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Liu Y, Lin S, Wang C, Li T, Zheng G, Sun W, An L, Bai Y, Wu F. Sex-Specific Effects of Environmental Exposure to the Antimicrobial Agents Benzalkonium Chloride and Triclosan on the Gut Microbiota and Health of Zebrafish ( Danio rerio). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:15450-15462. [PMID: 39141879 DOI: 10.1021/acs.est.4c03205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
The use of disinfectants containing benzalkonium chloride (BAC) has become increasingly widespread in response to triclosan (TCS) restrictions and the COVID-19 pandemic, leading to the increasing presence of BAC in aquatic ecosystems. However, the potential environmental health impacts of BAC on fish remain poorly explored. In this study, we show that BAC and TCS can induce the gut dysbiosis in zebrafish (Danio rerio), with substantial effects on health. Breeding pairs of adult zebrafish were exposed to environmentally relevant concentrations of BAC and TCS (0.4-40 μg/L) for 42 days. Both BAC and TCS exposure perturbed the gut microbiota, triggering the classical NF-κB signaling pathway and resulting in downstream pathological toxicity associated with inflammatory responses, histological damage, inhibited ingestion, and decreased survival. These effects were dose-dependent and sex-specific, as female zebrafish were more susceptible than male zebrafish. Furthermore, we found that BAC induced toxicity to a greater extent than the restricted TCS at environmentally relevant concentrations, which is particularly concerning. Our results suggest that environmental exposure to antimicrobial chemicals can have ecological consequences by perturbing the gut microbiota, a previously underappreciated target of such chemicals. Rigorous ecological analysis should be conducted before widely introducing replacement antimicrobial compounds into disinfecting products.
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Affiliation(s)
- Yueyue Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
- College of Water Science, Beijing Normal University, Beijing 100875, China
| | - Siyi Lin
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chen Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Tong Li
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guomao Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wen Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Lihui An
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yingchen Bai
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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Whatmough B, Holmes NA, Wilkinson B, Hutchings MI, Parra J, Duncan KR. Microbe Profile: Pseudonocardia: antibiotics for every niche. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001501. [PMID: 39297772 PMCID: PMC11412249 DOI: 10.1099/mic.0.001501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 08/27/2024] [Indexed: 09/25/2024]
Abstract
Pseudonocardia species comprise a genus of filamentous, sporulating bacteria belonging to the phylum Actinomycetota, formerly Actinobacteria. They are found in marine and freshwater sediments and soils and associated with marine animals, insects, and plants. To date, they have mostly been studied because of their mutually beneficial symbiosis with fungus-growing ants in the tribe Attini. They have also attracted interest due to their biosynthetic capabilities, including the production of variably glycosylated polyenes and other novel antifungal compounds, and for their capacity to grow on a variety of hydrocarbons. The majority of clinically used antibiotics are derived from the specialised metabolites of filamentous actinomycete bacteria and most of these come from the genus Streptomyces. However, in the quest for novel chemistry there is increasing interest in studying other filamentous actinomycete genera, including Pseudonocardia. Here we outline the biological properties, genome size and structure and key features of the genus Pseudonocardia, namely their specialised metabolites and ecological roles.
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Affiliation(s)
- Bonnie Whatmough
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Neil A. Holmes
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Matthew I. Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jonathan Parra
- Instituto de Investigaciones Farmacéuticas (INIFAR) and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
| | - Katherine R. Duncan
- Newcastle University, University of Newcastle Biosciences Institute, Newcastle Upon Tyne, NE2 4HH, UK
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Jiya N, Ghosh R, Shede P, Sharma A. Comparative analysis of bacterial diversity in accumulated snow and exposed sediments across Antarctic Islands. Braz J Microbiol 2024; 55:2355-2362. [PMID: 38748395 PMCID: PMC11405587 DOI: 10.1007/s42770-024-01360-8] [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: 12/30/2023] [Accepted: 04/11/2024] [Indexed: 09/18/2024] Open
Abstract
The Antarctic continent hosts exceptional niches, making it an ideal environment for studying polyextremophilic microorganisms. These organisms are uniquely shaped by the geographic niches and variations in soil types. Here we present, a culture-independent approach using DNA metabarcoding to assess the bacterial communities associated with accumulated snow and exposed sediments across different Antarctic islands situated in the Larsemann Hills, Antarctica. The exposed sediments (ES) were found to be more diverse than the accumulated snow (AS) sediments as represented by the alpha diversity metrics. Out of the total 303 amplicon sequence variants (ASVs) found at the genus level, 93 were unique to accumulated snow sediments and 97 were unique to exposed sediments. The bacterial community composition in accumulated snow was dominated by the phylum Actinobacteriota (24.7%). However, Pseudonocardia (11.9%), Crossiella (11%), and Rhodanobacter (9.1%) were the predominant genera. In contrast, in the exposed sediments, Bacteroidota (24.6%) was the most prevalent phylum, with Crossiella (17.1%), Rhodanobacter (11.1%), and Blastocatella (10%) as the most abundant genera. Metagenomic imputations revealed the abundance of gene families responsible for carbon metabolism, coping with environmental stresses through DNA repair mechanisms, and carbon fixation.
