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Dutta S, Kothari S, Singh D, Ghosh S, Narayan Sarangi A, Sanjita Behera S, Prajapati S, Kumar Sinha P, Prusty A, Tripathy S. Novel oceanic cyanobacterium isolated from Bangaram island with profound acid neutralizing ability is proposed as Leptolyngbya iicbica sp. nov. strain LK. Mol Phylogenet Evol 2024; 197:108092. [PMID: 38723790 DOI: 10.1016/j.ympev.2024.108092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 05/04/2024] [Indexed: 05/19/2024]
Abstract
An acid-neutralizing, filamentous, non-heterocytous, marine cyanobacterium named 'LK' has been isolated from the seashore of Bangaram Island, an atoll of Lakshadweep, India, and is described here as a novel species. LK has been characterized using morphological, ecological, and genomic features. Based on 16S rRNA, whole-genome sequencing, and marker gene-based analysis, LK has been identified as a new species. LK clustered with Leptolyngbya-like strains belonging to the LPP group but diverged from Leptolyngbya sensu stricto, indicating the polyphyletic nature of the Leptolyngbya genus. Leptolyngbya sp. SIOISBB and Halomicronema sp. CCY15110 were identified as LK's two closest phylogenetic neighbors in various phylogenetic studies. The analysis of 16S rRNA, ITS secondary structures, and genome relatedness indices such as AAI, ANI, and gANI strongly support LK as a novel species of the Leptolyngbya genus. The mechanism behind acid neutralization in LK has been delineated, attributing it to a surface phenomenon most likely due to the presence of salts of calcium, magnesium, sodium, and potassium. We name LK as Leptolyngbya iicbica strain LK which is a novel species with prominent acidic pH-neutralizing properties.
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Affiliation(s)
- Subhajeet Dutta
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shreya Kothari
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Smruti Sanjita Behera
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Molecular Genetics Division, CSIR Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Satish Prajapati
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Prasanta Kumar Sinha
- Advanced Materials and Chemical Characterisation Division (AMCCD), CSIR-Central Glass & Ceramic Research Institute (CGCRI), Kolkata 700 032, West Bengal, India
| | - Asharani Prusty
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Wu Y, Wang H, Peng L, Zhao H, Zhang Q, Tao Q, Tang X, Huang R, Li B, Wang C. Root-soil-microbiome interaction in the rhizosphere of Masson pine (Pinus massoniana) under different levels of heavy metal pollution. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116779. [PMID: 39083870 DOI: 10.1016/j.ecoenv.2024.116779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/05/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
Heavy metal pollution of the soil affects the environment and human health. Masson pine is a good candidate for phytoremediation of heavy metal in mining areas. Microorganisms in the rhizosphere can help with the accumulation of heavy metal in host plants. However, studies on its rhizosphere bacterial communities under heavy metal pollution are still limited. Therefore, in this study, the chemical and bacterial characteristics of Masson pine rhizosphere under four different levels of heavy metal pollution were investigated using 16 S rRNA gene sequencing, soil chemistry and analysis of plant enzyme activities. The results showed that soil heavy metal content, plant oxidative stress and microbial diversity damage were lower the farther they were from the mine dump. The co-occurrence network relationship of slightly polluted soils (C1 and C2) was more complicated than that of highly polluted soils (C3 and C4). Relative abundance analysis indicated Sphingomonas and Pseudolabrys were more abundant in slightly polluted soils (C1 and C2), while Gaiella and Haliangium were more abundant in highly polluted soils (C3 and C4). LEfSe analysis indicated Burkholderiaceae, Xanthobacteraceae, Gemmatimonadaceae, Gaiellaceae were significantly enriched in C1 to C4 site, respectively. Mantel analysis showed that available cadmium (Cd) contents of soil was the most important factor influencing the bacterial community assembly. Correlation analysis showed that eight bacterial genus were significantly positively associated with soil available Cd content. To the best of our knowledge, this is the first study to investigate the rhizospheric bacterial community of Masson pine trees under different degrees of heavy metal contamination, which lays the foundation for beneficial bacteria-based phytoremediation using Masson pines in the future.
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Affiliation(s)
- Yingjie Wu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| | - Haidong Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Lu Peng
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Haiyang Zhao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiannian Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyan Tang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Rong Huang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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Gallo G, Imbimbo P, Aulitto M. The Undeniable Potential of Thermophiles in Industrial Processes. Int J Mol Sci 2024; 25:7685. [PMID: 39062928 PMCID: PMC11276739 DOI: 10.3390/ijms25147685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Extremophilic microorganisms play a key role in understanding how life on Earth originated and evolved over centuries. Their ability to thrive in harsh environments relies on a plethora of mechanisms developed to survive at extreme temperatures, pressures, salinity, and pH values. From a biotechnological point of view, thermophiles are considered a robust tool for synthetic biology as well as a reliable starting material for the development of sustainable bioprocesses. This review discusses the current progress in the biomanufacturing of high-added bioproducts from thermophilic microorganisms and their industrial applications.
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Affiliation(s)
- Giovanni Gallo
- Division of Microbiology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany;
| | - Paola Imbimbo
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Sant’Angelo, 80126 Napoli, Italy
| | - Martina Aulitto
- Department of Biology, University of Napoli Federico II, Complesso Universitario Monte Sant’Angelo, 80126 Napoli, Italy
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Ali A, Vishnivetskaya TA, Chauhan A. Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches. Braz J Microbiol 2024:10.1007/s42770-024-01365-3. [PMID: 38758507 DOI: 10.1007/s42770-024-01365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/08/2024] [Indexed: 05/18/2024] Open
Abstract
The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530 m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change.
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Affiliation(s)
- Ahmad Ali
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India
| | | | - Archana Chauhan
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India.
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Aguilar C, Alwali A, Mair M, Rodriguez-Orduña L, Contreras-Peruyero H, Modi R, Roberts C, Sélem-Mojica N, Licona-Cassani C, Parkinson EI. Actinomycetota bioprospecting from ore-forming environments. Microb Genom 2024; 10:001253. [PMID: 38743050 PMCID: PMC11165632 DOI: 10.1099/mgen.0.001253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.
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Affiliation(s)
- César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Amir Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Madeline Mair
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Carson Roberts
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | | | | | - Elizabeth Ivy Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
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Hezbri K, Kammoun I, Sbissi I, Klenk HP, Montero-Calasanz MDC, Ghodhbane-Gtari F, Gtari M. Blastococcus brunescens sp. nov., a member of the Geodermatophilaceae isolated from sandstone collected from the Sahara Desert in Tunisia. Int J Syst Evol Microbiol 2024; 74. [PMID: 38568050 DOI: 10.1099/ijsem.0.006317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
The taxonomic position of strain BMG 8361T, isolated from sandstone collected in the Sahara Desert of Southern Tunisia, was refined through a polyphasic taxonomic investigation. Colonies of BMG 8361T were pale-orange coloured, irregular with a dry surface and produced a diffusible pink or brown pigment depending on media. The Gram-positive cells were catalase-positive and oxidase-negative. The strain exhibited growth at 10-40 °C and pH values ranging from 5.5 to 9.0, with optima at 28-35 °C and pH 6.5-8.0. Additionally, BMG 8361T demonstrated the ability to grow in the presence of up to 1 % NaCl (w/v) concentration. The peptidoglycan of the cell wall contained meso-diaminopimelic acid, glucose, galactose, xylose, ribose, and rhamnose. The predominant menaquinones consisted of MK-9(H4) and MK-9. The main polar lipids were phosphatidylcholine, phosphatidylinositol, glycophosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified lipids. Major cellular fatty acids were iso-C16 : 0, iso-C16 : 1 h, and C17 : 1 ω8c. Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences assigned strain BMG 8361T within the genus Blastococcus. The highest pairwise sequence similarity observed in the 16S rRNA gene was 99.5 % with Blastococcus haudaquaticus AT 7-14T. However, when considering digital DNA-DNA hybridization and average nucleotide identity, the highest values, 48.4 and 86.58 %, respectively, were obtained with Blastococcus colisei BMG 822T. These values significantly undershoot the recommended thresholds for establishing new species, corroborating the robust support for the distinctive taxonomic status of strain BMG 8361T within the genus Blastococcus. In conjunction with the phenotyping results, this compelling evidence leads to the proposal of a novel species we named Blastococcus brunescens sp. nov. with BMG 8361T (=DSM 46845T=CECT 8880T) as the type strain.
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Affiliation(s)
- Karima Hezbri
- University of Carthage, National Institute of Applied Sciences and Technology, USCR Molecular Bacteriology and Genomics, Carthage, Tunisia
| | - Ikram Kammoun
- University of Carthage, National Institute of Applied Sciences and Technology, USCR Molecular Bacteriology and Genomics, Carthage, Tunisia
| | - Imed Sbissi
- Arid Regions Institute, LR Pastoral Ecology, Medenine, Tunisia
| | - Hans-Peter Klenk
- Newcastle University, School of Natural and Environmental Sciences, Newcastle upon Tyne, UK
| | | | - Faten Ghodhbane-Gtari
- University of Carthage, National Institute of Applied Sciences and Technology, USCR Molecular Bacteriology and Genomics, Carthage, Tunisia
- University of La Manouba, Higher Institute of Biotechnology of Sidi-Thabet, Manouba, Tunisia
| | - Maher Gtari
- University of Carthage, National Institute of Applied Sciences and Technology, USCR Molecular Bacteriology and Genomics, Carthage, Tunisia
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Suárez‐Moo P, Prieto‐Davó A. Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications. Microbiologyopen 2024; 13:e1407. [PMID: 38593340 PMCID: PMC11003711 DOI: 10.1002/mbo3.1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 04/11/2024] Open
Abstract
Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.
