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Di Gregorio S, Niccolini L, Seggiani M, Strangis G, Barbani N, Vitiello V, Becarelli S, Petroni G, Yan X, Buttino I. Marine copepod culture as a potential source of bioplastic-degrading microbiome: The case of poly(butylene succinate-co-adipate). CHEMOSPHERE 2024; 362:142603. [PMID: 38885765 DOI: 10.1016/j.chemosphere.2024.142603] [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: 10/12/2023] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
The poly(butylene succinate-co-adipate) (PBSA) is emerging as environmentally sustainable polyester for applications in marine environment. In this work the capacity of microbiome associated with marine plankton culture to degrade PBSA, was tested. A taxonomic and functional characterization of the microbiome associated with the copepod Acartia tonsa, reared in controlled conditions, was analysed by 16S rDNA metabarcoding, in newly-formed adult stages and after 7 d of incubation. A predictive functional metagenomic profile was inferred for hydrolytic activities involved in bioplastic degradation with a particular focus on PBSA. The copepod-microbiome was also characterized in newly-formed carcasses of A. tonsa, and after 7 and 33 d of incubation in the plankton culture medium. Copepod-microbiome showed hydrolytic activities at all developmental stages of the alive copepods and their carcasses, however, the evenness of the hydrolytic bacterial community significantly increased with the time of incubation in carcasses. Microbial genera, never described in association with copepods: Devosia, Kordia, Lentibacter, Methylotenera, Rheinheimera, Marinagarivorans, Paraglaciecola, Pseudophaeobacter, Gaiella, Streptomyces and Kribbella sps., were retrieved. Kribbella sp. showed carboxylesterase activity and Streptomyces sp. showed carboxylesterase, triacylglycerol lipase and cutinase activities, that might be involved in PBSA degradation. A culturomic approach, adopted to isolate bacterial specimen from carcasses, led to the isolation of the bacterial strain, Vibrio sp. 01 tested for the capacity to promote the hydrolysis of the ester bonds. Granules of PBSA, incubated 82 d at 20 °C with Vibrio sp. 01, were characterized by scanning electron microscopy, infrared spectroscopy, thermogravimetric analysis, and differential scanning calorimetry, showing fractures compared to the control sample, and hydrolysis of ester bonds. These preliminary results are encouraging for further investigation on the ability of the microbiome associated with plankton to biodegrade polyesters, such as PBSA, and increasing knowledge on microorganisms involved in bioplastic degradation in marine environment.
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Affiliation(s)
- Simona Di Gregorio
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy
| | - Luca Niccolini
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy; Functional Biology and Plankton Genomic Lab. ISPRA - Italian Institute for Environmental Protection and Research, Via del Cedro n.38, 57122, Livorno, Italy
| | - Maurizia Seggiani
- Department of Civil and Industrial Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122, Pisa, Italy
| | - Giovanna Strangis
- Department of Civil and Industrial Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122, Pisa, Italy
| | - Niccoletta Barbani
- Department of Civil and Industrial Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122, Pisa, Italy
| | - Valentina Vitiello
- Functional Biology and Plankton Genomic Lab. ISPRA - Italian Institute for Environmental Protection and Research, Via del Cedro n.38, 57122, Livorno, Italy; Sino-Italian Joint Laboratory Functional Biology of Marine Biota, ISPRA, 57122, Livorno, Italy
| | - Simone Becarelli
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy
| | - Xiaojun Yan
- Sino-Italian Joint Laboratory Functional Biology of Marine Biota, ISPRA, 57122, Livorno, Italy; Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Isabella Buttino
- Functional Biology and Plankton Genomic Lab. ISPRA - Italian Institute for Environmental Protection and Research, Via del Cedro n.38, 57122, Livorno, Italy; Sino-Italian Joint Laboratory Functional Biology of Marine Biota, ISPRA, 57122, Livorno, Italy.
