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Zhang W, Zhou K, Huang L, Yang N, Lin L, Chen L, Yao J, Dong M, Shen J, Pan X. Biological characteristics and pathogenicity comparison of Nocardia seriolae isolated from Micropterus salmoides and Channa argus. Front Vet Sci 2024; 11:1367066. [PMID: 38659458 PMCID: PMC11040683 DOI: 10.3389/fvets.2024.1367066] [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: 01/08/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Nocardia seriolae is the primary pathogen causing nocardiosis in various fish species, leads to significant economic losses in the aquaculture industry. In this study, 10 bacterial strains isolated from Micropterus salmoides and Channa argus infected with nocardiosis, were identified as N. seriolae by physiological and biochemical identification, as well as 16S rDNA sequencing. Moreover, the key virulence-related genes such as ESX-1, T7SS-2, T7SS-3, EspG1, sodC, sod2 and ESAT6 were all positive, and showing high homology among different strains. Pathogenicity testing revealed mortality rates ranging from 70 to 100%, accompanied by the presence of white nodules in the viscera of deceased fish. The drug sensitivity test demonstrated that LY21811, the most lethal strain, exhibited high sensitivity to nine types of antibiotics, including azithromycin, doxycycline, florfenicol and compound sulfamethoxazole, yet showed complete resistance to β-lactam antibiotics. Additionally, the tannic acid also demonstrated potent inhibitory effects against LY21811, with a minimum inhibitory concentration of 0.0625 mg/mL. These results showed that N. seriolae originated from M. salmoides and C. argus in Zhejiang Province were highly conserved, demonstrating a high homogeneity in genetic characteristics, pathogenicity and antimicrobial susceptibilities. These results provide a foundation for further research on the pathogenic characteristics and disease prevention of N. seriolae infections.
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Affiliation(s)
- Wei Zhang
- School of Pharmacy, Qingdao University, Qingdao, China
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Kexin Zhou
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Lei Huang
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Na Yang
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Lingyun Lin
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Lu Chen
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Jiayun Yao
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Mingxin Dong
- School of Pharmacy, Qingdao University, Qingdao, China
| | - Jinyu Shen
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Xiaoyi Pan
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
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Guo H, Liu W, Xie Y, Wang Z, Huang C, Yi J, Yang Z, Zhao J, Yu X, Sibirina LA. Soil microbiome of shiro reveals the symbiotic relationship between Tricholoma bakamatsutake and Quercus mongolica. Front Microbiol 2024; 15:1361117. [PMID: 38601932 PMCID: PMC11004381 DOI: 10.3389/fmicb.2024.1361117] [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: 12/25/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Tricholoma bakamatsutake is a delicious and nutritious ectomycorrhizal fungus. However, its cultivation is hindered owing to limited studies on its symbiotic relationships. The symbiotic relationship between T. bakamatsutake and its host is closely related to the shiro, a complex network composed of mycelium, mycorrhizal roots, and surrounding soil. To explore the symbiotic relationship between T. bakamatsutake and its host, soil samples were collected from T. bakamatsutake shiro (Tb) and corresponding Q. mongolica rhizosphere (CK) in four cities in Liaoning Province, China. The physicochemical properties of all the soil samples were then analyzed, along with the composition and function of the fungal and bacterial communities. The results revealed a significant increase in total potassium, available nitrogen, and sand in Tb soil compared to those in CK soil, while there was a significant decrease in pH, total nitrogen, total phosphorus, available phosphorus, and silt. The fungal community diversity in shiro was diminished, and T. bakamatsutake altered the community structure of its shiro by suppressing other fungi, such as Russula (ectomycorrhizal fungus) and Penicillium (phytopathogenic fungus). The bacterial community diversity in shiro increased, with the aggregation of mycorrhizal-helper bacteria, such as Paenibacillus and Bacillus, and plant growth-promoting bacteria, such as Solirubrobacter and Streptomyces, facilitated by T. bakamatsutake. Microbial functional predictions revealed a significant increase in pathways associated with sugar and fat catabolism within the fungal and bacterial communities of shiro. The relative genetic abundance of carboxylesterase and gibberellin 2-beta-dioxygenase in the fungal community was significantly increased, which suggested a potential symbiotic relationship between T. bakamatsutake and Q. mongolica. These findings elucidate the microbial community and relevant symbiotic environment to better understand the relationship between T. bakamatsutake and Q. mongolica.
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Affiliation(s)
- Hongbo Guo
- College of Life Engineering, Shenyang Institute of Technology, Fushun, China
- Primorye State Agricultural Academy, Ussuriysk, Russia
| | - Weiye Liu
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Yuqi Xie
- College of Life Engineering, Shenyang Institute of Technology, Fushun, China
| | - Zhenyu Wang
- College of Life Engineering, Shenyang Institute of Technology, Fushun, China
| | - Chentong Huang
- College of Life Engineering, Shenyang Institute of Technology, Fushun, China
| | - Jingfang Yi
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Zhaoqian Yang
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Jiachen Zhao
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Xiaodan Yu
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Lidiya Alekseevna Sibirina
- Primorye State Agricultural Academy, Ussuriysk, Russia
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russia
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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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Jin W, Wang J, Yang X. Analysis of three cases with false positive PCR results of non tuberculosis mycobacterium. Respir Med Case Rep 2023; 47:101973. [PMID: 38260180 PMCID: PMC10801299 DOI: 10.1016/j.rmcr.2023.101973] [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: 03/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Background Real-time fluorescent quantitative PCR (RT-PCR) can effectively distinguish between Mycobacterium tuberculosis (MTB) and Non-tuberculosis mycobacterium (NTM), but when there are overlapping sequences between other pathogens (such as Nocardia otidiscaviarum, Mycobacterium parantracellulare, Mycolicibacterium fluoranthenivorans) and NTM, abnormal amplification curves may appear. Case presentation The clinical manifestations of the three patients were fever and respiratory symptoms. Chest CT showed "multiple lung infections". The acid-fast bacilli were negative by microscopic examination. The results of RT-PCR detection of Mycobacterium tuberculosis DNA showed that they are all NTM, while the results of DNA microarray method showed that there were no non-Mycobacterium tuberculosis. Identified by MALDI-TOF mass spectrometry, they are Nocardia otidiscaviarum, Mycobacterium parantracellale, Mycolicibacterium fluoranthenivorans. We found that the sequences of the above three bacteria can be combined with the primers and probes used for NTM PCR detection, resulting in false positive. Conclusions In the RT-PCR detection of mycobacteria, if there's abnormal amplification, and the mycobacterial species cannot be identified, the amplified products sequencing or MALDI- TOF mass spectrometry identification will help avoid the omission of rare pathogens.