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Affiliation(s)
- Pablo Suárez‐Moo
- Unidad de Química‐Sisal, Facultad de QuímicaUniversidad Nacional Autónoma de MéxicoSisalYucatánMéxico
| | - Alejandra Prieto‐Davó
- Unidad de Química‐Sisal, Facultad de QuímicaUniversidad Nacional Autónoma de MéxicoSisalYucatánMéxico
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Barnés-Guirado M, Stchigel AM, Cano-Lira JF. A New Genus of the Microascaceae (Ascomycota) Family from a Hypersaline Lagoon in Spain and the Delimitation of the Genus Wardomyces. J Fungi (Basel) 2024; 10:236. [PMID: 38667907 PMCID: PMC11051006 DOI: 10.3390/jof10040236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
The Saladas de Sástago-Bujaraloz is an endorheic and arheic complex of lagoons located in the Ebro Basin and protected by the Ramsar Convention on Wetlands. Due to the semi-arid climate of the region and the high salinity of their waters, these lagoons constitute an extreme environment. We surveyed the biodiversity of salt-tolerant and halophilic fungi residents of the Laguna de Pito, a lagoon belonging to this complex. Therefore, we collected several samples of water, sediments, and soil of the periphery. Throughout the study, we isolated 21 fungal species, including a strain morphologically related to the family Microascaceae. However, this strain did not morphologically match any of genera within this family. After an in-depth morphological characterization and phylogenetic analysis using a concatenated sequence dataset of four phylogenetically informative molecular markers (the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA (nrDNA); the D1-D2 domains of the 28S gene of the nuclear ribosomal RNA (LSU); and a fragment of the translation elongation factor 1-alpha (EF-1α) and the β-tubulin (tub2) genes), we established the new genus Dactyliodendromyces, with Dactyliodendromyces holomorphus as its species. Additionally, as a result of our taxonomic study, we reclassified the paraphyletic genus Wardomyces into three different genera: Wardomyces sensu stricto, Parawardomyces gen. nov., and Pseudowardomyces gen. nov., with Parawardomyces ovalis (formerly Wardomyces ovalis) and Pseudowardomyces humicola (formerly Wardomyces humicola) as the type species of their respective genera. Furthermore, we propose new combinations, including Parawardomyces giganteus (formerly Wardomyces giganteus) and Pseudowardomyces pulvinatus (formerly Wardomyces pulvinatus).
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Affiliation(s)
| | - Alberto Miguel Stchigel
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain; (M.B.-G.); (J.F.C.-L.)
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Khilyas IV, Markelova MI, Valeeva LR, Ivoilova TM, Shagimardanova E, Laikov AV, Elistratova AA, Berkutova ES, Lochnit G, Sharipova MR. Genomic insights and anti-phytopathogenic potential of siderophore metabolome of endolithic Nocardia mangyaensis NH1. Sci Rep 2024; 14:5676. [PMID: 38453942 PMCID: PMC10920908 DOI: 10.1038/s41598-024-54095-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/08/2024] [Indexed: 03/09/2024] Open
Abstract
Actinobacteria are one of the predominant groups that successfully colonize and survive in various aquatic, terrestrial and rhizhospheric ecosystems. Among actinobacteria, Nocardia is one of the most important agricultural and industrial bacteria. Screening and isolation of Nocardia related bacteria from extreme habitats such as endolithic environments are beneficial for practical applications in agricultural and environmental biotechnology. In this work, bioinformatics analysis revealed that a novel strain Nocardia mangyaensis NH1 has the capacity to produce structurally varied bioactive compounds, which encoded by non-ribosomal peptide synthases (NRPS), polyketide synthase (PKS), and post-translationally modified peptides (RiPPs). Among NRPS, five gene clusters have a sequence homology with clusters encoding for siderophore synthesis. We also show that N. mangyaensis NH1 accumulates both catechol- and hydroxamate-type siderophores simultaneously under iron-deficient conditions. Untargeted LC-MS/MS analysis revealed a variety of metabolites, including siderophores, lipopeptides, cyclic peptides, and indole-3-acetic acid (IAA) in the culture medium of N. mangyaensis NH1 grown under iron deficiency. We demonstrate that four CAS (chrome azurol S)-positive fractions display variable affinity to metals, with a high Fe3+ chelating capability. Additionally, three of these fractions exhibit antioxidant activity. A combination of iron scavenging metabolites produced by N. mangyaensis NH1 showed antifungal activity against several plant pathogenic fungi. We have shown that the pure culture of N. mangyaensis NH1 and its metabolites have no adverse impact on Arabidopsis seedlings. The ability of N. mangyaensis NH1 to produce siderophores with antifungal, metal-chelating, and antioxidant properties, when supplemented with phytohormones, has the potential to improve the release of macro- and micronutrients, increase soil fertility, promote plant growth and development, and enable the production of biofertilizers across diverse soil systems.
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Affiliation(s)
- Irina V Khilyas
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation.
| | - Maria I Markelova
- Laboratory of Multiomics Technologies of Living Systems, Institute Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Liia R Valeeva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Tatiana M Ivoilova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Elena Shagimardanova
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation
- Life Improvement by Future Technologies (LIFT) Center, Moscow, Russian Federation
| | - Alexander V Laikov
- Laboratory of Multiomics Technologies of Living Systems, Institute Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Anna A Elistratova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Ekaterina S Berkutova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Guenter Lochnit
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Margarita R Sharipova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
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Fenibo EO, Nkuna R, Matambo T. Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land. Sci Rep 2024; 14:3866. [PMID: 38365802 PMCID: PMC10873323 DOI: 10.1038/s41598-024-53147-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024] Open
Abstract
Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence for Oilfield Chemical Research, University of Port Harcourt, Choba, Rivers State, Nigeria.
| | - Rosina Nkuna
- Department of Biotechnology, Faculty of Applied and Computer Sciences, Vaal University of Technology, Vanderbijlpark 1900, Gauteng, South Africa
- Centre for Competence in Environmental Biotechnology, College of Animal and Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
| | - Tonderayi Matambo
- Centre for Competence in Environmental Biotechnology, College of Animal and Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
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van Bergeijk DA, Augustijn HE, Elsayed SS, Willemse J, Carrión VJ, Du C, Urem M, Grigoreva LV, Cheprasov MY, Grigoriev S, Jansen H, Wintermans B, Budding AE, Spaink HP, Medema MH, van Wezel GP. Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000-year-old mammoth. Environ Microbiol 2024; 26:e16589. [PMID: 38356049 DOI: 10.1111/1462-2920.16589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024]
Abstract
Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.
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Affiliation(s)
- Doris A van Bergeijk
- Department of Microbiology, Immunology and Transplantation (Laboratory of Molecular Bacteriology), KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Hannah E Augustijn
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | | | - Joost Willemse
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Victor J Carrión
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbiology, University of Málaga, Málaga, Spain
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Chao Du
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Mia Urem
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | | | | | | | - Bas Wintermans
- Department of Medical Microbiology, Adrz Hospital, Goes, The Netherlands
| | | | - Herman P Spaink
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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12
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Perez-Bou L, Muñoz-Palazon B, Gonzalez-Lopez J, Gonzalez-Martinez A, Correa-Galeote D. Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes. MICROBIAL ECOLOGY 2023; 87:14. [PMID: 38091083 DOI: 10.1007/s00248-023-02325-4] [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: 09/03/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023]
Abstract
Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.
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Affiliation(s)
- Lizandra Perez-Bou
- Department of Microbiology and Virology, Faculty of Biology, University of Havana, Havana, Cuba
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
| | - Barbara Muñoz-Palazon
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jesus Gonzalez-Lopez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Alejandro Gonzalez-Martinez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - David Correa-Galeote
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain.
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.
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13
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Razmilic V, Nouioui I, Karlyshev A, Jawad R, Trujillo ME, Igual JM, Andrews BA, Asenjo JA, Carro L, Goodfellow M. Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov., isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Central Andes in Chile. Int J Syst Evol Microbiol 2023; 73. [PMID: 38059605 DOI: 10.1099/ijsem.0.006189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Two novel Micromonospora strains, STR1-7T and STR1S-6T, were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora. They grew from 20 to 37 °C, from pH7 to 8 and in the presence of up to 3 %, w/v NaCl. The isolates formed distinct branches in Micromonospora gene trees based on 16S rRNA gene sequences and on a multi-locus sequence analysis of conserved house-keeping genes. A phylogenomic tree generated from the draft genomes of the isolates and their closest phylogenetic neighbours showed that isolate STR1-7T is most closely related to Micromonospora orduensis S2509T, and isolate STR1S-6 T forms a distinct branch that is most closely related to 12 validly named Micromonospora species, including Micromonospora saelicesensis the earliest proposed member of the group. The isolates were separated from one another and from their closest phylogenomic neighbours using a combination of chemotaxonomic, genomic and phenotypic features, and by low average nucleotide index and digital DNA-DNA hybridization values. Consequently, it is proposed that isolates STR1-7T and STR1S-6T be recognized as representing new species in the genus Micromonospora, namely as Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov.; the type strains are STR1-7T (=CECT 9665T=LMG 30768T) and STR1S-6T (=CECT 9666T=LMG 30770T), respectively. Genome mining showed that the isolates have the capacity to produce novel specialized metabolites, notably antibiotics and compounds that promote plant growth, as well as a broad-range of stress-related genes that provide an insight into how they cope with harsh abiotic conditions that prevail in high-altitude Atacama Desert soils.
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Affiliation(s)
- Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Andrey Karlyshev
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Rana Jawad
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Jose M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
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14
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Bootrak D, Rongsayamanont W, Jaidumrong T, Rongsayamanont C. Effect of phosphorylated polyvinyl alcohol matrix size of cell entrapment on partial nitrification of ammonia in wastewater. ENVIRONMENTAL TECHNOLOGY 2023; 44:4033-4045. [PMID: 35549830 DOI: 10.1080/09593330.2022.2078231] [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: 12/23/2021] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Partial nitrification is known as first and critical step for autotrophic nitrogen removal in high strength nitrogenous wastewater. Phosphorylated polyvinyl alcohol gel entrapment was used for suppressing oxygen to nitrite-oxidizing bacteria (NOB) in the gel matrix. The study investigated the effect of the size of gel matrix on partial nitrification. Results show that ammonia-oxidizing bacteria (AOB) proportion in the inoculum rather than the size of gel matrix governed ammonia oxidation. Nitrite oxidation depended on the size of gel matrix not the relative proportions of NOB and AOB in the inoculum. Larger size of gel matrix lead to less in situ oxygen penetration and available for NOB resulting in higher nitrite accumulation. This finding gains a better understanding of using suitable inoculum to control partial nitrification that is beneficial for the preparation of anaerobic ammonium oxidation-suited effluent.