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Charoenpol A, Crespy D, Schulte A, Suginta W. Immobilized chitinase as effective biocatalytic platform for producing bioactive di-N-acetyl chitobiose from recycled chitin food waste. BIORESOURCE TECHNOLOGY 2024; 406:130945. [PMID: 38901749 DOI: 10.1016/j.biortech.2024.130945] [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: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
Described is chitinase immobilization on magnetic nanoparticles (MNPs) as biocompatible support for enzymatic production of di-N-acetyl chitobiose from chitin waste. Chitinase immobilization was feasible with an immobilization yield of 88.9 ± 1.6 % with 97.8 ± 1.0 % retention of activity and compared to free enzyme work, immobilization conferred better thermal and storage stability. As practical benefit the attachment to magnetic nanocarriers enabled easy enzyme recovery after repeated application runs and thus sustainable reuse. In fixed state chitinase retained a remarkable 39.7 ± 2.6 % of the starting activity after 16 reaction cycles. Furthermore, immobilized chitinase showed higher catalytic activity than free chitinase in converting shrimp shells and squid-pens chitins into di-N-acetyl chitobiose in a single-step reaction. The final yield of purified compound was 37.0 ± 1.2 % from shrimp shells and 61.1 ± 0.5 % from squid-pens chitin. In conclusion, an efficient MNP-based chitinase immobilization system with the potential for large-scale production was developed.
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Affiliation(s)
- Ailada Charoenpol
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong 21210, Thailand
| | - Daniel Crespy
- Department of Materials Science and Engineering, School of Molecular Science and Engineering (MSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong 21210, Thailand
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong 21210, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong 21210, Thailand.
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Guo X, Zhang X, Shao H, McMinn A, Liang Y, Wang M. A novel flavobacterial phage abundant during green tide, representing a new viral family, Zblingviridae. Appl Environ Microbiol 2024; 90:e0036724. [PMID: 38953371 PMCID: PMC11267871 DOI: 10.1128/aem.00367-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Flavobacteriia are the dominant and active bacteria during algal blooms and play an important role in polysaccharide degradation. However, little is known about phages infecting Flavobacteriia, especially during green tide. In this study, a novel virus, vB_TgeS_JQ, infecting Flavobacteriia was isolated from the surface water of the Golden Beach of Qingdao, China. Transmission electron microscopy demonstrated that vB_TgeS_JQ had the morphology of siphovirus. The experiments showed that it was stable from -20°C to 45°C and pH 5 to pH 8, with latent and burst periods both lasting for 20 min. Genomic analysis showed that the phage vB_TgeS_JQ contained a 40,712-bp dsDNA genome with a GC content of 30.70%, encoding 74 open-reading frames. Four putative auxiliary metabolic genes were identified, encoding electron transfer-flavoprotein dehydrogenase, calcineurin-like phosphoesterase, phosphoribosyl-ATP pyrophosphohydrolase, and TOPRIM nucleotidyl hydrolase. The abundance of phage vB_TgeS_JQ was higher during Ulva prolifera (U. prolifera) blooms compared with other marine environments. The phylogenetic and comparative genomic analyses revealed that vB_TgeS_JQ exhibited significant differences from all other phage isolates in the databases and therefore was classified as an undiscovered viral family, named Zblingviridae. In summary, this study expands the knowledge about the genomic, phylogenetic diversity and distribution of flavobacterial phages (flavophages), especially their roles during U. prolifera blooms. IMPORTANCE The phage vB_TgeS_JQ was the first flavobacterial phage isolated during green tide, representing a new family in Caudoviricetes and named Zblingviridae. The abundance of phage vB_TgeS_JQ was higher during the Ulva prolifera blooms. This study provides insights into the genomic, phylogenetic diversity, and distribution of flavophages, especially their roles during U. prolifera blooms.
