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Guden RM, Haegeman A, Ruttink T, Moens T, Derycke S. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach. Mol Ecol 2024; 33:e17331. [PMID: 38533629 DOI: 10.1111/mec.17331] [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: 06/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.
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Affiliation(s)
- Rodgee Mae Guden
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Moens
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Oostende, Belgium
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2
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Du T, Zhang L, Chen Y, Zhang Y, Zhu H, Xu Z, Tan B, You C, Liu Y, Wang L, Liu S, Xu H, Xu L, Li H. Decreased snow depth inhibits litter decomposition via changes in litter microbial biomass and enzyme activity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171078. [PMID: 38382615 DOI: 10.1016/j.scitotenv.2024.171078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/04/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Decreased snow depth resulting from global warming has the potential to significantly impact biogeochemical cycles in cold forests. However, the specific mechanisms of how snow reduction affects litter decomposition and the underlying microbial processes remain unclear, this knowledge gap limits our ability to precisely predict ecological processes within cold forest ecosystems under climate change. Hence, a field experiment was conducted in a subalpine forest in southwestern China, involving a gradient of snow reduction levels (control, 50 %, 100 %) to investigate the effects of decreased snow on litter decomposition, as well as microbial biomass and activity, specifically focused on two common species: red birch (Betula albosinensis) and masters larch (Larix mastersiana). After one year of incubation, the decomposition rate (k-value) of the two types of litter ranged from 0.12 to 0.24 across three snow treatments. A significant lower litter mass loss, microbial biomass and enzyme activity were observed under decreased snow depth in winter. Furthermore, a hysteresis inhibitory effect of snow reduction on hydrolase activity was observed in the following growing season. Additionally, the high initial quality (lower C/N ratio) of red birch litter facilitated the colonization by a greater quantity of microorganisms, making it more susceptible to snow reduction compared to the low-quality masters larch litter. Structural equation models indicated that decreased snow depth hindered litter decomposition by altering the biological characterization of litter (e.g., microbial biomass and enzyme activity) and environmental variables (e.g., mean temperature and moisture content). The findings suggest that the potential decline in snow depth could inhibit litter decomposition by reducing microbial biomass and activity, implying that the future climate change may alter the material cycling processes in subalpine forest ecosystems.
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Affiliation(s)
- Ting Du
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhang
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yulian Chen
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhang
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Hemeng Zhu
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenfeng Xu
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Tan
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengming You
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Liu
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Lixia Wang
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Sining Liu
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongwei Xu
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Xu
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Han Li
- College of Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China.
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3
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Lau NS, Furusawa G. Polysaccharide degradation in Cellvibrionaceae: Genomic insights of the novel chitin-degrading marine bacterium, strain KSP-S5-2, and its chitinolytic activity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169134. [PMID: 38070563 DOI: 10.1016/j.scitotenv.2023.169134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/02/2023] [Accepted: 12/03/2023] [Indexed: 01/18/2024]
Abstract
In this study, we present the genome characterization of a novel chitin-degrading strain, KSP-S5-2, and comparative genomics of 33 strains of Cellvibrionaceae. Strain KSP-S5-2 was isolated from mangrove sediment collected in Balik Pulau, Penang, Malaysia, and its 16S rRNA gene sequence showed the highest similarity (95.09%) to Teredinibacter franksiae. Genome-wide analyses including 16S rRNA gene sequence similarity, average nucleotide identity, digital DNA-DNA hybridization, and phylogenomics, suggested that KSP-S5-2 represents a novel species in the family Cellvibrionaceae. The Cellvibrionaceae pan-genome exhibited high genomic variability, with only 1.7% representing the core genome, while the flexible genome showed a notable enrichment of genes related to carbohydrate metabolism and transport pathway. This observation sheds light on the genetic plasticity of the Cellvibrionaceae family and the gene pools that form the basis for the evolution of polysaccharide-degrading capabilities. Comparative analysis of the carbohydrate-active enzymes across Cellvibrionaceae strains revealed that the chitinolytic system is not universally present within the family, as only 18 of the 33 genomes encoded chitinases. Strain KSP-S5-2 displayed an expanded repertoire of chitinolytic enzymes (25 GH18, two GH19 chitinases, and five GH20 β-N-acetylhexosaminidases) but lacked genes for agar, xylan, and pectin degradation, indicating specialized enzymatic machinery focused primarily on chitin degradation. Further, the strain degraded 90% of chitin after 10 days of incubation. In summary, our findings provided insights into strain KSP-S5-2's genomic potential, the genetics of its chitinolytic system, genomic diversity within the Cellvibrionaceae family in terms of polysaccharide degradation, and its application for chitin degradation.
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Affiliation(s)
- Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia.
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4
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Subramanian K, Balaraman D, Panangal M, Nageswara Rao T, Perumal E, R A, Kumarappan A, Sampath Renuga P, Arumugam S, Thirunavukkarasu R, Aruni W, Yousef AlOmar S. Bioconversion of chitin waste through Stenotrophomonas maltophilia for production of chitin derivatives as a Seabass enrichment diet. Sci Rep 2022; 12:4792. [PMID: 35314727 PMCID: PMC8938544 DOI: 10.1038/s41598-022-08371-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
Marine wastes pose a great threat to the ecosystem leading to severe environmental hazards and health issues particularly the shellfish wastes. The shellfish waste which contains half of the amount of chitin can be efficiently transformed into useful products. Various approaches for the hydrolysis of chitin like physical, chemical, and enzymatic processes are there. Still, the use of enzyme chitinase is well documented as an effective and eco-friendly method. The present study summarizes the isolation of chitinase enzyme producing bacteria from different shrimp waste disposal sites in Parangipettai (India), and the possible use of an enzyme hydrolyzate as an immunostimulant to Asian Seabass (Lates calcarifer). The potential chitinase-producing bacteria were identified by 16S rRNA gene sequencing as Stenotrophomonas maltophilia. After purification, the chitinase specific activity was 5.01 (U/ml) and the protein content was 72 mg and the recovery rate was 48.06%. The optimum pH and temperature for the chitinolytic activity were 6.5 and at 35-50 °C, respectively. The animal experiment trial was done with our feed supplements which included 0.0 (control), 0.5%, 1% and 2% of chitin degraded product. All the supplementary feed had an optimal 42% (w/w) of crude protein. The feed protein level was 41-43% on average and gross energy was 13-17 kcal/g and the feed was observed to exhibit a significantly higher (p < 0.05) survival rate, condition factor, specific growth rates, and body weight gain was also found to be promising compared to other fishes fed with control diet only. The red blood cells (RBC) and white blood cell (WBC) counts were found to increase significantly after being challenged with infection in animals fed with chitin derivatives from 1st week to 3rd week when compared to the control. The hematocrit (Hct) values were low on the 2nd and 3rd week in infected fish fed with chitin derivatives. This low level was due to infection lyses of the red blood cells and increased nitro blue tetrazolium reduction. The control diet-fed fish showed 70% mortality but the chitin derivative supplemented fishes showed only 20% mortality post-infection. The results of the study encompass that the use of chitin-derivate enriched feed further is taken into large-scale approaches thereby benefitting the aquaculture sector.
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Affiliation(s)
- Kumaran Subramanian
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, 600119, India.
- Department of Biotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India.
| | | | - Mani Panangal
- Department of Biotechnology, Annai College of Arts & Science, Kumbakonam, Tamil Nadu, India.
| | - Tentu Nageswara Rao
- Department of Chemistry, Krishna University, Machilipatnam, Andra Pradesh, India
| | - Elumalai Perumal
- Department of Pharmacology, Saveetha Dental College and Hospital, Chennai, Tamil Nadu, India
| | - Amutha R
- Department of Biotechnology, Periyar University PG Extension Center, Dharmapuri, Tamil Nadu, India
| | - Alagappan Kumarappan
- Molecular Biology Laboratory (Pure Health), Al Qassimi Women's and Children's Hospital, Wasit Street, Sharjah, United Arab Emirates
| | - Pugazhvendan Sampath Renuga
- Department of Zoology, Annamalai University, Annamalai Nagar, Cuddalore, Tamilnadu, 608002, India
- Department of Zoology, Arignar Anna Government Arts College, Thiruvalluvar University, Cheyyar, Tamilnadu, 604407, India
| | - Suresh Arumugam
- Central Research Laboratory, Meenakshi Medical College Hospital & Research Institute, Kanchipuram, Tamil Nadu, India
| | - Rajasekar Thirunavukkarasu
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, 600119, India
| | - Wilson Aruni
- United States Department of Veterans Affairs, Loma Linda University, Loma Linda, CA, 92354, USA
| | - Suliman Yousef AlOmar
- Zoology Department, College of Science, Kind Saud University, Riyadh, 11451, Kingdom of Saudi Arabia.
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Garber AI, Zehnpfennig JR, Sheik CS, Henson MW, Ramírez GA, Mahon AR, Halanych KM, Learman DR. Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy. mSphere 2021; 6:e0077021. [PMID: 34817234 PMCID: PMC8612310 DOI: 10.1128/msphere.00770-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.
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Affiliation(s)
- Arkadiy I. Garber
- Biodesign Center for Mechanisms for Evolution, Arizona State University, Tempe, Arizona, USA
| | | | - Cody S. Sheik
- Biology Department and Large Lakes Observatory, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Michael W. Henson
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Gustavo A. Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
- Department of Marine Biology, Haifa University, Haifa, Israel
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Kenneth M. Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Deric R. Learman
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
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6
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Multifunctional fluorescent probes for high-throughput characterization of hexosaminidase enzyme activity. Bioorg Chem 2021; 119:105532. [PMID: 34883361 DOI: 10.1016/j.bioorg.2021.105532] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/29/2021] [Accepted: 11/25/2021] [Indexed: 12/28/2022]
Abstract
Microbial polysaccharides composed of N-acetylglucosamine (GlcNAc), such as chitin, peptidoglycan and poly-β-(1 → 6)-GlcNAc (dPNAG), play a critical role in maintaining cell integrity or in facilitating biofilm formation in numerous fungal and bacterial pathogens. Glycosyl hydrolase enzymes that catalyze the degradation of these β-GlcNAc containing polysaccharides play important roles in normal microbial cell physiology and can also be exploited as biocatalysts with applications as anti-fungal, anti-bacterial, or biofilm dispersal agents. Assays to rapidly detect and characterize the activity of such glycosyl hydrolase enzymes can facilitate their development as biocatalyst, however, currently available probes such as 4-methylumbelliferyl-β-GlcNAc (4MU-GlcNAc) are not universally accepted as substrates, and their fluorescent signal is sensitive to changes in pH. Here, we present the development of a new multifunctional fluorescent substrate analog for the detection and characterization of hexosaminidase enzyme activity containing a 7-amino-4-methyl coumarin (AMC) carbamate aglycone. This probe is widely tolerated as a substrate for exo-acting β-hexosaminidase, family 19 endo-chitinase, and the dPNAG hydrolase enzyme Dispersin B (DspB) and enables detection of hexosaminidase enzyme activity via either single wavelength fluorescent measurements or ratiometric fluorescent detection. We demonstrate the utility of this probe to screen for recombinant DspB activity in Escherichia coli cell lysates, and for the development of a high-throughput assay to screen for DspB inhibitors.
