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Deng J, Xu W, Lv G, Yuan H, Zhang QH, Wickham JD, Xu L, Zhang L. Associated bacteria of a pine sawyer beetle confer resistance to entomopathogenic fungi via fungal growth inhibition. ENVIRONMENTAL MICROBIOME 2022; 17:47. [PMID: 36085246 PMCID: PMC9463743 DOI: 10.1186/s40793-022-00443-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND The entomopathogenic Beauveria bassiana is a popular fungus used to control the Japanese pine sawyer, Monochamus alternatus Hope, the key vector of pine wood nematode (Bursaphelenchus xylophilus) that is the causal agent of pine wilt disease, resulting in devastating losses of pines in China and Portugal. However, recent studies have demonstrated that some insect-associated bacteria might decrease fungal toxicity and further undermine its biological control efficacy against M. alternatus. Thus, it is of great significance to uncover whether and how associated bacteria of M. alternatus become involved in the infection process of B. bassiana. RESULTS Here, we show that axenic M. alternatus larvae died significantly faster than non-axenic larvae infected by four increasing concentrations of B. bassiana spores (Log-rank test, P < 0.001). The infection of B. bassiana significantly changed the richness and structure of the beetle-associated bacterial community both on the cuticle and in the guts of M. alternatus; meanwhile, the abundance of Pseudomonas and Serratia bacteria were significantly enriched as shown by qPCR. Furthermore, these two bacteria genera showed a strong inhibitory activity against B. bassiana (One-way ANOVA, P < 0.001) by reducing the fungal conidial germination and growth rather than regulating host immunity. CONCLUSIONS This study highlights the role of insect-associated bacteria in the interaction between pest insects and entomopathogenic fungi, which should be taken into consideration when developing microbial-based pest control strategies.
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Affiliation(s)
- Jundan Deng
- Anhui Provincial Key Laboratory of Microbial Control, Anhui Agricultural University, Hefei, 230036, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Weikang Xu
- Anhui Provincial Key Laboratory of Microbial Control, Anhui Agricultural University, Hefei, 230036, China
| | - Guochang Lv
- Anhui Provincial Key Laboratory of Microbial Control, Anhui Agricultural University, Hefei, 230036, China
| | - Hang Yuan
- Anhui Provincial Key Laboratory of Microbial Control, Anhui Agricultural University, Hefei, 230036, China
| | - Qing-He Zhang
- Sterling International, Inc., Spokane, WA, 99216, USA
| | - Jacob D Wickham
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prospect, Moscow, Russia, 119071
| | - Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Longwa Zhang
- Anhui Provincial Key Laboratory of Microbial Control, Anhui Agricultural University, Hefei, 230036, China.
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Yurgel SN, Nadeem M, Cheema M. Microbial Consortium Associated with Crustacean Shells Composting. Microorganisms 2022; 10:1033. [PMID: 35630475 PMCID: PMC9145653 DOI: 10.3390/microorganisms10051033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
Soil microbes play an essential role in the biodegradation of crustacean shells, which is the process of sustainable bioconversion to chitin derivatives ultimately resulting in the promotion of plant growth properties. While a number of microorganisms with chitinolytic properties have been characterized, little is known about the microbial taxa that participate in this process either by active chitin degradation or by facilitation of this activity through nutritional cooperation and composting with the chitinolytic microorganisms. In this study, we evaluated the transformation of the soil microbiome triggered by close approximation to the green crab shell surface. Our data indicate that the microbial community associated with green crab shell matter undergoes significant specialized changes, which was reflected in a decreased fungal and bacterial Shannon diversity and evenness and in a dramatic alteration in the community composition. The relative abundance of several bacterial and fungal genera including bacteria Flavobacterium, Clostridium, Pseudomonas, and Sanguibacter and fungi Mortierella, Mycochlamys, and Talaromyces were increased with approximation to the shell surface. Association with the shell triggered significant changes in microbial cooperation that incorporate microorganisms that were previously reported to be involved in chitin degradation as well as ones with no reported chitinolytic activity. Our study indicates that the biodegradation of crab shells in soil incorporates a consortium of microorganisms that might provide a more efficient way for bioconversion.
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Affiliation(s)
- Svetlana N. Yurgel
- USDA-ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA
| | - Muhammad Nadeem
- School of Science and the Environment, Grenfell Campus, Memorial University of Newfoundland and Labrador, Corner Brook, NL A2H 5G4, Canada; (M.N.); (M.C.)
| | - Mumtaz Cheema
- School of Science and the Environment, Grenfell Campus, Memorial University of Newfoundland and Labrador, Corner Brook, NL A2H 5G4, Canada; (M.N.); (M.C.)