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Affiliation(s)
| | | | - Xin Yang
- The clinical Laboratory, Yantai Yuhuangding Hospital, 20 Yuhuangding East Road, Yantai 264000, Shandong, China
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Alotaibi F, Lee SJ, Lahrach Z, St-Arnaud M, Hijri M. Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil. Microorganisms 2023; 11:2972. [PMID: 38138115 PMCID: PMC10745995 DOI: 10.3390/microorganisms11122972] [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: 10/24/2023] [Revised: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
The bacterial strain WB46 was isolated from the rhizosphere of willow plants (Salix purpurea L.) growing in soil contaminated with petroleum hydrocarbons. The strain was subjected to whole-genome shotgun sequencing using Illumina HiSeq. Its draft genome is 7.15 Mb, with a 69.55% GC content, containing 6387 protein-coding genes and 51 tRNA and 15 rRNA sequences. The quality and reliability of the genome were assessed using CheckM, attaining an estimated genome completeness of 98.75% and an estimated contamination of 1.68%. These results indicate a high-quality genome (>95%) and low contamination (<5%). Many of these genes are responsible for petroleum hydrocarbon degradation, such as alkane 1-monooxygenase (alkB) and naphthalene dioxygenase (ndo). 16S rRNA gene analysis, including in silico DNA-DNA hybridization (DDH) and average nucleotide identity (ANI), showed that strain WB46 belongs to the genus Nocardia, and the most closely related species is Nocardia asteroides. The strain WB46 showed a distance of 63.4% and sequence identity of 88.63%, respectively. These values fall below the threshold levels of 70% and 95%, respectively, suggesting that the strain WB46 is a new species. We propose the name of Nocardia canadensis sp. nov. for this new species. Interestingly, the sequence divergence of the 16S rRNA gene showed that the divergence only occurred in the V2 region. Therefore, the conventional V3-V4, V5-V7, or V8-V9 targeting metabarcoding, among others, would not be able to assess the diversity related to this new species.
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Affiliation(s)
- Fahad Alotaibi
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
- Department of Soil Science, King Saud University, Riyadh 11564, Saudi Arabia
| | - Soon-Jae Lee
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
| | - Zakaria Lahrach
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir 43150, Morocco
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; (S.-J.L.); (Z.L.); (M.S.-A.)
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir 43150, Morocco
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Ahsan T, Tian PC, Gao J, Wang C, Liu C, Huang YQ. Effects of microbial agent and microbial fertilizer input on soil microbial community structure and diversity in a peanut continuous cropping system. J Adv Res 2023:S2090-1232(23)00367-3. [PMID: 38030126 DOI: 10.1016/j.jare.2023.11.028] [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: 09/09/2023] [Revised: 11/11/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023] Open
Abstract
INTRODUCTION The soil harbors a diverse array of microorganisms, and these are essential components of terrestrial ecosystems. The presence of microorganisms in the soil, particularly in the rhizosphere, is closely linked to plant growth and soil fertility. OBJECTIVE The primary objective of this study is to assess the potential advantages of integrating microbial inoculants with compound fertilizer in enhancing peanut yield. METHODS We utilized Illumina MiSeq high-throughput sequencing technology to conduct our investigation. The experimental design consists of four treatment groups: compound fertilizers (CF), compound fertilizers supplemented with microbial agents (CF + MA), compound fertilizers supplemented with microbial fertilizers (CF + MF), and compound fertilizers supplemented with both microbial agents and microbial fertilizers (CF + MM). RESULTS The experimental results demonstrated a significant increase in peanut yield upon application of CF + MA, CF + MF, and CF + MM treatments. During the blossom stage and pod-setting stage, the soil's catalase, urease, and acid phosphatase activities were significantly increased in the CF + MA, and CF + MM treatments compared to the CF treatment. The application of CF + MA resulted in an increase in bacterial richness in the rhizosphere soil of peanuts, as indicated by the sequencing results. The application of CF + MA, CF + MF, and CF + MM resulted in a reduction of fungal diversity. Proteobacteria, Actinobacteria, and Acidobacteria were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the dominant phyla in the fungal component of the rhizosphere soil microbiome across all experimental treatments. CONCLUSION Microbial agents and fertilizers modify the peanut rhizosphere soil's microbial community structure, as per our findings. The abundance of potentially beneficial bacteria (Bradyrhizobium, Rhizobium, and Burkholderia) and fungi (Trichoderma and Cladophialophora) could increase, while pathogenic fungi (Penicillium and Fusarium) decreased, thereby significantly promoting plant growth and yield of peanut.
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Affiliation(s)
- Taswar Ahsan
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Pei-Cong Tian
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Jie Gao
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Chen Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Chuang Liu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Yu-Qian Huang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
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Saad H, Majer T, Bhattarai K, Lampe S, Nguyen DT, Kramer M, Straetener J, Brötz-Oesterhelt H, Mitchell DA, Gross H. Bioinformatics-guided discovery of biaryl-linked lasso peptides. Chem Sci 2023; 14:13176-13183. [PMID: 38023510 PMCID: PMC10664482 DOI: 10.1039/d3sc02380j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Using mass spectrometry, stable isotope incorporation, and extensive 2D-NMR spectrometry, we report the structural characterization of two unique examples of (C-N) biaryl-linked lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with a Trp-Tyr crosslink, while longipepetin A, from Longimycelium tulufanense, features a Trp-Trp linkage. Besides the unusual bicyclic frame, a Met of longipepetin A undergoes S-methylation to yield a trivalent sulfonium, a heretofore unprecedented RiPP modification. A bioinformatic survey revealed additional lasso peptide BGCs containing P450 enzymes which await future characterization. Lastly, nocapeptin A bioactivity was assessed against a panel of human and bacterial cell lines with modest growth-suppression activity detected towards Micrococcus luteus.