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7
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Li T, Jiang A, Di Y, Zhang D, Zhu X, Deng L, Ding X, Chen S. Novel BaSnO
3
/TiO
2
@HNTs Heterojunction Composites with Highly Enhanced Photocatalytic Activity and Stability. ChemistrySelect 2021. [DOI: 10.1002/slct.202102834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Taishan Li
- College of Materials and Chemistry & Chemical Engineering Chengdu University of Technology Chengdu 610059 China
| | - Ao Jiang
- College of Materials and Chemistry & Chemical Engineering Chengdu University of Technology Chengdu 610059 China
| | - Yuli Di
- College of Materials and Chemistry & Chemical Engineering Chengdu University of Technology Chengdu 610059 China
- Department School of Science Xichang University Xichang 615000 China
| | - Dafu Zhang
- College of Materials and Chemistry & Chemical Engineering Chengdu University of Technology Chengdu 610059 China
- Pangang Group research institute CO. Ltd. State Key Laboratory of comprehensive utilization of vanadium and titanium Panzhihua 617000 China
| | - Xiaodong Zhu
- College of Materials and Chemistry & Chemical Engineering Chengdu University of Technology Chengdu 610059 China
- College of Mechanical Engineering Chengdu University Chengdu 610106 China
| | - Lin Deng
- College of Materials and Chemistry & Chemical Engineering Chengdu University of Technology Chengdu 610059 China
- School of Biological and Chemical Engineering Panzhihua University Panzhihua 617000 China
| | - Xiaoyu Ding
- College of Materials and Chemistry & Chemical Engineering Chengdu University of Technology Chengdu 610059 China
| | - Shanhua Chen
- College of Materials and Chemistry & Chemical Engineering Chengdu University of Technology Chengdu 610059 China
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8
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Perkins AK, Rose AL, Grossart HP, Rojas-Jimenez K, Barroso Prescott SK, Oakes JM. Oxic and Anoxic Organic Polymer Degradation Potential of Endophytic Fungi From the Marine Macroalga, Ecklonia radiata. Front Microbiol 2021; 12:726138. [PMID: 34733248 PMCID: PMC8558676 DOI: 10.3389/fmicb.2021.726138] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.
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Affiliation(s)
- Anita K. Perkins
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
- Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Andrew L. Rose
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
- Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Hans-Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, Berlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Selva K. Barroso Prescott
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | - Joanne M. Oakes
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
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9
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Marinho CM, Garmyn D, Ga L, Brunhede MZ, O'Byrne C, Piveteau P. Investigation of the roles of AgrA and σB regulators in Listeria monocytogenes adaptation to roots and soil. FEMS Microbiol Lett 2021; 367:5775477. [PMID: 32124918 DOI: 10.1093/femsle/fnaa036] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 03/02/2020] [Indexed: 02/07/2023] Open
Abstract
Little is known about the regulatory mechanisms that ensure the survival of the food-borne bacterial pathogen Listeria monocytogenes in the telluric environment and on roots. Earlier studies have suggested a regulatory overlap between the Agr cell-cell communication system and the general stress response regulator σB. Here, we investigated the contribution of these two systems to root colonisation and survival in sterilised and biotic soil. The ability to colonise the roots of the grass Festuca arundinacea was significantly compromised in the double mutant (∆agrA∆sigB). In sterile soil at 25°C, a significant defect was observed in the double mutant, suggesting some synergy between these systems. However, growth was observed and similar population dynamics were shown in the parental strain, ΔagrA and ΔsigB mutants. In biotic soil at 25°C, viability of the parental strain declined steadily over a two-week period highlighting the challenging nature of live soil environments. Inactivation of the two systems further decreased survival. The synergistic effect of Agr and σB was stronger in biotic soil. Transcriptional analysis confirmed the expected effects of the mutations on known Agr- and σB-dependent genes. Data highlight the important role that these global regulatory systems play in the natural ecology of this pathogen.
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Affiliation(s)
- Catarina M Marinho
- Université de Bourgogne Franche-Comté, Esplanade Erasme BP27877, 21078 Dijon Cedex, France.,Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, 17 Rue Sully, 21000 Dijon Cedex, France.,National University of Ireland, Galway, School of Natural Sciences, Department of Microbiology, Bacterial Stress Response Group, University Road H91 TK33, Galway, Ireland
| | - Dominique Garmyn
- Université de Bourgogne Franche-Comté, Esplanade Erasme BP27877, 21078 Dijon Cedex, France.,Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, 17 Rue Sully, 21000 Dijon Cedex, France
| | - Laurent Ga
- Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, 17 Rue Sully, 21000 Dijon Cedex, France.,AgroSup Dijon, 26 Boulevard Dr Petitjean BP8799, 21079 Dijon Cedex, France
| | - Maja Z Brunhede
- Université de Bourgogne Franche-Comté, Esplanade Erasme BP27877, 21078 Dijon Cedex, France.,Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, 17 Rue Sully, 21000 Dijon Cedex, France
| | - Conor O'Byrne
- National University of Ireland, Galway, School of Natural Sciences, Department of Microbiology, Bacterial Stress Response Group, University Road H91 TK33, Galway, Ireland
| | - Pascal Piveteau
- Université de Bourgogne Franche-Comté, Esplanade Erasme BP27877, 21078 Dijon Cedex, France.,Institut National de la Recherche Agronomique, UMR 1347 Agroécologie, 17 Rue Sully, 21000 Dijon Cedex, France.,AgroSup Dijon, 26 Boulevard Dr Petitjean BP8799, 21079 Dijon Cedex, France
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10
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Jayaraman S, Naorem A, Lal R, Dalal RC, Sinha N, Patra A, Chaudhari S. Disease-Suppressive Soils-Beyond Food Production: a Critical Review. JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION 2021; 21:1437-1465. [PMID: 33746349 PMCID: PMC7953945 DOI: 10.1007/s42729-021-00451-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/21/2021] [Indexed: 05/09/2023]
Abstract
In the pursuit of higher food production and economic growth and increasing population, we have often jeopardized natural resources such as soil, water, vegetation, and biodiversity at an alarming rate. In this process, wider adoption of intensive farming practices, namely changes in land use, imbalanced fertilizer application, minimum addition of organic residue/manure, and non-adoption of site-specific conservation measures, has led to declining in soil health and land degradation in an irreversible manner. In addition, increasing use of pesticides, coupled with soil and water pollution, has led the researchers to search for an environmental-friendly and cost-effective alternatives to controlling soil-borne diseases that are difficult to control, and which significantly limit agricultural productivity. Since the 1960s, disease-suppressive soils (DSS) have been identified and studied around the world. Soil disease suppression is the reduction in the incidence of soil-borne diseases even in the presence of a host plant and inoculum in the soil. The disease-suppressive capacity is mainly attributed to diverse microbial communities present in the soil that could act against soil-borne pathogens in multifaceted ways. The beneficial microorganisms employ some specific functions such as antibiosis, parasitism, competition for resources, and predation. However, there has been increasing evidence on the role of soil abiotic factors that largely influence the disease suppression. The intricate interactions of the soil, plant, and environmental components in a disease triangle make this process complex yet crucial to study to reduce disease incidence. Increasing resistance of the pathogen to presently available chemicals has led to the shift from culturable microbes to unexplored and unculturable microbes. Agricultural management practices such as tillage, fertilization, manures, irrigation, and amendment applications significantly alter the soil physicochemical environment and influence the growth and behaviour of antagonistic microbes. Plant factors such as age, type of crop, and root behaviour of the plant could stimulate or limit the diversity and structure of soil microorganisms in the rhizosphere. Further, identification and in-depth of disease-suppressive soils could lead to the discovery of more beneficial microorganisms with novel anti-microbial and plant promoting traits. To date, several microbial species have been isolated and proposed as key contributors in disease suppression, but the complexities as well as the mechanisms of the microbial and abiotic interactions remain elusive for most of the disease-suppressive soils. Thus, this review critically explores disease-suppressive attributes in soils, mechanisms involved, and biotic and abiotic factors affecting DSS and also briefly reviewing soil microbiome for anti-microbial drugs, in fact, a consequence of DSS phenomenon.
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Affiliation(s)
- Somasundaram Jayaraman
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - A.K. Naorem
- ICAR– Central Arid Zone Research Institute, Regional Research Station-Kukma, Bhuj, Gujarat 370105 India
| | - Rattan Lal
- Carbon Management Sequestration Center, The Ohio State University, 2021 Coffey Rd, Columbus, OH USA
| | - Ram C. Dalal
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD 4072 Australia
| | - N.K. Sinha
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - A.K. Patra
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - S.K. Chaudhari
- Indian Council of Agricultural Research, KAB-II, New Delhi, India
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Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review. SUSTAINABILITY 2020. [DOI: 10.3390/su13010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.
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Zegeye EK, Sadler NC, Lomas GX, Attah IK, Jansson JK, Hofmockel KS, Anderton CR, Wright AT. Activity-Based Protein Profiling of Chitin Catabolism. Chembiochem 2020; 22:717-723. [PMID: 33049124 DOI: 10.1002/cbic.202000616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/12/2020] [Indexed: 01/09/2023]
Abstract
The microbial catabolism of chitin, an abundant and ubiquitous environmental organic polymer, is a fundamental cog in terrestrial and aquatic carbon and nitrogen cycles. Despite the importance of this critical bio-geochemical function, there is a limited understanding of the synergy between the various hydrolytic and accessory enzymes involved in chitin catabolism. To address this deficit, we synthesized activity-based probes (ABPs) designed to target active chitinolytic enzymes by modifying the chitin subunits N-acetyl glucosamine and chitotriose. The ABPs were used to determine the active complement of chitinolytic enzymes produced over time by the soil bacterium Cellvibrio japonicus treated with various C substrates. We demonstrate the utility of these ABPs in determining the synergy between various enzymes involved in chitin catabolism. The strategy can be used to gain molecular-level insights that can be used to better understand microbial roles in soil bio-geochemical cycling in the face of a changing climate.