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3
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Embacher J, Neuhauser S, Zeilinger S, Kirchmair M. Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus Serpula lacrymans. J Fungi (Basel) 2021; 7:354. [PMID: 33946450 PMCID: PMC8147175 DOI: 10.3390/jof7050354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022] Open
Abstract
The dry rot fungus Serpula lacrymans causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Using a cultivation-based approach, we show that S. lacrymans has many co-existing, mainly Gram-positive, bacteria and demonstrate differences in the communities associated with distinct fungal parts. Bacteria isolated from the fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were less abundant. Fluorescence in situ hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells scattered across and within tissues, sometimes also attached to fungal spores. In co-culture, some bacterial isolates caused growth inhibition of S. lacrymans, and vice versa, and some induced fungal pigment production. It was found that 25% of the isolates could degrade pectin, 43% xylan, 17% carboxymethylcellulose, and 66% were able to depolymerize starch. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria influence the behavior of S. lacrymans in culture.
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Affiliation(s)
| | | | | | - Martin Kirchmair
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria; (J.E.); (S.N.); (S.Z.)
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Marian M, Fujikawa T, Shimizu M. Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114. Arch Microbiol 2021; 203:3373-3388. [PMID: 33880605 DOI: 10.1007/s00203-021-02327-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022]
Abstract
Mitsuaria sp. TWR114 is a biocontrol agent against tomato bacterial wilt (TBW). We aimed to gain genomic insights relevant to the biocontrol mechanisms and colonization ability of this strain. The draft genome size was found to be 5,632,523 bp, with a GC content of 69.5%, assembled into 1144 scaffolds. Genome annotation predicted a total of 4675 protein coding sequences (CDSs), 914 pseudogenes, 49 transfer RNAs, 3 noncoding RNAs, and 2 ribosomal RNAs. Genome analysis identified multiple CDSs associated with various pathways for the metabolism and transport of amino acids and carbohydrates, motility and chemotactic capacities, protection against stresses (oxidative, antibiotic, and phage), production of secondary metabolites, peptidases, quorum-quenching enzymes, and indole-3-acetic acid, as well as protein secretion systems and their related appendages. The genome resource will extend our understanding of the genomic features related to TWR114's biocontrol and colonization abilities and facilitate its development as a new biopesticide against TBW.
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Affiliation(s)
- Malek Marian
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.,College of Agriculture, Ibaraki University, Ami, Inashiki, Ibaraki, 300-0393, Japan
| | - Takashi Fujikawa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8605, Japan
| | - Masafumi Shimizu
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
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Noskov YA, Kabilov MR, Polenogova OV, Yurchenko YA, Belevich OE, Yaroslavtseva ON, Alikina TY, Byvaltsev AM, Rotskaya UN, Morozova VV, Glupov VV, Kryukov VY. A Neurotoxic Insecticide Promotes Fungal Infection in Aedes aegypti Larvae by Altering the Bacterial Community. MICROBIAL ECOLOGY 2021; 81:493-505. [PMID: 32839879 DOI: 10.1007/s00248-020-01567-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
Symbiotic bacteria have a significant impact on the formation of defensive mechanisms against fungal pathogens and insecticides. The microbiome of the mosquito Aedes aegypti has been well studied; however, there are no data on the influence of insecticides and pathogenic fungi on its structure. The fungus Metarhizium robertsii and a neurotoxic insecticide (avermectin complex) interact synergistically, and the colonization of larvae with hyphal bodies is observed after fungal and combined (conidia + avermectins) treatments. The changes in the bacterial communities (16S rRNA) of Ae. aegypti larvae under the influence of fungal infection, avermectin toxicosis, and their combination were studied. In addition, we studied the interactions between the fungus and the predominant cultivable bacteria in vitro and in vivo after the coinfection of the larvae. Avermectins increased the total bacterial load and diversity. The fungus decreased the diversity and insignificantly increased the bacterial load. Importantly, avermectins reduced the relative abundance of Microbacterium (Actinobacteria), which exhibited a strong antagonistic effect towards the fungus in in vitro and in vivo assays. The avermectin treatment led to an increased abundance of Chryseobacterium (Flavobacteria), which exerted a neutral effect on mycosis development. In addition, avermectin treatment led to an elevation of some subdominant bacteria (Pseudomonas) that interacted synergistically with the fungus. We suggest that avermectins change the bacterial community to favor the development of fungal infection.