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Affiliation(s)
- Namrata Jiya
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
- Department of Microbiology, MES' Abasaheb Garware College (Autonomous), Pune, India
| | - Rochita Ghosh
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Prafulla Shede
- Department of Microbiology, MES' Abasaheb Garware College (Autonomous), Pune, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India.
- School of Agriculture, Graphic Era Hill University, Dehradun, India.
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Worsley SF, Davies CS, Lee CZ, Mannarelli ME, Burke T, Komdeur J, Dugdale HL, Richardson DS. Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population. Mol Ecol 2024; 33:e17477. [PMID: 39010794 DOI: 10.1111/mec.17477] [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: 01/11/2024] [Revised: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 07/17/2024]
Abstract
In humans, gut microbiome (GM) differences are often correlated with, and sometimes causally implicated in, ageing. However, it is unclear how these findings translate in wild animal populations. Studies that investigate how GM dynamics change within individuals, and with declines in physiological condition, are needed to fully understand links between chronological age, senescence and the GM, but have rarely been done. Here, we use longitudinal data collected from a closed population of Seychelles warblers (Acrocephalus sechellensis) to investigate how bacterial GM alpha diversity, composition and stability are associated with host senescence. We hypothesised that GM diversity and composition will differ, and become more variable, in older adults, particularly in the terminal year prior to death, as the GM becomes increasingly dysregulated due to senescence. However, GM alpha diversity and composition remained largely invariable with respect to adult age and did not differ in an individual's terminal year. Furthermore, there was no evidence that the GM became more heterogenous in senescent age groups (individuals older than 6 years), or in the terminal year. Instead, environmental variables such as season, territory quality and time of day, were the strongest predictors of GM variation in adult Seychelles warblers. These results contrast with studies on humans, captive animal populations and some (but not all) studies on non-human primates, suggesting that GM deterioration may not be a universal hallmark of senescence in wild animal species. Further work is needed to disentangle the factors driving variation in GM-senescence relationships across different host taxa.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | - Chuen Zhang Lee
- School of Biological Sciences, University of East Anglia, Norfolk, UK
| | | | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Nature Seychelles, Mahé, Republic of Seychelles
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Sun RZ, Wang YY, Liu XQ, Yang ZL, Deng X. Structure and dynamics of microbial communities associated with the resurrection plant Boea hygrometrica in response to drought stress. PLANTA 2024; 260:24. [PMID: 38858226 DOI: 10.1007/s00425-024-04459-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
MAIN CONCLUSION The resurrection plant Boea hygrometrica selectively recruits and assembles drought-specific microbial communities across the plant-soil compartments, which may benefit plant growth and fitness under extreme drought conditions. Plant-associated microbes are essential for facilitating plant growth and fitness under drought stress. The resurrection plant Boea hygrometrica in natural habitats with seasonal rainfall can survive rapid desiccation, yet their interaction with microbiomes under drought conditions remains unexplored. This study examined the bacterial and fungal microbiome structure and drought response across plant-soil compartments of B. hygrometrica by high-throughput amplicon sequencing of 16S rRNA gene and internal transcribed spacer. Our results demonstrated that the diversity, composition, and functional profile of the microbial community varied considerably across the plant-soil compartments and were strongly affected by drought stress. Bacterial and fungal diversity was significantly reduced from soil to endosphere and belowground to aboveground compartments. The compartment-specific enrichment of the dominant bacteria phylum Cyanobacteriota and genus Methylorubrum in leaf endosphere, genera Pseudonocardia in rhizosphere soil and Actinoplanes in root endosphere, and fungal phylum Ascomycota in the aboveground compartments and genera Knufia in root endosphere and Cladosporium in leaf endosphere composed part of the core microbiota with corresponding enrichment of beneficial functions for plant growth and fitness. Moreover, the recruitment of dominant microbial genera Sphingosinicella and Plectosphaerella, Ceratobasidiaceae mycorrhizal fungi, and numerous plant growth-promoting bacteria involving nutrient supply and auxin regulation was observed in desiccated B. hygrometrica plants. Our results suggest that the stable assembled drought-specific microbial community of B. hygrometrica may contribute to plant survival under extreme environments and provide valuable microbial resources for the microbe-mediated drought tolerance enhancement in crops.
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Affiliation(s)
- Run-Ze Sun
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- China National Botanical Garden, 100093, Beijing, China.
| | - Yuan-Yuan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiao-Qiang Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhao-Lin Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xin Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- China National Botanical Garden, 100093, Beijing, China.