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Affiliation(s)
- Xiaoyue Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
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Chaulagain D, Shamabadi NS, Leslie SA, Karig DK. From Natural Microbe Screening to Sustained Chitinase Activity in Exogenous Hosts. ACS Synth Biol 2024; 13:1165-1176. [PMID: 38587290 DOI: 10.1021/acssynbio.3c00637] [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] [Indexed: 04/09/2024]
Abstract
Genetic parts and hosts can be sourced from nature to realize new functions for synthetic biology or to improve performance in a particular application environment. Here, we proceed from the discovery and characterization of new parts to stable expression in new hosts with a particular focus on achieving sustained chitinase activity. Chitinase is a key enzyme for various industrial applications that require the breakdown of chitin, the second most abundant biopolymer on the earth. Diverse microbes exhibit chitinase activity, but for applications, the environmental conditions for optimal enzyme activity and microbe fitness must align with the application context. Achieving sustained chitinase activity under broad conditions in heterologous hosts has also proven difficult due to toxic side effects. Toward addressing these challenges, we first screen ocean water samples to identify microbes with chitinase activity. Next, we perform whole genome sequencing and analysis and select a chitinase gene for heterologous expression. Then, we optimize transformation methods for target hosts and introduce chitinase. Finally, to achieve robust function, we optimize ribosome binding sites and discover a beneficial promoter that upregulates chitinase expression in the presence of colloidal chitin in a sense-and-respond fashion. We demonstrate chitinase activity for >21 days in standard (Escherichia coli) and nonstandard (Roseobacter denitrificans) hosts. Besides enhancing chitinase applications, our pipeline is extendable to other functions, identifies natural microbes that can be used directly in non-GMO contexts, generates new parts for synthetic biology, and achieves weeks of stable activity in heterologous hosts.
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Affiliation(s)
- Diptee Chaulagain
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Narges S Shamabadi
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Skylar A Leslie
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - David K Karig
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
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5
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Yang J, Zhang L, Lin S, Li W, Liu C, Yan J, Li S, Long L. Structural insights of a SusD-like protein in marine Bacteroidetes bacteria reveal the molecular basis for chitin recognition and acquisition. FEBS J 2024; 291:584-595. [PMID: 37845429 DOI: 10.1111/febs.16974] [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: 07/24/2023] [Revised: 09/02/2023] [Accepted: 10/12/2023] [Indexed: 10/18/2023]
Abstract
Efficient recognition and transportation of chitin oligosaccharides are crucial steps for the utilization of chitin by heterotrophic bacteria. In this study, we employed structural biological and biochemical approaches to investigate the substrate recognition and acquisition mechanism of a novel chitin-binding SusD-like protein, AqSusD, which is derived from the chitin utilization gene cluster of a marine Bacteroides strain (Aquimarina sp. SCSIO 21287). We resolved the crystal structures of the AqSusD apo-protein and its complex with chitin oligosaccharides. Our results revealed that some crucial residues (Gln67, Phe87, and Asp276) underwent significant conformational changes to form tighter substrate binding sites for ligand binding. Moreover, we identified the functions of key amino acid residues and discovered that π-π stacking and hydrogen bonding between AqSusD and the ligand played significant roles in recognition of the protein for chitin oligosaccharide binding. Based on our findings and previous investigations, we put forward a model for the mechanism of chitin oligosaccharide recognition, capture, and transport by AqSusD, in collaboration with the membrane protein AqSusC. Our study deepens the understanding of the molecular-level "selfish" use of polysaccharides such as chitin by Bacteroides.