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Affiliation(s)
- Y A Noskov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091.
- National Research Tomsk State University, Tomsk, Russia, 634050.
| | - M R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630090
| | - O V Polenogova
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - Y A Yurchenko
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - O E Belevich
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - O N Yaroslavtseva
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - T Y Alikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630090
| | - A M Byvaltsev
- Novosibirsk State University, Novosibirsk, Russia, 630090
| | - U N Rotskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - V V Morozova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630090
| | - V V Glupov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
| | - V Y Kryukov
- Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia, 630091
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Paenibacillus lutrae sp. nov., A Chitinolytic Species Isolated from A River Otter in Castril Natural Park, Granada, Spain. Microorganisms 2019; 7:microorganisms7120637. [PMID: 31810255 PMCID: PMC6955709 DOI: 10.3390/microorganisms7120637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 11/16/2022] Open
Abstract
A highly chitinolytic facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive, rod-shaped bacterial strain N10T was isolated from the feces of a river otter in the Castril Natural Park (Granada, Spain). It is a slightly halophilic, motile, catalase-, oxidase-, ACC deaminase- and C4 and C8 lipase-positive strain. It is aerobic, respiratory and has a fermentative metabolism using oxygen as an electron acceptor, produces acids from glucose and can fix nitrogen. Phylogenetic analysis of the 16S rRNA gene sequence, multilocus sequence analysis (MLSA) of 16S rRNA, gyrB, recA and rpoB, as well as phylogenomic analyses indicate that strain N10T is a novel species of the genus Paenibacillus, with the highest 16S rRNA sequence similarity (95.4%) to P. chitinolyticus LMG 18047T and <95% similarity to other species of the genus Paenibacillus. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANIb) were 21.1% and <75%, respectively. Its major cellular fatty acids were anteiso-C15:0, C16:0, and iso-C15:0. G + C content ranged between 45%–50%. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with chemotaxonomic and phenotypic data, we demonstrate that type strain N10T (= CECT 9541T =LMG 30535T) is a novel species of genus Paenibacillus and the name Paenibacillus lutrae sp. nov. is proposed.
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7
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Rodrigues AA, Araújo MVF, Soares RS, Oliveira BFRDE, Ribeiro IDA, Sibov ST, Vieira JDG. Isolation and prospection of diazotrophic rhizobacteria associated with sugarcane under organic management. AN ACAD BRAS CIENC 2018; 90:3813-3829. [PMID: 30379271 DOI: 10.1590/0001-3765201820180319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/27/2018] [Indexed: 11/22/2022] Open
Abstract
Microorganisms associated with organic management are essential in nutrient transformation and release for plant use. The present study aimed to isolate, identify and characterize plant growth promoting diazotrophic rhizobacteria associated with sugarcane under organic management. Rhizospheres of organic sugarcane varieties IAC 911099 and CTC4 were sampled and inoculated onto nitrogen free NFb and Burk media. The isolated microorganisms were screened in vitro concerning their ability to produce plant growth promoting factors. Eighty-one bacteria were isolated; 45.6% were positive for the nifH gene and produced at least one of the evaluated plant growth promotion factors. The production of indole-3-acetic acid was observed in 46% of the isolates, while phosphate solubilization was observed in 86.5%. No isolates were hydrogen cyanide producers, while 81% were ammonia producers, 19% produced cellulases and 2.7%, chitinases. Microorganisms belonging to the Burkholderia genus were able to inhibit Fusarium moniliforme growth in vitro. Plant growth promoting microorganisms associated with organic sugarcane, especially belonging to Burkholderia, Sphingobium, Rhizobium and Enterobacter genera, can be environmentally friendly alternatives to improve sugarcane production.