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Affiliation(s)
- Darak Bootrak
- Faculty of Environmental Management, Prince of Songkla University, Songkhla, Thailand
| | | | - Tunyakamon Jaidumrong
- Faculty of Environmental Management, Prince of Songkla University, Songkhla, Thailand
| | - Chaiwat Rongsayamanont
- Faculty of Environmental Management, Prince of Songkla University, Songkhla, Thailand
- Environmental Assessment and Technology for Hazardous Waste Management Research Center, Faculty of Environmental Management, Prince of Songkla University, Songkhla, Thailand
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15
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Liu L, Liu Y, Liu S, Nikandrova AA, Imamutdinova AN, Lukianov DA, Osterman IA, Sergiev PV, Zhang B, Zhang D, Li F, Sun C. Bioprospecting for the soil-derived actinobacteria and bioactive secondary metabolites on the Western Qinghai-Tibet Plateau. Front Microbiol 2023; 14:1247001. [PMID: 37886074 PMCID: PMC10599150 DOI: 10.3389/fmicb.2023.1247001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Introduction The increase in incidence of multidrug-resistant bacteria and the inadequacy of new antimicrobial drugs have led to a widespread outbreak of bacterial antimicrobial resistance. To discover new antibiotics, biodiversity, and novelty of culturable actinobacteria dwelled in soil of the Western Qinghai-Tibet Plateau were investigated. By integrating antibacterial assay with omics tools, Amycolatopsis sp. A133, a rare actinobacterial strain and its secondary metabolites were further studied. Method Culture-dependent method was used to obtain actinobacterial strains from two soil samples collected from Ali region in Qinghai-Tibet Plateau. The cultural extractions of representative strains were assayed against "ESKAPE" pathogens by paper-disk diffusion method and the double fluorescent protein reporter "pDualrep2" system. An Amycolatopsis strain coded as A133 was prioritized and its secondary metabolites were further analyzed and annotated by omics tools including antiSMASH and GNPS (Global Natural Social Molecular Networking). The predicted rifamycin analogs produced by Amycolatopsis sp. A133 were isolated and identified by chromatographic separation, such as Sephadex LH-20 and HPLC, and spectral analysis, such as NMR and UPLC-HRESI-MS/MS, respectively. Results A total of 406 actinobacteria strains affiliated to 36 genera in 17 families of 9 orders were isolated. Out of 152 representative strains, 63 isolates exhibited antagonistic activity against at least one of the tested pathogens. Among them, 7 positive strains were identified by the "pDualrep2" system as either an inhibitor of protein translation or DNA biosynthesis. The cultural broth of Amycolatopsis sp. A133 exhibited a broader antimicrobial activity and can induce expression of TurboRFP. The secondary metabolites produced by strain A133 was annotated as rifamycins and zampanolides by antiSMASH and GNPS analysis. Five members of rifamycins, including rifamycin W, protorifamycin I, rifamycin W-M1, proansamycin B, and rifamycin S, were purified and identified. Rifamycin W-M1, was found as a new member of the naturally occurring rifamycin group of antibiotics. Discussion Assisted by omics tools, the successful and highly efficient discovery of rifamycins, a group of clinically used antibiotics from actinobacteria in Ali area encouraged us to devote more energy to explore new antibiotics from the soils on the Western Tibetan Plateau.
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Affiliation(s)
- Lifang Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuyu Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shaowei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Arina A. Nikandrova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arina N. Imamutdinova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Benyin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Dejun Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Feina Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
| | - Chenghang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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16
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Faulkner M, Hoeven R, Kelly PP, Sun Y, Park H, Liu LN, Toogood HS, Scrutton NS. Chemoautotrophic production of gaseous hydrocarbons, bioplastics and osmolytes by a novel Halomonas species. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:152. [PMID: 37821908 PMCID: PMC10568851 DOI: 10.1186/s13068-023-02404-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Production of relatively low value, bulk commodity chemicals and fuels by microbial species requires a step-change in approach to decrease the capital and operational costs associated with scaled fermentation. The utilisation of the robust and halophilic industrial host organisms of the genus Halomonas could dramatically decrease biomanufacturing costs owing to their ability to grow in seawater, using waste biogenic feedstocks, under non-sterile conditions. RESULTS We describe the isolation of Halomonas rowanensis, a novel facultative chemoautotrophic species of Halomonas from a natural brine spring. We investigated the ability of this species to produce ectoine, a compound of considerable industrial interest, under heterotrophic conditions. Fixation of radiolabelled NaH14CO3 by H. rowanensis was confirmed in mineral medium supplied with thiosulfate as an energy source. Genome sequencing suggested carbon fixation proceeds via a reductive tricarboxylic acid cycle, and not the Calvin-Bensen-Bassham cycle. The mechanism of energy generation to support chemoautotrophy is unknown owing to the absence of an annotated SOX-based thiosulfate-mediated energy conversion system. We investigated further the biotechnological potential of the isolated H. rowanensis by demonstrating production of the gaseous hydrocarbon (bio-propane), bioplastics (poly-3-hydroxybutyrate) and osmolytes (ectoine) under heterotrophic and autotrophic CO2 fixation growth conditions. CONCLUSIONS This proof-of-concept study illustrates the value of recruiting environmental isolates as industrial hosts for chemicals biomanufacturing, where CO2 utilisation could replace, or augment, the use of biogenic feedstocks in non-sterile, industrialised bioreactors.
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Affiliation(s)
- Matthew Faulkner
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Robin Hoeven
- C3 Biotechnologies Ltd, 20 Mannin Way, Caton Road, Lancaster, LA1 35W, Lancashire, UK
- Engineering Building A, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Paul P Kelly
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - Helen Park
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - Helen S Toogood
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- C3 Biotechnologies Ltd, 20 Mannin Way, Caton Road, Lancaster, LA1 35W, Lancashire, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- C3 Biotechnologies Ltd, 20 Mannin Way, Caton Road, Lancaster, LA1 35W, Lancashire, UK.
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17
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Sriragavi G, Sangeetha M, Santhakumar M, Lokesh E, Nithyalakshmi M, Saleel CA, Balagurunathan R. Exploring Antibacterial Properties of Bioactive Compounds Isolated from Streptomyces sp. in Bamboo Rhizosphere Soil. ACS OMEGA 2023; 8:36333-36343. [PMID: 37810705 PMCID: PMC10552487 DOI: 10.1021/acsomega.3c04954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
The increasing concern over multidrug resistance in pathogens has led to an ongoing search for novel antibiotics derived from soil actinobacteria. In this current investigation, actinobacteria were isolated from the rhizosphere of bamboo plants collected within the Megamalai forest of the Western Ghats in the Theni zone of Tamil Nadu, India. These actinobacteria were subjected to characterization, and their growth conditions were optimized to enhance the production of bioactive compounds. To assess antibacterial properties, the isolated Actinobacteria underwent testing using the agar plug method. The strain exhibiting notable antibacterial activity underwent further characterization through 16s rRNA gene sequencing and subsequent phylogenetic analysis. Employing response surface methodology (RSM), cultural conditions were fine-tuned. Bioactive compounds were extracted from the culture medium using ethyl acetate, and their antibacterial and antioxidant effects were evaluated through disc diffusion and DPPH radical scavenging methods, respectively. Ethyl acetate extracts were analyzed by using FT-IR and GC-MS techniques. In total, nine strains of Actinobacteria were isolated from the rhizosphere soil of bamboo. Among these, strain BS-16 displayed remarkable antibacterial activity against three strains: Staphylococcus aureus (19 mm), Bacillus subtilis (12 mm), and Streptococcus pyogenes (10 mm). This strain was identified as Streptomyces sp. The optimal conditions for bioactive compound production were determined as follows: malt extract (10 g), yeast extract (5 g), dextrose (5 g), pH 6.5, and temperature 30 °C. After a 7-day incubation period, the results showed a 6% increase in production. The ethyl acetate fraction derived from strain BS-16 exhibited dose-dependent antibacterial and antioxidant activities. FT-IR and GC-MS analyses revealed the presence of active compounds with antibacterial effects within the extract. Consequently, further investigation into the BS-16 strain holds promise for scaling up the production of bioactive compounds possessing antibacterial and antioxidant properties.
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Affiliation(s)
- Govindaraj Sriragavi
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Murthy Sangeetha
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Munusamy Santhakumar
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Elumalai Lokesh
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Mohanam Nithyalakshmi
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
| | - Chanduveetil Ahamed Saleel
- Department
of Mechanical Engineering, College of Engineering, King Khalid University, P.O. Box 394, Abha 61421, Saudi Arabia
| | - Ramasamy Balagurunathan
- Actinobacterial
Research Laboratory, Department of Microbiology, Periyar University, Salem 636011, Tamilnadu, India
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18
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Liu SW, Zhai XX, Liu D, Liu YY, Sui LY, Luo KK, Yang Q, Li FN, Nikandrova AA, Imamutdinova AN, Lukianov DA, Osterman IA, Sergiev PV, Zhang BY, Zhang DJ, Xue CM, Sun CH. Bioprospecting of Actinobacterial Diversity and Antibacterial Secondary Metabolites from the Sediments of Four Saline Lakes on the Northern Tibetan Plateau. Microorganisms 2023; 11:2475. [PMID: 37894133 PMCID: PMC10609225 DOI: 10.3390/microorganisms11102475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
The Tibetan Plateau, known as the "Roof of the World" and "The Third Pole", harbors numerous saline lakes primarily distributed in the Northern Tibetan Plateau. However, the challenging conditions of high altitude, low oxygen level, and harsh climate have limited investigations into the actinobacteria from these saline lakes. This study focuses on investigating the biodiversity and bioactive secondary metabolites of cultivable actinobacteria isolated from the sediments of four saline lakes on the Northern Tibetan Plateau. A total of 255 actinobacterial strains affiliated with 21 genera in 12 families of 7 orders were recovered by using the pure culture technique and 16S rRNA gene phylogenetic analysis. To facilitate a high-throughput bioactivity evaluation, 192 isolates underwent OSMAC cultivation in a miniaturized 24-well microbioreactor system (MATRIX cultivation). The antibacterial activity of crude extracts was then evaluated in a 96-well plate antibacterial assay. Forty-six strains demonstrated antagonistic effects against at least one tested pathogen, and their underlying antibacterial mechanisms were further investigated through a dual-fluorescent reporter assay (pDualrep2). Two Streptomyces strains (378 and 549) that produce compounds triggering DNA damage were prioritized for subsequent chemical investigations. Metabolomics profiling involving HPLC-UV/vis, UPLC-QTOF-MS/MS, and molecular networking identified three types of bioactive metabolites belonging to the aromatic polyketide family, i.e., cosmomycin, kidamycin, and hedamycin. In-depth analysis of the metabolomic data unveiled some potentially novel anthracycline compounds. A genome mining study based on the whole-genome sequences of strains 378 and 549 identified gene clusters potentially responsible for cosmomycin and kidamycin biosynthesis. This work highlights the effectiveness of combining metabolomic and genomic approaches to rapidly identify bioactive chemicals within microbial extracts. The saline lakes on the Northern Tibetan Plateau present prospective sources for discovering novel actinobacteria and biologically active compounds.