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Affiliation(s)
- Elias K Zegeye
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Natalie C Sadler
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Gerard X Lomas
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Isaac K Attah
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
- Department of Ecology, Evolution and Organismal Biology Iowa State University, 251 Bessey Hall, Ames, Iowa (USA) 50011
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Aaron T Wright
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
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Stutzmann S, Blokesch M. Comparison of chitin-induced natural transformation in pandemic Vibrio cholerae O1 El Tor strains. Environ Microbiol 2020; 22:4149-4166. [PMID: 32860313 PMCID: PMC7693049 DOI: 10.1111/1462-2920.15214] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/23/2022]
Abstract
The human pathogen Vibrio cholerae serves as a model organism for many important processes ranging from pathogenesis to natural transformation, which has been extensively studied in this bacterium. Previous work has deciphered important regulatory circuits involved in natural competence induction as well as mechanistic details related to its DNA acquisition and uptake potential. However, since competence was first reported for V. cholerae in 2005, many researchers have struggled with reproducibility in certain strains. In this study, we therefore compare prominent seventh pandemic V. cholerae isolates, namely strains A1552, N16961, C6706, C6709, E7946, P27459, and the close relative MO10, for their natural transformability and decipher underlying defects that mask the high degree of competence conservation. Through a combination of experimental approaches and comparative genomics based on new whole‐genome sequences and de novo assemblies, we identify several strain‐specific defects, mostly in genes that encode key players in quorum sensing. Moreover, we provide evidence that most of these deficiencies might have recently occurred through laboratory domestication events or through the acquisition of mobile genetic elements. Lastly, we highlight that differing experimental approaches between research groups might explain more of the variations than strain‐specific alterations.
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Affiliation(s)
- Sandrine Stutzmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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Mehmood MA, Zhao H, Cheng J, Xie J, Jiang D, Fu Y. Sclerotia of a phytopathogenic fungus restrict microbial diversity and improve soil health by suppressing other pathogens and enriching beneficial microorganisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 259:109857. [PMID: 32072956 DOI: 10.1016/j.jenvman.2019.109857] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Sclerotinia sclerotiorum, a notorious soil-borne pathogen of various important crops, produces numerous sclerotia to oversummer in the soil. Considering that sclerotia may also be attacked by other microbes in the soil, we hypothesized that sclerotia in soil may affect the community of soil microbes directly and/or indirectly. In this study, we inoculated sclerotia of S. sclerotiorum in soil collected from the field to observe changes in microbial diversity over three months using 16S rRNA and ITS2 sequencing techniques. Alpha diversity indices exhibited a decline in the diversity of microbial communities, while permanova results confirmed a significant difference in the microbial communities of sclerotia-amended and non-amended soil samples. In sclerotia-amended soil, fungal diversity showed enrichment of antagonists such as Clonostachys, Trichoderma, and Talaromyces and a drastic reduction in the plant pathogenic microbes compared to the non-amended soil. Sclerotia not only activated the antagonists but also enhanced the abundance of plant growth-promoting bacteria, such as Chitinophaga, Burkholderia, and Dyella. Moreover, the presence of sclerotia curtailed the growth of several notorious plant pathogenic fungi belonging to various genera such as Fusarium, Colletotrichum, Cladosporium, Athelia, Alternaria, and Macrophomina. Thus, we conclude that S. sclerotiorum when dormant in soil can reduce the diversity of soil microbes, including suppressing plant pathogens and enriching beneficial microbes. To the best of our knowledge, this is the first time a plant pathogen has been found in soil that can significantly suppress other pathogens. Our findings may provide novel cues to understand the ecology of crop pathogens in soil and maintaining soil conditions that could be beneficial for constructing a healthy soil microorganism community required for mitigating soil-borne diseases.
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Affiliation(s)
- Mirza Abid Mehmood
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Department of Plant Pathology, Muhammad Nawaz Shareef University of Agriculture, Multan, Punjab, Pakistan
| | - Huizhang Zhao
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Jiasen Cheng
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Jiatao Xie
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Yanping Fu
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China.
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Matthey N, Stutzmann S, Stoudmann C, Guex N, Iseli C, Blokesch M. Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae. eLife 2019; 8:48212. [PMID: 31478834 PMCID: PMC6783263 DOI: 10.7554/elife.48212] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/03/2019] [Indexed: 01/28/2023] Open
Abstract
Natural competence for transformation is a primary mode of horizontal gene transfer. Competent bacteria are able to absorb free DNA from their surroundings and exchange this DNA against pieces of their own genome when sufficiently homologous. However, the prevalence of non-degraded DNA with sufficient coding capacity is not well understood. In this context, we previously showed that naturally competent Vibrio cholerae use their type VI secretion system (T6SS) to actively acquire DNA from non-kin neighbors. Here, we explored the conditions of the DNA released through T6SS-mediated killing versus passive cell lysis and the extent of the transfers that occur due to these conditions. We show that competent V. cholerae acquire DNA fragments with a length exceeding 150 kbp in a T6SS-dependent manner. Collectively, our data support the notion that the environmental lifestyle of V. cholerae fosters the exchange of genetic material with sufficient coding capacity to significantly accelerate bacterial evolution.
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Affiliation(s)
- Noémie Matthey
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (Swiss Federal Institute of Technology Lausanne; EPFL), Lausanne, Switzerland
| | - Sandrine Stutzmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (Swiss Federal Institute of Technology Lausanne; EPFL), Lausanne, Switzerland
| | - Candice Stoudmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (Swiss Federal Institute of Technology Lausanne; EPFL), Lausanne, Switzerland
| | - Nicolas Guex
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (Swiss Federal Institute of Technology Lausanne; EPFL), Lausanne, Switzerland
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Microbial Succession of Anaerobic Chitin Degradation in Freshwater Sediments. Appl Environ Microbiol 2019; 85:AEM.00963-19. [PMID: 31285190 PMCID: PMC6715849 DOI: 10.1128/aem.00963-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/29/2019] [Indexed: 12/23/2022] Open
Abstract
Chitin is the most abundant biopolymer in aquatic environments, with a direct impact on the carbon and nitrogen cycles. Despite its massive production as a structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in predominantly anoxic freshwater sediments and the responsible microorganisms. We proved that chitin is readily degraded under anoxic conditions and linked this to a succession of the members of the responsible microbial community over a 43-day period. While Fibrobacteres and Firmicutes members were driving the early and late phases of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded toward the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments. Chitin is massively produced by freshwater plankton species as a structural element of their exoskeleton or cell wall. At the same time, chitin does not accumulate in the predominantly anoxic sediments, underlining its importance as carbon and nitrogen sources for sedimentary microorganisms. We studied chitin degradation in littoral sediment of Lake Constance, Central Europe’s third largest lake. Turnover of the chitin analog methyl-umbelliferyl-N,N-diacetylchitobioside (MUF-DC) was highest in the upper oxic sediment layer, with 5.4 nmol MUF-DC h−1 (g sediment [dry weight])−1. In the underlying anoxic sediment layers, chitin hydrolysis decreased with depth from 1.1 to 0.08 nmol MUF-DC h−1 (g sediment [dry weight])−1. Bacteria involved in chitin degradation were identified by 16S rRNA (gene) amplicon sequencing of anoxic microcosms incubated in the presence of chitin compared to microcosms amended either with N-acetylglucosamine as the monomer of chitin or no substrate. Chitin degradation was driven by a succession of bacteria responding specifically to chitin only. The early phase (0 to 9 days) was dominated by Chitinivibrio spp. (Fibrobacteres). The intermediate phase (9 to 21 days) was characterized by a higher diversity of chitin responders, including, besides Chitinivibrio spp., also members of the phyla Bacteroidetes, Proteobacteria, Spirochaetes, and Chloroflexi. In the late phase (21 to 43 days), the Chitinivibrio populations broke down with a parallel strong increase of Ruminiclostridium spp. (formerly Clostridium cluster III, Firmicutes), which became the dominating chitin responders. Our study provides quantitative insights into anaerobic chitin degradation in lake sediments and linked this to a model of microbial succession associated with this activity. IMPORTANCE Chitin is the most abundant biopolymer in aquatic environments, with a direct impact on the carbon and nitrogen cycles. Despite its massive production as a structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in predominantly anoxic freshwater sediments and the responsible microorganisms. We proved that chitin is readily degraded under anoxic conditions and linked this to a succession of the members of the responsible microbial community over a 43-day period. While Fibrobacteres and Firmicutes members were driving the early and late phases of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded toward the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments.
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Xaxiri NA, Nikouli E, Berillis P, Kormas KA. Bacterial biofilm development during experimental degradation of Melicertus kerathurus exoskeleton in seawater. AIMS Microbiol 2019; 4:397-412. [PMID: 31294223 PMCID: PMC6604942 DOI: 10.3934/microbiol.2018.3.397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/29/2018] [Indexed: 11/28/2022] Open
Abstract
Chitinolytic bacteria are widespread in marine and terrestrial environment, and this is rather a reflection of their principle growth substrate's ubiquity, chitin, in our planet. In this paper, we investigated the development of naturally occurring bacterial biofilms on the exoskeleton of the shrimp Melicertus kerathurus during its degradation in sea water. During a 12-day experiment with exoskeleton fragments in batch cultures containing only sea water as the growth medium at 18 °C in darkness, we analysed the formation and succession of biofilms by scanning electron microscopy and 16S rRNA gene diversity by next generation sequencing. Bacteria belonging to the γ- and α-Proteobacteria and Bacteroidetes showed marked (less or more than 10%) changes in their relative abundance from the beginning of the experiment. These bacterial taxa related to known chitinolytic bacteria were the Pseudolateromonas porphyrae, Halomonasaquamarina, Reinekea aestuarii, Colwellia asteriadis and Vibrio crassostreae. These bacteria could be considered as appropriate candidates for the degradation of chitinous crustacean waste from the seafood industry as they dominated in the biofilms developed on the shrimp's exoskeleton in natural sea water with no added substrates and the degradation of the shrimp exoskeleton was also evidenced.
