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McClure R, Naylor D, Farris Y, Davison M, Fansler SJ, Hofmockel KS, Jansson JK. Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome. Front Microbiol 2020; 11:1987. [PMID: 32983014 PMCID: PMC7479069 DOI: 10.3389/fmicb.2020.01987] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
The soil microbiome is central to the cycling of carbon and other nutrients and to the promotion of plant growth. Despite its importance, analysis of the soil microbiome is difficult due to its sheer complexity, with thousands of interacting species. Here, we reduced this complexity by developing model soil microbial consortia that are simpler and more amenable to experimental analysis but still represent important microbial functions of the native soil ecosystem. Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source. Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation. Several soil consortia were derived that had tractable richness (30–50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. The resulting consortia could be stored as glycerol or lyophilized stocks at −80°C and revived while retaining community composition, greatly increasing their use as tools for the research community at large. One of the consortia that was particularly stable was chosen as a model soil consortium (MSC-1) for further analysis. MSC-1 species interactions were studied using both pairwise co-cultivation in liquid media and during growth in soil under several perturbations. Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa. These experiments demonstrate the success of an approach based on naturally enriching a community of interacting species that can be stored, revived, and shared. The knowledge gained from querying these communities and their interactions will enable better understanding of the soil microbiome and the roles these interactions play in this environment.
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Affiliation(s)
- Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Dan Naylor
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Michelle Davison
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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Qin J, Tong Z, Zhan Y, Buisson C, Song F, He K, Nielsen-LeRoux C, Guo S. A Bacillus thuringiensis Chitin-Binding Protein is Involved in Insect Peritrophic Matrix Adhesion and Takes Part in the Infection Process. Toxins (Basel) 2020; 12:toxins12040252. [PMID: 32294913 PMCID: PMC7232397 DOI: 10.3390/toxins12040252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 11/16/2022] Open
Abstract
Bacillus thuringiensis (Bt) is used for insect pest control, and its larvicidal activity is primarily attributed to Cry toxins. Other factors participate in infection, and limited information is available regarding factors acting on the peritrophic matrix (PM). This study aimed to investigate the role of a Bt chitin-binding protein (CBPA) that had been previously shown to be expressed at pH 9 in vitro and could therefore be expressed in the alkaline gut of lepidopteron larvae. A ∆cbpA mutant was generated that was 10-fold less virulent than wild-type Bt HD73 towards Ostrinia furnacalis neonate larvae, indicating its important role in infection. Purified recombinant Escherichia coli CBPA was shown to have a chitin affinity, thus indicating a possible interaction with the chitin-rich PM. A translational GFP-CBPA fusion elucidated the localization of CBPA on the bacterial surface, and the transcriptional activity of the promoter PcbpA was immediately induced and confirmed at pH 9. Next, in order to connect surface expression and possible in vivo gut activity, last instar Galleria mellonella (Gm) larvae (not susceptible to Bt HD-73) were used as a model to follow CBPA in gut expression, bacterial transit, and PM adhesion. CBPA-GFP was quickly expressed in the Gm gut lumen, and more Bt HD73 strain bacteria adhered to the PM than those of the ∆cbpA mutant strain. Therefore, CBPA may help to retain the bacteria, via the PM binding, close to the gut surface and thus takes part in the early steps of Bt gut interactions.
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Affiliation(s)
- Jiaxin Qin
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Zongxing Tong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yiling Zhan
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Christophe Buisson
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kanglai He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Christina Nielsen-LeRoux
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Correspondence: (C.N.-L.); (S.G.); Tel.: +33-01-3465-2101 (C.N.-L.); +86-10-6891-4495 (S.G.)
| | - Shuyuan Guo
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
- Correspondence: (C.N.-L.); (S.G.); Tel.: +33-01-3465-2101 (C.N.-L.); +86-10-6891-4495 (S.G.)
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Sehar U, Mehmood MA, Hussain K, Nawaz S, Nadeem S, Siddique MH, Nadeem H, Gull M, Ahmad N, Sohail I, Gill SS, Majeed S. Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4. Bioinformation 2013; 9:901-7. [PMID: 24307767 PMCID: PMC3842575 DOI: 10.6026/97320630009901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 10/19/2013] [Indexed: 11/23/2022] Open
Abstract
This paper presents an in silico characterization of the chitin binding protein CBP50 from B. thuringiensis serovar konkukian S4 through homology modeling and molecular docking. The CBP50 has shown a modular structure containing an N-terminal CBM33 domain, two consecutive fibronectin-III (Fn-III) like domains and a C-terminal CBM5 domain. The protein presented a unique modular structure which could not be modeled using ordinary procedures. So, domain wise modeling using MODELLER and docking analyses using Autodock Vina were performed. The best conformation for each domain was selected using standard procedure. It was revealed that four amino acid residues Glu-71, Ser-74, Glu-76 and Gln-90 from N-terminal domain are involved in protein-substrate interaction. Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding. Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.