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Kitson L, Becker AAMJ, Hartmann K, Bergmann M, Sepulveda-Garcia P, Canales N, Muller A. Characterizing the blood microbiota in healthy and febrile domestic cats via 16s rRNA sequencing. Sci Rep 2024; 14:10584. [PMID: 38719878 PMCID: PMC11079020 DOI: 10.1038/s41598-024-61023-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
This study aimed to evaluate the blood bacterial microbiota in healthy and febrile cats. High-quality sequencing reads from the 16S rRNA gene variable region V3-V4 were obtained from genomic blood DNA belonging to 145 healthy cats, and 140 febrile cats. Comparisons between the blood microbiota of healthy and febrile cats revealed dominant presence of Actinobacteria, followed by Firmicutes and Proteobacteria, and a lower relative abundance of Bacteroidetes. Upon lower taxonomic levels, the bacterial composition was significantly different between healthy and febrile cats. The families Faecalibacterium and Kineothrix (Firmicutes), and Phyllobacterium (Proteobacteria) experienced increased abundance in febrile samples. Whereas Thioprofundum (Proteobacteria) demonstrated a significant decrease in abundance in febrile. The bacterial composition and beta diversity within febrile cats was different according to the affected body system (Oral/GI, systemic, skin, and respiratory) at both family and genus levels. Sex and age were not significant factors affecting the blood microbiota of febrile cats nor healthy ones. Age was different between young adult and mature adult healthy cats. Alpha diversity was unaffected by any factors. Overall, the findings suggest that age, health status and nature of disease are significant factors affecting blood microbiota diversity and composition in cats, but sex is not.
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Affiliation(s)
- Liam Kitson
- Graduate Program, Ross University School of Veterinary Medicine, West Farm, West Indies, Saint Kitts and Nevis
| | - Anne A M J Becker
- One Health Center for Zoonoses and Tropical Veterinary Medicine, Biomedical Sciences Department, Ross University School of Veterinary Medicine, West Farm, West Indies, Saint Kitts and Nevis
| | - Katrin Hartmann
- LMU Small Animal Clinic, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Michèle Bergmann
- LMU Small Animal Clinic, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Paulina Sepulveda-Garcia
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Escuela de Graduados, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Nivia Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Ananda Muller
- One Health Center for Zoonoses and Tropical Veterinary Medicine, Biomedical Sciences Department, Ross University School of Veterinary Medicine, West Farm, West Indies, Saint Kitts and Nevis.
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Duan Y, Siegenthaler A, Skidmore AK, Chariton AA, Laros I, Rousseau M, De Groot GA. Forest top canopy bacterial communities are influenced by elevation and host tree traits. ENVIRONMENTAL MICROBIOME 2024; 19:21. [PMID: 38581032 PMCID: PMC10998314 DOI: 10.1186/s40793-024-00565-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/26/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce). RESULTS We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families. CONCLUSIONS While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.
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Affiliation(s)
- Yiwei Duan
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands.
| | - Andjin Siegenthaler
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - Andrew K Skidmore
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - Anthony A Chariton
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ivo Laros
- Wageningen Environmental Research, Wageningen UR, P.O. Box 46, 6700 AA, Wageningen, The Netherlands
| | - Mélody Rousseau
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - G Arjen De Groot
- Wageningen Environmental Research, Wageningen UR, P.O. Box 46, 6700 AA, Wageningen, The Netherlands
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Teo WFA, Devaraj K, Nor MNM, Li WJ, Tan GYA. Sciscionella sediminilitoris sp. nov., a Marine Actinomycete Isolated from Cape Rochado, Malaysia, and the Emendations to the Description of the Genus Sciscionella. Curr Microbiol 2024; 81:124. [PMID: 38551738 DOI: 10.1007/s00284-024-03634-8] [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: 07/12/2023] [Accepted: 02/01/2024] [Indexed: 04/02/2024]
Abstract
In this study, we employed a polyphasic approach to determine the taxonomic position of a newly isolated actinomycete, designated SE31T, obtained from a sediment sample collected at Cape Rochado, Malaysia. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain SE31T belonged to the family Pseudonocardiaceae and exhibited the highest sequence similarity (98.9%) to Sciscionella marina. Further genomic analysis demonstrated a 93.4% average nucleotide identity and 54.4% digital DNA-DNA hybridization relatedness between strain SE31T and S. marina. The chemotaxonomic characteristics of strain SE31T were typical of the genus Sciscionella, including cell-wall chemotype IV (with meso-diaminopimelic acid as the diagnostic diamino acid, and arabinose and galactose as whole-cell sugars). The identified polar lipids of strain SE31T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, and hydroxyphosphatidymethylethanolamine. The primary menaquinone observed was MK-9(H4), and the major cellular fatty acid was iso-C16:0. The genomic DNA size of strain SE31T was determined to be 7.4 Mbp with a G+C content of 68.7%. Based on these comprehensive findings, strain SE31T represents a novel species within the genus Sciscionella, in which the name Sciscionella sediminilitoris sp. nov. is proposed. The type strain of Sciscionella sediminilitoris is SE31T (= DSM 46824T = TBRC 5134T).
