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Ben Abdallah M, Chamkha M, Karray F, Sayadi S. Microbial diversity in polyextreme salt flats and their potential applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11371-11405. [PMID: 38180652 DOI: 10.1007/s11356-023-31644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.
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Affiliation(s)
- Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018, Sfax, Tunisia.
| | - Mohamed Chamkha
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018, Sfax, Tunisia
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018, Sfax, Tunisia
| | - Sami Sayadi
- Biotechnology Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, 2713, Doha, Qatar
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Judicial Opinions 112–122. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Opinion 112 denies the request to place
Seliberia
Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject
Shewanella irciniae
Lee et al. 2006 and Opinion 114 denies the request to reject the name
Enterobacter siamensis
Khunthongpan et al. 2014. Opinion 115 rejects the epithet of
Moorella thermoautotrophica
(Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate
Methylothermus subterraneus
Hirayama et al. 2011 as the type species of the genus
Methylothermus
is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name
Flaviaesturariibacter
is treated, as are the analogous cases of
Fredinandcohnia
and
Hydrogeniiclostidium
. The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and
Hydrogeniiclostridium
, respectively. Opinion 119 concludes that assigning
Actinomycetales
Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class
Actinobacteria
Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but
Actinomycetales
is also assigned as type of
Actinomycetes
Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name
Amycolatopsis albidoflavus
is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of
Mollicutes
proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.
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Raeisnia N, Arefian E, Amoozegar MA. Microbial Community of an 11th Century Manuscript by Both Culture-Dependent and -Independent Approaches. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722300117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Zainul Kamal S, Koyama M, Syukri F, Toda T, Tran QNM, Nakasaki K. Effect of enzymatic pre-treatment on thermophilic composting of shrimp pond sludge to improve ammonia recovery. ENVIRONMENTAL RESEARCH 2022; 204:112299. [PMID: 34743806 DOI: 10.1016/j.envres.2021.112299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
In recent years, attempts have been made to develop a thermophilic composting process for organic sludge to produce ammonia gas for high value-added algal production. However, the hydrolysis of non-dissolved organic nitrogen in sludge is a bottleneck for ammonia conversion. The aim of this study was to identify enzymes that enhance sludge hydrolysis in a thermophilic composting system for ammonia recovery from shrimp pond sludge. This was achieved by screening useful enzymes to degrade non-dissolved nitrogen and subsequently investigating their effectiveness in lab-scale composting systems. Among the four hydrolytic enzyme classes assessed (lysozyme, protease, phospholipase, and collagenase), proteases from Streptomyces griseus were the most effective at hydrolysing non-dissolved nitrogen in the sludge. After composting sludge pre-treated with proteases, the final amount of non-dissolved nitrogen was 46.2% of the total N in the control sample and 22.3% of the total N in the protease sample, thus increasing the ammonia (gaseous and in-compost) conversion efficiency from 41.5% to 56.4% of the total N. The decrease in non-dissolved nitrogen was greater in the protease sample than in the control sample during the pre-treatment period, and no difference was observed during the subsequent composting period. These results suggest that Streptomyces proteases hydrolyse the organic nitrogen fraction, which cannot be degraded by the bacterial community in the compost. Functional potential analysis of the bacterial community using PICRUSt2 suggested that 4 (EC:3.4.21.80, EC:3.4.21.81, EC:3.4.21.82, and EC:3.4.24.77) out of 13 endopeptidase genes in S. griseus were largely absent in the compost bacterial community and that they play a key role in the hydrolysis of non-dissolved nitrogen. This is the first study to identify the enzymes that enhance the hydrolysis of shrimp pond sludge and to show that the thermophilic bacterial community involved in composting has a low ability to secrete these enzymes.
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Affiliation(s)
- Syazni Zainul Kamal
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan; Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis, Kompleks Pengajian Jejawi 3, 02600, Arau, Perlis, Malaysia
| | - Mitsuhiko Koyama
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Fadhil Syukri
- Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Tatsuki Toda
- Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan
| | - Quyen Ngoc Minh Tran
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kiyohiko Nakasaki
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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Jin CZ, Jin L, Liu MJ, Lee JM, Park DJ, Kim CJ. Solihabitans fulvus gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005110] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic study was carried out on an actinobacterial strain (AN110305T) isolated from soil sampled in the Republic of Korea. Cells of the strain were Gram-stain-positive, aerobic, non-motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of strain AN110305T with
Actinomycetia
, with highest pairwise sequence similarities to
Goodfellowiella coeruleoviolacea
DSM 43935T (97.6%),
Umezawaea tangerina
MK27-91F2T (97.0%),
Kutzneria chonburiensis
NBRC 110610T (96.9%),
Kutzneria buriramensis
A-T 1846T (96.8%),
Umezawaea endophytica
YIM 2047XT (96.8%),
Kutzneria albida
NRRL B-24060T (96.7%) and
Saccharothrix coeruleofusca
NRRL B-16115T (96.6%). Cells of strain AN110305T formed pale-yellow colonies on Reasoner's 2A agar. MK-9 (H4) (68%) and MK-10 (H4) (32%) were the predominant menaquinones. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethyl ethanolamine, hydroxy-phosphatidylethanolamine, an unidentified aminolipid and an unidentified aminophospholipid were major polar lipids. Iso-C16:0 (24.5%), anteiso-C15:0 (19.3%), anteiso-C17:0 (15.7%) and iso-C15:0 (15.2%) were the major fatty acids and meso-diaminopimelic acid was the pepdidoglycan. The cell-wall sugars were composed of galactose, glucose, mannose and ribose. The genomic DNA G+C content was 70.7 mol%. Based on genotypic and phenotypic data, strain AN110305T could be distinguished from all genera within the family
Pseudonocardiaceae
and represents a novel genus and species named Solihabitans fulvus gen. nov., sp nov. The type strain is AN110305T (=KCTC 39307T =DSM 103572T).