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Affiliation(s)
- Nikolina-Alexandra Xaxiri
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Eleni Nikouli
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Panagiotis Berillis
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Konstantinos Ar Kormas
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
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Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S. Ecological Functions of Agricultural Soil Bacteria and Microeukaryotes in Chitin Degradation: A Case Study. Front Microbiol 2019; 10:1293. [PMID: 31281293 PMCID: PMC6596343 DOI: 10.3389/fmicb.2019.01293] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/23/2019] [Indexed: 11/24/2022] Open
Abstract
Chitin provides a valuable carbon and nitrogen source for soil microorganisms and is a major component of particulate organic matter in agricultural soils. To date, there is no information on interaction and interdependence in chitin-degrading soil microbiomes. Since microbial chitin degradation occurs under both oxic and anoxic conditions and both conditions occur simultaneously in soil, the comparison of the active microbiome members under both conditions can reveal key players for the overall degradation in aerated soil. A time-resolved 16S rRNA stable isotope probing experiment was conducted with soil material from the top soil layer of a wheat-covered field. [13CU]-chitin was largely mineralized within 20 days under oxic conditions. Cellvibrio, Massilia, and several Bacteroidetes families were identified as initially active chitin degraders. Subsequently, Planctomycetes and Verrucomicrobia were labeled by assimilation of 13C carbon either from [13CU]-chitin or from 13C-enriched components of primary chitin degraders. Bacterial predators (e.g., Bdellovibrio and Bacteriovorax) were labeled, too, and non-labeled microeukaryotic predators (Alveolata) increased their relative abundance toward the end of the experiment (70 days), indicating that chitin degraders were subject to predation. Trophic interactions differed substantially under anoxic and oxic conditions. Various fermentation types occurred along with iron respiration. While Acidobacteria and Chloroflexi were the first taxa to be labeled, although at a low 13C level, Firmicutes and uncultured Bacteroidetes were predominantly labeled at a much higher 13C level during the later stages, suggesting that the latter two bacterial taxa were mainly responsible for the degradation of chitin and also provided substrates for iron reducers. Eventually, our study revealed that (1) hitherto unrecognized Bacteria were involved in a chitin-degrading microbial food web of an agricultural soil, (2) trophic interactions were substantially shaped by the oxygen availability, and (3) detectable predation was restricted to oxic conditions. The gained insights into trophic interactions foster our understanding of microbial chitin degradation, which is in turn crucial for an understanding of soil carbon dynamics.
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Affiliation(s)
- Adam S Wieczorek
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, Aalborg, Denmark
| | | | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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20
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Killer toxin-like chitinases in filamentous fungi: Structure, regulation and potential roles in fungal biology. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Wörner S, Pester M. The Active Sulfate-Reducing Microbial Community in Littoral Sediment of Oligotrophic Lake Constance. Front Microbiol 2019; 10:247. [PMID: 30814991 PMCID: PMC6381063 DOI: 10.3389/fmicb.2019.00247] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/30/2019] [Indexed: 11/16/2022] Open
Abstract
Active sulfate-reducing microorganisms (SRM) in freshwater sediments are under-examined, despite the well-documented cryptic sulfur cycle occurring in these low-sulfate habitats. In Lake Constance sediment, sulfate reduction rates of up to 1,800 nmol cm-3 day-1 were previously measured. To characterize its SRM community, we used a tripartite amplicon sequencing approach based on 16S rRNA genes, 16S rRNA, and dsrB transcripts (encoding the beta subunit of dissimilatory sulfite reductase). We followed the respective amplicon dynamics in four anoxic microcosm setups supplemented either with (i) chitin and sulfate, (ii) sulfate only, (iii) chitin only, or (iv) no amendment. Chitin was used as a general substrate for the whole carbon degradation chain. Sulfate turnover in sulfate-supplemented microcosms ranged from 38 to 955 nmol day-1 (g sediment f. wt.)-1 and was paralleled by a decrease of 90–100% in methanogenesis as compared to the respective methanogenic controls. In the initial sediment, relative abundances of recognized SRM lineages accounted for 3.1 and 4.4% of all bacterial 16S rRNA gene and 16S rRNA sequences, respectively. When normalized against the 1.4 × 108 total prokaryotic 16S rRNA gene copies as determined by qPCR and taking multiple rrn operons per genome into account, this resulted in approximately 105–106 SRM cells (g sediment f. wt.)-1. The three amplicon approaches jointly identified Desulfobacteraceae and Syntrophobacteraceae as the numerically dominant and transcriptionally most active SRM in the initial sediment. This was corroborated in the time course analyses of sulfate-consuming sediment microcosms irrespective of chitin amendment. Uncultured dsrAB family-level lineages constituted in sum only 1.9% of all dsrB transcripts, with uncultured lineage 5 and 6 being transcriptionally most active. Our study is the first holistic molecular approach to quantify and characterize active SRM including uncultured dsrAB lineages not only in Lake Constance but for lake sediments in general.
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Affiliation(s)
- Susanne Wörner
- Department of Biology, University of Konstanz, Konstanz, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell cultures, Braunschweig, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell cultures, Braunschweig, Germany.,Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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22
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Kumar A, Zhang KYJ. Human Chitinases: Structure, Function, and Inhibitor Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:221-251. [PMID: 31102249 DOI: 10.1007/978-981-13-7318-3_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chitinases are glycosyl hydrolases that hydrolyze the β-(1-4)-linkage of N-acetyl-D-glucosamine units present in chitin polymers. Chitinases are widely distributed enzymes and are present in a wide range of organisms including insects, plants, bacteria, fungi, and mammals. These enzymes play key roles in immunity, nutrition, pathogenicity, and arthropod molting. Humans express two chitinases, chitotriosidase 1 (CHIT1) and acid mammalian chitinase (AMCase) along with several chitinase-like proteins (CLPs). Human chitinases are reported to play a protective role against chitin-containing pathogens through their capability to degrade chitin present in the cell wall of pathogens. Now, human chitinases are gaining attention as the key players in innate immune response. Although the exact mechanism of their role in immune response is not known, studies in recent years begin to relate chitin recognition and degradation with the activation of signaling pathways involved in inflammation. The roles of both CHIT1 and AMCase in the development of various diseases have been revealed and several classes of inhibitors have been developed. However, a clear understanding could not be established due to complexities in the design of the right experiment for studying the role of human chitinase in various diseases. In this chapter, we will first outline the structural features of CHIT1 and AMcase. We will then review the progress in understanding the role of human chitinases in the development of various diseases. Finally, we will summarize the inhibitor discovery efforts targeting both CHIT1 and AMCase.
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Affiliation(s)
- Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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23
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Itoh T, Kimoto H. Bacterial Chitinase System as a Model of Chitin Biodegradation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:131-151. [PMID: 31102245 DOI: 10.1007/978-981-13-7318-3_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chitin, a structural polysaccharide of β-1,4-linked N-acetyl-D-glucosamine residues, is the second most abundant natural biopolymer after cellulose. The metabolism of chitin affects the global carbon and nitrogen cycles, which are maintained by marine and soil-dwelling bacteria. The degradation products of chitin metabolism serve as important nutrient sources for the chitinolytic bacteria. Chitinolytic bacteria have elaborate enzymatic systems for the degradation of the recalcitrant chitin biopolymer. This chapter introduces chitin degradation and utilization systems of the chitinolytic bacteria. These bacteria secrete many chitin-degrading enzymes, including processive chitinases, endo-acting non-processive chitinases, lytic polysaccharide monooxygenases, and N-acetyl-hexosaminidases. Bacterial chitinases play a fundamental role in the degradation of chitin. Enzymatic properties, catalytic mechanisms, and three-dimensional structures of chitinases have been extensively studied by many scientists. These enzymes can be exploited to produce a range of chitin-derived products, e.g., biocontrol agents against many plant pathogenic fungi and insects. We introduce bacterial chitinases in terms of their reaction modes and structural features.
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Affiliation(s)
- Takafumi Itoh
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195, Japan.
| | - Hisashi Kimoto
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195, Japan
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24
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Chen XW, Wong JTF, Chen ZT, Tang TWL, Guo HW, Leung AOW, Ng CWW, Wong MH. Effects of biochar on the ecological performance of a subtropical landfill. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:963-975. [PMID: 30743893 DOI: 10.1016/j.scitotenv.2018.06.379] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/25/2018] [Accepted: 06/29/2018] [Indexed: 06/09/2023]
Abstract
Landfills commonly occupy large areas of land that may be ecologically important. Ecological restoration of landfill cover is a necessary approach to rebuild sustainable habitats. However, unfavourable soil conditions and invasion by exotic plants in certain regions hinder the restoration. In this study, the effects of biochar as a soil amendment on the restoration of a landfill cover were investigated under field condition. Topsoils of a landfill cover in the subtropical region (Shenzhen, China) were mixed with 0, 5 and 10% (v/v) of biochar. Soil pH, electronic conductivity, organic matter, total organic carbon, water content, total N and total P were enhanced by biochar amendment. After nine months of self-succession, plant productivity, species richness and diversity were enhanced by biochar. The structures of soil bacterial and arbuscular mycorrhizal (AM) fungal communities were changed, and species richness and diversity were moderately promoted. Enhanced plant growth and diversity were probably attributed to a number of enhanced bacterial functions related to nutrient cycling including aerobic ammonia oxidation, aerobic nitrite oxidation, nitrification, sulphur respiration, nitrate respiration, nitrogen respiration, ureolysis, chemoheterotrophy and fermentation. The higher abundances of bacteria Streptomyces sp. and Pseudomonas sp. in biochar treatments potentially enhanced the AM fungal diversity. The bacterial diversity was more related to the soil properties, especially pH, than AM fungi. Continuous monitoring is necessary to track the changes of species composition and ecological functions over time. This is the first comprehensive study on the effects of biochar on the ecological performance of a man-made ecosystem. In addition to agricultural application, biochar can be used for restoring degraded lands.
