosic materials.

A Specific Short Dextrin-Hydrolyzing Extracellular Glucosidase from the Thermophilic Fungus Thermoascus aurantiacus 179-5: Ana Flavia Azevedo Carvalho , Aline Zorzetto Gonclves , Roberto da Silva , Eleni Gomes; J. Microbiol. 2006;44(3):276-283.; DOI: https://doi.org/2385 [pii]

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Abstract: The thermophilic fungus Thermoascus aurantiacus 179-5 produced large quantities of a glucosidase which preferentially hydrolyzed maltose over starch. Enzyme production was high in submerged fermentation, with a maximal activity of 30 U/ml after 336 h of fermentation. In solid-state fermentation, the activity of the enzyme was 22 U/ml at 144 h in medium containing wheat bran and 5.8 U/ml at 48 h when cassava pulp was used as the culture medium. The enzyme was specific for maltose, very slowly hydrolyzed starch, dextrins (2-7G) and the synthetic substrate (α-PNPG), and did not hydrolyze sucrose. These properties suggest that the enzyme is a type II α-glucosidase. The optimum temperature of the enzyme was 70?. In addition, the enzyme was highly thermostable (100% stability for 10 h at 60? and a half-life of 15 min at 80?), and stable within a wide pH range.

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