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Affiliation(s)
- Shao-Wei Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Xiao-Xu Zhai
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Di Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Yu-Yu Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Li-Ying Sui
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ke-Ke Luo
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Qin Yang
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Fei-Na Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing 100045, China;
| | - Arina A. Nikandrova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Arina N. Imamutdinova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ben-Yin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
| | - De-Jun Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
| | - Chun-Mei Xue
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Cheng-Hang Sun
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
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19
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Hong Q, Guo MM, Yang J, Wei X, Liao L, Xin XJ, Zhang D, An FL. Four previously undescribed diketopiperazines from marine fungus Aspergillus puniceus FAHY0085 and their effects on liver X receptor α. PHYTOCHEMISTRY 2023; 214:113816. [PMID: 37536654 DOI: 10.1016/j.phytochem.2023.113816] [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: 04/16/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
Four previously undescribed diketopiperazine-type alkaloids including one oxepin-containing diketopiperazine-type alkaloid, oxepinamide L (1), three 4-quinazolinone alkaloids, puniceloids E-G (10-12), together with 12 known analogues, protuboxepin D (2), oxepinamides D-G, J-K and I (3-9), puniceloids B-D (13-15) and protubonine B (16), were isolated from the culture of the marine-derived fungus Aspergillus puniceus FAHY0085. The structures of the previously undescribed compounds were comprehensively elucidated by detailed interpretation of their NMR and HRESIMS data. Their absolute configurations were unambiguously determined by ROESY experiments, Marfey's method, calculated ECD experiments and single-crystal X-ray diffraction analysis. Compounds (3-4, 6-8, 14-15) were evaluated for their cytotoxic activity against HepG2, MCF-7, SW1116 and HeLa cells and compound 6 and 14 showed moderate cytotoxic activity against HeLa cells with IC50 49.61 ± 2.91 and 28.38 ± 1.57 μM, respectively. Compounds (1-8, 11-15) were screened for their transcriptional activation of liver X receptor α and compound 11 with known compounds 13-15 showed significant transcriptional activation of liver X receptor α with EC50 values in the range 2-50 μM.
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Affiliation(s)
- Qi Hong
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Miao-Miao Guo
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, No. 11/33, Fucheng Road, Beijing, 100048, China
| | - Jin Yang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xing Wei
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Li Liao
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, 200136, China; School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiu-Juan Xin
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Di Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China; Jiangsu Institute of Marine Resources Development, School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, PR China.
| | - Fa-Liang An
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, No.4, Lane 218, Haiji Sixth Road, Shanghai, 201306, China.
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20
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Li S, Lian WH, Han JR, Ali M, Lin ZL, Liu YH, Li L, Zhang DY, Jiang XZ, Li WJ, Dong L. Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis. NPJ Biofilms Microbiomes 2023; 9:67. [PMID: 37736746 PMCID: PMC10516943 DOI: 10.1038/s41522-023-00439-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
- School of Life Science, Jiaying University, Meizhou, 514015, China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Dong-Ya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Xian-Zhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
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21
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Barosa B, Ferrillo A, Selci M, Giardina M, Bastianoni A, Correggia M, di Iorio L, Bernardi G, Cascone M, Capuozzo R, Intoccia M, Price R, Vetriani C, Cordone A, Giovannelli D. Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy. Front Microbiol 2023; 14:1134114. [PMID: 37637107 PMCID: PMC10452888 DOI: 10.3389/fmicb.2023.1134114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.
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Affiliation(s)
- Bernardo Barosa
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Matteo Selci
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Marco Giardina
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Alessia Bastianoni
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Monica Correggia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Luciano di Iorio
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Martina Cascone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Rosaria Capuozzo
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Michele Intoccia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Roy Price
- School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Costantino Vetriani
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
| | - Angelina Cordone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples “Federico II”, Naples, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
- Istituto per le Risorse Biologiche e Biotecnologiche Marine, Consiglio Nazionale Delle Ricerche, CNR-IRBIM, Ancona, Italy
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, Japan
- Marine Chemistry and Geochemistry Department–Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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22
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Sajjad W, Nadeem M, Alam T, Rehman AU, Abbasi SW, Ahmad S, Din G, Khan S, Badshah M, Gul S, Farman M, Shah AA. Biological Evaluation and Computational Studies of Methoxy-flavones from Newly Isolated Radioresistant Micromonospora aurantiaca Strain TMC-15. Appl Biochem Biotechnol 2023; 195:4915-4935. [PMID: 37115385 DOI: 10.1007/s12010-023-04517-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/29/2023]
Abstract
This study aims to determine UV-B resistance and to investigate computational analysis and antioxidant potential of methoxy-flavones of Micromonospora aurantiaca TMC-15 isolated from Thal Desert, Pakistan. The cellular extract was purified through solid-phase extraction and UV-Vis spectrum analysis indicated absorption peaks at λmax 250 nm, 343 nm, and 380 nm that revealed the presence of methoxy-flavones named eupatilin and 5-hydroxyauranetin. The flavones were evaluated for their antioxidant as well as protein and lipid peroxidation inhibition potential using di(phenyl)-(2,4,6-trinitrophenyl) iminoazanium (DPPH), 2,4-dinitrophenyl hydrazine (DNPH), and thiobarbituric acid reactive substances (TBARS) assays, respectively. The methoxy-flavones were further studied for their docking affinity and interaction dynamics to determine their structural and energetic properties at the atomic level. The antioxidant potential, protein, and lipid oxidation inhibition and DNA damage preventive abilities were correlated as predicted by computational analysis. The eupatilin and 5-hydroxyauranetin binding potential to their targeted proteins 1N8Q and 1OG5 is - 4.1 and - 7.5 kcal/mol, respectively. Moreover, the eupatiline and 5-hydroxyauranetin complexes illustrate van der Waals contacts and strong hydrogen bonds to their respective enzymes target. Both in vitro studies and computational analysis results revealed that methoxy-flavones of Micromonospora aurantiaca TMC-15 can be used against radiation-mediated oxidative damages due to its kosmotrophic nature. The demonstration of good antioxidant activities not only protect DNA but also protein and lipid oxidation and therefore could be a good candidate in radioprotective drugs and as sunscreen due to its kosmotropic nature.
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Affiliation(s)
- Wasim Sajjad
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Mahnoor Nadeem
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Tayyaba Alam
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Asim Ur Rehman
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Ghufranud Din
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
- Department of Medical Laboratory Technology, University of Haripur, Haripur, 22620, Pakistan
| | - Samiullah Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Malik Badshah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Sarah Gul
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Muhammad Farman
- Department of Chemistry, Faculty of Natural Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
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23
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Chavarria-Quicaño E, Contreras-Jácquez V, Carrillo-Fasio A, De la Torre-González F, Asaff-Torres A. Native Bacillus paralicheniformis isolate as a potential agent for phytopathogenic nematodes control. Front Microbiol 2023; 14:1213306. [PMID: 37588888 PMCID: PMC10425774 DOI: 10.3389/fmicb.2023.1213306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/07/2023] [Indexed: 08/18/2023] Open
Abstract
Phytopathogenic nematodes (PPNs) are responsible for substantial damages within agricultural crops worldwide which can be controlled employing beneficial microorganisms and/or their metabolites in an ecofriendly way. Nevertheless, the success of the control regards not only on the virulence of the strains or the toxicity of their metabolites but also on their ability to colonize and remain in the rhizospheric environment, particularly in those crops affected by abiotic stresses promoted by the climate change. Consequently, the bioprospection of beneficial microorganisms able to control PPNs and to thrive in adverse conditions has attracted attention. On this way, deserts are perfect ecological niches to isolate microorganisms adapted to harsh enviroments. The purpose of this research was to isolate and characterize bacteria from rhizospheric soil samples collected in the Northwestern Desert of Mexico with potential for PPNs control. As first screening, secretomes of each isolate were tested in vitro for nematicidal activity (NA). Then, activities from secretomes and endospores from the selected isolate were confirmed in vivo assays. From 100 thermotolerant isolates, the secretome of the isolate identified as Bacillus paralicheniformis TB197 showed the highest NA (>95%) against Meloidogyne incognita, both in vitro and in vivo tests, suppressing infections caused by M. enterolobii in tomato crops, too. In open field tests, the endospores of TB197 strain showed a reduction of 81% in the infection severity caused by M. enterolobii (p ≤ 0.05), while the galling index (GI) was reduced 84% (p ≤ 0.05) in tomato greenhouse-tests. Also, a reduction of the root necrosis (81%) caused by Radopholus similis in banana plantations (p ≤ 0.05), compared to the control was observed. Owing to their efficacy in controlling PPNs infections, the endospores and secondary metabolites of B. paralicheniformis TB197 strain could be used in bionematicidal formulations.
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Affiliation(s)
- Estefany Chavarria-Quicaño
- Laboratory of Industrial Biotechnology, Department of Food Science, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Victor Contreras-Jácquez
- Laboratory of Industrial Biotechnology, Department of Food Science, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Armando Carrillo-Fasio
- Laboratory of Nematology, Centro de Investigación en Alimentación y Desarrollo, Culiacán, Mexico
| | | | - Ali Asaff-Torres
- Laboratory of Industrial Biotechnology, Department of Food Science, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
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24
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Kiss A, Hariri Akbari F, Marchev A, Papp V, Mirmazloum I. The Cytotoxic Properties of Extreme Fungi's Bioactive Components-An Updated Metabolic and Omics Overview. Life (Basel) 2023; 13:1623. [PMID: 37629481 PMCID: PMC10455657 DOI: 10.3390/life13081623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 08/27/2023] Open
Abstract
Fungi are the most diverse living organisms on planet Earth, where their ubiquitous presence in various ecosystems offers vast potential for the research and discovery of new, naturally occurring medicinal products. Concerning human health, cancer remains one of the leading causes of mortality. While extensive research is being conducted on treatments and their efficacy in various stages of cancer, finding cytotoxic drugs that target tumor cells with no/less toxicity toward normal tissue is a significant challenge. In addition, traditional cancer treatments continue to suffer from chemical resistance. Fortunately, the cytotoxic properties of several natural products derived from various microorganisms, including fungi, are now well-established. The current review aims to extract and consolidate the findings of various scientific studies that identified fungi-derived bioactive metabolites with antitumor (anticancer) properties. The antitumor secondary metabolites identified from extremophilic and extremotolerant fungi are grouped according to their biological activity and type. It became evident that the significance of these compounds, with their medicinal properties and their potential application in cancer treatment, is tremendous. Furthermore, the utilization of omics tools, analysis, and genome mining technology to identify the novel metabolites for targeted treatments is discussed. Through this review, we tried to accentuate the invaluable importance of fungi grown in extreme environments and the necessity of innovative research in discovering naturally occurring bioactive compounds for the development of novel cancer treatments.