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Affiliation(s)
- Xun Wen Chen
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - James Tsz Fung Wong
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Zhan Ting Chen
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Thomas Wui Lung Tang
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Hao Wen Guo
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Anna Oi Wah Leung
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Charles Wang Wai Ng
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
| | - Ming Hung Wong
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China; Consortium on Health, Environment, Education and Research (CHEER), and Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong SAR, China; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China.
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25
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Steven J. VD, Richard M. L. Chitins and chitinase activity in airway diseases. J Allergy Clin Immunol 2018; 142:364-369. [PMID: 29959948 PMCID: PMC6078791 DOI: 10.1016/j.jaci.2018.06.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/19/2018] [Accepted: 06/22/2018] [Indexed: 01/04/2023]
Abstract
Chitin, one of the most abundant biopolymers on Earth, is bound and degraded by chitinases, specialized enzymes that are similarly widespread in nature. Chitin catabolism affects global carbon and nitrogen cycles through a host of diverse biological processes, but recent work has focused attention on systems of chitin recognition and degradation conserved in mammals, connecting an ancient pathway of polysaccharide processing to human diseases influenced by persistent immune triggering. Here we review current advances in our understanding of how chitin-chitinase interactions affect mucosal immune feedback mechanisms essential to maintaining homeostasis and organ health.
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Affiliation(s)
- Van Dyken Steven J.
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO USA.
| | - Locksley Richard M.
- Howard Hughes Medical Institute, Departments of Medicine and Microbiology / Immuology, University of California San Francisco, San Francisco, CA, USA.
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26
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Abstract
Vibrio is a genus of ubiquitous heterotrophic bacteria found in aquatic environments. Although they are a small percentage of the bacteria in these environments, vibrios can predominate during blooms. Vibrios also play important roles in the degradation of polymeric substances, such as chitin, and in other biogeochemical processes. Vibrios can be found as free-living bacteria, attached to particles, or associated with other organisms in a mutualistic, commensal, or pathogenic relationship. This review focuses on vibrio ecology and genome plasticity, which confers an ability to adapt to new niches and is driven, at least in part, by horizontal gene transfer (HGT). The extent of HGT and its role in pathogen emergence are discussed based on genomic studies of environmental and pathogenic vibrios, mobile genetically encoded virulence factors, and mechanistic studies on the different modes of HGT.
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Affiliation(s)
- Frédérique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, F-29280 Plouzané, France.,Laboratoire de Biologie Intégrative des Modèles Marins, Station Biologique de Roscoff, CNRS UMR 8227, UPMC Paris 06, Sorbonne Universités, F-29688 Roscoff CEDEX, France;
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland;
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27
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Nguyen STC, Freund HL, Kasanjian J, Berlemont R. Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. Appl Microbiol Biotechnol 2018; 102:1629-1637. [PMID: 29359269 DOI: 10.1007/s00253-018-8778-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 11/30/2022]
Abstract
The enzymatic deconstruction of structural polysaccharides, which relies on the production of specific glycoside hydrolases (GHs), is an essential process across environments. Over the past few decades, researchers studying the diversity and evolution of these enzymes have isolated and biochemically characterized thousands of these proteins. The carbohydrate-active enzymes database (CAZy) lists these proteins and provides some metadata. Here, the sequences and metadata of characterized sequences derived from GH families associated with the deconstruction of cellulose, xylan, and chitin were collected and discussed. First, although few polyspecific enzymes are identified, characterized GH families are mostly monospecific. Next, the taxonomic distribution of characterized GH mirrors the distribution of identified sequences in sequenced genomes. This provides a rationale for connecting the identification of GH sequences to specific reactions or lineages. Finally, we tested the annotation of the characterized GHs using HMM scan and the protein families database (Pfam). The vast majority of GHs targeting cellulose, xylan, and chitin can be identified using this publicly accessible approach.
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Affiliation(s)
- Stanley T C Nguyen
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Hannah L Freund
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Joshua Kasanjian
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Renaud Berlemont
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA.
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28
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Chitinase Expression in Listeria monocytogenes Is Influenced by lmo0327, Which Encodes an Internalin-Like Protein. Appl Environ Microbiol 2017; 83:AEM.01283-17. [PMID: 28887418 PMCID: PMC5666140 DOI: 10.1128/aem.01283-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/23/2017] [Indexed: 02/02/2023] Open
Abstract
The chitinolytic system of Listeria monocytogenes thus far comprises two chitinases, ChiA and ChiB, and a lytic polysaccharide monooxygenase, Lmo2467. The role of the system in the bacterium appears to be pleiotropic, as besides mediating the hydrolysis of chitin, the second most ubiquitous carbohydrate in nature, the chitinases have been deemed important for the colonization of unicellular molds, as well as mammalian hosts. To identify additional components of the chitinolytic system, we screened a transposon mutant library for mutants exhibiting impaired chitin hydrolysis. The screening yielded a mutant with a transposon insertion in a locus corresponding to lmo0327 of the EGD-e strain. lmo0327 encodes a large (1,349 amino acids [aa]) cell wall-associated protein that has been proposed to possess murein hydrolase activity. The single inactivation of lmo0327, as well as of lmo0325 that codes for a putative transcriptional regulator functionally related to lmo0327, led to an almost complete abolishment of chitinolytic activity. The effect could be traced at the transcriptional level, as both chiA and chiB transcripts were dramatically decreased in the lmo0327 mutant. In accordance with that, we could barely detect ChiA and ChiB in the culture supernatants of the mutant strain. Our results provide new information regarding the function of the lmo0325-lmo0327 locus in L. monocytogenes and link it to the expression of chitinolytic activity. IMPORTANCE Many bacteria from terrestrial and marine environments express chitinase activities enabling them to utilize chitin as the sole source of carbon and nitrogen. Interestingly, several bacterial chitinases may also be involved in host pathogenesis. For example, in the important foodborne pathogen Listeria monocytogenes, the chitinases ChiA and ChiB and the lytic polysaccharide monooxygenase Lmo2467 are implicated in chitin assimilation but also act as virulence factors during the infection of mammalian hosts. Therefore, it is important to identify their regulators and induction cues to understand how the different roles of the chitinolytic system are controlled and mediated. Here, we provide evidence for the importance of lmo0327 and lmo0325, encoding a putative internalin/autolysin and a putative transcriptional activator, respectively, in the efficient expression of chitinase activity in L. monocytogenes and thereby provide new information regarding the function of the lmo0325-lmo0327 locus.
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29
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Elizalde-Peña E, Quintero-Ortega I, Zárate-Triviño D, Nuño-Licona A, Gough J, Sanchez I, Medina D, Luna-Barcenas G. (Chitosan- g -glycidyl methacrylate)-xanthan hydrogel implant in Wistar rats for spinal cord regeneration. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 78:892-900. [DOI: 10.1016/j.msec.2017.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 12/09/2016] [Accepted: 03/01/2017] [Indexed: 12/01/2022]
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30
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Veliz EA, Martínez-Hidalgo P, Hirsch AM. Chitinase-producing bacteria and their role in biocontrol. AIMS Microbiol 2017; 3:689-705. [PMID: 31294182 PMCID: PMC6604996 DOI: 10.3934/microbiol.2017.3.689] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/19/2017] [Indexed: 11/30/2022] Open
Abstract
Chitin is an important component of the exteriors of insects and fungi. Upon degradation of chitin by a number of organisms, severe damage and even death may occur in pathogens and pests whose external surfaces contain this polymer. Currently, chemical fungicides and insecticides are the major means of controlling these disease-causing agents. However, due to the potential harm that these chemicals cause to the environment and to human and animal health, new strategies are being developed to replace or reduce the use of fungal- and pest-killing compounds in agriculture. In this context, chitinolytic microorganisms are likely to play an important role as biocontrol agents and pathogen antagonists and may also function in the control of postharvest rot. In this review, we discuss the literature concerning chitin and the basic knowledge of chitin-degrading enzymes, and also describe the biocontrol effects of chitinolytic microorganisms and their potential use as more sustainable pesticides and fungicides in the field.
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Affiliation(s)
- Esteban A Veliz
- Department of Molecular Cell and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, 90095-1606, USA
| | | | - Ann M Hirsch
- Department of Molecular Cell and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, 90095-1606, USA
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31
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Laycock B, Nikolić M, Colwell JM, Gauthier E, Halley P, Bottle S, George G. Lifetime prediction of biodegradable polymers. Prog Polym Sci 2017. [DOI: 10.1016/j.progpolymsci.2017.02.004] [Citation(s) in RCA: 301] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Biancalana F, Kopprio GA, Lara RJ, Alonso C. A protocol for the simultaneous identification of chitin-containing particles and their associated bacteria. Syst Appl Microbiol 2017. [PMID: 28648723 DOI: 10.1016/j.syapm.2017.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Chitin is the second most abundant polymer on Earth, playing a crucial role in the biogeochemical cycles. A core issue for studying its processing in aquatic systems is the identification and enumeration of chitin-containing particles and organisms, ideally in a manner that can be directly linked to bulk chitin quantification. The aim of this study was the development of such a technique. We successfully combined the methodology of bulk chitin determination using wheat germ agglutinin (FITC-WGA) for staining chitin-containing particles and organisms along with CARD-FISH staining of either chitin-containing eukaryotic cells or bacteria associated with them. Environmental chitin staining was successfully applied to natural water samples. Fungal hyphae, diatoms, and dinoflagellates, sestonic aggregates and chitin-containing structures derived from metazoa were observed. Also, hybridized bacteria attached to chitinaceous debris were clearly visualized. Finally, as proof of principle, cultured yeast cells were simultaneously-targeted by FITC-WGA and the EUK516 probe without exhibiting any interference between both stains. The presented approach appears as a powerful tool to evaluate the contribution of different size classes and organisms to chitin production and consumption, opening the possibility for application of single-cell approaches targeting the ecophysiology of chitin transformations in aquatic systems.