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Affiliation(s)
- Ariana A Rodrigues
- Laboratório de Microbiologia Ambiental e Biotecnologia, Departamento de Biotecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Av. Universitária, s/n, 74605-050 Goiânia, GO, Brazil
| | - Marcus Vinícius F Araújo
- Laboratório de Microbiologia Ambiental e Biotecnologia, Departamento de Biotecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Av. Universitária, s/n, 74605-050 Goiânia, GO, Brazil
| | - Renan S Soares
- Laboratório de Microbiologia Ambiental e Biotecnologia, Departamento de Biotecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Av. Universitária, s/n, 74605-050 Goiânia, GO, Brazil
| | - Bruno F R DE Oliveira
- Laboratório de Bacteriologia Molecular e Marinha, Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rua Professor Rodolpho Paulo Rocco, 373, 21941-590 Rio de Janeiro, RJ, Brazil
| | - Igor D A Ribeiro
- Centro de Microbiologia Agrícola, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, 91540-000 Porto Alegre, RS, Brazil
| | - Sergio T Sibov
- Laboratório de Cultura de Tecidos, Departamento de Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goiás, Av. Esperança, s/n, 74690-900 Goiânia, GO, Brazil
| | - José Daniel G Vieira
- Laboratório de Microbiologia Ambiental e Biotecnologia, Departamento de Biotecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Av. Universitária, s/n, 74605-050 Goiânia, GO, Brazil
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Morohoshi T, Ogata K, Okura T, Sato S. Molecular Characterization of the Bacterial Community in Biofilms for Degradation of Poly(3-Hydroxybutyrate-co-3-Hydroxyhexanoate) Films in Seawater. Microbes Environ 2018; 33:19-25. [PMID: 29386425 PMCID: PMC5877338 DOI: 10.1264/jsme2.me17052] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Microplastics are fragmented pieces of plastic in marine environments, and have become a serious environmental issue. However, the dynamics of the biodegradation of plastic in marine environments have not yet been elucidated in detail. Polyhydroxyalkanoates (PHAs) are biodegradable polymers that are synthesized by a wide range of microorganisms. One of the PHA derivatives, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) has flexible material properties and a low melting temperature. After an incubation in seawater samples, a significant amount of biofilms were observed on the surfaces of PHBH films, and some PHBH films were mostly or partially degraded. In the biofilms that formed on the surfaces of unbroken PHBH films, the most dominant operational taxonomic units (OTUs) showed high similarity with the genus Glaciecola in the family Alteromonadaceae. On the other hand, the dominant OTUs in the biofilms that formed on the surfaces of broken PHBH films were assigned to the families Rhodobacteraceae, Rhodospirillaceae, and Oceanospirillaceae, and the genus Glaciecola mostly disappeared. The bacterial community in the biofilms on PHBH films was assumed to have dynamically changed according to the progression of degradation. Approximately 50 colonies were isolated from the biofilm samples that formed on the PHBH films and their PHBH-degrading activities were assessed. Two out of three PHBH-degrading isolates showed high similarities to Glaciecola lipolytica and Aestuariibacter halophilus in the family Alteromonadaceae. These results suggest that bacterial strains belonging to the family Alteromonadaceae function as the principal PHBH-degrading bacteria in these biofilms.
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Affiliation(s)
- Tomohiro Morohoshi
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University
| | - Kento Ogata
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University
| | - Tetsuo Okura
- GP Business Development Division, Kaneka Corporation
| | - Shunsuke Sato
- GP Business Development Division, Kaneka Corporation
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Mitsuaria noduli sp. nov., isolated from the root nodules of Robinia pseudoacacia in a lead–zinc mine. Int J Syst Evol Microbiol 2018; 68:87-92. [DOI: 10.1099/ijsem.0.002459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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10
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Affiliation(s)
- Koki Toyota
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology,
2–24–16 Nakacho, Koganei, Tokyo, 184–8588,
Japan
- Senior Editor, Microbes and Environments, E-mail:
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Characterization of Thermotolerant Chitinases Encoded by a Brevibacillus laterosporus Strain Isolated from a Suburban Wetland. Genes (Basel) 2015; 6:1268-82. [PMID: 26690223 PMCID: PMC4690040 DOI: 10.3390/genes6041268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/20/2015] [Accepted: 11/27/2015] [Indexed: 11/16/2022] Open
Abstract
To isolate and characterize chitinases that can be applied with practical advantages, 57 isolates of chitin-degrading bacteria were isolated from the soil of a suburban wetland. 16S rRNA gene analysis revealed that the majority of these strains belonged to two genera, Paenibacillus and Brevibacillus. Taking thermostability into account, the chitinases (ChiA and ChiC) of a B. laterosporus strain were studied further. Ni-NTA affinity-purified ChiA and ChiC were optimally active at pH 7.0 and 6.0, respectively, and showed high temperature stability up to 55 °C. Kinetic analysis revealed that ChiC has a lower affinity and stronger catalytic activity toward colloidal chitin than ChiA. With their stability in a broad temperature range, ChiA and ChiC can be utilized for the industrial bioconversion of chitin wastes into biologically active products.