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Affiliation(s)
- Attila Kiss
- Agro-Food Science Techtransfer and Innovation Centre, Faculty for Agro, Food and Environmental Science, Debrecen University, 4032 Debrecen, Hungary;
| | - Farhad Hariri Akbari
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Andrey Marchev
- Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000 Plovdiv, Bulgaria
| | - Viktor Papp
- Department of Botany, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary;
| | - Iman Mirmazloum
- Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary
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25
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Wijayawardene NN, Boonyuen N, Ranaweera CB, de Zoysa HKS, Padmathilake RE, Nifla F, Dai DQ, Liu Y, Suwannarach N, Kumla J, Bamunuarachchige TC, Chen HH. OMICS and Other Advanced Technologies in Mycological Applications. J Fungi (Basel) 2023; 9:688. [PMID: 37367624 DOI: 10.3390/jof9060688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.
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Affiliation(s)
- Nalin N Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
- Section of Genetics, Institute for Research and Development in Health and Social Care, No: 393/3, Lily Avenue, Off Robert Gunawardane Mawatha, Battaramulla 10120, Sri Lanka
| | - Nattawut Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chathuranga B Ranaweera
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, General Sir John Kotelawala Defence University Sri Lanka, Kandawala Road, Rathmalana 10390, Sri Lanka
| | - Heethaka K S de Zoysa
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Rasanie E Padmathilake
- Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Pulliyankulama, Anuradhapura 50000, Sri Lanka
| | - Faarah Nifla
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Dong-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Yanxia Liu
- Guizhou Academy of Tobacco Science, No.29, Longtanba Road, Guanshanhu District, Guiyang 550000, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thushara C Bamunuarachchige
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Huan-Huan Chen
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Agricultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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26
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Schultz J, Modolon F, Peixoto RS, Rosado AS. Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles. Front Microbiol 2023; 14:1167718. [PMID: 37333658 PMCID: PMC10272570 DOI: 10.3389/fmicb.2023.1167718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.
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Affiliation(s)
- Júnia Schultz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Flúvio Modolon
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Shaffer JMC, Giddings LA, Samples RM, Mikucki JA. Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat. Front Microbiol 2023; 14:1156033. [PMID: 37250028 PMCID: PMC10213415 DOI: 10.3389/fmicb.2023.1156033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01's genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC-MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.
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Affiliation(s)
- Jacob M. C. Shaffer
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | | | - Robert M. Samples
- Department of Chemistry, Smith College, Northampton, MA, United States
| | - Jill A. Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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Shumilov OI, Kasatkina EA, Kirtsideli IY, Makarov DV. Tolerance of Rare-Earth Elements in Extremophile Fungus Umbelopsis isabellina from Polar Loparite Ore Tailings in Northwestern Russia. J Fungi (Basel) 2023; 9:jof9050506. [PMID: 37233217 DOI: 10.3390/jof9050506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023] Open
Abstract
In this study, extremophile fungal species isolated from pure loparite-containing sands and their tolerance/resistance to the lanthanides Ce and Nd were investigated. The loparite-containing sands were collected at the tailing dumps of an enterprise developing a unique polar deposit of niobium, tantalum and rare-earth elements (REEs) of the cerium group: the Lovozersky Mining and Processing Plant (MPP), located in the center of the Kola Peninsula (northwestern Russia). From the 15 fungal species found at the site, one of the most dominant isolates was identified by molecular analysis as the zygomycete fungus Umbelopsis isabellina (GenBank accession no. OQ165236). Fungal tolerance/resistance was evaluated using different concentrations of CeCl3 and NdCl3. Umbelopsis isabellina exhibited a higher degree of tolerance/resistance to cerium and neodymium than did the other dominant isolates (Aspergillus niveoglaucus, Geomyces vinaceus and Penicillium simplicissimum). The fungus began to be inhibited only after being exposed to 100 mg L-1 of NdCl3. The toxic effects of Ce were not observed in fungus growth until it was subjected to 500 mg∙L-1 of CeCl3. Moreover, only U. isabellina started to grow after extreme treatment with 1000 mg∙L-1 of CeCl3 one month after inoculation. This work indicates, for the first time, the potential of Umbelopsis isabellina to remove REEs from the loparite ore tailings, making it a suitable candidate for the development of bioleaching methods.
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Affiliation(s)
- Oleg I Shumilov
- Institute of North Industrial Ecology Problems, Kola Science Centre, Russian Academy of Sciences, 184209 Apatity, Russia
| | - Elena A Kasatkina
- Institute of North Industrial Ecology Problems, Kola Science Centre, Russian Academy of Sciences, 184209 Apatity, Russia
| | - Irina Y Kirtsideli
- Komarov Botanical Institute, Russian Academy of Sciences, 197376 Saint Petersburg, Russia
| | - Dmitry V Makarov
- Institute of North Industrial Ecology Problems, Kola Science Centre, Russian Academy of Sciences, 184209 Apatity, Russia
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Alhadrami HA, Sayed AM, Hassan HM, Rateb ME. Aloin A inhibits SARS CoV-2 replication by targeting its binding with ACE2 - Evidence from modeling-supported molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:11647-11656. [PMID: 36755429 DOI: 10.1080/07391102.2023.2175262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/01/2023] [Indexed: 02/10/2023]
Abstract
The current study aimed to expand on the recently published results and assess the inhibitory efficacy of aloin A against SARS CoV-2. In vitro testing of aloin A against SARS CoV-2 proteases (i.e., MPro and PLPro) showed weak to moderate activity (IC50 = 68.56 ± 1.13 µM and 24.77 ± 1.57 µM, respectively). However, aloin A was able to inhibit the replication of SARS CoV-2 in Vero E6 cells efficiently with an IC50 of 0.095 ± 0.022 µM. Depending on the reported poor permeability of aloin A alongside its insignificant protease inhibitory activities presented in this study, we ran a number of extensive virtual screenings and physics-based simulations to determine the compound's potential mode of action. As a result, RBD-ACE2 was identified as a key target for aloin A. Results from 600 ns-long molecular dynamics (MD) simulation experiments pointed to aloin A's role as an RBD-ACE2 destabilizer. Therefore, the results of this work may pave the way for further development of this scaffold and the eventual production of innovative anti-SARS CoV-2 medicines with several mechanisms of action.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hani A Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Molecular Diagnostic Laboratory, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, King Abdulaziz University Hospital, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Hossam M Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Mostafa E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, Scotland
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Pushparaj K, Meyyazhagan A, Bhotla HK, Arumugam VA, Pappuswamy M, Vadivalagan C, Hakeem KR, Balasubramanian B, Liu W, Mousavi Khaneghah A. The crux of bioactive metabolites in endophytic and thermophilic fungi and their proximal prospects in biotechnological and industrial domains. Toxicon 2023; 223:107007. [PMID: 36563862 DOI: 10.1016/j.toxicon.2022.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Fungi are ubiquitous in distribution and are found in grasses to hot springs. Their mode of nutrition provides sustenance for living and propagation. Ironically, varied fungal species have developed customized strategies for protection and survival by producing diverse secondary metabolites. The review aimed to project the contrasting potential features of the endophytic and thermophilic fungi groups. The metabolites and the enzymes of endophytic and thermophilic fungi served as the backbone to thrive and adapt within-host and in extreme conditions like higher pH, heat, and salinity, respectively. Identification, knowledge of their biochemistry and pathway, exploration, production, and utilization of these bioactive molecules in various commercial, industrial, and pharmaceutical domains were briefly discussed. The uniqueness of endophytes includes stress management and improved biomass production of the host, green fuel production, omnipresence, selected triple-symbiosis with the virus, synthesis of polyketides, and other active metabolites are widely used in biomedical applications and agriculture management. This review attempted to limelight the specific applications of thermophilic fungal metabolites and the roles of thermo-stable enzymes in bioprospecting. Moreover, probing the metabolites of thermophiles rendered novel antibiotic compounds, which were proven effective against multi-drug resistant bacteria and harboured the potential to curtail infectious diseases.
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Affiliation(s)
- Karthika Pushparaj
- Department of Zoology, School of Biosciences, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641 043, Tamil Nadu, India
| | - Arun Meyyazhagan
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | - Haripriya Kuchi Bhotla
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | - Vijaya Anand Arumugam
- Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, 641 046, Tamil Nadu, India
| | - Manikantan Pappuswamy
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | | | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | | | - Wenchao Liu
- Department of Animal Science, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China.
| | - Amin Mousavi Khaneghah
- Department of Fruit and Vegetable Product Technology, Prof. WacławDąbrowski Institute of Agricultural and Food Biotechnology - State Research Institute, 36 Rakowiecka St., 02-532, Warsaw, Poland; Department of Technology of Chemistry, Azerbaijan State Oil and Industry University, Baku, Azerbaijan.