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Affiliation(s)
- Florencia Biancalana
- Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Sur, Florida 4750, B8000FWB Bahía Blanca, Argentina.
| | - Germán A Kopprio
- Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Sur, Florida 4750, B8000FWB Bahía Blanca, Argentina; Leibniz Center for Tropical Marine Ecology (ZMT), Fahrenheitstr. 6, 28359 Bremen, Germany
| | - Rubén J Lara
- Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Sur, Florida 4750, B8000FWB Bahía Blanca, Argentina
| | - Cecilia Alonso
- Microbial Ecology of Aquatic Transitional Systems Research Group, Centro Universitario Región Este, Universidad de la República, Ruta nacional N°9, 2700 Rocha, Uruguay
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33
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Ilangumaran G, Stratton G, Ravichandran S, Shukla PS, Potin P, Asiedu S, Prithiviraj B. Microbial Degradation of Lobster Shells to Extract Chitin Derivatives for Plant Disease Management. Front Microbiol 2017; 8:781. [PMID: 28529501 PMCID: PMC5418339 DOI: 10.3389/fmicb.2017.00781] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/18/2017] [Indexed: 11/13/2022] Open
Abstract
Biodegradation of lobster shells by chitinolytic microorganisms are an environment safe approach to utilize lobster processing wastes for chitin derivation. In this study, we report degradation activities of two microbes, "S223" and "S224" isolated from soil samples that had the highest rate of deproteinization, demineralization and chitinolysis among ten microorganisms screened. Isolates S223 and S224 had 27.3 and 103.8 protease units mg-1 protein and 12.3 and 11.2 μg ml-1 of calcium in their samples, respectively, after 1 week of incubation with raw lobster shells. Further, S223 contained 23.8 μg ml-1 of N-Acetylglucosamine on day 3, while S224 had 27.3 μg ml-1 on day 7 of incubation with chitin. Morphological observations and 16S rDNA sequencing suggested both the isolates were Streptomyces. The culture conditions were optimized for efficient degradation of lobster shells and chitinase (∼30 kDa) was purified from crude extract by affinity chromatography. The digested lobster shell extracts induced disease resistance in Arabidopsis by induction of defense related genes (PR1 > 500-fold, PDF1.2 > 40-fold) upon Pseudomonas syringae and Botrytis cinerea infection. The study suggests that soil microbes aid in sustainable bioconversion of lobster shells and extraction of chitin derivatives that could be applied in plant protection.
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Affiliation(s)
- Gayathri Ilangumaran
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, TruroNS, Canada
| | - Glenn Stratton
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, TruroNS, Canada
| | - Sridhar Ravichandran
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, TruroNS, Canada
| | - Pushp S. Shukla
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, TruroNS, Canada
| | | | - Samuel Asiedu
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, TruroNS, Canada
| | - Balakrishnan Prithiviraj
- Marine Bio-products Research Laboratory, Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, TruroNS, Canada
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34
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Li HM, Sullivan R, Moy M, Kobayashi DY, Belanger FC. Expression of a novel chitinase by the fungal endophyte in Poa ampla. Mycologia 2017. [DOI: 10.1080/15572536.2005.11832951] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | | | - Faith C. Belanger
- Department of Plant Biology and Pathology, Cook College, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey 08903
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35
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Thimoteo SS, Glogauer A, Faoro H, de Souza EM, Huergo LF, Moerschbacher BM, Pedrosa FO. A broad pH range and processive chitinase from a metagenome library. ACTA ACUST UNITED AC 2017; 50:e5658. [PMID: 28076454 PMCID: PMC5264535 DOI: 10.1590/1414-431x20165658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/25/2016] [Indexed: 01/14/2023]
Abstract
Chitinases are hydrolases that degrade chitin, a polymer of N-acetylglucosamine
linked β(1-4) present in the exoskeleton of crustaceans, insects, nematodes and
fungal cell walls. A metagenome fosmid library from a wastewater-contaminated soil
was functionally screened for chitinase activity leading to the isolation and
identification of a chitinase gene named metachi18A. The
metachi18A gene was subcloned and overexpressed in
Escherichia coli BL21 and the MetaChi18A chitinase was purified
by affinity chromatography as a 6xHis-tagged fusion protein. The MetaChi18A enzyme is
a 92-kDa protein with a conserved active site domain of glycosyl hydrolases family
18. It hydrolyses colloidal chitin with an optimum pH of 5 and temperature of 50°C.
Moreover, the enzyme retained at least 80% of its activity in the pH range from 4 to
9 and 98% at 600 mM NaCl. Thin layer chromatography analyses identified chitobiose as
the main product of MetaChi18A on chitin polymers as substrate. Kinetic analysis
showed inhibition of MetaChi18A activity at high concentrations of colloidal chitin
and 4-methylumbelliferyl N,N′-diacetylchitobiose and sigmoid kinetics at low
concentrations of colloidal chitin, indicating a possible conformational change to
lead the chitin chain from the chitin-binding to the catalytic domain. The observed
stability and activity of MetaChi18A over a wide range of conditions suggest that
this chitinase, now characterized, may be suitable for application in the industrial
processing of chitin.
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Affiliation(s)
- S S Thimoteo
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - A Glogauer
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil.,Agência de Inovação, Instituto de Tecnologia do Paraná - Tecpar, Curitiba, PR, Brasil
| | - H Faoro
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil.,Instituto Carlos Chagas, Fiocruz, Curitiba, PR, Brasil
| | - E M de Souza
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L F Huergo
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - B M Moerschbacher
- Institute for Biology and Biotechnology of Plants, WWU Münster University, Münster, Germany
| | - F O Pedrosa
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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36
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Paulsen SS, Andersen B, Gram L, Machado H. Biological Potential of Chitinolytic Marine Bacteria. Mar Drugs 2016; 14:md14120230. [PMID: 27999269 PMCID: PMC5192467 DOI: 10.3390/md14120230] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 12/26/2022] Open
Abstract
Chitinolytic microorganisms secrete a range of chitin modifying enzymes, which can be exploited for production of chitin derived products or as fungal or pest control agents. Here, we explored the potential of 11 marine bacteria (Pseudoalteromonadaceae, Vibrionaceae) for chitin degradation using in silico and phenotypic assays. Of 10 chitinolytic strains, three strains, Photobacterium galatheae S2753, Pseudoalteromonas piscicida S2040 and S2724, produced large clearing zones on chitin plates. All strains were antifungal, but against different fungal targets. One strain, Pseudoalteromonas piscicida S2040, had a pronounced antifungal activity against all seven fungal strains. There was no correlation between the number of chitin modifying enzymes as found by genome mining and the chitin degrading activity as measured by size of clearing zones on chitin agar. Based on in silico and in vitro analyses, we cloned and expressed two ChiA-like chitinases from the two most potent candidates to exemplify the industrial potential.
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Affiliation(s)
- Sara Skøtt Paulsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Birgitte Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Henrique Machado
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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Nakamura T, Yonezawa Y, Tsuchiya Y, Niiyama M, Ida K, Oshima M, Morita J, Uegaki K. Substrate recognition of N,N′-diacetylchitobiose deacetylase from Pyrococcus horikoshii. J Struct Biol 2016; 195:286-293. [DOI: 10.1016/j.jsb.2016.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 10/21/2022]
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Kimyon Ö, Ulutürk ZI, Nizalapur S, Lee M, Kutty SK, Beckmann S, Kumar N, Manefield M. N-Acetylglucosamine Inhibits LuxR, LasR and CviR Based Quorum Sensing Regulated Gene Expression Levels. Front Microbiol 2016; 7:1313. [PMID: 27602027 PMCID: PMC4993992 DOI: 10.3389/fmicb.2016.01313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/09/2016] [Indexed: 12/19/2022] Open
Abstract
N-acetyl glucosamine, the monomer of chitin, is an abundant source of carbon and nitrogen in nature as it is the main component and breakdown product of many structural polymers. Some bacteria use N-acyl-L-homoserine lactone (AHL) mediated quorum sensing (QS) to regulate chitinase production in order to catalyze the cleavage of chitin polymers into water soluble N-acetyl-D-glucosamine (NAG) monomers. In this study, the impact of NAG on QS activities of LuxR, LasR, and CviR regulated gene expression was investigated by examining the effect of NAG on QS regulated green fluorescent protein (GFP), violacein and extracellular chitinase expression. It was discovered that NAG inhibits AHL dependent gene transcription in AHL reporter strains within the range of 50-80% reduction at low millimolar concentrations (0.25-5 mM). Evidence is presented supporting a role for both competitive inhibition at the AHL binding site of LuxR type transcriptional regulators and catabolite repression. Further, this study shows that NAG down-regulates CviR induced violacein production while simultaneously up-regulating CviR dependent extracellular enzymes, suggesting that an unknown NAG dependent regulatory component influences phenotype expression. The quorum sensing inhibiting activity of NAG also adds to the list of compounds with known quorum sensing inhibiting activities.
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Affiliation(s)
- Önder Kimyon
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW, Australia
| | - Zehra I Ulutürk
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW, Australia
| | | | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW, Australia
| | - Samuel K Kutty
- School of Chemistry, University of New South Wales, Sydney NSW, Australia
| | - Sabrina Beckmann
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW, Australia
| | - Naresh Kumar
- School of Chemistry, University of New South Wales, Sydney NSW, Australia
| | - Mike Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW, Australia
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A Structurally Novel Chitinase from the Chitin-Degrading Hyperthermophilic Archaeon Thermococcus chitonophagus. Appl Environ Microbiol 2016; 82:3554-3562. [PMID: 27060120 DOI: 10.1128/aem.00319-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A structurally novel chitinase, Tc-ChiD, was identified from the hyperthermophilic archaeon Thermococcus chitonophagus, which can grow on chitin as the sole organic carbon source. The gene encoding Tc-ChiD contains regions corresponding to a signal sequence, two chitin-binding domains, and a putative catalytic domain. This catalytic domain shows no similarity with previously characterized chitinases but resembles an uncharacterized protein found in the mesophilic anaerobic bacterium Clostridium botulinum Two recombinant Tc-ChiD proteins were produced in Escherichia coli, one without the signal sequence [Tc-ChiD(ΔS)] and the other corresponding only to the putative catalytic domain [Tc-ChiD(ΔBD)]. Enzyme assays using N-acetylglucosamine (GlcNAc) oligomers indicated that both proteins hydrolyze GlcNAc oligomers longer than (GlcNAc)4 Chitinase assays using colloidal chitin suggested that Tc-ChiD is an exo-type chitinase that releases (GlcNAc)2 or (GlcNAc)3 Analysis with GlcNAc oligomers modified with p-nitrophenol suggested that Tc-ChiD recognizes the reducing end of chitin chains. While Tc-ChiD(ΔBD) displayed a higher initial velocity than that of Tc-ChiD(ΔS), we found that the presence of the two chitin-binding domains significantly enhanced the thermostability of the catalytic domain. In T. chitonophagus, another chitinase ortholog that is similar to the Thermococcus kodakarensis chitinase ChiA is present and can degrade chitin from the nonreducing ends. Therefore, the presence of multiple chitinases in T. chitonophagus with different modes of cleavage may contribute to its unique ability to efficiently degrade chitin. IMPORTANCE A structurally novel chitinase, Tc-ChiD, was identified from Thermococcus chitonophagus, a hyperthermophilic archaeon. The protein contains a signal peptide for secretion, two chitin-binding domains, and a catalytic domain that shows no similarity with previously characterized chitinases. Tc-ChiD thus represents a new family of chitinases. Tc-ChiD is an exo-type chitinase that recognizes the reducing end of chitin chains and releases (GlcNAc)2 or (GlcNAc)3 As a thermostable chitinase that recognizes the reducing end of chitin chains was not previously known, Tc-ChiD may be useful in a wide range of enzyme-based technologies to degrade and utilize chitin.