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Affiliation(s)
- Ujala Sehar
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University Faisalabad, Faisalabad, Pakistan
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Sehar U, Mehmood MA, Nawaz S, Nadeem S, Hussain K, Sohail I, Tabassum MR, Gill SS, Saqib A. Three dimensional (3D) structure prediction and substrate-protein interaction study of the chitin binding protein CBP24 from B. thuringiensis. Bioinformation 2013; 9:725-9. [PMID: 23976829 PMCID: PMC3746096 DOI: 10.6026/97320630009725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 07/25/2013] [Indexed: 12/03/2022] Open
Abstract
Bacillus thuringiensis is an insecticidal bacterium whose chitinolytic system has been exploited to improve insect resistance in crops. In the present study, we studied the CBP24 from B. thuringiensis using homology modeling and molecular docking. The primary and secondary structure analyses showed CBP24 is a positively charged protein and contains single domain that belongs to family CBM33. The 3D model after refinement was used to explore the chitin binding characteristics of CBP24 using AUTODOCK. The docking analyses have shown that the surface exposed hydrophilic amino acid residues Thr-103, Lys-112 and Ser-162 interact with substrate through H-bonding. While, the amino acids resides Glu-39, Tyr-46, Ser-104 and Asn-109 were shown to have polar interactions with the substrate. The binding energy values evaluation of docking depicts a stable intermolecular conformation of the docked complex. The functional characterization of the CBP24 will elucidate the substrate-interaction pathway of the protein in specific and the carbohydrate binding proteins in general leading towards the exploration and exploitation of the prokaryotic substrate utilization pathways.
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Affiliation(s)
- Ujala Sehar
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Salman Nawaz
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Shahid Nadeem
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Khadim Hussain
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Iqra Sohail
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Muhammad Rizwan Tabassum
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Saba Shahid Gill
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
| | - Anam Saqib
- Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University, Faisalabad, Pakistan
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Chu HH, Hoang V, Hofemeister J, Schrempf H. A Bacillus amyloliquefaciens ChbB protein binds beta- and alpha-chitin and has homologues in related strains. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1793-1803. [PMID: 11429457 DOI: 10.1099/00221287-147-7-1793] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A small (19.8 kDa) protein was identified in Bacillus amyloliquefaciens ALKO 2718 cultures during growth in the presence of yeast extract and chitin, but not with glucose. The protein targets beta-chitin best, then alpha-chitin, but barely any other polysaccharide. This described chitin-binding protein (ChbB) is the first of its type from a Bacillus strain and cross-reacts with antibodies raised against the Streptomyces alpha-chitin-binding protein CHB1. Using reverse genetics, the chromosomal chbB gene of strain ALKO 2718 was identified, cloned and sequenced. ChbB shares several motifs with the alpha-chitin-binding proteins CHB1 and CHB2 of Streptomyces and CBP21 of Serratia marcescens predominantly targeting beta-chitin. Synthesis was repressed by glucose and the presence of cre boxes suggests catabolite control. Using PCR, Southern hybridization and anti-ChbB antibodies, the presence of a chbB gene, as well as of a ChbB protein homologue, was ascertained in several tested B. amyloliquefaciens strains, but not in Bacillus subtilis 168. Contrary to B. subtilis 168, all B. amyloliquefaciens strains secreted varying amounts of enzymic activity, degrading carboxymethyl chitin coupled with Remazol brilliant violet.
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Affiliation(s)
- Hoang Ha Chu
- FB Biologie/Chemie, Universität Osnabrück, Barbarastraße 11, 49069 Osnabrück, Germany2
- Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Abteilung Molekulare Genetik, Corrensstraße 3, 06466 Gatersleben, Germany1
| | - Viet Hoang
- Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Abteilung Molekulare Genetik, Corrensstraße 3, 06466 Gatersleben, Germany1
| | - Jürgen Hofemeister
- Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Abteilung Molekulare Genetik, Corrensstraße 3, 06466 Gatersleben, Germany1
| | - Hildgund Schrempf
- FB Biologie/Chemie, Universität Osnabrück, Barbarastraße 11, 49069 Osnabrück, Germany2
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