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Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Thomas Majer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Keshab Bhattarai
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Sarah Lampe
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Dinh T Nguyen
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Markus Kramer
- Institute of Organic Chemistry, University of Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Jan Straetener
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen Tübingen Germany
| | - Douglas A Mitchell
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen Tübingen Germany
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Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia. PLoS Negl Trop Dis 2021; 15:e0009665. [PMID: 34437546 PMCID: PMC8437295 DOI: 10.1371/journal.pntd.0009665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/13/2021] [Accepted: 07/19/2021] [Indexed: 01/23/2023] Open
Abstract
Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus. Nocardia species can be responsible for opportunistic infections in humans, causing a variety of clinical presentations. They can also cause mycetoma in a normal host through direct inoculation. Although these species are often overlooked and misunderstood by modern medicine, they can cause life-threatening infections. However, most of our knowledge about Nocardia is based upon case reports and a few small studies of limited scope. This study provides an overview of the taxonomic and evolutionary structure of the genus Nocardia through extensive analysis of genome sequences. Our work aids the field by dissecting the genetic diversity of this species and improving the identification scheme for Nocardia species.
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Ericsson AC, Busi SB, Davis DJ, Nabli H, Eckhoff DC, Dorfmeyer RA, Turner G, Oswalt PS, Crim MJ, Bryda EC. Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration. Anim Microbiome 2021; 3:55. [PMID: 34353374 PMCID: PMC8340428 DOI: 10.1186/s42523-021-00116-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/27/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. Commercial RAS must be allowed to equilibrate following installation, before fish can be introduced. There is little information available regarding the bacterial community structure in commercial zebrafish housing systems, or the time-point at which the system or biofilter reaches a microbiological equilibrium in RAS in general. METHODS A zebrafish housing system was monitored at multiple different system sites including tank water in six different tanks, pre- and post-particulate filter water, the fluidized bed biofilter substrate, post-carbon filter water, and water leaving the ultra-violet (UV) disinfection unit and entering the tanks. All of these samples were collected in quadruplicate, from prior to population of the system with zebrafish through 18 weeks post-population, and analyzed using both 16S rRNA amplicon sequencing and culture using multiple agars and annotation of isolates via matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. Sequencing data were analyzed using traditional methods, network analyses of longitudinal data, and integration of culture and sequence data. RESULTS The water microbiome, dominated by Cutibacterium and Staphylococcus spp., reached a relatively stable richness and composition by approximately three to four weeks post-population, but continued to evolve in composition throughout the study duration. The microbiomes of the fluidized bed biofilter and water leaving the UV disinfection unit were distinct from water at all other sites. Core taxa detected using molecular methods comprised 36 amplicon sequence variants, 15 of which represented Proteobacteria including multiple members of the families Burkholderiaceae and Sphingomonadaceae. Culture-based screening yielded 36 distinct isolates, and showed moderate agreement with sequencing data. CONCLUSIONS The microbiome of commercial RAS used for research zebrafish reaches a relatively stable state by four weeks post-population and would be expected to be suitable for experimental use following that time-point.
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Affiliation(s)
- Aaron C. Ericsson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- University of Missouri Metagenomics Center, Columbia, MO USA
| | - Susheel B. Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Daniel J. Davis
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- Animal Modeling Core, University of Missouri, Columbia, MO USA
| | - Henda Nabli
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
| | | | - Rebecca A. Dorfmeyer
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- University of Missouri Metagenomics Center, Columbia, MO USA
| | - Giedre Turner
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- University of Missouri Metagenomics Center, Columbia, MO USA
| | - Payton S. Oswalt
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
| | | | - Elizabeth C. Bryda
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO USA
- Animal Modeling Core, University of Missouri, Columbia, MO USA
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Engelbrecht A, Saad H, Gross H, Kaysser L. Natural Products from Nocardia and Their Role in Pathogenicity. Microb Physiol 2021; 31:217-232. [PMID: 34139700 DOI: 10.1159/000516864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022]
Abstract
Nocardia spp. are filamentous Actinobacteria of the order Corynebacteriales and mostly known for their ability to cause localized and systemic infections in humans. However, the onset and progression of nocardiosis is only poorly understood, in particular the mechanisms of strain-specific presentations. Recent genome sequencing has revealed an extraordinary capacity for the production of specialized small molecules. Such secondary metabolites are often crucial for the producing microbe to survive the challenges of different environmental conditions. An interesting question thus concerns the role of these natural products in Nocardia-associated pathogenicity and immune evasion in a human host. In this review, a summary and discussion of Nocardia metabolites is presented, which may play a part in nocardiosis because of their cytotoxic, immunosuppressive and metal-chelating properties or otherwise vitally important functions. This review also contains so far unpublished data concerning the biosynthesis of these molecules that were obtained by detailed bioinformatic analyses.
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Affiliation(s)
- Alicia Engelbrecht
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Hamada Saad
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Department of Phytochemistry and Plant Systematics, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt
| | - Harald Gross
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Institute for Drug Discovery, University of Leipzig, Leipzig, Germany
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11
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Assil Z, Esegbue O, Mašek O, Gutierrez T, Free A. Specific enrichment of hydrocarbonclastic bacteria from diesel-amended soil on biochar particles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143084. [PMID: 33131874 DOI: 10.1016/j.scitotenv.2020.143084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Biochar has been proposed as a suitable biostimulant for the remediation of hydrocarbon contamination, and also has the potential to act as a carrier for hydrocarbonoclastic microorganisms which could bioaugment endogenous microbial communities. However, the evidence regarding the biostimulatory effects of biochars on hydrocarbon bioremediation is somewhat equivocal, possibly due to variability of the physicochemical properties of biochar and soil across studies. Here, we use standard biochars with defined properties produced from softwood pellets (SWP) and rice husk (RH) at pyrolysis temperatures of 550 °C or 700 °C to test the effects of biochar amendment on microbial community composition and hydrocarbon degradation in soil microcosms contaminated with diesel oil. Combining this approach for the first time with specific analysis of microbial community composition using amplicon sequence variants (ASVs), we find that oil contamination causes extreme short-term loss of soil microbial diversity, and highly-specific selection of a limited set of genera defined by 13 ASVs. Biochar ameliorates the short-term loss of diversity, and in the longer term (9 weeks), changes community composition in a type-specific manner. The majority of the 13 selected ASVs are further enriched on biochar particles, although SWP biochars perform better than RH biochar in enrichment of putative hydrocarbonoclastic Aquabacterium spp. However, complete degradation of normal (n) alkanes from the aliphatic hydrocarbon fraction is prevented in the presence of biochar amendment, possibly due to their adsorption onto the char surface. Furthermore, we show that putative hydrocarbon degraders released from diesel-amended soil can subsequently be enriched to high levels on SWP biochar particles in growth medium supplemented with diesel oil as the sole carbon source; these include selected ASVs representing the genera Rhodococcus, Aquabacterium, and Cavicella. This work suggests that use of biochar pre-enriched with endogenous, conditionally-rare hydrocarbon degrading bacteria is a promising strategy for bioaugmentation of diesel-contaminated soils.