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Mazumdar R, Dutta PP, Saikia J, Borah JC, Thakur D. Streptomyces sp. Strain PBR11, a Forest-Derived Soil Actinomycetia with Antimicrobial Potential. Microbiol Spectr 2023; 11:e0348922. [PMID: 36719230 PMCID: PMC10101066 DOI: 10.1128/spectrum.03489-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/21/2022] [Indexed: 02/01/2023] Open
Abstract
The Actinomycetia isolate PBR11 was isolated from the forest rhizosphere soil of Pobitora Wildlife Sanctuary (PWS), Assam, India. The isolate was identified as Streptomyces sp. with 92.91% sequence similarity to their closest type strain, Streptomyces atrovirens NRRL B-16357 DQ026672. The strain demonstrated significant antimicrobial activity against 19 test pathogens, including multidrug-resistant (MDR) clinical isolates and dermatophytes. Phenol, 2,5-bis(1,1-dimethylethyl), is the major chemical compound detected by gas chromatography-mass spectrometry in the ethyl acetate extract of PBR11 (EtAc-PBR11). The presence of the PKS type II gene (type II polyketide synthases) and chitinase gene suggested that it has been involved in the production of antimicrobial compounds. Metabolic profiling of the EtAc-PBR11 was performed by thin-layer chromatography and flash chromatography resulted in the extraction of two bioactive fractions, namely, PBR11Fr-1 and PBR11Fr-2. Liquid chromatography-tandem mass spectrometry analysis of both the fractions demonstrated the presence of significant antimicrobial compounds, including ethambutol. This is the first report on the detection of antituberculosis drug in the bioactive fractions of Streptomyces sp. PBR11. EtAc-PBR11 and PBR11Fr-1 showed the lowest MIC values (>0.097 and >0.048 μg/mL, respectively) against Candida albicans MTCC 227, whereas they showed the highest MIC values (>0.390 and >0.195 μg/mL, respectively) against Escherichia coli ATCC BAA-2469. The effects of PBR11Fr-1 were investigated on the pathogens by using a scanning electron microscope. The results indicated major morphological alterations in the cytoplasmic membrane. PBR11Fr-1 exhibited low cytotoxicity on normal hepatocyte cell line (CC-1) and the percent cell viability started to decline as the concentration increased from 50 μg/mL (87.07% ± 3.22%) to 100 μg/mL (81.26% ± 2.99%). IMPORTANCE Novel antibiotic breakthroughs are urgently required to combat antimicrobial resistance. Actinomycetia are the principal producers of antibiotics. The present study demonstrated the broad-spectrum antimicrobial potential of an Actinomycetia strain Streptomyces sp. strain PBR11 isolated from the PWS of Assam, India, which represents diverse, poorly screened habitats for novel microorganisms. The strain displayed 92.4% sequence similarity with genes of the closest type strain, indicating that the strain may represent a novel taxon within the phylum Actinomycetota. The metabolomics studies of EtAc-PBR11 revealed structurally diverse antimicrobial agents, including the detection of the antituberculosis drug ethambutol, in the bioactive fraction of Streptomyces sp. PBR11 for the first time. The PBR11 strain also yielded positive results for the antibiotic synthesis gene and the chitinase gene, both of which are responsible for broad-spectrum antimicrobial activity. This suggests that the untouched forest ecosystems have a tremendous potential to harbor potent actinomycetia for future drug discovery.
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Affiliation(s)
- Rajkumari Mazumdar
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
- Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | | | - Juri Saikia
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
- Department of Biotechnology, Gauhati University, Guwahati, India
| | - Jagat Chandra Borah
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
| | - Debajit Thakur
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
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Świecimska M, Golińska P, Goodfellow M. Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy. Front Microbiol 2023; 13:1054384. [PMID: 36741889 PMCID: PMC9893292 DOI: 10.3389/fmicb.2022.1054384] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Introduction Filamentous actinomycetes, notably members of the genus Streptomyces, remain a rich source of new specialized metabolites, especially antibiotics. In addition, they are also a valuable source of anticancer and biocontrol agents, biofertilizers, enzymes, immunosuppressive drugs and other biologically active compounds. The new natural products needed for such purposes are now being sought from extreme habitats where harsh environmental conditions select for novel strains with distinctive features, notably an ability to produce specialized metabolites of biotechnological value. Methods A culture-based bioprospecting strategy was used to isolate and screen filamentous actinomycetes from three poorly studied extreme biomes. Actinomycetes representing different colony types growing on selective media inoculated with environmental suspensions prepared from high-altitude, hyper-arid Atacama Desert soils, a saline soil from India and from a Polish pine forest soil were assigned to taxonomically predictive groups based on characteristic pigments formed on oatmeal agar. One hundred and fifteen representatives of the colour-groups were identified based on 16S rRNA gene sequences to determine whether they belonged to validly named or to putatively novel species. The antimicrobial activity of these isolates was determined using a standard plate assay. They were also tested for their capacity to produce hydrolytic enzymes and compounds known to promote plant growth while representative strains from the pine forest sites were examined to determine their ability to inhibit the growth of fungal and oomycete plant pathogens. Results Comparative 16S rRNA gene sequencing analyses on isolates representing the colour-groups and their immediate phylogenetic neighbours showed that most belonged to either rare or novel species that belong to twelve genera. Representative isolates from the three extreme biomes showed different patterns of taxonomic diversity and characteristic bioactivity profiles. Many of the isolates produced bioactive compounds that inhibited the growth of one or more strains from a panel of nine wild strains in standard antimicrobial assays and are known to promote plant growth. Actinomycetes from the litter and mineral horizons of the pine forest, including acidotolerant and acidophilic strains belonging to the genera Actinacidiphila, Streptacidiphilus and Streptomyces, showed a remarkable ability to inhibit the growth of diverse fungal and oomycete plant pathogens. Discussion It can be concluded that selective isolation and characterization of dereplicated filamentous actinomyctes from several extreme biomes is a practical way of generating high quality actinomycete strain libraries for agricultural, industrial and medical biotechnology.
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Affiliation(s)
- Magdalena Świecimska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland,*Correspondence: Magdalena Świecimska, ✉
| | - Patrycja Golińska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland,Patrycja Golińska, ✉
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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Saadouli I, Marasco R, Mejri L, Hamden H, Guerfali MM, Stathopoulou P, Daffonchio D, Cherif A, Ouzari HI, Tsiamis G, Mosbah A. Diversity and adaptation properties of actinobacteria associated with Tunisian stone ruins. Front Microbiol 2022; 13:997832. [PMID: 36583041 PMCID: PMC9793712 DOI: 10.3389/fmicb.2022.997832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major challenge and an opportunity to characterize new strains equipped with valuable biological activity. Here, we explored the diversity and adaptation strategies of total bacterial communities associated with Roman stone ruins in Tunisia by considering the effects of geo-climatic regions and stone geochemistry. Environmental 16S rRNA gene amplicon was performed on DNA extracted from stones samples collected in three different sampling sites in Tunisia, along an almost 400km aridity transect, encompassing Mediterranean, semiarid and arid climates. The library was sequenced on an Illumina MiSeq sequencing platform. The cultivable Actinobacteria were isolated from stones samples using the dilution plate technique. A total of 71 strains were isolated and identified based on 16S rRNA gene sequences. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. Amplicon sequencing showed that stone ruins bacterial communities were consistently dominated by Cyanobacteria, followed by Proteobacteria and Actinobacteria along the aridity gradient. However, the relative abundance of the bacterial community components changed according to the geo-climatic origin. Stone geochemistry, particularly the availability of magnesium, chromium, and copper, also influenced the bacterial communities' diversity. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. All the cultivated bacteria belonged to the Actinobacteria class, and the most abundant genera were Streptomyces, Kocuria and Arthrobacter. They were able to tolerate high temperatures (up to 45°C) and salt accumulation, and they produced enzymes involved in nutrients' solubilization, such as phosphatase, amylase, protease, chitinase, and cellulase. Actinobacteria members also had an important role in the co-occurrence interactions among bacteria, favoring the community interactome and stabilization. Our findings provide new insights into actinobacteria's diversity, adaptation, and role within the microbiome associated with stone ruins.
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Affiliation(s)
- Ilhem Saadouli
- Laboratory of Microorganisms and Active Biomolecules, LMBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lassaad Mejri
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, Sidi Thabet, Tunisia
| | - Haytham Hamden
- Laboratory of Biotechnology and Nuclear Technologies, LR16CNSTN02, National Centre of Nuclear Sciences and Technologies, Sidi Thabet, Tunisia
| | - Meriem M’saad Guerfali
- Laboratory of Biotechnology and Nuclear Technologies, LR16CNSTN02, National Centre of Nuclear Sciences and Technologies, Sidi Thabet, Tunisia
| | - Panagiota Stathopoulou
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, Agrinio, Greece
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ameur Cherif
- BVBGR-LR11ES31, Higher Institute of Biotechnology Sidi Thabet, University of Manouba, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Hadda-Imene Ouzari
- Laboratory of Microorganisms and Active Biomolecules, LMBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia,*Correspondence: Hadda-Imene Ouzari,
| | - George Tsiamis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, Agrinio, Greece,George Tsiamis,
| | - Amor Mosbah
- BVBGR-LR11ES31, Higher Institute of Biotechnology Sidi Thabet, University of Manouba, Biotechpole Sidi Thabet, Ariana, Tunisia,Amor Mosbah,
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Xu Z, Eichler B, Klausner EA, Duffy-Matzner J, Zheng W. Lead/Drug Discovery from Natural Resources. Molecules 2022; 27:molecules27238280. [PMID: 36500375 PMCID: PMC9736696 DOI: 10.3390/molecules27238280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Natural products and their derivatives have been shown to be effective drug candidates against various diseases for many years. Over a long period of time, nature has produced an abundant and prosperous source pool for novel therapeutic agents with distinctive structures. Major natural-product-based drugs approved for clinical use include anti-infectives and anticancer agents. This paper will review some natural-product-related potent anticancer, anti-HIV, antibacterial and antimalarial drugs or lead compounds mainly discovered from 2016 to 2022. Structurally typical marine bioactive products are also included. Molecular modeling, machine learning, bioinformatics and other computer-assisted techniques that are very important in narrowing down bioactive core structural scaffolds and helping to design new structures to fight against key disease-associated molecular targets based on available natural products are considered and briefly reviewed.
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Affiliation(s)
- Zhihong Xu
- Department of Chemistry and Biochemistry, Augustana University, 2001 S Summit Ave., Sioux Falls, SD 57197, USA
- Institute of Interventional & Vascular Surgery, Tongji University, Shanghai 200072, China
- Department of Pharmaceutical Sciences, South College School of Pharmacy, 400 Goody’s Lane, Knoxville, TN 37922, USA
- Correspondence: ; Tel.: +1-(605)-274-5008
| | - Barrett Eichler
- Department of Chemistry and Biochemistry, Augustana University, 2001 S Summit Ave., Sioux Falls, SD 57197, USA
| | - Eytan A. Klausner
- Department of Pharmaceutical Sciences, South College School of Pharmacy, 400 Goody’s Lane, Knoxville, TN 37922, USA
| | - Jetty Duffy-Matzner
- Department of Chemistry and Biochemistry, Augustana University, 2001 S Summit Ave., Sioux Falls, SD 57197, USA
| | - Weifan Zheng
- Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, 1801 Fayetteville St., Durham, NC 27707, USA
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Liu L, Qian X, Yang T, Fang D, Qin Z, Ren B, Li G. Cyclopiazonic Acid and Okaramine Analogues, Including Chlorinated Compounds, from Chrysosporium undulatum YT-1. JOURNAL OF NATURAL PRODUCTS 2022; 85:2547-2556. [PMID: 36268672 DOI: 10.1021/acs.jnatprod.2c00445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Eight new cyclopiazonic acid (1-8) and five new okaramine (9-13) alkaloids together with 13 known compounds were isolated from the fungus Chrysosporium undulatum YT-1. Compounds 2, 4, 5, 7, 10, 11, and 13 were chlorinated indole alkaloids. The structures of compounds 1-13 were elucidated by HRESIMS and NMR spectroscopic data. Their relative and absolute configurations were established by J-based configuration analysis, NOESY, NOEDIFF experiments, ECD spectroscopic data, and biogenetic considerations. Compound 4 inhibited the growth of Bacillus subtilis with an MIC value of 6.3 μg/mL. Compounds 9-11 exhibited strong insecticidal capacity against the third instar larvae of silkworm and cotton bollworm (LD50: ≤7.56 μg/g). At 40 μM, compound 1 showed obvious neuroprotection to the PC12 cells with 6-OHDA treatment.