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12
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Jankiewicz U, Swiontek Brzezinska M. Purification, characteristics and identification of chitinases synthesized by the bacterium Serratia plymuthica MP44 antagonistic against phytopathogenic fungi. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815050105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Tsurumaru H, Okubo T, Okazaki K, Hashimoto M, Kakizaki K, Hanzawa E, Takahashi H, Asanome N, Tanaka F, Sekiyama Y, Ikeda S, Minamisawa K. Metagenomic analysis of the bacterial community associated with the taproot of sugar beet. Microbes Environ 2015; 30:63-9. [PMID: 25740621 PMCID: PMC4356465 DOI: 10.1264/jsme2.me14109] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 10(5) reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 10(5) reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the (15)N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.
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Affiliation(s)
- Koki Toyota
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology
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15
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Narihiro T, Kamagata Y. Cultivating yet-to-be cultivated microbes: the challenge continues. Microbes Environ 2013; 28:163-5. [PMID: 23727826 PMCID: PMC4070670 DOI: 10.1264/jsme2.me2802rh] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, Tsukuba, Ibaraki 305–8566, Japan.
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Jacquiod S, Franqueville L, Cécillon S, M. Vogel T, Simonet P. Soil bacterial community shifts after chitin enrichment: an integrative metagenomic approach. PLoS One 2013; 8:e79699. [PMID: 24278158 PMCID: PMC3835784 DOI: 10.1371/journal.pone.0079699] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/25/2013] [Indexed: 11/19/2022] Open
Abstract
Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome.
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Affiliation(s)
- Samuel Jacquiod
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
- Microbial Molecular Ecology Group, Section of Microbiology, København Universitat, København, Denmark
| | - Laure Franqueville
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Sébastien Cécillon
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Timothy M. Vogel
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
- * E-mail:
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17
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Wang K, Yan PS, Cao LX, Ding QL, Shao C, Zhao TF. Potential of chitinolytic Serratia marcescens strain JPP1 for biological control of Aspergillus parasiticus and aflatoxin. BIOMED RESEARCH INTERNATIONAL 2013; 2013:397142. [PMID: 23865052 PMCID: PMC3705848 DOI: 10.1155/2013/397142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/08/2013] [Accepted: 06/09/2013] [Indexed: 11/17/2022]
Abstract
Serratia marcescens strain JPP1 was isolated from peanut hulls in Huai'an city, Jiangsu Province, China. Its potential to inhibit the mycelial growth of Aspergillus parasiticus and the subsequent aflatoxin production was evaluated. The strain JPP1 could produce chitinase to degrade fungal cell walls, which was the main mechanism of strain JPP1 for biocontrol. Scanning electron microscopy of fungi treated with the crude chitinase revealed abnormal morphological changes. While the strain was grown in the peanut hulls-based medium, the chitinase activity reached 7.39 units. RT-PCR analysis showed that the crude chitinase repressed the transcription of genes involved in the aflatoxin gene cluster, such as aflR, aflC (pksL1), and aflO (dmtA) genes. By visual agar plate assay and tip culture method, the strain JPP1 exhibited remarkable inhibitory effect on mycelia growth (antifungal ratio >95%) and subsequent aflatoxin production (antiaflatoxigenic ratio >98%). An in vitro assay with seed coating agent of bacterial suspension showed that strain JPP1 effectively reduced fungal growth and subsequent aflatoxin production on peanut seeds, and its antagonistic effect was superior to the common agricultural fungicide of carbendazim. These characteristics suggest that S. marcescens JPP1 strain could potentially be utilized for the biological control of phytopathogenic fungi and aflatoxin in Chinese peanut main producing areas.