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Affiliation(s)
- Jian Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Shanshan Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chen Liu
- Guangzhou Quality Supervision and Testing Institute, China
| | - Jingheng Yan
- Guangzhou Quality Supervision and Testing Institute, China
| | - Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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Miksch S, Orellana LH, Oggerin de Orube M, Vidal-Melgosa S, Solanki V, Hehemann JH, Amann R, Knittel K. Taxonomic and functional stability overrules seasonality in polar benthic microbiomes. THE ISME JOURNAL 2024; 18:wrad005. [PMID: 38365229 PMCID: PMC10811738 DOI: 10.1093/ismejo/wrad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 02/18/2024]
Abstract
Coastal shelf sediments are hot spots of organic matter mineralization. They receive up to 50% of primary production, which, in higher latitudes, is strongly seasonal. Polar and temperate benthic bacterial communities, however, show a stable composition based on comparative 16S rRNA gene sequencing despite different microbial activity levels. Here, we aimed to resolve this contradiction by identifying seasonal changes at the functional level, in particular with respect to algal polysaccharide degradation genes, by combining metagenomics, metatranscriptomics, and glycan analysis in sandy surface sediments from Isfjorden, Svalbard. Gene expressions of diverse carbohydrate-active enzymes changed between winter and spring. For example, β-1,3-glucosidases (e.g. GH30, GH17, GH16) degrading laminarin, an energy storage molecule of algae, were elevated in spring, while enzymes related to α-glucan degradation were expressed in both seasons with maxima in winter (e.g. GH63, GH13_18, and GH15). Also, the expression of GH23 involved in peptidoglycan degradation was prevalent, which is in line with recycling of bacterial biomass. Sugar extractions from bulk sediments were low in concentrations during winter but higher in spring samples, with glucose constituting the largest fraction of measured monosaccharides (84% ± 14%). In porewater, glycan concentrations were ~18-fold higher than in overlying seawater (1107 ± 484 vs. 62 ± 101 μg C l-1) and were depleted in glucose. Our data indicate that microbial communities in sandy sediments digest and transform labile parts of photosynthesis-derived particulate organic matter and likely release more stable, glucose-depleted residual glycans of unknown structures, quantities, and residence times into the ocean, thus modulating the glycan composition of marine coastal waters.
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Affiliation(s)
- Sebastian Miksch
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Luis H Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Monike Oggerin de Orube
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Silvia Vidal-Melgosa
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Vipul Solanki
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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Lane DM, Valentine DL, Peng X. Genomic analysis of the marine yeast Rhodotorula sphaerocarpa ETNP2018 reveals adaptation to the open ocean. BMC Genomics 2023; 24:695. [PMID: 37986036 PMCID: PMC10662464 DOI: 10.1186/s12864-023-09791-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Despite a rising interest in the diversity and ecology of fungi in marine environments, there are few published genomes of fungi isolated from the ocean. The basidiomycetous yeast (unicellular fungus) genus Rhodotorula are prevalent and abundant in the open ocean, and they have been isolated from a wide range of other environments. Many of these environments are nutrient poor, such as the Antarctica and the Atacama deserts, raising the question as to how Rhodotorula yeasts may have adapted their metabolic strategies to optimize survival under low nutrient conditions. In order to understand their adaptive strategies in the ocean, the genome of R. sphaerocarpa ETNP2018 was compared to that of fourteen representative Rhodotorula yeasts, isolated from a variety of environments. RESULTS Rhodotorula sphaerocarpa ETNP2018, a strain isolated from the oligotrophic part of the eastern tropical North Pacific (ETNP) oxygen minimum zone (OMZ), hosts the smallest of the fifteen genomes and yet the number of protein-coding genes it possesses is on par with the other strains. Its genome exhibits a distinct reduction in genes dedicated to Major Facilitator Superfamily transporters as well as biosynthetic enzymes. However, its core metabolic pathways are fully conserved. Our research indicates that the selective pressures of the ETNP OMZ favor a streamlined genome with reduced overall biosynthetic potential balanced by a stable set of core metabolisms and an expansion of mechanisms for nutrient acquisition. CONCLUSIONS In summary, this study offers insights into the adaptation of fungi to the oligotrophic ocean and provides valuable information for understanding the ecological roles of fungi in the ocean.
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Affiliation(s)
- Dylan M Lane
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA
| | - David L Valentine
- Marine Science Institute, University of California, Santa Barbara, CA, USA
- Department of Earth Science, University of California, Santa Barbara, CA, USA
| | - Xuefeng Peng
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA.
- Marine Science Institute, University of California, Santa Barbara, CA, USA.