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Affiliation(s)
- Lingyan Liu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xueqing Qian
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Tao Yang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Dongmei Fang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhangyi Qin
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Bo Ren
- Key Laboratory of Standardization of Chinese Herbal Medicine, Ministry of Education, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Guoyou Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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Seshadri R, Roux S, Huber KJ, Wu D, Yu S, Udwary D, Call L, Nayfach S, Hahnke RL, Pukall R, White JR, Varghese NJ, Webb C, Palaniappan K, Reimer LC, Sardà J, Bertsch J, Mukherjee S, Reddy T, Hajek PP, Huntemann M, Chen IMA, Spunde A, Clum A, Shapiro N, Wu ZY, Zhao Z, Zhou Y, Evtushenko L, Thijs S, Stevens V, Eloe-Fadrosh EA, Mouncey NJ, Yoshikuni Y, Whitman WB, Klenk HP, Woyke T, Göker M, Kyrpides NC, Ivanova NN. Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes. CELL GENOMICS 2022; 2:100213. [PMID: 36778052 PMCID: PMC9903846 DOI: 10.1016/j.xgen.2022.100213] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 07/19/2022] [Accepted: 10/16/2022] [Indexed: 11/13/2022]
Abstract
The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.
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Affiliation(s)
- Rekha Seshadri
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Corresponding author
| | - Simon Roux
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Katharina J. Huber
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dongying Wu
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Sora Yu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dan Udwary
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lee Call
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Stephen Nayfach
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Richard L. Hahnke
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Rüdiger Pukall
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Neha J. Varghese
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Cody Webb
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Lorenz C. Reimer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Joaquim Sardà
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jonathon Bertsch
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - T.B.K. Reddy
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Patrick P. Hajek
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Marcel Huntemann
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - I-Min A. Chen
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alex Spunde
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Nicole Shapiro
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Zong-Yen Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center, Beijing, China
| | - Lyudmila Evtushenko
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, All-Russian Collection of Microorganisms (VKM), Pushchino, Russia
| | - Sofie Thijs
- Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Vincent Stevens
- Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Emiley A. Eloe-Fadrosh
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nigel J. Mouncey
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido 060-8589, Japan
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany,Corresponding author
| | - Nikos C. Kyrpides
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia N. Ivanova
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA,Corresponding author
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Yong D, Li Y, Gong K, Yu Y, Zhao S, Duan Q, Ren C, Li A, Fu J, Ni J, Zhang Y, Li R. Biocontrol of strawberry gray mold caused by Botrytis cinerea with the termite associated Streptomyces sp. sdu1201 and actinomycin D. Front Microbiol 2022; 13:1051730. [PMID: 36406410 PMCID: PMC9674021 DOI: 10.3389/fmicb.2022.1051730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Strawberry gray mold caused by Botrytis cinerea is one of the most severe diseases in pre- and post-harvest periods. Although fungicides have been an effective way to control this disease, they can cause serious “3R” problems (Resistance, Resurgence and Residue). In this study, Streptomyces sp. sdu1201 isolated from the hindgut of the fungus-growing termite Odontotermes formosanus revealed significant antifungal activity against B. cinerea. Four compounds (1–4) were isolated from Streptomyces sp. sdu1201 and further identified as actinomycins by the HRMS and 1D NMR data. Among them, actinomycin D had the strongest inhibitory activity against B. cinerea with the EC50 value of 7.65 μg mL−1. The control effect of actinomycin D on strawberry gray mold was also tested on fruits and leaves in vitro, and its control efficiency on leaves was 78.77% at 3 d. Moreover, actinomycin D can also inhibit the polarized growth of germ tubes of B. cinerea. Therefore, Streptomyces sp. sdu1201 and actinomycin D have great potential to gray mold as biocontrol agents.
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Affiliation(s)
- Daojing Yong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Qingdao Zhongda Agritech Co., Ltd., Qingdao, China
| | - Yue Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kai Gong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yingying Yu
- Qingdao Zhongda Agritech Co., Ltd., Qingdao, China
| | - Shuai Zhao
- Qingdao Zhongda Agritech Co., Ltd., Qingdao, China
| | - Qiong Duan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Cailing Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jun Fu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jinfeng Ni
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Jinfeng Ni,
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Youming Zhang,
| | - Ruijuan Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Ruijuan Li,
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Danilova OA, Ianutsevich EA, Bondarenko SA, Antropova AB, Tereshina VM. Membrane Lipids and Osmolytes Composition of Xerohalophilic Fungus Aspergillus penicillioides during Growth on High NaCl and Glycerol Media. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601373] [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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Kribbellichelins A and B, Two New Antibiotics from Kribbella sp. CA-293567 with Activity against Several Human Pathogens. Molecules 2022; 27:molecules27196355. [PMID: 36234892 PMCID: PMC9570599 DOI: 10.3390/molecules27196355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 12/04/2022] Open
Abstract
Current needs in finding new antibiotics against emerging multidrug-resistant superbugs are pushing the scientific community into coming back to Nature for the discovery of novel active structures. Recently, a survey of halophilic actinomyectes from saline substrates of El Saladar del Margen, in the Cúllar-Baza depression (Granada, Spain), led us to the isolation and identification of 108 strains from the rhizosphere of the endemic plant Limonium majus. Evaluation of the potential of these strains to produce new anti-infective agents against superbug pathogens was performed through fermentation in 10 different culture media using an OSMAC approach and assessment of the antibacterial and antifungal properties of their acetone extracts. The study allowed the isolation of two novel antibiotic compounds, kribbellichelin A (1) and B (2), along with the known metabolites sandramycin (3), coproporphyrin III (4), and kribelloside C (5) from a bioassay-guided fractionation of scaled-up active extracts of the Kribbella sp. CA-293567 strain. The structures of the new molecules were elucidated by ESI-qTOF-MS/MS, 1D and 2D NMR, and Marfey’s analysis for the determination of the absolute configuration of their amino acid residues. Compounds 1–3 and 5 were assayed against a panel of relevant antibiotic-resistant pathogenic strains and evaluated for cytotoxicity versus the human hepatoma cell line HepG2 (ATCC HB-8065). Kribbellichelins A (1) and B (2) showed antimicrobial activity versus Candida albicans ATCC-64124, weak potency against Acinetobacter baumannii MB-5973 and Pseudomonas aeruginosa MB-5919, and an atypical dose-dependent concentration profile against Aspergillus fumigatus ATCC-46645. Sandramycin (3) confirmed previously reported excellent growth inhibition activity against MRSA MB-5393 but also presented clear antifungal activity against C. albicans ATCC-64124 and A. fumigatus ATCC-46645 associated with lower cytotoxicity observed in HepG2, whereas Kribelloside C (5) displayed high antifungal activity only against A. fumigatus ATCC-46645. Herein, we describe the processes followed for the isolation, structure elucidation, and potency evaluation of these two new active compounds against a panel of human pathogens as well as, for the first time, the characterization of the antifungal activities of sandramycin (3).
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40
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Two new 22-membered macrolides from Streptomyces sp. HU210. J Antibiot (Tokyo) 2022; 75:650-653. [DOI: 10.1038/s41429-022-00563-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/20/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022]
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Montuori E, Capalbo A, Lauritano C. Marine Compounds for Melanoma Treatment and Prevention. Int J Mol Sci 2022; 23:ijms231810284. [PMID: 36142196 PMCID: PMC9499452 DOI: 10.3390/ijms231810284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/11/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Melanoma is considered a multifactorial disease etiologically divided into melanomas related to sun exposure and those that are not, but also based on their mutational signatures, anatomic site, and epidemiology. The incidence of melanoma skin cancer has been increasing over the past decades with 132,000 cases occurring globally each year. Marine organisms have been shown to be an excellent source of natural compounds with possible bioactivities for human health applications. In this review, we report marine compounds from micro- and macro-organisms with activities in vitro and in vivo against melanoma, including the compound Marizomib, isolated from a marine bacterium, currently in phase III clinical trials for melanoma. When available, we also report active concentrations, cellular targets and mechanisms of action of the mentioned molecules. In addition, compounds used for UV protection and melanoma prevention from marine sources are discussed. This paper gives an overview of promising marine molecules which can be studied more deeply before clinical trials in the near future.
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Affiliation(s)
- Eleonora Montuori
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
| | - Anita Capalbo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
| | - Chiara Lauritano
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
- Correspondence: ; Tel.: +39-0815833221
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Yang T, Yang K, Zhang Y, Zhou R, Zhang F, Zhan G, Guo Z. Metabolites with antioxidant and α-glucosidase inhibitory activities produced by the endophytic fungi Aspergillus niger from Pachysandra terminalis. Biosci Biotechnol Biochem 2022; 86:1343-1348. [PMID: 35973685 DOI: 10.1093/bbb/zbac137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/06/2022] [Indexed: 11/13/2022]
Abstract
One new compound and 13 known compounds were isolated from Aspergillus niger, a plant endophytic fungus of Pachysandra terminalis collected from Qinling Mountains, Xi'an, China. The structure of new compound 1 was classically determined by extensive spectroscopic analysis. Compounds 5, 6, 8, and 14 were firstly reported from Aspergillus, while compound 2 was isolated from A. niger for the first time. All isolated compounds were further evaluated for their antioxidant and α-glucosidase inhibitory activities. Compounds 2 and 3 exhibited significant antioxidant activities with IC50 values of 31.64 μm and 24.32 μm, respectively, similar to the positive control ascorbic acid. Additionally, compound 1 displayed remarkable inhibitory activity against α-glucosidase with an IC50 value of 96.25 μm, which was 3.4-fold more potent than that of the positive control acarbose. Compound 1 has great potential for development as a new lead compound owing to its simple structure and remarkable biological activity.
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Affiliation(s)
- Tao Yang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, P. R. China
| | - Kailing Yang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, P. R. China
| | - Yu Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, P. R. China
| | - Ruixi Zhou
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, P. R. China
| | - Fuxin Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, P. R. China
| | - Guanqun Zhan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, P. R. China
| | - Zengjun Guo
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, P. R. China
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Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica. Extremophiles 2022; 26:24. [PMID: 35829965 PMCID: PMC9279279 DOI: 10.1007/s00792-022-01271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 06/06/2022] [Indexed: 11/12/2022]
Abstract
Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota, particularly the Streptomyces. Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene amplicon sequencing data from 18 Herring Island soils and selected the soil sample with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota. These strains encompassed thirty-five ‘species’ groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.