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Affiliation(s)
- Zhansaya Assil
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | | | - Ondřej Mašek
- UK Biochar Research Centre, School of GeoSciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Andrew Free
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
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12
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The Sorghum bicolor Root Exudate Sorgoleone Shapes Bacterial Communities and Delays Network Formation. mSystems 2021; 6:6/2/e00749-20. [PMID: 33727394 PMCID: PMC8546980 DOI: 10.1128/msystems.00749-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary and secondary metabolites exuded from roots are key drivers of root-soil microbe interactions that contribute to the structure and function of microbial communities. Studies with model plants have begun to reveal the complex interactions between root exudates and soil microbes, but little is known about the influence of specialized exudates from crop plants. The aims of this work were to understand whether sorgoleone, a unique lipophilic secondary benzoquinone exuded only from the root hairs of sorghum, influences belowground microbial community structure in the field, to assess the effect of purified sorgoleone on the cultured bacteria from field soils, and to determine whether sorgoleone inhibits nitrification under field conditions. Studies were conducted comparing wild-type sorghum and lines with genetically reduced sorgoleone exudation. In the soil near roots and rhizosphere, sorgoleone influenced microbial community structure as measured by β-diversity and network analysis. Under greenhouse conditions, the soil nitrogen content was an important factor in determining the impacts of sorgoleone. Sorgoleone delayed the formation of the bacterial and archaeal networks early in plant development and only inhibited nitrification at specific sampling times under field conditions. Sorgoleone was also shown to both inhibit and promote cultured bacterial isolate growth in laboratory tests. These findings provide new insights into the role of secondary metabolites in shaping the composition and function of the sorghum root-associated bacterial microbiomes. Understanding how root exudates modify soil microbiomes may potentially unlock an important tool for enhancing crop sustainability and yield in our changing environment.IMPORTANCE Plant roots exude a complex mixture of metabolites into the rhizosphere. Primary and secondary metabolites exuded from roots are key drivers of root-soil microbe interactions that contribute to the structure and function of microbial communities in agricultural and natural ecosystems. Previous work on plant root exudates and their influence on soil microbes has mainly been restricted to model plant species. Plant are a diverse group of organisms and produce a wide array of different secondary metabolites. Therefore, it is important to go beyond studies of model plants to fully understand the diverse repertoire of root exudates in crop plant species that feed human populations. Extending studies to a wider array of root exudates will provide a more comprehensive understanding of how the roots of important food crops interact with highly diverse soil microbial communities. This will provide information that could lead to tailoring root exudates for the development of more beneficial plant-soil microbe interactions that will benefit agroecosystem productivity.
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Wolański M, Krawiec M, Schwarz PN, Stegmann E, Wohlleben W, Buchmann A, Gross H, Eitel M, Koch P, Botas A, Méndez C, Núñez LE, Morís F, Cortés J, Zakrzewska‐Czerwińska J. A novel LysR-type regulator negatively affects biosynthesis of the immunosuppressant brasilicardin. Eng Life Sci 2021; 21:4-18. [PMID: 33531886 PMCID: PMC7837296 DOI: 10.1002/elsc.202000038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 11/16/2022] Open
Abstract
Brasilicardin A (BraA) is a promising immunosuppressive compound produced naturally by the pathogenic bacterium Nocardia terpenica IFM 0406. Heterologous host expression of brasilicardin gene cluster showed to be efficient to bypass the safety issues, low production levels and lack of genetic tools related with the use of native producer. Further improvement of production yields requires better understanding of gene expression regulation within the BraA biosynthetic gene cluster (Bra-BGC); however, the only so far known regulator of this gene cluster is Bra12. In this study, we discovered the protein LysRNt, a novel member of the LysR-type transcriptional regulator family, as a regulator of the Bra-BGC. Using in vitro approaches, we identified the gene promoters which are controlled by LysRNt within the Bra-BGC. Corresponding genes encode enzymes involved in BraA biosynthesis as well as the key Bra-BGC regulator Bra12. Importantly, we provide in vivo evidence that LysRNt negatively affects production of brasilicardin congeners in the heterologous host Amycolatopsis japonicum. Finally, we demonstrate that some of the pathway related metabolites, and their chemical analogs, can interact with LysRNt which in turn affects its DNA-binding activity.