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Affiliation(s)
- Wee Fei Aaron Teo
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management and Innovation Complex, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kavimalar Devaraj
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Muhammad Nuruddin Mohd Nor
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Faculty of Plantation and Agrotechnology, UiTM Cawangan Melaka, Kampus Jasin, Merlimau, 77300, Melaka, Malaysia
| | - 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, People's Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management and Innovation Complex, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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Lin H, Peddada SD. Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures. Nat Methods 2024; 21:83-91. [PMID: 38158428 PMCID: PMC10776411 DOI: 10.1038/s41592-023-02092-7] [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: 04/04/2023] [Accepted: 10/17/2023] [Indexed: 01/03/2024]
Abstract
Microbiome differential abundance analysis methods for two groups are well-established in the literature. However, many microbiome studies involve more than two groups, sometimes even ordered groups such as stages of a disease, and require different types of comparison. Standard pairwise comparisons are inefficient in terms of power and false discovery rates. In this Article, we propose a general framework, ANCOM-BC2, for performing a wide range of multigroup analyses with covariate adjustments and repeated measures. We illustrate our methodology through two real datasets. The first example explores the effects of aridity on the soil microbiome, and the second example investigates the effects of surgical interventions on the microbiome of patients with inflammatory bowel disease.
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Affiliation(s)
- Huang Lin
- Biostatistics and Computational Biology Branch, NIEHS, NIH, Research Triangle Park, NC, USA
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD, USA
| | - Shyamal Das Peddada
- Biostatistics and Computational Biology Branch, NIEHS, NIH, Research Triangle Park, NC, USA.
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10
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Parra J, Beaton A, Seipke RF, Wilkinson B, Hutchings MI, Duncan KR. Antibiotics from rare actinomycetes, beyond the genus Streptomyces. Curr Opin Microbiol 2023; 76:102385. [PMID: 37804816 DOI: 10.1016/j.mib.2023.102385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 10/09/2023]
Abstract
Throughout the golden age of antibiotic discovery, Streptomyces have been unsurpassed for their ability to produce bioactive metabolites. Yet, this success has been hampered by rediscovery. As we enter a new stage of biodiscovery, omics data and existing scientific repositories can enable informed choices on the biodiversity that may yield novel antibiotics. Here, we focus on the chemical potential of rare actinomycetes, defined as bacteria within the order Actinomycetales, but not belonging to the genus Streptomyces. They are named as such due to their less-frequent isolation under standard laboratory practices, yet there is increasing evidence to suggest these biologically diverse genera harbour considerable biosynthetic and chemical diversity. In this review, we focus on examples of successful isolation and genera that have been the focus of more concentrated biodiscovery efforts, we survey the representation of rare actinomycete taxa, compared with Streptomyces, across natural product data repositories in addition to its biosynthetic potential. This is followed by an overview of clinically useful drugs produced by rare actinomycetes and considerations for future biodiscovery efforts. There is much to learn about these underexplored taxa, and mounting evidence suggests that they are a fruitful avenue for the discovery of novel antimicrobials.
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Affiliation(s)
- Jonathan Parra
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José 11501-2060, Costa Rica; Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
| | - Ainsley Beaton
- John Innes Centre, Department of Molecular Microbiology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ryan F Seipke
- University of Leeds, Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, Leeds LS2 9JT, UK
| | - Barrie Wilkinson
- John Innes Centre, Department of Molecular Microbiology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew I Hutchings
- John Innes Centre, Department of Molecular Microbiology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow G4 0RE, UK.
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11
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Mlewski EC, Saona LA, Boidi FJ, Chiappero MF, Vaieretti MV, Soria M, Farías ME, Izquierdo AE. Exploring Soil Bacterial Diversity in Relation to Edaphic Physicochemical Properties of High-altitude Wetlands from Argentine Puna. MICROBIAL ECOLOGY 2023; 87:6. [PMID: 38030916 DOI: 10.1007/s00248-023-02316-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023]
Abstract
High Andean wetlands, particularly those known as vegas or bofedales, are essential conservation ecosystems due to their significant contribution to ecosystem services. The soil microbial communities in these ecosystems play a crucial role in fundamental processes such as decomposition and nutrient cycling, sustaining life in the region. However, at present, these microbial communities are poorly understood. In order to contribute to this knowledge, we aimed to characterize and compare the microbial communities from soils of seven Argentine Puna vegas and to analyze their association with soil physicochemical characteristics. Proteobacteria (Gamma and Alphaproteobacteria) was the dominant phylum across all vegas, followed in abundance by Actinobacteriota, Desulfobacterota, and Chloroflexi. Furthermore, the abundance of specific bacterial families and genera varied significantly between the vegas; some of them can be associated with plant growth-promoting bacteria such as Rhodomicrobium in La Quebradita and Quebrada del Diablo, Bacillus in Antofalla and Las Quinuas. Laguna Negra showed no shared ASVs with abundance in genera such as Sphingomonas and Pseudonocardia. The studied vegas also differed in their soil physicochemical properties; however, associations between the composition of microbial communities with the edaphic parameters measured were not found. These results suggest that other environmental factors (e.g., geographic, climatic, and plant communities' characteristics) could determine soil microbial diversity patterns. Further investigations are needed to be focused on understanding the composition and function of microorganisms in the soil associated with specific vegetation types in these high-altitude wetlands, which will provide valuable insights into the ecological dynamics of these ecosystems for conservation strategies.
