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Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:microorganisms10122355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
| | - Mohammad J. Taherzadeh
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
- Correspondence:
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Yasir M, Qureshi AK, Khan I, Bibi F, Rehan M, Khan SB, Azhar EI. Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 23:17-27. [PMID: 30589606 DOI: 10.1089/omi.2018.0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates. Most of the hot springs had a neutral pH and a temperature range of 45-89°C. Relatively higher colony-forming units (1.9 ± 0.45 × 104) were observed with 60°C incubation of an 89°C sediment sample from the hot spring at Ain al Harra1. Among the 536 purified isolates, 6 novel candidate species were found, and the remaining isolates represented 139 distinct species. Several species, such as Bacillus cereus, Bacillus subtilis, and Bacillus schlegelii, were ubiquitous in the hot springs sampled, but 102 of the identified species were uniquely distributed among the hot springs. Sixteen of the isolated thermophilic bacteria, including Geobacillus kaustophilus, Thermus oshimai, and Brevibacillus thermoruber, grew at ≥60°C. In addition, 21 species exhibited hydrolytic enzymatic activity. Most of these species belonged to Bacillus and Brevibacillus. Overall, this study contributes to global knowledgebase on bacterial communities by comprehensively profiling culture-based bacterial diversity in the hot springs of Saudi Arabia. Further studies are required for investigating bacteria from hot springs by a metagenomic approach.
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Affiliation(s)
- Muhammad Yasir
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arooj K Qureshi
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Imran Khan
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,2 State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology Taipa, Macau, China
| | - Fehmida Bibi
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Rehan
- 3 King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sher Bahadar Khan
- 4 Department of Chemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,5 Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Cihan AC, Yildiz ED, Sahin E, Mutlu O. Introduction of novel thermostable α-amylases from genus Anoxybacillus and proposing to group the Bacillaceae related α-amylases under five individual GH13 subfamilies. World J Microbiol Biotechnol 2018; 34:95. [PMID: 29904894 DOI: 10.1007/s11274-018-2478-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/12/2018] [Indexed: 11/25/2022]
Abstract
Among the thermophilic Bacillaceae family members, α-amylase production of 15 bacilli from genus Anoxybacillus was investigated, some of which are biotechnologically important. These Anoxybacillus α-amylase genes displayed ≥ 91.0% sequence similarities to Anoxybacillus enzymes (ASKA, ADTA and GSX-BL), but relatively lower similarities to Geobacillus (≤ 69.4% to GTA, Gt-amyII), and Bacillus aquimaris (≤ 61.3% to BaqA) amylases, all formerly proposed only in a Glycoside Hydrolase 13 (GH13) subfamily. The phylogenetic analyses of 63 bacilli-originated protein sequences among 93 α-amylases revealed the overall relationships within Bacillaceae amylolytic enzymes. All bacilli α-amylases formed 5 clades different from 15 predefined GH13 subfamilies. Their phylogenetic findings, taxonomic relationships, temperature requirements, and comparisonal structural analyses (including their CSR-I-VII regions, 12 sugar- and 4 calcium-binding sites, presence or absence of the complete catalytic machinery, and their currently unassigned status in a valid GH13 subfamiliy) revealed that these five GH13 α-amylase clades related to familly share some common characteristics, but also display differentiative features from each other and the preclassified ones. Based on these findings, we proposed to divide Bacillaceae related GH13 subfamilies into 5 individual groups: the novel a2 subfamily clustered around α-amylase B2M1-A (Anoxybacillus sp.), the a1, a3 and a4 subfamilies (including the representatives E184aa-A (Anoxybacillus sp.), ATA (Anoxybacillus tepidamans), and BaqA,) all of which were composed from the division of the previously grouped single subfamily around α-amylase BaqA, and the undefinite subfamily formerly defined as xy including Bacillus megaterium NL3.
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Affiliation(s)
- Arzu Coleri Cihan
- Faculty of Science, Department of Biology, Ankara University, Tandogan, 06100, Ankara, Turkey.
| | | | - Ergin Sahin
- Faculty of Science, Department of Biology, Ankara University, Tandogan, 06100, Ankara, Turkey
| | - Ozal Mutlu
- Faculty of Arts and Sciences, Department of Biology, Marmara University, Goztepe, 34722, Istanbul, Turkey
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Coleri Cihan A, Karaca B, Ozel BP, Kilic T. Determination of the biofilm production capacities and characteristics of members belonging to Bacillaceae family. World J Microbiol Biotechnol 2017; 33:118. [DOI: 10.1007/s11274-017-2271-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 04/25/2017] [Indexed: 10/19/2022]
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Sultanpuram VR, Mothe T. Salipaludibacillus aurantiacus gen. nov., sp. nov. a novel alkali tolerant bacterium, reclassification of Bacillus agaradhaerens as Salipaludibacillus agaradhaerens comb. nov. and Bacillus neizhouensis as Salipaludibacillus neizhouensis comb. nov. Int J Syst Evol Microbiol 2016; 66:2747-2753. [DOI: 10.1099/ijsem.0.001117] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Thirumala Mothe
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Nalgonda, Telangana, India
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Abstract
Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.
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Addou NA, Schumann P, Spröer C, Ben Hania W, Hacene H, Fauque G, Cayol JL, Fardeau ML. Melghiribacillus thermohalophilus gen. nov., sp. nov., a novel filamentous, endospore-forming, thermophilic and halophilic bacterium. Int J Syst Evol Microbiol 2015; 65:1172-1179. [DOI: 10.1099/ijs.0.000075] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel filamentous, endospore-forming, thermophilic and moderately halophilic bacterium designated strain Nari2AT was isolated from soil collected from an Algerian salt lake, Chott Melghir. The novel isolate was Gram-staining-positive, aerobic, catalase-negative and oxidase-positive. Optimum growth occurred at 50–55 °C, 7–10 % (w/v) NaCl and pH 7–8. The strain exhibited 95.4, 95.4 and 95.2 % 16S rRNA gene sequence similarity to
Thalassobacillus devorans
G19.1T,
Sediminibacillus halophilus
EN8dT and
Virgibacillus kekensis
YIM-kkny16T, respectively. The major menaquinone was MK-7. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, three unknown phosphoglycolipids and two unknown phospholipids. The predominant cellular fatty acids were iso-C15 : 0 and iso-C17 : 0. The DNA G+C content was 41.9 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain Nari2AT is considered to represent a novel species of a new genus in the family
Bacillaceae
, order
Bacillales
, for which the name Melghiribacillus thermohalophilus gen. nov., sp. nov. is proposed. The type strain of Melghiribacillus thermohalophilus is Nari2AT ( = DSM 25894T = CCUG 62543T).
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Affiliation(s)
- Nariman Ammara Addou
- Laboratoire de Biologie Cellulaire et Moléculaire (Equipe de Microbiologie), Université des Sciences et de la Technologie Houari Boumediène, BP 32, El Alia 16111 Bab Ezzouar, Algiers, Algeria
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288 Marseille, France
| | - Peter Schumann
- Leibniz Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Wajdi Ben Hania
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288 Marseille, France
| | - Hocine Hacene
- Laboratoire de Biologie Cellulaire et Moléculaire (Equipe de Microbiologie), Université des Sciences et de la Technologie Houari Boumediène, BP 32, El Alia 16111 Bab Ezzouar, Algiers, Algeria
| | - Guy Fauque
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288 Marseille, France
| | - Jean-Luc Cayol
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288 Marseille, France
| | - Marie-Laure Fardeau
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, 13288 Marseille, France
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