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Corrêa ANR, Ferreira CD. Mycotoxins in Grains and Cereals Intended for Human Consumption: Brazilian Legislation, Occurrence Above Maximum Levels and Co-Occurrence. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2022.2098318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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45
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Antimicrobial Potential of Streptomyces spp. Isolated from the Rift Valley Regions of Ethiopia. Adv Pharmacol Pharm Sci 2022; 2022:1724906. [PMID: 35734196 PMCID: PMC9208996 DOI: 10.1155/2022/1724906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/06/2022] [Indexed: 11/17/2022] Open
Abstract
The study was undertaken to isolate, screen, and identify actinomycetes with antimicrobial metabolites. Twenty-one composite soil samples were randomly collected from various unique agroecological niches in the Rift Valley of Ethiopia. The soil samples were serially diluted and spread on starch casein agar medium supplemented with 50 μg/ml cycloheximide and 25 μg/ml nalidixic acid. Two hundred and forty-nine (249) actinomycetes cultures were isolated and screened by cross streaking against various human pathogens. Twenty-four isolates with pronounced antimicrobial activity were selected for identification and further screening. Among the isolates, 172 (69.1%) showed antimicrobial activities against tested pathogens. The inhibition zone of the isolates ranged from 5 ± 0.31 to >40 mm during primary screening. The antimicrobial activity of the crude extracts of promising isolates showed a statistically significant difference (P < 0.05) between them and the control. The isolates RVE129 and RVE217 showed the maximum zone of inhibition at 27 ± 0.6 mm and 26 ± 0.6 mm, respectively, against S. aureus, and the results were higher than the standard drug streptomycin (25 ± 0.58 mm). The inhibition zone of crude extracts from RVE129 was at the maximum of 22 ± 0.0 mm against P. aeruginosa, almost comparable to the standard drug streptomycin (24 ± 0.58 mm). Crude extract from the isolates RVE129 and RVE187 showed higher inhibition zones of 22 ± 0.6 mm and 16 ± 0.33 mm against A. niger ATCC10535, which, however, were smaller than those obtained with the standard drug amphotericin B (29 ± 0.6 mm). Twenty-four actinomycete strains with remarkable bioactivity were characterized using various cultural, morphological, physiological, and biochemical characteristics and assigned under the genus Streptomycetes. The finding of the current study indicates that Streptomyces sp. isolated from the Rift Valley of Ethiopia was found to possess a broad spectrum of bioactivity against a range of human pathogens.
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Orlandi VT, Martegani E, Giaroni C, Baj A, Bolognese F. Bacterial pigments: A colorful palette reservoir for biotechnological applications. Biotechnol Appl Biochem 2022; 69:981-1001. [PMID: 33870552 PMCID: PMC9544673 DOI: 10.1002/bab.2170] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 04/09/2021] [Indexed: 12/12/2022]
Abstract
Synthetic derivatives are currently used instead of pigments in many applicative fields, from food to feed, from pharmaceutical to diagnostic, from agronomy to industry. Progress in organic chemistry allowed to obtain rather cheap compounds covering the whole color spectrum. However, several concerns arise from this chemical approach, as it is mainly based on nonrenewable resources such as fossil oil, and the toxicity or carcinogenic properties of products and/or precursors may be harmful for personnel involved in the productive processes. In this scenario, microorganisms and their pigments represent a colorful world to discover and reconsider. Each living bacterial strain may be a source of secondary metabolites with peculiar functions. The aim of this review is to link the physiological role of bacterial pigments with their potential use in different biotechnological fields. This enormous potential supports the big challenge for the development of strategies useful to identify, produce, and purify the right pigment for the desired application. At the end of this ideal journey through the world of bacterial pigments, the attention will be focused on melanin compounds, whose production relies upon different techniques ranging from natural producers, heterologous hosts, or isolated enzymes. In a green workflow, the microorganisms represent the starting and final point of pigment production.
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Affiliation(s)
| | - Eleonora Martegani
- Department of Biotechnologies and Life SciencesUniversity of InsubriaVareseItaly
| | - Cristina Giaroni
- Department of Medicine and SurgeryUniversity of InsubriaVareseItaly
| | - Andreina Baj
- Department of Medicine and SurgeryUniversity of InsubriaVareseItaly
| | - Fabrizio Bolognese
- Department of Biotechnologies and Life SciencesUniversity of InsubriaVareseItaly
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Exploring the Diversity and Antibacterial Potentiality of Cultivable Actinobacteria from the Soil of the Saxaul Forest in Southern Gobi Desert in Mongolia. Microorganisms 2022; 10:microorganisms10050989. [PMID: 35630432 PMCID: PMC9147431 DOI: 10.3390/microorganisms10050989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/10/2022] Open
Abstract
Saxaul (Haloxylon ammodendron) is the most widespread plant community in the Gobi Desert in Mongolia, which plays important roles in wind control, sand fixation and water conservation. Investigations of soil-derived actinobacteria inhabiting in the saxaul forest in Gobi Desert in Mongolia have been scarce. In this study, biodiversity of culturable actinobacteria isolated from soil of the saxaul forest in Southern Gobi Aimak (Southern Gobi Province) of Mongolia was characterized and their potential to produce compounds with antibacterial activities was assessed. A total of 172 actinobacterial strains were recovered by culture-based approaches and were phylogenetically affiliated into 22 genera in 13 families of seven orders. Forty-nine actinobacterial isolates were selected to evaluate the antibacterial activities and their underlying mechanism of action was screened by means of a dual-fluorescent reporter assay (pDualrep2). Twenty-three isolates exhibited antagonistic activity against at least one of the tested pathogens, of which two Streptomyces strains can attenuate protein translation by ribosome stalling. Combinational strategies based on modern metabolomics, including bioassay-guided thin-layer chromatography (TLC), UPLC-QTOF-MS/MS based structural annotation and enhanced molecular networking successfully annotated chloramphenicol, althiomycin and granaticin and their derivatives as the antibacterial compounds from extracts in three Streptomyces strains, respectively. This work demonstrates that UPLC-MS/MS-based structural identification and enhanced molecular networking are effective strategies to rapidly illuminate the bioactive chemicals in the microbial extracts. Meanwhile, our results show that the saxaul forest in Mongolia Gobi Desert is a prospective source for discovering novel actinobacteria and biologically active compounds.
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Kochhar N, I․K K, Shrivastava S, Ghosh A, Rawat VS, Sodhi KK, Kumar M. Perspectives on the microorganism of extreme environments and their applications. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100134. [PMID: 35909612 PMCID: PMC9325743 DOI: 10.1016/j.crmicr.2022.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/21/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
The applications of extremophiles in various fields like biotechnology, biodegradation, bioremediation, biorefinery and astrobiology along with other industries like pharmaceuticals, food, agricultural, cosmetics, and textile. Further research in biodegradation, bioremediation and generation of biofuels using extremophiles is required considering the current climate crisis as it helps in reduction of environmental contamination load. The importance of promoting the use of extremophiles in food and agricultural industries and how extremophiles can be the key to achieving the Sustainable Development Goal of global food security. Keeping in mind the current global scenario with regards to the Covid-19 pandemic, our paper also focuses on the importance of by-products of extremophiles like biosurfactants in the vaccine production process. For advancement of the astrobiology sector, more PFA sites should be located and the extremophiles inhabiting them should be studied.
Extremophiles are organisms that can survive and thrive in conditions termed as “extreme” by human beings. Conventional methods cannot be applied under extreme conditions like temperature and pH fluctuations, high salinity, etc. for a variety of reasons. Extremophiles can function and are adapted to thrive in these environments and are sustainable, cheaper, and efficient, therefore, they serve as better alternatives to the traditional methods. They adapt to these environments with biochemical and physiological changes and produce products like extremolytes, extremozymes, biosurfactants, etc., which are found to be useful in a wide range of industries like sustainable agriculture, food, cosmetics, and pharmaceuticals. These products also play a crucial role in bioremediation, production of biofuels, biorefinery, and astrobiology. This review paper comprehensively lists out the current applications of extremophiles and their products in various industries and explores the prospects of the same. They help us understand the underlying basis of biological mechanisms exploring the boundaries of life and thus help us understand the origin and evolution of life on Earth. This helps us in the research for extra-terrestrial life and space exploration. The structure and biochemical properties of extremophiles along with any possible long-term effects of their applications need to be investigated further.
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Affiliation(s)
- Nikita Kochhar
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
| | - Kavya I․K
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
| | | | - Anshika Ghosh
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
| | | | - Kushneet Kaur Sodhi
- Department of Zoology, Hansraj College, University of Delhi, Delhi-110007, India
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Mohit Kumar
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
- Department of Zoology, University of Delhi, Delhi-110007, India
- Corresponding author.
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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Vuong P, Wise MJ, Whiteley AS, Kaur P. Small investments with big returns: environmental genomic bioprospecting of microbial life. Crit Rev Microbiol 2022; 48:641-655. [PMID: 35100064 DOI: 10.1080/1040841x.2021.2011833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms and their natural products are major drivers of ecological processes and industrial applications. Microbial bioprospecting has been critical for the advancement in various fields such as pharmaceuticals, sustainable industries, food security and bioremediation. Next generation sequencing has been paramount in the exploration of diverse environmental microbiomes. It presents a culture-independent approach to investigating hitherto uncultured taxa, resulting in the creation of massive sequence databases, which are available in the public domain. Genome mining searches available (meta)genomic data for target biosynthetic genes, and combined with the large-scale public data, this in-silico bioprospecting method presents an efficient and extensive way to uncover microbial bioproducts. Bioinformatic tools have progressed to a stage where we can recover genomes from the environment; these metagenome-assembled genomes present a way to understand the metabolic capacity of microorganisms in a physiological and ecological context. Environmental sampling been extensive across various ecological settings, including microbiomes with unique physicochemical properties that could influence the discovery of novel functions and metabolic pathways. Although in-silico methods cannot completely substitute in-vitro studies, the contextual information it provides is invaluable for understanding the ecological and taxonomic distribution of microbial genotypes and to form effective strategies for future microbial bioprospecting efforts.
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Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Michael J Wise
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia
| | - Andrew S Whiteley
- Centre for Environment & Life Sciences, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Australia
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
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