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Jiang Z, Liu S, Zhang D, Sha Z. The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean. MICROBIAL ECOLOGY 2023; 86:2781-2789. [PMID: 37552473 PMCID: PMC10640468 DOI: 10.1007/s00248-023-02284-w] [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: 01/28/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.
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Affiliation(s)
- Zhichen Jiang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sizhen Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dechao Zhang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laoshan Laboratory, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhongli Sha
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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9
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Gonfa TG, Negessa AK, Bulto AO. Isolation, screening, and identification of chitinase-producing bacterial strains from riverbank soils at Ambo, Western Ethiopia. Heliyon 2023; 9:e21643. [PMID: 38027800 PMCID: PMC10665737 DOI: 10.1016/j.heliyon.2023.e21643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Chitinases are hydrolytic enzymes that dissolve the glycosidic linkages in chitin. Chitin is a cell wall component of fungi and fund in exoskeleten of worms and arthropods. Chitinase has been applied in agriculture, as a biopesticide for the control of plant fungal infections, in medicine, and in waste management. This research aimed to isolate, screen, and identification of chitinase-producing bacteria from riverbank soils. Twenty nine chitinolytic bacteria were isolated from the river bank soil samples, from which 9 of them had strong chitinolytic properties. Chitinase production was determined by zones of hydrolysis produced after 96 h of incubation at 37 °C. The different bacterial isolates were characterized morphologically, microscopically, and biochemically and finally eight strain were identified at species level by Matrix Assisted Laser Desorption Ionization - Time of Flight Mass Spectrometry (MALDI-TOF MS). From the eight, bacterial isolates investigated in this study Stenotrophomonas maltophilia showed the highest chitinase enzyme activity (625 μg/mL) followed by Pseudomonas putida with the enzyme activity of (553 μg/mL) and the least enzyme activity was recorded for Lilliottia amnigena (80 μg/mL). An incubation temperature of 45 °C, neutral pH and an incubation period of 96 h are found to be the optimum condition for the chitinase enzyme production from Stenotrophomonas maltophilia. The results of this study indicated the possibility of the production of chitinase from the chitinolytic bacterial isolates, which was highly useful for a variety of applications, including biocontrol of harmful insects and pathogenic fungi as well as in the biochemical, pharmaceutical, and medical sectors.
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Affiliation(s)
- Teshome Gudeta Gonfa
- Kotebe University of Education, College of Natural and Computational Sciences, Department of Biology, Addis Ababa, Ethiopia
| | - Asefa Keneni Negessa
- Kotebe University of Education, College of Natural and Computational Sciences, Department of Biology, Addis Ababa, Ethiopia
- Ambo Ubiversity, College of Natural and Computational Sceicnes, Department of Biology, Ambo, Ethiopia
- Animal Health Institute, Sebeta, Ethiopia
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10
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Jeong GJ, Khan F, Tabassum N, Kim YM. Chitinases as key virulence factors in microbial pathogens: Understanding their role and potential as therapeutic targets. Int J Biol Macromol 2023; 249:126021. [PMID: 37506799 DOI: 10.1016/j.ijbiomac.2023.126021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Chitinases are crucial for the survival of bacterial and fungal pathogens both during host infection and outside the host in the environment. Chitinases facilitate adhesion onto host cells, act as virulence factors during infection, and provide protection from the host immune system, making them crucial factors in the survival of microbial pathogens. Understanding the mechanisms behind chitinase action is beneficial to design novel therapeutics to control microbial infections. This review explores the role of chitinases in the pathogenesis of bacterial, fungal, and viral infections. The mechanisms underlying the action of chitinases of bacterial, fungal, and viral pathogens in host cells are thoroughly reviewed. The evolutionary relationships between chitinases of various bacterial, fungal, and viral pathogens are discussed to determine their involvement in processes, such as adhesion and host immune system modulation. Gaining a better understanding of the distribution and activity of chitinases in these microbial pathogens can help elucidate their role in the invasion and infection of host cells.