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Affiliation(s)
- Estela Cecilia Mlewski
- Instituto Multidisciplinario de Biología Vegetal (IMBiV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
- Facultad de Ciencias Exactas Físicas y Naturales, Centro de Ecología y Recursos Naturales Renovables (CERNAR), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Luis A Saona
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Flavia Jaquelina Boidi
- Instituto Nacional de Tecnología Agropecuaria (INTA), EEA Rafaela, Rafaela, Argentina
- Instituto de Investigación de la Cadena Láctea (IDICAL, CONICET-INTA), Rafaela, Argentina
| | - M Fernanda Chiappero
- Instituto Multidisciplinario de Biología Vegetal (IMBiV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Victoria Vaieretti
- Instituto Multidisciplinario de Biología Vegetal (IMBiV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Mariana Soria
- PUNABIO S.A. Campus USP-T Av. Solano Vera y Camino a Villa Nougués San Pablo, Tucumán, Argentina
| | - María Eugenia Farías
- PUNABIO S.A. Campus USP-T Av. Solano Vera y Camino a Villa Nougués San Pablo, Tucumán, Argentina
| | - Andrea E Izquierdo
- Instituto Multidisciplinario de Biología Vegetal (IMBiV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina.
- Facultad de Ciencias Naturales y Exactas e Instituto M. Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina.
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12
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Wang Z, Zhang N, Li C, Shao L. Diversity of antibiotic resistance genes in soils with four different fertilization treatments. Front Microbiol 2023; 14:1291599. [PMID: 37928655 PMCID: PMC10623414 DOI: 10.3389/fmicb.2023.1291599] [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: 09/09/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Although the enrichment of resistance genes in soil has been explored in recent years, there are still some key questions to be addressed regarding the variation of ARG composition in soil with different fertilization treatments, such as the core ARGs in soil after different fertilization treatments, the correlation between ARGs and bacterial taxa, etc. For soils after different fertilization treatments, the distribution and combination of ARG in three typical fertilization methods (organic fertilizer alone, chemical fertilizer alone, and conventional fertilizer) and non-fertilized soils were investigated in this study using high-throughput fluorescence quantitative PCR (HT-qPCR) technique. The application of organic fertilizers significantly increased the abundance and quantity of ARGs and their subtypes in the soil compared to the non-fertilized soil, where sul1 was the ARGs specific to organic fertilizers alone and in higher abundance. The conventional fertilizer application also showed significant enrichment of ARGs, which indicated that manure addition often had a more decisive effect on ARGs in soil than chemical fertilizers, and three bacteria, Pseudonocardia, Irregularibacter, and Castllaniella, were the key bacteria affecting ARG changes in soil after fertilization. In addition, nutrient factors and heavy metals also affect the distribution of ARGs in soil and are positively correlated. This paper reveals the possible reasons for the increase in the number of total soil ARGs and their relative abundance under different fertilization treatments, which has positive implications for controlling the transmission of ARGs through the soil-human pathway.
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Affiliation(s)
- Zhuoran Wang
- Key Laboratory of Groundwater Resources and Environment of Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Na Zhang
- Jilin Bishuiyuan Water Science and Technology Ltd., Co., Changchun, Jilin, China
| | - Chunming Li
- Jilin Bishuiyuan Water Science and Technology Ltd., Co., Changchun, Jilin, China
| | - Liang Shao
- Jilin Bishuiyuan Water Science and Technology Ltd., Co., Changchun, Jilin, China
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13
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Amin H, Šantl-Temkiv T, Cramer C, Finster K, Real FG, Gislason T, Holm M, Janson C, Jögi NO, Jogi R, Malinovschi A, Marshall IPG, Modig L, Norbäck D, Shigdel R, Sigsgaard T, Svanes C, Thorarinsdottir H, Wouters IM, Schlünssen V, Bertelsen RJ. Indoor Airborne Microbiome and Endotoxin: Meteorological Events and Occupant Characteristics Are Important Determinants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:11750-11766. [PMID: 37523308 PMCID: PMC10433529 DOI: 10.1021/acs.est.3c01616] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 08/02/2023]
Abstract
Airborne bacteria and endotoxin may affect asthma and allergies. However, there is limited understanding of the environmental determinants that influence them. This study investigated the airborne microbiomes in the homes of 1038 participants from five cities in Northern Europe: Aarhus, Bergen, Reykjavik, Tartu, and Uppsala. Airborne dust particles were sampled with electrostatic dust fall collectors (EDCs) from the participants' bedrooms. The dust washed from the EDCs' clothes was used to extract DNA and endotoxin. The DNA extracts were used for quantitative polymerase chain (qPCR) measurement and 16S rRNA gene sequencing, while endotoxin was measured using the kinetic chromogenic limulus amoebocyte lysate (LAL) assay. The results showed that households in Tartu and Aarhus had a higher bacterial load and diversity than those in Bergen and Reykjavik, possibly due to elevated concentrations of outdoor bacterial taxa associated with low precipitation and high wind speeds. Bergen-Tartu had the highest difference (ANOSIM R = 0.203) in β diversity. Multivariate regression models showed that α diversity indices and bacterial and endotoxin loads were positively associated with the occupants' age, number of occupants, cleaning frequency, presence of dogs, and age of the house. Further studies are needed to understand how meteorological factors influence the indoor bacterial community in light of climate change.