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Affiliation(s)
| | - Michał Krawiec
- Faculty of BiotechnologyUniversity of WrocławWrocławPoland
| | - Paul N. Schwarz
- Department of Microbiology and BiotechnologyInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
| | - Evi Stegmann
- Department of Microbiology and BiotechnologyInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- German Centre for Infection Research (DZIF)Partner Site TübingenTübingenGermany
| | - Wolfgang Wohlleben
- Department of Microbiology and BiotechnologyInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- German Centre for Infection Research (DZIF)Partner Site TübingenTübingenGermany
| | - Anina Buchmann
- German Centre for Infection Research (DZIF)Partner Site TübingenTübingenGermany
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenTübingenGermany
- Present address:
Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Harald Gross
- German Centre for Infection Research (DZIF)Partner Site TübingenTübingenGermany
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenTübingenGermany
| | - Michael Eitel
- Department of Pharmaceutical ChemistryInstitute of Pharmaceutical SciencesUniversity of TübingenTübingenGermany
| | - Pierre Koch
- Department of Pharmaceutical ChemistryInstitute of Pharmaceutical SciencesUniversity of TübingenTübingenGermany
| | - Alma Botas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de AsturiasUniversidad de OviedoOviedoSpain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de AsturiasUniversidad de OviedoOviedoSpain
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Microbial risk assessment of Nocardia cyriacigeorgica in polluted environments, case of urban rainfall water. Comput Struct Biotechnol J 2020; 19:384-400. [PMID: 33489008 PMCID: PMC7787915 DOI: 10.1016/j.csbj.2020.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 12/29/2022] Open
Abstract
Urban infiltration basins are a reservoir of a high diversity of Nocardia encompassing both pathogenic and not-pathogenic species. Relative abundance of pathogenic Nocardia species presents a positive correlation with metal trace elements. High infraspecific variability within N. cyriacigeorgica, forming three phylogroups. Environmental N. cyriacigeorgica strains may be as virulent as clinical GUH-2 strain. hsp65 marker can be used by metabarcoding approach for assessment of environmental Nocardia biodiversity.
Urban Infiltration Basins (UIBs) are used to manage urban runoff transfers and feed aquifers. These UIBs can accumulate urban pollutants and favor the growth of potentially pathogenic biological agents as Nocardia. Objectives To assess the spatio-temporal dynamics of pathogenic Nocardia in UIBs and to stablish phylogenetic relationships between clinical and UIB N. cyriacigeorgica strains. To assess pathogenicity associated with environmental N. cyriacigeorgica using an animal model, and to identify genetic elements that may be associated to its virulence. Methods A well-characterized UIB in terms of chemical pollutants from Lyon area was used in this study during a whole year. Cultural and Next-Generation-Sequencing methods were used for Nocardia detection and typing. Clinical and environmental isolates phylogenetic relationships and virulences were compared with Multilocus-Sequence-Analysis study together with a murine model. Results In autumn, N. cyriacigeorgica and N. nova were the pathogenic most prevalent species in the UIB. The complex N. abscessus/asiatica was also detected together with some other non-pathogenic species. The presence of pathogenic Nocardia was positively correlated to metallic trace elements. Up to 1.0 × 103 CFU/g sediment of N. cyriacigeorgica and 6 OTUs splited in two different phylogroups were retrieved and were close to clinical strains. The EML446 tested UIB isolate showed significant infectivity in mice with pulmonary damages similar to clinical clone (GUH-2). Conclusion Hsp65 marker-based metabarcoding approach allowed detecting N. cyriacigeogica as the most abundant Nocardia pathogenic species in a UIB. Metal trace elements-polluted environments can be reservoirs of pathogenic Nocardia which may have a similar virulence to clinical strains.
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Cheng H, Zhang D, Huang B, Song Z, Ren L, Hao B, Liu J, Zhu J, Fang W, Yan D, Li Y, Wang Q, Cao A. Organic fertilizer improves soil fertility and restores the bacterial community after 1,3-dichloropropene fumigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:140345. [PMID: 32806339 DOI: 10.1016/j.scitotenv.2020.140345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Although fumigants can effectively control soil-borne diseases they are typically harmful to beneficial microorganisms unless methods are developed to encourage their survival after fumigation. The soil fumigant 1,3-dichloropropene (1,3-D) is widely used because of its effective management of pathogenic nematodes and weeds. After fumigation with 1,3-D, Bacillus subtilis and Trichoderma harzianum fertilizer (either singularly or together) or humic acid were added to soil that had been used to produce tomatoes under continuous production for >20 years. We evaluated changes to the soil's physicochemical properties and enzyme activity in response to these fertilizer treatments, and the effects of these changes on beneficial bacteria. Fertilizer applied after fumigation increased the content of ammonium nitrogen, nitrate nitrogen, available phosphorus, available potassium and organic matter, and it promoted an increase in pH and electrical conductivity. The activity of urease, sucrase and catalase enzymes in the soil increased after fumigation. Taxonomic identification of bacteria using genetic analysis techniques showed that fertilizer applied after fumigation increased the abundance of Actinobacteria and the relative abundance of the biological control genera Sphingomona, Pseudomonas, Bacillus and Lysobacter. The abundance of these beneficial bacteria increased significantly when B. subtilis and T. harzianum were applied together. These results showed that fertilizer applied after fumigation can increase the abundance of beneficial microorganisms in the soil within a short period of time, which improved the soil's fertility, ecological balance and potentially crop quality and yield.
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Affiliation(s)
- Hongyan Cheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhaoxin Song
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lirui Ren
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Baoqiang Hao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiahong Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100029, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100029, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100029, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100029, China.
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Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans. Microorganisms 2020; 8:microorganisms8060900. [PMID: 32549367 PMCID: PMC7355893 DOI: 10.3390/microorganisms8060900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 01/08/2023] Open
Abstract
Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).
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Zhang D, Yan D, Cheng H, Fang W, Huang B, Wang X, Wang X, Yan Y, Ouyang C, Li Y, Wang Q, Cao A. Effects of multi-year biofumigation on soil bacterial and fungal communities and strawberry yield. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 256:113415. [PMID: 31672346 DOI: 10.1016/j.envpol.2019.113415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/31/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Biofumigation is an effective, non-chemical method to control soil-borne pests and diseases and to maximize crop yield. We studied the responses of soil bacterial and fungal communities, the soil's nutritional state and strawberry yield, when the soil was biofumigated each year for five consecutive years using fresh chicken manure (BioFum). BioFum significantly increased the soil's NH4+-N, NO3--N, available P and K and organic matter. Fusarium spp. and Phytophthora spp. which are known to cause plant disease, were significantly decreased after BioFum. In addition, Biofum increased the soil's temperature, enhanced chlorophyll levels in the leaves of strawberry plants, and the soluble sugar and ascorbic acid content in strawberry fruit. We used high-throughput gene sequencing to monitor changes in the soil's bacterial and fungal communities. Although BioFum significantly decreased the diversity of these communities, it increased the relative abundance of some biological control agents in the phylum Actinobacteria and the genera Pseudomonas, Bacillus and Chaetomium. An increase in these biological control agents would reduce the incidence of soil-borne pathogens and plant disease. Although strawberry marketable yield using BioFum was higher in the first three years, the decline in the final two years could be due to the accumulation of P and K which may have delayed flowering and fruiting. Methods to overcome yield losses using BioFum need to be developed in the future. Our research, however, showed that BioFum enhanced soil fertility, reduced the presence of soil pathogens, increased the relative abundance of beneficial bacteria and fungi and improved strawberry quality. Unlike chemical soil treatments that can cause pest and disease resistance when used continuously over many years, our multi-year research program on BioFum showed that this treatment provided significant benefits to the soil, plant and strawberry fruit.