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Affiliation(s)
- Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
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11
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Cardozo FA, Feitosa V, Mendonça CMN, da Silva FVS, Converti A, de Souza Oliveira RP, Pessoa A. Enhanced production of N-acetyl-glucosaminidase by marine Aeromonas caviae CHZ306 in bioreactor. Braz J Microbiol 2023; 54:1533-1545. [PMID: 37610567 PMCID: PMC10485184 DOI: 10.1007/s42770-023-01088-x] [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: 05/31/2022] [Accepted: 07/31/2023] [Indexed: 08/24/2023] Open
Abstract
N-Acetyl-glucosaminidases (GlcNAcases) are exoenzymes found in a wide range of living organisms, which have gained great attention in the treatment of disorders related to diabetes, Alzheimer's, Tay-Sachs', and Sandhoff's diseases; the control of phytopathogens; and the synthesis of bioactive GlcNAc-containing products. Aiming at future industrial applications, in this study, GlcNAcase production by marine Aeromonas caviae CHZ306 was enhanced first in shake flasks in terms of medium composition and then in bench-scale stirred-tank bioreactor in terms of physicochemical conditions. Stoichiometric balance between the bioavailability of carbon and nitrogen in the formulated culture medium, as well as the use of additional carbon and nitrogen sources, played a central role in improving the bioprocess, considerably increasing the enzyme productivity. The optimal cultivation medium was composed of colloidal α-chitin, corn steep liquor, peptone A, and mineral salts, in a 5.2 C:N ratio. Optimization of pH, temperature, colloidal α-chitin concentration, and kLa conditions further increased GlcNAcase productivity. Under optimized conditions in bioreactor (i.e., 34 °C, pH 8 and kLa 55.2 h-1), GlcNAcase activity achieved 173.4 U.L-1 after 12 h of cultivation, and productivity no less than 14.45 U.L-1.h-1 corresponding to a 370-fold enhancement compared to basal conditions.
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Affiliation(s)
- Flávio Augusto Cardozo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brasil.
| | - Valker Feitosa
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brasil
- Departamento de Medicina e Enfermagem, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, Brasil
| | - Carlos Miguel Nóbrega Mendonça
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brasil
- CICECO - Instituto de Materiais de Aveiro, Departamento de Química, Universidade de Aveiro, Aveiro, Portugal
| | - Francisco Vitor Santos da Silva
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brasil
| | - Attilio Converti
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brasil
- Dipartimento di Ingegneria Civile, Chimica e Ambientale, Università di Genova, Genova, Italia
| | | | - Adalberto Pessoa
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brasil
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12
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Guessous G, Patsalo V, Balakrishnan R, Çağlar T, Williamson JR, Hwa T. Inherited chitinases enable sustained growth and rapid dispersal of bacteria from chitin particles. Nat Microbiol 2023; 8:1695-1705. [PMID: 37580592 DOI: 10.1038/s41564-023-01444-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 07/04/2023] [Indexed: 08/16/2023]
Abstract
Many biogeochemical functions involve bacteria utilizing solid substrates. However, little is known about the coordination of bacterial growth with the kinetics of attachment to and detachment from such substrates. In this quantitative study of Vibrio sp. 1A01 growing on chitin particles, we reveal the heterogeneous nature of the exponentially growing culture comprising two co-existing subpopulations: a minority replicating on chitin particles and a non-replicating majority which was planktonic. This partition resulted from a high rate of cell detachment from particles. Despite high detachment, sustained exponential growth of cells on particles was enabled by the enrichment of extracellular chitinases excreted and left behind by detached cells. The 'inheritance' of these chitinases sustains the colonizing subpopulation despite its reduced density. This simple mechanism helps to circumvent a trade-off between growth and dispersal, allowing particle-associated marine heterotrophs to explore new habitats without compromising their fitness on the habitat they have already colonized.
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Affiliation(s)
- Ghita Guessous
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Vadim Patsalo
- Department of Integrative Structural and Computational Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
- DataBricks, San Diego, CA, USA
| | - Rohan Balakrishnan
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Tolga Çağlar
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
- San Diego Supercomputer Center, La Jolla, CA, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, CA, USA.