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Affiliation(s)
- Chun-Zhi Jin
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - Min-Jiao Liu
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jong-Min Lee
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Dong-Jin Park
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Chang-Jin Kim
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Teo WFA, Tan GYA, Li WJ. Taxonomic note on the family Pseudonocardiaceae based on phylogenomic analysis and descriptions of Allosaccharopolyspora gen. nov. and Halosaccharopolyspora gen. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34714227 DOI: 10.1099/ijsem.0.005075] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of members within the family Pseudonocardiaceae were assessed based on phylogenomic trees reconstructed using core-proteome and genome blast distance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the family Pseudonocardiaceae were analysed using overall genome-related indices based on average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values. The family Pseudonocardiaceae consists of the type genus Pseudonocardia, as well as the genera Actinoalloteichus, Actinocrispum, Actinokineospora, Actinomycetospora, Actinophytocola, Actinopolyspora, Actinorectispora, Actinosynnema, Allokutzneria, Allosaccharopolyspora gen. nov., Amycolatopsis, Bounagaea, Crossiella, Gandjariella, Goodfellowiella, Haloactinomyces, Haloechinothrix, Halopolyspora, Halosaccharopolyspora gen. nov., Herbihabitans, Kibdelosporangium, Kutzneria, Labedaea, Lentzea, Longimycelium, Prauserella, Saccharomonospora, Saccharopolyspora, Saccharothrix, Salinifilum, Sciscionella, Streptoalloteichus, Tamaricihabitans, Thermocrispum, Thermotunica and Umezawaea. The G+C contents of the Pseudonocardiaceae genomes ranged from 66.2 to 74.6 mol% and genome sizes ranged from 3.69 to 12.28 Mbp. Based on the results of phylogenomic analysis, the names Allosaccharopolyspora coralli comb. nov., Halosaccharopolyspora lacisalsi comb. nov. and Actinoalloteichus caeruleus comb. nov. are proposed. This study revealed that Actinokineospora mzabensis is a heterotypic synonym of Actinokineospora spheciospongiae, Lentzea deserti is a heterotypic synonym of Lentzea atacamensis, Prauserella endophytica is a heterotypic synonym of Prauserella coralliicola, and Prauserella flava and Prauserella sediminis are heterotypic synonyms of Prauserella salsuginis. This study addresses the nomenclature conundrums of Actinoalloteichus cyanogriseus and Streptomyces caeruleus as well as Micropolyspora internatus and Saccharomonospora viridis.
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Affiliation(s)
- Wee Fei Aaron Teo
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala, Lumpur, Malaysia
| | - Geok Yuan Annie Tan
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala, Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala, Lumpur, Malaysia
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, PR China
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Riahi HS, Heidarieh P, Fatahi-Bafghi M. Genus Pseudonocardia: What we know about its biological properties, abilities and current application in biotechnology. J Appl Microbiol 2021; 132:890-906. [PMID: 34469043 DOI: 10.1111/jam.15271] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
The genus Pseudonocardia belongs to a group of Actinomycetes, and is a member of the family Pseudonocardiacea. The members of this genus are aerobic, Gram-positive, non-motile bacteria that are commonly found in soil, plant and environment. Although this genus has a low clinical significance; however, it has an important role in biotechnology due to the production of secondary metabolites, some of which have anti-bacterial, anti-fungal and anti-tumour effects. The use of phenotypic tests, such as gelatinase activity, starch hydrolysis, catalase and oxidase tests, as well as molecular methods, such as polymerase chain reaction, are necessary for Pseudonocardia identification at the genus and species levels.
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Affiliation(s)
- Hanieh Sadat Riahi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Parvin Heidarieh
- Department of Bacteriology and Virology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Thermo-halotolerant mycelial bacteria from Algerian soils: Isolation, taxonomy and antagonistic properties. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.101972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China. PLoS One 2020; 15:e0236006. [PMID: 32649724 PMCID: PMC7351256 DOI: 10.1371/journal.pone.0236006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
Halophiles are relatively unexplored as potential sources of novel species.
However, little is known about the culturable bacterial diversity thrive in
hypersaline lakes. In this work, a total of 343 bacteria from sediment samples
of Aiding Lake, China, were isolated using nine different media supplemented
with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria
recovered from the different media varied, indicating the need to optimize the
isolation conditions. The results showed an unexpected level of bacterial
diversity, with four phyla (Actinobacteria,
Firmicutes, Proteobacteria, and
Rhodothermaeota), fourteen orders
(Actinopolysporales, Alteromonadales,
Bacillales, Balneolales,
Chromatiales, Glycomycetales,
Jiangellales, Micrococcales,
Micromonosporales, Oceanospirillales,
Pseudonocardiales, Rhizobiales,
Streptomycetales, and
Streptosporangiales), including 17 families, 43 genera
(including two novel genera), and 71 species (including four novel species). The
predominant phyla included Actinobacteria and Firmicutes and the predominant
genera included Actinopolyspora,
Gracilibacillus, Halomonas,
Nocardiopsis, and Streptomyces. To our
knowledge, this is the first time that members of phylum
Rhodothermaeota were identified in sediment samples from a
salt lake.
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