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Affiliation(s)
- Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China
| | - Hongyan Cheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xianli Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoning Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yue Yan
- Agricultural Environmental Protection and Rural Energy Principal Station of Shandong Province, Shandong, 250014, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China.
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Dhakal D, Rayamajhi V, Mishra R, Sohng JK. Bioactive molecules from Nocardia: diversity, bioactivities and biosynthesis. ACTA ACUST UNITED AC 2019; 46:385-407. [DOI: 10.1007/s10295-018-02120-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Abstract
Nocardia spp. are catalase positive, aerobic, and non-motile Gram-positive filamentous bacteria. Many Nocarida spp. have been reported as unusual causes of diverse clinical diseases in both humans and animals. Therefore, they have been studied for a long time, primarily focusing on strain characterization, taxonomic classification of new isolates, and host pathophysiology. Currently, there are emerging interests in isolating bioactive molecules from diverse actinobacteria including Nocardia spp. and studying their biosynthetic mechanisms. In addition, these species possess significant metabolic capacity, which has been utilized for generating diverse functionalized bioactive molecules by whole cell biotransformation. This review summarizes the structural diversity and biological activities of compounds biosynthesized or biotransformed by Nocardia spp. Furthermore, the recent advances on biosynthetic mechanisms and genetic engineering approaches for enhanced production or structural/functional modification are presented.
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Affiliation(s)
- Dipesh Dhakal
- 0000 0004 0533 4202 grid.412859.3 Department of Life Science and Biochemical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
| | - Vijay Rayamajhi
- 0000 0004 0533 4202 grid.412859.3 Department of Life Science and Biochemical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
| | - Ravindra Mishra
- 0000 0004 0533 4202 grid.412859.3 Department of Life Science and Biochemical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
| | - Jae Kyung Sohng
- 0000 0004 0533 4202 grid.412859.3 Department of Life Science and Biochemical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
- 0000 0004 0533 4202 grid.412859.3 Department of BT-Convergent Pharmaceutical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
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Mishra R, Dhakal D, Han JM, Lim HN, Jung HJ, Yamaguchi T, Sohng JK. Production of a Novel Tetrahydroxynaphthalene (THN) Derivative from Nocardia sp. CS682 by Metabolic Engineering and Its Bioactivities. Molecules 2019; 24:molecules24020244. [PMID: 30634706 PMCID: PMC6358914 DOI: 10.3390/molecules24020244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/26/2018] [Accepted: 01/08/2019] [Indexed: 11/16/2022] Open
Abstract
Nargenicin A1 is major secondary metabolite produced by Nocardia sp. CS682, with an effective antibacterial activity against various Gram-positive bacteria. Most Nocardia spp. have metabolic ability to produce compounds of diverse nature, so one-strain-many-compounds (OSMAC) approach can be applied for obtaining versatile compounds from these strains. In this study, we characterized a novel 1, 3, 6, 8-tetrahydroxynaphthalene (THN) derivative by metabolic engineering approach leading to the inactivation of nargenicin A1 biosynthesis. By using genome mining, metabolite profiling, and bioinformatics, the biosynthetic gene cluster and biosynthetic mechanism were elucidated. Further, the antibacterial, anticancer, melanin formation, and UV protective properties for isolated THN compound were performed. The compound did not exhibit significant antibacterial and cytotoxic activities, but it exhibited promising UV protection effects. Thus, metabolic engineering is an effective strategy for discovering novel bioactive molecules.
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Affiliation(s)
- Ravindra Mishra
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
| | - Dipesh Dhakal
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
| | - Jang Mi Han
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
| | - Haet Nim Lim
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
| | - Hye Jin Jung
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
| | - Tokutaro Yamaguchi
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, 70 Sun Moon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea.
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Lacombe-Harvey MÈ, Brzezinski R, Beaulieu C. Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution. Appl Microbiol Biotechnol 2018; 102:7219-7230. [PMID: 29931600 PMCID: PMC6097792 DOI: 10.1007/s00253-018-9149-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 12/20/2022]
Abstract
Actinobacteria, a large group of Gram-positive bacteria, secrete a wide range of extracellular enzymes involved in the degradation of organic compounds and biopolymers including the ubiquitous aminopolysaccharides chitin and chitosan. While chitinolytic enzymes are distributed in all kingdoms of life, actinobacteria are recognized as particularly good decomposers of chitinous material and several members of this taxon carry impressive sets of genes dedicated to chitin and chitosan degradation. Degradation of these polymers in actinobacteria is dependent on endo- and exo-acting hydrolases as well as lytic polysaccharide monooxygenases. Actinobacterial chitinases and chitosanases belong to nine major families of glycosyl hydrolases that share no sequence similarity. In this paper, the distribution of chitinolytic actinobacteria within different ecosystems is examined and their chitinolytic machinery is described and compared to those of other chitinolytic organisms.