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Affiliation(s)
- Hesham Amin
- Department
of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Tina Šantl-Temkiv
- Section
for Microbiology, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | - Christine Cramer
- Department
of Public Health, Environment, Work and Health, Danish Ramazzini Center, Aarhus University, 8000 Aarhus, Denmark
- Department
of Occupational Medicine, Danish Ramazzini Center, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Kai Finster
- Section
for Microbiology, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | | | | | - Mathias Holm
- Department
of Occupational and Environmental Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Christer Janson
- Department
of Medical Sciences: Respiratory, Allergy, Sleep Research, Uppsala University, 751 85 Uppsala, Sweden
- Department
of Medical Sciences: Clinical Physiology, Uppsala University, 751
85 Uppsala, Sweden
| | - Nils Oskar Jögi
- Department
of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Rain Jogi
- Tartu
University Hospital, Lung Clinic, 50406 Tartu, Estonia
| | - Andrei Malinovschi
- Department
of Medical Sciences: Clinical Physiology, Uppsala University, 751
85 Uppsala, Sweden
| | - Ian P. G. Marshall
- Section
for Microbiology, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | - Lars Modig
- Division
of Occupational and Environmental Medicine, Department of Public Health
and Clinical Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Dan Norbäck
- Department of Medical
Sciences, Occupational and Environmental Medicine, Uppsala University, 751
85 Uppsala, Sweden
| | - Rajesh Shigdel
- Department
of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Torben Sigsgaard
- Department
of Public Health, Environment, Work and Health, Danish Ramazzini Center, Aarhus University, 8000 Aarhus, Denmark
| | - Cecilie Svanes
- Department of Occupational Medicine, Haukeland
University Hospital, 5053 Bergen, Norway
- Centre for International Health, University
of Bergen Department of Global Public Health and Primary Care, 5009 Bergen, Norway
| | - Hulda Thorarinsdottir
- Department of Anesthesia
and Intensive Care, Landspitali University
Hospital, 101 Reykjavik, Iceland
| | - Inge M. Wouters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Vivi Schlünssen
- Department
of Public Health, Environment, Work and Health, Danish Ramazzini Center, Aarhus University, 8000 Aarhus, Denmark
| | - Randi J. Bertelsen
- Department
of Clinical Science, University of Bergen, 5021 Bergen, Norway
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14
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Ajeethan N, Ali S, Fuller KD, Abbey L, Yurgel SN. Apple Root Microbiome as Indicator of Plant Adaptation to Apple Replant Diseased Soils. Microorganisms 2023; 11:1372. [PMID: 37374874 DOI: 10.3390/microorganisms11061372] [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: 03/12/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023] Open
Abstract
The tree fruit industry in Nova Scotia, Canada, is dominated by the apple (Malus domestica) sector. However, the sector is faced with numerous challenges, including apple replant disease (ARD), which is a well-known problem in areas with intensive apple cultivation. A study was performed using 16S rRNA/18S rRNA and 16S rRNA/ITS2 amplicon sequencing to assess soil- and root-associated microbiomes, respectively, from mature apple orchards and soil microbiomes alone from uncultivated soil. The results indicated significant (p < 0.05) differences in soil microbial community structure and composition between uncultivated soil and cultivated apple orchard soil. We identified an increase in the number of potential pathogens in the orchard soil compared to uncultivated soil. At the same time, we detected a significant (p < 0.05) increase in relative abundances of several potential plant-growth-promoting or biocontrol microorganisms and non-fungal eukaryotes capable of promoting the proliferation of bacterial biocontrol agents in orchard soils. Additionally, the apple roots accumulated several potential PGP bacteria from Proteobacteria and Actinobacteria phyla, while the relative abundances of fungal taxa with the potential to contribute to ARD, such as Nectriaceae and plant pathogenic Fusarium spp., were decreased in the apple root microbiome compared to the soil microbiome. The results suggest that the health of a mature apple tree can be ascribed to a complex interaction between potential pathogenic and plant growth-promoting microorganisms in the soil and on apple roots.
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Affiliation(s)
- Nivethika Ajeethan
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro NS B2N 5E3, Canada
- Department of Biosystems Technology, Faculty of Technology, University of Jaffna, Kilinochchi 44000, Sri Lanka
| | - Shawkat Ali
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville NS B4N 1J5, Canada
| | - Keith D Fuller
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville NS B4N 1J5, Canada
| | - Lord Abbey
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro NS B2N 5E3, Canada
| | - Svetlana N Yurgel
- USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA
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15
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Cantera S, Di Benedetto F, Tumulero BF, Sousa DZ. Microbial conversion of carbon dioxide and hydrogen into the fine chemicals hydroxyectoine and ectoine. BIORESOURCE TECHNOLOGY 2023; 374:128753. [PMID: 36801441 DOI: 10.1016/j.biortech.2023.128753] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
This study explores a novel conversion of CO2 into the chemicals hydroxyectoine and ectoine, which are compounds with high retail values in the pharmaceutical industry. Firstly, 11 species of microbes able to use CO2 and H2 and that have the genes for ectoines synthesis (ectABCD) were identified through literature search and genomic mining. Laboratory tests were then conducted to ascertain the capacity of these microbes to produce ectoines from CO2. Results showed that the most promising bacteria for CO2 to ectoines bioconversion areHydrogenovibrio marinus, Rhodococcus opacus, and Hydrogenibacillus schlegelii.Upon salinity and H2/CO2/O2 ratio optimization,H. marinus accumulated 85 mg of ectoine g biomass-1. Interestingly, R.opacusand H. schlegelii mainly produced hydroxyectoine (53 and 62 mg g biomass-1), which has a higher commercial value. Overall, these results constitute the first proof of a novel valorization platform of CO2 and lay the foundation for a new economic niche aimed at CO2 recircularization into pharmaceuticals.