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Affiliation(s)
- Kai Wang
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Pei-sheng Yan
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Li-xin Cao
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Qing-long Ding
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Chi Shao
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
| | - Teng-fei Zhao
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China
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18
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Someya N, Ohdaira Kobayashi Y, Tsuda S, Ikeda S. Molecular characterization of the bacterial community in a potato phytosphere. Microbes Environ 2013; 28:295-305. [PMID: 23748858 PMCID: PMC4070957 DOI: 10.1264/jsme2.me13006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The bacterial community of a potato phytosphere at the flowering stage was examined using both culture-dependent and -independent methods. Tissues (leaves, stems, roots and tubers) were sampled from field-grown potato plants (cultivar Matilda), and the clone libraries of 16S rRNA genes and the isolate collections using R2A medium were constructed. By analyzing the combined data set of 16S rRNA gene sequences from both clone libraries and isolate collections, 82 genera from 8 phyla were found and 237 OTUs (≥97% identity) at species level were identified across the potato phytosphere. The statistical analyses of clone libraries suggested that stems harbor the lowest diversity among the tissues examined. The phylogenetic analyses revealed that the most dominant phylum was shown to be Proteobacteria for all tissues (62.0%-89.7% and 57.7%-72.9%, respectively), followed by Actinobacteria (5.0%-10.7% and 14.6%-39.4%, respectively). The results of principal coordinates analyses of both clone libraries and isolate collections indicated that distinct differences were observed between above- and below-ground tissues for bacterial community structures. The results also revealed that leaves harbored highly similar community structures to stems, while the tuber community was shown to be distinctly different from the stem and root communities.
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Affiliation(s)
- Nobutaka Someya
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
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19
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Affiliation(s)
- Masahito Hayatsu
- National Institute for Agro-Environmental Sciences, Tsukuba, Japan.
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20
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Zindel R, Ofek M, Minz D, Palevsky E, Zchori‐Fein E, Aebi A. The role of the bacterial community in the nutritional ecology of the bulb mite
Rhizoglyphus robini
(Acari: Astigmata: Acaridae). FASEB J 2013; 27:1488-97. [DOI: 10.1096/fj.12-216242] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Renate Zindel
- Agroscope Reckenholz‐Tänikon, Research Station ARTZürichSwitzerland
| | - Maya Ofek
- Institute of Soil, Water, and Environmental Sciences, Agricultural Research OrganizationBet DaganIsrael
| | - Dror Minz
- Institute of Soil, Water, and Environmental Sciences, Agricultural Research OrganizationBet DaganIsrael
| | - Eric Palevsky
- Department of EntomologyNewe Ya'ar Research CenterAgricultural Research OrganizationRamat YishayIsrael
| | - Einat Zchori‐Fein
- Department of EntomologyNewe Ya'ar Research CenterAgricultural Research OrganizationRamat YishayIsrael
| | - Alexandre Aebi
- Agroscope Reckenholz‐Tänikon, Research Station ARTZürichSwitzerland
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21
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Wang K, Yan PS, Ding QL, Wu QX, Wang ZB, Peng J. Diversity of culturable root-associated/endophytic bacteria and their chitinolytic and aflatoxin inhibition activity of peanut plant in China. World J Microbiol Biotechnol 2012; 29:1-10. [PMID: 23108663 DOI: 10.1007/s11274-012-1135-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/14/2012] [Indexed: 10/27/2022]
Abstract
A total of 72 isolates of root-associated/endophytic (RAE) bacteria were isolated from peanut plants grown in the main producing areas of 6 provinces in China. The 16S rRNA gene sequences of these isolates were determined and phylogenetic analyses revealed that 72 isolates belonged to the classes Bacilli (49 isolates) and Gammaproteobacteria (23 isolates). The majority of RAE bacteria in Bacilli belonged to 2 genera, Bacillus and Lysinibacillus (48 and 1) while those in Gammaproteobacteria belonged to the genera Enterobacter, Serratia, Stenotrophomonas, and Pseudomonas (7, 11, 3 and 2 isolates, respectively). This is the first report of Lysinibacillus xylanilyticus isolate as biocontrol agent against AFs. All of the selected RAE bacteria showed inhibitory activities against Aspergillus parasiticus (A. parasiticus) growth and/or aflatoxins (AFs) production by visual agar plate assay and tip culture method. Most of the RAE bacteria strains (96 % strains) were determined to have decreased mycelia growth or AFs production levels by >50 % (p < 0.05). Bacterial isolates were further characterized for chitinolytic activity and 22 strains (30 % strains) of identified RAE bacteria degraded colloidal chitin on the chitin medium plate. Ten selected chitinolytic RAE bacteria were tested for antifungal activity on peanuts and most of them significantly decreased mycelial growth and AFs production levels by >90 %. These results showed a wide distribution of biological control bacteria against AFs in Chinese peanut main producing areas and the selected RAE bacteria could potentially be utilized for the biocontrol of toxicogenic fungi.
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Affiliation(s)
- Kai Wang
- School of Municipal & Environmental Engineering, Harbin Institute of Technology, 150090 Harbin, China.
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