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Affiliation(s)
| | - Ryszard Brzezinski
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Carole Beaulieu
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
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21
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Han HJ, Kwak MJ, Ha SM, Yang SJ, Kim JD, Cho KH, Kim TW, Cho MY, Kim BY, Jung SH, Chun J. Genomic characterization of Nocardia seriolae strains isolated from diseased fish. Microbiologyopen 2018; 8:e00656. [PMID: 30117297 PMCID: PMC6436429 DOI: 10.1002/mbo3.656] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 11/24/2022] Open
Abstract
Members of the genus Nocardia are widespread in diverse environments; a wide range of Nocardia species are known to cause nocardiosis in several animals, including cat, dog, fish, and humans. Of the pathogenic Nocardia species, N. seriolae is known to cause disease in cultured fish, resulting in major economic loss. We isolated two N. seriolae strains, CK‐14008 and EM15050, from diseased fish and sequenced their genomes using the PacBio sequencing platform. To identify their genomic features, we compared their genomes with those of other Nocardia species. Phylogenetic analysis showed that N. seriolae shares a common ancestor with a putative human pathogenic Nocardia species. Moreover, N. seriolae strains were phylogenetically divided into four clusters according to host fish families. Through genome comparison, we observed that the putative pathogenic Nocardia strains had additional genes for iron acquisition. Dozens of antibiotic resistance genes were detected in the genomes of N. seriolae strains; most of the antibiotics were involved in the inhibition of the biosynthesis of proteins or cell walls. Our results demonstrated the virulence features and antibiotic resistance of fish pathogenic N. seriolae strains at the genomic level. These results may be useful to develop strategies for the prevention of fish nocardiosis.
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Affiliation(s)
- Hyun-Ja Han
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | | | - Sung-Min Ha
- ChunLab Inc., Seoul, Korea.,Laboratory of evolutionary bioinformatics, Seoul National University, Seoul, Korea
| | | | - Jin Do Kim
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | | | | | - Mi Young Cho
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | | | - Sung-Hee Jung
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Jongsik Chun
- ChunLab Inc., Seoul, Korea.,Laboratory of evolutionary bioinformatics, Seoul National University, Seoul, Korea
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22
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Zhang S, Liu X, Jiang Q, Shen G, Ding W. Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity. AMB Express 2017; 7:178. [PMID: 28921475 PMCID: PMC5603465 DOI: 10.1186/s13568-017-0475-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/05/2017] [Indexed: 11/10/2022] Open
Abstract
Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high throughput Illumina sequencing and Biolog ECO microplates to determine the bacterial community and microbial metabolic activity in ginger harvest fields of non-fumigation (NF), chloropicrin-fumigation for 1 year (F_1) and continuous chloropicrin-fumigation for 3 years (F_3). The results showed that microbial richness and diversity in F_3 were the lowest, while the metabolic activity had no significant difference. With the increase of fumigation years, the incidence of bacterial wilt was decreased, the relative abundance of Actinobacteria and Saccharibacteria were gradually increased. Using LEfSe analyses, we found that Saccharibacteria was the most prominent biomarker in F_3. Eight genera associated with antibiotic production in F_3 were screened out, of which seven belonged to Actinobacteria, and one belonged to Bacteroidetes. The study indicated that with the increase of fumigation years, soil antibacterial capacity may be increased (possible reason for reduced the incidence of bacterial wilt), and Saccharibacteria played a potential role in evaluating the biological effects of continuous fumigation.
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Affiliation(s)
- Shuting Zhang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
| | - Xiaojiao Liu
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, Netherlands
| | - Qipeng Jiang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
| | - Guihua Shen
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
| | - Wei Ding
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715 China
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23
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Yasuike M, Nishiki I, Iwasaki Y, Nakamura Y, Fujiwara A, Shimahara Y, Kamaishi T, Yoshida T, Nagai S, Kobayashi T, Katoh M. Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species. PLoS One 2017; 12:e0173198. [PMID: 28257489 PMCID: PMC5336288 DOI: 10.1371/journal.pone.0173198] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/16/2017] [Indexed: 01/15/2023] Open
Abstract
Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages. The virulence factor candidates provide an essential basis for understanding their pathogenic mechanisms at the molecular level by the fish nocardiosis research community in future studies. We also found many potential antibiotic resistance genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N. cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes were present in all five Nocardia genomes (core genes) and 1,982 genes were unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a greater number of mobile elements and genes of unknown function that comprise the differences in structure and gene content from the other Nocardia genomes. In addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC transport system. Because of limited resources in ocean environments, these N. seriolae UTF1 specific ABC transporters might facilitate adaptation strategies essential for marine environment survival. Thus, the availability of the complete N. seriolae UTF1 genome sequence will provide a valuable resource for comparative genomic studies of N. seriolae isolates, as well as provide new insights into the ecological and functional diversity of the genus Nocardia.
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Affiliation(s)
- Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Yoshiko Shimahara
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Saiki, Oita, Japan
| | - Takashi Kamaishi
- Fisheries Agency, Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo, Japan
| | | | - Satoshi Nagai
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Takanori Kobayashi
- Headquarters, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masaya Katoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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Hara S, Ishikawa N, Hara Y, Nehira T, Sakai K, Gonoi T, Ishibashi M. Nabscessins A and B, Aminocyclitol Derivatives from Nocardia abscessus IFM 10029 T. JOURNAL OF NATURAL PRODUCTS 2017; 80:565-568. [PMID: 28112922 DOI: 10.1021/acs.jnatprod.6b00935] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Two new aminocyclitol amide derivatives, nabscessins A (1) and B (2), were isolated from the culture broth of a pathogenic actinomycete species, Nocardia abscessus IFM 10029T. The structures of nabscessins A and B were elucidated by spectral studies, and the compounds showed antifungal activity against Cryptococcus neoformans, with IC50 values of 32 and 16 μg/mL, respectively.