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Affiliation(s)
- Sara Cantera
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands.
| | - Francesca Di Benedetto
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Ben F Tumulero
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
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16
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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
| | - Patrycja Golińska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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17
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Dacewicz E, Lenart-Boroń A. Waste Polyurethane Foams as Biomass Carriers in the Treatment Process of Domestic Sewage with Increased Ammonium Nitrogen Content. MATERIALS (BASEL, SWITZERLAND) 2023; 16:619. [PMID: 36676355 PMCID: PMC9862140 DOI: 10.3390/ma16020619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/25/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
In order to understand the mechanisms of microbial growth on waste polyurethane sponge materials, their effectiveness as biomass carriers in domestic sewage with increased ammonium nitrogen content treatment was assessed. Comparative experiments were carried out in microreactors under steady conditions of batch culture, which allowed for an assessment of different carriers, in the form of flexible foams, rigid foams, and flexible foams placed in full casings. In the studies conducted in continuous cultures, biomass carriers selected in batch culture were used as fillings in the column model. The structure of the microbial community inhabiting the spongy material was determined and the pollutant-removing process from real domestic sewage was assessed. Analyzes using the Illumina sequencing technique allowed for demonstrating that Nitrosomonas and Nitrospira were the predominant nitrifiers in the biomass carrier in the form of waste polyurethane foams (PUF). It was found that anammox bacteria, the presence of which-as unidentified Planctomycetes-was confirmed in the polyurethane sponge material, were also responsible for the high removal of N-NH4+. Burkholderia and Sphingopyxis phyla were identified as the dominant denitrifying bacteria involved in the treatment of domestic sewage with increased content of ammonium nitrogen. The biomass carrier in the form of waste PUF placed additionally in full casings proved to be more beneficial for the proliferation of bacteria involved in nitrification and denitrification processes. On the other hand, waste foams without casings proved to be more suitable for the growth of microorganisms known to perform partial denitrification and may accumulate nitrites (Staphylococcus, Dokdonella). Additionally, the presence of Devosia and Pseudonocardia, which participated in the phosphorus removal process, was found in the waste PUR foams.
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Affiliation(s)
- Ewa Dacewicz
- Department of Sanitary Engineering and Water Management, Faculty of Environmental Engineering and Land Surveying, University of Agriculture in Kraków, Adam Mickiewicz Ave. 24/28, 30-059 Kraków, Poland
| | - Anna Lenart-Boroń
- Department of Microbiology and Biomonitoring, Faculty of Agriculture and Economics, University of Agriculture in Kraków, Adam Mickiewicz Ave. 24/28, 30-059 Kraków, Poland
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18
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Pipite A, Lockhart PJ, McLenachan PA, Christi K, Kumar D, Prasad S, Subramani R. Isolation, antibacterial screening, and identification of bioactive cave dwelling bacteria in Fiji. Front Microbiol 2022; 13:1012867. [PMID: 36605510 PMCID: PMC9807670 DOI: 10.3389/fmicb.2022.1012867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteria are well known producers of bioactive secondary metabolites, including some of the most effective antibiotics in use today. While the caves of Oceania are still largely under-explored, they form oligotrophic and extreme environments that are a promising source for identifying novel species of bacteria with biologically active compounds. By using selective media that mimicked a cave environment, and pretreatments that suppressed the growth of fast-growing bacteria, we have cultured genetically diverse bacteria from a limestone cave in Fiji. Partial 16S rRNA gene sequences from isolates were determined and compared with 16S rRNA gene sequences in EzBioCloud and SILVA data bases. Fifty-five isolates purified from culture had Actinomycete-like morphologies and these were investigated for antibacterial activity. Initial screening using a cross streak test with pathogenic bacteria indicated that 34 of the isolates had antibacterial properties. The best matches for the isolates are bacteria with potential uses in the manufacture of antibiotics and pesticides, in bioremediation of toxic waste, in biomining, in producing bioplastics, and in plant growth promotion. Nineteen bacteria were confirmed as Actinomycetes. Thirteen were from the genus Streptomyces and six from genera considered to be rare Actinomycetes from Pseudonocardia, Kocuria, Micromonospora, Nonomuraea. Ten isolates were Firmicutes from the genera Bacillus, Lysinbacillus, Psychrobacillus and Fontibacillus. Two were Proteobacteria from the genera Mesorhizobium and Cupriavidus. Our findings identify a potentially rich source of microbes for applications in biotechnologies.