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13
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Arnold ND, Garbe D, Brück TB. Proteomic and Transcriptomic Analyses to Decipher the Chitinolytic Response of Jeongeupia spp. Mar Drugs 2023; 21:448. [PMID: 37623729 PMCID: PMC10455584 DOI: 10.3390/md21080448] [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: 07/25/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023] Open
Abstract
In nature, chitin, the most abundant marine biopolymer, does not accumulate due to the action of chitinolytic organisms, whose saccharification systems provide instructional blueprints for effective chitin conversion. Therefore, discovery and deconstruction of chitinolytic machineries and associated enzyme systems are essential for the advancement of biotechnological chitin valorization. Through combined investigation of the chitin-induced secretome with differential proteomic and transcriptomic analyses, a holistic system biology approach has been applied to unravel the chitin response mechanisms in the Gram-negative Jeongeupia wiesaeckerbachi. Hereby, the majority of the genome-encoded chitinolytic machinery, consisting of various glycoside hydrolases and a lytic polysaccharide monooxygenase, could be detected extracellularly. Intracellular proteomics revealed a distinct translation pattern with significant upregulation of glucosamine transport, metabolism, and chemotaxis-associated proteins. While the differential transcriptomic results suggested the overall recruitment of more genes during chitin metabolism compared to that of glucose, the detected protein-mRNA correlation was low. As one of the first studies of its kind, the involvement of over 350 unique enzymes and 570 unique genes in the catabolic chitin response of a Gram-negative bacterium could be identified through a three-way systems biology approach. Based on the cumulative data, a holistic model for the chitinolytic machinery of Jeongeupia spp. is proposed.
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Affiliation(s)
| | | | - Thomas B. Brück
- TUM School of Natural Sciences, Department of Chemistry, Technical University of Munich, Werner-Siemens Chair for Synthetic Biotechnology (WSSB), Lichtenbergstr. 4, 85748 Garching, Germany; (N.D.A.); (D.G.)
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14
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Basawa R, Kabra S, Khile DA, Faruk Abbu RU, Parekkadan SJ, Thomas NA, Kim SK, Raval R. Repurposing chitin-rich seafood waste for warm-water fish farming. Heliyon 2023; 9:e18197. [PMID: 37519647 PMCID: PMC10372652 DOI: 10.1016/j.heliyon.2023.e18197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
The pisciculture industry has grown multi-fold over the past few decades. However, a surge in development and nutrient demand has led to the establishment of numerous challenges. Being a potential solution, chitosan has gained attention as a bio nanocomposite for its well-acclaimed properties including biodegradability, non-toxicity, immunomodulatory effects, antimicrobial activity, and biocompatibility. This biopolymer and its derivatives can be transformed into various structures, like micro and nanoparticles, for various purposes. Consequently, with regards to these properties chitin and its derivatives extend their application into drug delivery, food supplementation, vaccination, and preservation. This review focuses on the clinical advancements made in fish biotechnology via chitosan and its derivatives and highlights its prospective expansion into the pisciculture industry-in particular, warm-water species.