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Lv M, Hu Y, Gänzle MG, Lin J, Wang C, Cai J. Preparation of chitooligosaccharides from fungal waste mycelium by recombinant chitinase. Carbohydr Res 2016; 430:1-7. [PMID: 27153004 DOI: 10.1016/j.carres.2016.04.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/05/2016] [Accepted: 04/13/2016] [Indexed: 11/27/2022]
Abstract
This study aimed to develop an enzymatic method for conversion of chitin from fungal waste mycelia to chitooligosaccharides. The recombinant chitinase LlChi18A from Lactococcus lactis was over-expressed by Escherichia coli BL21 (DE3) and purified by affinity chromatography. The enzymatic properties of the purified enzyme were studied by chitin oligosaccharides. Waste mycelium was pre-treated by alkaline. The optimal conditions for hydrolysis of fungal chitin by recombinant chitinase were determined by Schales method. HPLC/ESI-MS was used to determine the content of N-acetylglucosamine and chitooligosaccharides after hydrolysis. The level of reducing sugar released from pretreated mycelium by chitinase increased with the reaction time during 6 days. The main product in the hydrolysates was N,N'-diacetylchitobiose. After hydrolysis by chitinase for 5 d, the yield of N,N'-diacetylchitobiose from waste mycelium was around 10% with estimated purity of around 70%. Combination of chitinase and snailase remarkably increased the yield to 24% with purity of 78%. Fungal mycelium which contains chitin is a new potential source for obtaining food grade chitooligosaccharides.
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Affiliation(s)
- Mengyuan Lv
- College of Bioengineering, Faculty of Light Industry, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Ying Hu
- College of Bioengineering, Faculty of Light Industry, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, Hubei 430068, China; Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta T6E 2P5, Canada.
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta T6E 2P5, Canada; School of Food and Pharmaceutical Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Jianguo Lin
- College of Bioengineering, Faculty of Light Industry, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Changgao Wang
- College of Bioengineering, Faculty of Light Industry, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Jun Cai
- College of Bioengineering, Faculty of Light Industry, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, Hubei 430068, China
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Mendoza-Becerril MA, Maronna MM, Pacheco MLAF, Simões MG, Leme JM, Miranda LS, Morandini AC, Marques AC. An evolutionary comparative analysis of the medusozoan (Cnidaria) exoskeleton. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12415] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- María A. Mendoza-Becerril
- Department of Zoology; Institute of Biosciences; University of São Paulo; Rua do Matão, Trav. 14, 101 05508-090 São Paulo Brazil
| | - Maximiliano M. Maronna
- Department of Zoology; Institute of Biosciences; University of São Paulo; Rua do Matão, Trav. 14, 101 05508-090 São Paulo Brazil
| | - Mírian L. A. F. Pacheco
- Department of Biology; Federal University of Sao Carlos; Rodovia João Leme dos Santos - até km 104.000 Parque Reserva Fazenda Imperial 18052780 Sorocaba São Paulo Brazil
| | - Marcello G. Simões
- Department of Zoology; Laboratory of Paleozoology; São Paulo State University Botucatu; Jardim Santo Inácio (Rubião Junior) 18618970 Botucatu São Paulo Brazil
| | - Juliana M. Leme
- Department of Sedimentary and Environmental Geology; Institute of Geosciences; University of São Paulo; Rua do Lago, 562 05508-080 São Paulo Brazil
| | - Lucília S. Miranda
- Department of Zoology; Institute of Biosciences; University of São Paulo; Rua do Matão, Trav. 14, 101 05508-090 São Paulo Brazil
| | - André C. Morandini
- Department of Zoology; Institute of Biosciences; University of São Paulo; Rua do Matão, Trav. 14, 101 05508-090 São Paulo Brazil
| | - Antonio C. Marques
- Department of Zoology; Institute of Biosciences; University of São Paulo; Rua do Matão, Trav. 14, 101 05508-090 São Paulo Brazil
- Center for Marine Biology; University of São Paulo; Rodovia Manoel H. Do Rego km 131.5 CEP 11600-000 São Sebastião São Paulo Brazil
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Mycelial development preceding basidioma formation in Moniliophthora perniciosa is associated to chitin, sugar and nutrient metabolism alterations involving autophagy. Fungal Genet Biol 2016; 86:33-46. [DOI: 10.1016/j.fgb.2015.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 12/02/2015] [Accepted: 12/12/2015] [Indexed: 02/07/2023]
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43
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Dai J, Qu H, Yu Z, Yang J, Zhang H. Computational analysis of AnmK-like kinase: New insights into the cell wall metabolism of fungi. J Theor Biol 2015; 379:59-65. [PMID: 25979372 DOI: 10.1016/j.jtbi.2015.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 04/13/2015] [Accepted: 05/02/2015] [Indexed: 02/02/2023]
Abstract
1,6-Anhydro-N-acetylmuramic acid kinase (AnmK) is the unique enzyme that marks the recycling of the cell wall of Escherichia coli. Here, 81 fungal AnmK-like kinase sequences from 57 fungal species were searched in the NCBI database and a phylogenetic tree was constructed. The three-dimensional structure of an AnmK-like kinase, levoglucosan kinase (LGK) of the yeast Lipomyces starkeyi, was modeled; molecular docking revealed that AnmK and LGK are conserved proteins, and 187Asp, 212Asp are enzymatic residues, respectively. Analysis suggests that 1,6-anhydro-N-acetylglucosamine (anhGlcNAc) and/or 1,6-anhydro-β-d-glucosamine (anhGlcN) would be the appropriate substrates of AnmK-like kinases. Also, the counterparts of other characteristic enzymes of cell wall recycling of bacteria were found in fungi. Taken together, it is proposed that a putative recycling of anhGlcNAc/anhGlcN, which is associated with the hydrolysis of cell walls, exists in fungi. This computational analysis will provide new insights into the metabolism of fungal cell walls.
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Affiliation(s)
- Jianghong Dai
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, No. 68 Xuefu Road (S), Evergreen Garden, Wuhan 430023, PR China; College of Resources & Environment, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China.
| | - Hong Qu
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, No. 5 Yiheyuan Road, Beijing 100871, PR China.
| | - Zhisheng Yu
- College of Resources & Environment, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Jiangke Yang
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, No. 68 Xuefu Road (S), Evergreen Garden, Wuhan 430023, PR China
| | - Hongxun Zhang
- College of Resources & Environment, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
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Yang B, Zhang M, Li L, Pu F, You W, Ke C. Molecular Analysis of Atypical Family 18 Chitinase from Fujian Oyster Crassostrea angulata and Its Physiological Role in the Digestive System. PLoS One 2015; 10:e0129261. [PMID: 26046992 PMCID: PMC4457423 DOI: 10.1371/journal.pone.0129261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 05/06/2015] [Indexed: 11/23/2022] Open
Abstract
Chitinolytic enzymes have an important physiological significance in immune and digestive systems in plants and animals, but chitinase has not been identified as having a role in the digestive system in molluscan. In our study, a novel chitinase homologue, named Ca-Chit, has been cloned and characterized as the oyster Crassostrea angulate. The 3998bp full-length cDNA of Ca-Chit consisted of 23bp 5-UTR, 3288 ORF and 688bp 3-UTR. The deduced amino acids sequence shares homologue with the chitinase of family 18. The molecular weight of the protein was predicted to be 119.389 kDa, with a pI of 6.74. The Ca-Chit protein was a modular enzyme composed of a glycosyl hydrolase family 18 domain, threonine-rich region profile and a putative membrane anchor domain. Gene expression profiles monitored by quantitative RT-PCR in different adult tissues showed that the mRNA of Ca-Chit expressed markedly higher visceral mass than any other tissues. The results of the whole mount in-situ hybridization displayed that Ca-Chit starts to express the visceral mass of D-veliger larvae and then the digestive gland forms a crystalline structure during larval development. Furthermore, the adult oysters challenged by starvation indicated that the Ca-Chit expression would be regulated by feed. All the observations made suggest that Ca-Chit plays an important role in the digestive system of the oyster, Crassostrea angulate.