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Affiliation(s)
- Atanas Pipite
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji,*Correspondence: Atanas Pipite,
| | - Peter J. Lockhart
- School of Natural Sciences, Massey University, Palmerston North, New Zealand,Peter J. Lockhart,
| | | | - Ketan Christi
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji
| | - Dinesh Kumar
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji
| | - Surendra Prasad
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji
| | - Ramesh Subramani
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji
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19
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Wu Y, Wang B, Wu L, Liu S, Yue L, Wu J, Chen D. Fifty-year habitat subdivision enhances soil microbial biomass and diversity across subtropical land-bridge islands. Front Microbiol 2022; 13:1063340. [PMID: 36569066 PMCID: PMC9780280 DOI: 10.3389/fmicb.2022.1063340] [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: 10/07/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Although habitat loss and subdivision are considered main causes of sharp declines in biodiversity, there is still great uncertainty concerning the response of soil microbial biomass, diversity, and assemblage to habitat subdivision at the regional scale. Here, we selected 61 subtropical land-bridge islands (with small, medium, and large land areas) with a 50-year history of habitat subdivision and 9 adjacent mainland sites to investigate how habitat subdivision-induced unequal-sized patches and isolation affects biomass, diversity, and assemblages of soil bacteria and fungi. We found that the soil bacterial and fungal biomass on all unequal-sized islands were higher than that on mainland, while soil bacterial and fungal richness on the medium-sized islands were higher than that on mainland and other-sized islands. The habitat subdivision-induced increases in microbial biomass or richness were mainly associated with the changes in subdivision-specified habitat heterogeneities, especial for soil pH and soil moisture. Habitat subdivision reduced soil bacterial dissimilarity on medium-sized islands but did not affect soil fungal dissimilarity on islands of any size. The habitat fragment-induced changes in soil microbial dissimilarity were mainly associated with microbial richness. In summary, our results based on the responses of soil microbial communities from subtropical land-bridge islands are not consistent with the island biogeographical hypotheses but are to some extent consistent with the tradeoff between competition and dispersal. These findings indicate that the response of soil microbial communities to habitat subdivision differed by degree of subdivision and strongly related to habitat heterogeneity, and the distribution of microbial diversity among islands is also affected by tradeoff between competition and dispersal.
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Affiliation(s)
- Ying Wu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China,Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China,Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Bing Wang
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Liji Wu
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Shengen Liu
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Lingyan Yue
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Jianping Wu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China,Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, Kunming, China,Jianping Wu,
| | - Dima Chen
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China,*Correspondence: Dima Chen,
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20
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Fang Z, Zhang Q, Zhang L, She J, Li J, Zhang W, Zhang H, Zhu Y, Zhang C. Antifungal Macrolides Kongjuemycins from Coral-Associated Rare Actinomycete Pseudonocardia kongjuensis SCSIO 11457. Org Lett 2022; 24:3482-3487. [PMID: 35476540 DOI: 10.1021/acs.orglett.2c01089] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Four new macrolides, kongjuemycins A and B1-B3 (1-4), were isolated from a coral-associated actinomycete Pseudonocardia kongjuensis SCSIO 11457. Their structures were characterized by comprehensive spectroscopic analysis and single-crystal X-ray diffraction. The absolute configurations of 1 and 2 were established by electronic circular dichroism calculation and the modified Mosher's method. Kongjuemycins displayed antifungal activity against three phytopathogenic fungi.
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Affiliation(s)
- Zhuangjie Fang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
| | - Jianglian She
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
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Li J, Wang B, Yang Q, Si H, Zhao Y, Zheng Y, Peng W. Enabling Efficient Genetic Manipulations in a Rare Actinomycete Pseudonocardia alni Shahu. Front Microbiol 2022; 13:848964. [PMID: 35308340 PMCID: PMC8928166 DOI: 10.3389/fmicb.2022.848964] [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: 01/05/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudonocardia species are emerging as important microorganisms of global concern with unique and increasingly significant ecological roles and represent a prominent source of bioactive natural products, but genetic engineering of these organisms for biotechnological applications is greatly hindered due to the limitation of efficient genetic manipulation tools. In this regard, we report here the establishment of an efficient genetic manipulation system for a newly isolated strain, Pseudonocardia alni Shahu, based on plasmid conjugal transfer from Escherichia coli to Pseudonocardia. Conjugants were yielded upon determining the optimal ratio between the donor and recipient cells, and designed genome modifications were efficiently accomplished, including exogenous gene integration based on an integrative plasmid and chromosomal stretch removal by homologous recombination using a suicidal non-replicating vector. Collectively, this work has made the P. alni Shahu accessible for genetic engineering, and provided an important reference for developing genetic manipulation methods in other rare actinomycetes.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Baiyang Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qing Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Han Si
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yuting Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yanli Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- *Correspondence: Yanli Zheng,
| | - Wenfang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Engineering Research Center for Bio-enzyme Catalysis, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
- Wenfang Peng,
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