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Affiliation(s)
- Shoko Hara
- Graduate School of Pharmaceutical Sciences, Chiba University , 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Naoki Ishikawa
- Graduate School of Pharmaceutical Sciences, Chiba University , 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Yasumasa Hara
- Graduate School of Pharmaceutical Sciences, Chiba University , 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Tatsuo Nehira
- Graduate School of Integrated Arts and Sciences, Hiroshima University , 1-7-1 Kagamiyama, Higashi-hiroshima, 739-8521, Japan
| | - Kanae Sakai
- Medical Mycology Research Center, Chiba University , 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University , 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Masami Ishibashi
- Graduate School of Pharmaceutical Sciences, Chiba University , 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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25
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Liu X, Zhang S, Jiang Q, Bai Y, Shen G, Li S, Ding W. Using community analysis to explore bacterial indicators for disease suppression of tobacco bacterial wilt. Sci Rep 2016; 6:36773. [PMID: 27857159 PMCID: PMC5114674 DOI: 10.1038/srep36773] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 10/20/2016] [Indexed: 12/20/2022] Open
Abstract
Although bacterial communities play important roles in the suppression of pathogenic diseases and crop production, little is known about the bacterial communities associated with bacterial wilt. Based on 16S rRNA gene sequencing, statistical analyses of microbial communities in disease-suppressive and disease-conducive soils from three districts during the vegetation period of tobacco showed that Proteobacteria was the dominant phylum, followed by Acidobacteria. Only samples from September were significantly correlated to disease factors. Fifteen indicators from taxa found in September (1 class, 2 orders, 3 families and 9 genera) were identified in the screen as being associated with disease suppression, and 10 of those were verified for potential disease suppression in March. Kaistobacter appeared to be the genus with the most potential for disease suppression. Elucidating microbially mediated natural disease suppression is fundamental to understanding microecosystem responses to sustainable farming and provides a possible approach for modeling disease-suppressive indicators. Here, using cluster analysis, MRPP testing, LEfSe and specific filters for a Venn diagram, we provide insight into identifying possible indicators of disease suppression of tobacco bacterial wilt.
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Affiliation(s)
- Xiaojiao Liu
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Shuting Zhang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Qipeng Jiang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Yani Bai
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Guihua Shen
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Shili Li
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
| | - Wei Ding
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing, China
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26
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Bourguignon N, Bargiela R, Rojo D, Chernikova TN, de Rodas SAL, García-Cantalejo J, Näther DJ, Golyshin PN, Barbas C, Ferrero M, Ferrer M. Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data. World J Microbiol Biotechnol 2016; 32:201. [PMID: 27785708 DOI: 10.1007/s11274-016-2163-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
The analysis of catabolic capacities of microorganisms is currently often achieved by cultivation approaches and by the analysis of genomic or metagenomic datasets. Recently, a microarray system designed from curated key aromatic catabolic gene families and key alkane degradation genes was designed. The collection of genes in the microarray can be exploited to indicate whether a given microbe or microbial community is likely to be functionally connected with certain degradative phenotypes, without previous knowledge of genome data. Herein, this microarray was applied to capture new insights into the catabolic capacities of copper-resistant actinomycete Amycolatopsis tucumanensis DSM 45259. The array data support the presumptive ability of the DSM 45259 strain to utilize single alkanes (n-decane and n-tetradecane) and aromatics such as benzoate, phthalate and phenol as sole carbon sources, which was experimentally validated by cultivation and mass spectrometry. Interestingly, while in strain DSM 45259 alkB gene encoding an alkane hydroxylase is most likely highly similar to that found in other actinomycetes, the genes encoding benzoate 1,2-dioxygenase, phthalate 4,5-dioxygenase and phenol hydroxylase were homologous to proteobacterial genes. This suggests that strain DSM 45259 contains catabolic genes distantly related to those found in other actinomycetes. Together, this study not only provided new insight into the catabolic abilities of strain DSM 45259, but also suggests that this strain contains genes uncommon within actinomycetes.
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Affiliation(s)
- Natalia Bourguignon
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Rafael Bargiela
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain
| | | | - Sara A López de Rodas
- Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Jesús García-Cantalejo
- Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Daniela J Näther
- Institute for Microbiology, Biocentre, Goethe University, Frankfurt, Germany
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Gwynedd, LL57 2UW, UK
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain
| | - Marcela Ferrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Manuel Ferrer
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
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Dhakal D, Kumar Jha A, Pokhrel A, Shrestha A, Sohng JK. Genetic Manipulation of
Nocardia
Species. ACTA ACUST UNITED AC 2016; 40:10F.2.1-10F.2.18. [DOI: 10.1002/9780471729259.mc10f02s40] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Dipesh Dhakal
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
| | - Amit Kumar Jha
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
| | - Anaya Pokhrel
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
| | - Anil Shrestha
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
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28
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Lasker BA, Bell M, Klenk HP, Schumann P, Brown JM. Nocardia arizonensis sp. nov., obtained from human respiratory specimens. Antonie van Leeuwenhoek 2015; 108:1129-37. [DOI: 10.1007/s10482-015-0566-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/20/2015] [Indexed: 11/24/2022]
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29
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Luo Q, Hiessl S, Poehlein A, Daniel R, Steinbüchel A. Insights into the microbial degradation of rubber and gutta-percha by analysis of the complete genome of Nocardia nova SH22a. Appl Environ Microbiol 2014; 80:3895-907. [PMID: 24747905 PMCID: PMC4054215 DOI: 10.1128/aem.00473-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/14/2014] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of Nocardia nova SH22a was determined in light of the remarkable ability of rubber and gutta-percha (GP) degradation of this strain. The genome consists of a circular chromosome of 8,348,532 bp with a G+C content of 67.77% and 7,583 predicted protein-encoding genes. Functions were assigned to 72.45% of the coding sequences. Among them, a large number of genes probably involved in the metabolism of xenobiotics and hardly degradable compounds, as well as genes that participate in the synthesis of polyketide- and/or nonribosomal peptide-type secondary metabolites, were detected. Based on in silico analyses and experimental studies, such as transposon mutagenesis and directed gene deletion studies, the pathways of rubber and GP degradation were proposed and the relationship between both pathways was unraveled. The genes involved include, inter alia, genes participating in cell envelope synthesis (long-chain-fatty-acid-AMP ligase and arabinofuranosyltransferase), β-oxidation (α-methylacyl-coenzyme A [α-methylacyl-CoA] racemase), propionate catabolism (acyl-CoA carboxylase), gluconeogenesis (phosphoenolpyruvate carboxykinase), and transmembrane substrate uptake (Mce [mammalian cell entry] transporter). This study not only improves our insights into the mechanism of microbial degradation of rubber and GP but also expands our knowledge of the genus Nocardia regarding metabolic diversity.
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Affiliation(s)
- Quan Luo
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Sebastian Hiessl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany King Abdulaziz University, Faculty of Biology, Jeddah, Saudi Arabia
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