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Affiliation(s)
- Bingye Yang
- Xiamen Medical College, Xiamen, 361008, PR China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, PR China
- College of Ocean and Earth Science, Xiamen University, Xiamen, 361005, PR China
| | - Mingming Zhang
- College of Life Science, Xiamen University, Xiamen, 361005, PR China
| | - Lingling Li
- College of Life Science, Xiamen University, Xiamen, 361005, PR China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, PR China
- College of Ocean and Earth Science, Xiamen University, Xiamen, 361005, PR China
| | - Weiwei You
- College of Ocean and Earth Science, Xiamen University, Xiamen, 361005, PR China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, PR China
- College of Ocean and Earth Science, Xiamen University, Xiamen, 361005, PR China
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Cretoiu MS, Berini F, Kielak AM, Marinelli F, van Elsas JD. A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil. Appl Microbiol Biotechnol 2015; 99:8199-215. [PMID: 26040993 PMCID: PMC4561078 DOI: 10.1007/s00253-015-6639-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 12/04/2022]
Abstract
Here, we report on the construction of a metagenomic library from a chitin-amended disease-suppressive agricultural soil and its screening for genes that encode novel chitinolytic enzymes. The library, constructed in fosmids in an Escherichia coli host, comprised 145,000 clones containing inserts of sizes of 21 to 40 kb, yielding a total of approximately 5.8 GB of cloned soil DNA. Using genetic screenings by repeated PCR cycles aimed to detect gene sequences of the bacterial chitinase A-class (hereby named chi A genes), we identified and characterized five fosmids carrying candidate genes for chitinolytic enzymes. The analysis thus allowed access to the genomic (fosmid-borne) context of these genes. Using the chiA-targeted PCR, which is based on degenerate primers, the five fosmids all produced amplicons, of which the sequences were related to predicted chitinolytic enzyme-encoding genes of four different host organisms, including Stenotrophomonas maltophilia. Sequencing and de novo annotation of the fosmid inserts confirmed that each one of these carried one or more open reading frames that were predicted to encode enzymes active on chitin, including one for a chitin deacetylase. Moreover, the genetic contexts in which the putative chitinolytic enzyme-encoding genes were located were unique per fosmid. Specifically, inserts from organisms related to Burkholderia sp., Acidobacterium sp., Aeromonas veronii, and the chloroflexi Nitrolancetus hollandicus and/or Ktedonobacter racemifer were obtained. Remarkably, the S. maltophilia chiA-like gene was found to occur in two different genetic contexts (related to N. hollandicus/K. racemifer), indicating the historical occurrence of genetic reshufflings in this part of the soil microbiota. One fosmid containing the insert composed of DNA from the N. hollandicus-like organism (denoted 53D1) was selected for further work. Using subcloning procedures, its putative gene for a chitinolytic enzyme was successfully brought to expression in an E. coli host. On the basis of purified protein preparations, the produced protein was characterized as a chitobiosidase of 43.6 kDa, with a pI of 4.83. Given its activity spectrum, it can be typified as a halotolerant chitobiosidase.
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Affiliation(s)
- Mariana Silvia Cretoiu
- />Department of Microbial Ecology, CEES, University of Groningen, Groningen, The Netherlands
- />Department of Marine Microbiology, Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands
| | - Francesca Berini
- />Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- />“The Protein Factory” Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | - Anna Maria Kielak
- />Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO), Wageningen, The Netherlands
| | - Flavia Marinelli
- />Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- />“The Protein Factory” Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | - Jan Dirk van Elsas
- />Department of Microbial Ecology, CEES, University of Groningen, Groningen, The Netherlands
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Tzelepis G, Dubey M, Jensen DF, Karlsson M. Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea. MICROBIOLOGY-SGM 2015; 161:1407-19. [PMID: 25881898 DOI: 10.1099/mic.0.000096] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Clonostachysrosea is a mycoparasitic fungal species that is an efficient biocontrol agent against many plant diseases. During mycoparasitic interactions, one of the most crucial steps is the hydrolysis of the prey's fungal cell wall, which mainly consists of glucans, glycoproteins and chitin. Chitinases are hydrolytic enzymes responsible for chitin degradation and it is suggested that they play an important role in fungal-fungal interactions. Fungal chitinases belong exclusively to the glycoside hydrolase (GH) family 18.These GH18 proteins are categorized into three distinct phylogenetic groups (A, B and C), subdivided into several subgroups. In this study, we identified 14 GH18 genes in the C. rosea genome, which is remarkably low compared with the high numbers found in mycoparasitic Trichoderma species. Phylogenetic analysis revealed that C. rosea contains eight genes in group A, two genes in group B, two genes in group C, one gene encoding a putative ENGase (endo-β-N-acetylglucosaminidase) and the ech37 gene, which is of bacterial origin. Gene expression analysis showed that only two genes had higher transcription levels during fungal-fungal interactions, while eight out of 14 GH18 genes were triggered by chitin. Furthermore, deletion of the C group chiC2 gene decreased the growth inhibitory activity of C. rosea culture filtrates against Botrytis cinerea and Rhizoctonia solani, although the biocontrol ability of C. rosea against B. cinerea was not affected. In addition, a potential role of the CHIC2 chitinase in the sporulation process was revealed. These results provide new information about the role of GH18 proteins in mycoparasitic interactions.
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Affiliation(s)
- Georgios Tzelepis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden
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Lo Scrudato M, Borgeaud S, Blokesch M. Regulatory elements involved in the expression of competence genes in naturally transformable Vibrio cholerae. BMC Microbiol 2014; 14:327. [PMID: 25539806 PMCID: PMC4299799 DOI: 10.1186/s12866-014-0327-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/16/2014] [Indexed: 11/19/2022] Open
Abstract
Background The human pathogen Vibrio cholerae normally enters the developmental program of natural competence for transformation after colonizing chitinous surfaces. Natural competence is regulated by at least three pathways in this organism: chitin sensing/degradation, quorum sensing and carbon catabolite repression (CCR). The cyclic adenosine monophosphate (cAMP) receptor protein CRP, which is the global regulator of CCR, binds to regulatory DNA elements called CRP sites when in complex with cAMP. Previous studies in Haemophilus influenzae suggested that the CRP protein binds competence-specific CRP-S sites under competence-inducing conditions, most likely in concert with the master regulator of transformation Sxy/TfoX. Results In this study, we investigated the regulation of the competence genes qstR and comEA as an example of the complex process that controls competence gene activation in V. cholerae. We identified previously unrecognized putative CRP-S sites upstream of both genes. Deletion of these motifs significantly impaired natural transformability. Moreover, site-directed mutagenesis of these sites resulted in altered gene expression. This altered gene expression also correlated directly with protein levels, bacterial capacity for DNA uptake, and natural transformability. Conclusions Based on the data provided in this study we suggest that the identified sites are important for the expression of the competence genes qstR and comEA and therefore for natural transformability of V. cholerae even though the motifs might not reflect bona fide CRP-S sites.
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Borodina TN, Grigoriev DO, Carillo MA, Hartmann J, Moehwald H, Shchukin DG. Preparation of multifunctional polysaccharide microcontainers for lipophilic bioactive agents. ACS APPLIED MATERIALS & INTERFACES 2014; 6:6570-8. [PMID: 24708592 DOI: 10.1021/am406039r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Chitosan/xanthan gum microcontainers with a core-shell structure formed due to chemical interactions between polysaccharide chains induced by ultrasonication are presented. Containers were prepared by sonication of water-immiscible (oil-like) liquids in the solution of polysaccharides. One-step fabrication of the container permanent shell is possible, because of the contribution of ultrasonically caused formation of hydrogen bonds and amide linkages. We synthesized containers in a wide size range from 350 nm to 7500 nm, varying in oil/water ratio. The microcontainers were modified with oppositely charged polyelectrolytes and microparticles, which could be used to impart the specified properties to the system. The biocide 4,5-dichloro-2-n-octyl-4-isothiazoline-3-one (DCOIT) was loaded into the proposed containers by utilizing its solution as an oil phase. The following incorporation of the DCOIT containers into the polymer coating demonstrated more sustained antimicrobial activity (∼30%) of the biocide in the encapsulated state, compared to its non-encapsulated form.
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Affiliation(s)
- Tatiana N Borodina
- Laboratory of Bioorganic Structures, Shubnikov Institute of Crystallography Russian Academy of Sciences, Moscow, Russia
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Mine S, Niiyama M, Hashimoto W, Ikegami T, Koma D, Ohmoto T, Fukuda Y, Inoue T, Abe Y, Ueda T, Morita J, Uegaki K, Nakamura T. Expression from engineeredEscherichia colichromosome and crystallographic study of archaealN,N′-diacetylchitobiose deacetylase. FEBS J 2014; 281:2584-96. [DOI: 10.1111/febs.12805] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 03/31/2014] [Accepted: 04/03/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Shouhei Mine
- National Institute of Advanced Industrial Science and Technology; Osaka Japan
| | - Mayumi Niiyama
- National Institute of Advanced Industrial Science and Technology; Osaka Japan
| | - Wakana Hashimoto
- National Institute of Advanced Industrial Science and Technology; Osaka Japan
- Faculty of Human Life and Science; Doshisha Women's College of Liberal Arts; Kyoto Japan
| | | | - Daisuke Koma
- Osaka Municipal Technical Research Institute; Japan
| | | | - Yohta Fukuda
- Graduate School of Engineering; Osaka University; Japan
| | | | - Yoshito Abe
- Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Junji Morita
- Faculty of Human Life and Science; Doshisha Women's College of Liberal Arts; Kyoto Japan
| | - Koichi Uegaki
- National Institute of Advanced Industrial Science and Technology; Osaka Japan
| | - Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology; Osaka Japan
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Paspaliari DK, Mollerup MS, Kallipolitis BH, Ingmer H, Larsen MH. Chitinase expression in Listeria monocytogenes is positively regulated by the Agr system. PLoS One 2014; 9:e95385. [PMID: 24752234 PMCID: PMC3994053 DOI: 10.1371/journal.pone.0095385] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/25/2014] [Indexed: 11/23/2022] Open
Abstract
The food-borne pathogen Listeria monocytogenes encodes two chitinases, ChiA and ChiB, which allow the bacterium to hydrolyze chitin, the second most abundant polysaccharide in nature. Intriguingly, despite the absence of chitin in human and mammalian hosts, both of the chitinases have been deemed important for infection, through a mechanism that, at least in the case of ChiA, involves modulation of host immune responses. In this study, we show that the expression of the two chitinases is subject to regulation by the listerial agr system, a homologue of the agr quorum-sensing system of Staphylococcus aureus, that has so far been implicated in virulence and biofilm formation. We demonstrate that in addition to these roles, the listerial agr system is required for efficient chitin hydrolysis, as deletion of agrD, encoding the putative precursor of the agr autoinducer, dramatically decreased chitinolytic activity on agar plates. Agr was specifically induced in response to chitin addition in stationary phase and agrD was found to regulate the amount of chiA, but not chiB, transcripts. Although the transcript levels of chiB did not depend on agrD, the extracellular protein levels of both chitinases were reduced in the ΔagrD mutant. The regulatory effect of agr on chiA is potentially mediated through the small RNA LhrA, which we show here to be negatively regulated by agr. LhrA is in turn known to repress chiA translation by binding to the chiA transcript and interfering with ribosome recruitment. Our results highlight a previously unrecognized role of the agr system and suggest that autoinducer-based regulation of chitinolytic systems may be more commonplace than previously thought.
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Affiliation(s)
- Dafni Katerina Paspaliari
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Maria Storm Mollerup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Birgitte H. Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Marianne Halberg Larsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail:
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