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Affiliation(s)
- Renuka Basawa
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Suhani Kabra
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Dnyanada Anil Khile
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Rahil Ummar Faruk Abbu
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Serin Joby Parekkadan
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Naomi Ann Thomas
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Se Kwon Kim
- Department of Marine Science and Convergence Engineering, College of Science and Technology, Hanyang University, Erica 55 Hanyangdae-ro, Sangnol-gu, Ansan-si 11558, Gyeonggi-do, Republic of Korea
| | - Ritu Raval
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
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15
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Ibrahim MA, Alhalafi MH, Emam EAM, Ibrahim H, Mosaad RM. A Review of Chitosan and Chitosan Nanofiber: Preparation, Characterization, and Its Potential Applications. Polymers (Basel) 2023; 15:2820. [PMID: 37447465 DOI: 10.3390/polym15132820] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
Chitosan is produced by deacetylating the abundant natural chitin polymer. It has been employed in a variety of applications due to its unique solubility as well as its chemical and biological properties. In addition to being biodegradable and biocompatible, it also possesses a lot of reactive amino side groups that allow for chemical modification and the creation of a wide range of useful derivatives. The physical and chemical characteristics of chitosan, as well as how it is used in the food, environmental, and medical industries, have all been covered in a number of academic publications. Chitosan offers a wide range of possibilities in environmentally friendly textile processes because of its superior absorption and biological characteristics. Chitosan has the ability to give textile fibers and fabrics antibacterial, antiviral, anti-odor, and other biological functions. One of the most well-known and frequently used methods to create nanofibers is electrospinning. This technique is adaptable and effective for creating continuous nanofibers. In the field of biomaterials, new materials include nanofibers made of chitosan. Numerous medications, including antibiotics, chemotherapeutic agents, proteins, and analgesics for inflammatory pain, have been successfully loaded onto electro-spun nanofibers, according to recent investigations. Chitosan nanofibers have several exceptional qualities that make them ideal for use in important pharmaceutical applications, such as tissue engineering, drug delivery systems, wound dressing, and enzyme immobilization. The preparation of chitosan nanofibers, followed by a discussion of the biocompatibility and degradation of chitosan nanofibers, followed by a description of how to load the drug into the nanofibers, are the first issues highlighted by this review of chitosan nanofibers in drug delivery applications. The main uses of chitosan nanofibers in drug delivery systems will be discussed last.
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Affiliation(s)
- Marwan A Ibrahim
- Department of Biology, College of Science, Majmaah University, Al-Majmaah 11952, Saudi Arabia
- Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Mona H Alhalafi
- Department of Chemistry, College of Science, Majmaah University, Al-Majmaah 11952, Saudi Arabia
| | - El-Amir M Emam
- Faculty of Applied Arts, Textile Printing, Dyeing and Finishing Department, Helwan University, Cairo 11795, Egypt
| | - Hassan Ibrahim
- Pretreatment and Finishing of Cellulosic Fibers Department, Textile Research and Technology Institute, National Research Centre, Cairo 12622, Egypt
| | - Rehab M Mosaad
- Department of Biology, College of Science, Majmaah University, Al-Majmaah 11952, Saudi Arabia
- Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo 11566, Egypt
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16
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Rowley AF, Coates CJ. Shell disease syndromes of decapod crustaceans. Environ Microbiol 2023; 25:931-947. [PMID: 36708190 PMCID: PMC10946978 DOI: 10.1111/1462-2920.16344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/26/2023] [Indexed: 01/29/2023]
Abstract
The term shell disease subsumes a number of debilitating conditions affecting the outer integument (the carapace) of decapod crustaceans, such as lobsters and crabs. Herein, we seek to find commonality in the aetiology and pathology of such conditions, and those cases that result in the progressive erosion of the cuticle through to the visceral tissues by a cocktail of microbial-derived enzymes including lipases, proteases and chitinases. Aquimarina spp. are involved in shell disease in many different crustaceans across a wide geographical area, but the overall view is that the condition is polymicrobial in nature leading to dysbiosis within the microbial consortium of the damaged cuticle. The role of environment, decapod behaviour and physiology in triggering this disease is also reviewed. Finally, we provide a conceptual model for disease aetiology and suggest several avenues for future research that could improve our understanding of how such factors trigger, or exacerbate, this condition.
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Affiliation(s)
- Andrew F. Rowley
- Department of Biosciences, Faculty of Science and EngineeringSwansea UniversitySwanseaUK
| | - Christopher J. Coates
- Department of Zoology, School of Natural SciencesZoology, Ryan InstituteSchool of Natural Sciences, University of GalwayGalwayIreland
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17
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Cheng M, Shao Z, Wang X, Lu C, Li S, Duan D. Novel Chitin Deacetylase from Thalassiosira weissflogii Highlights the Potential for Chitin Derivative Production. Metabolites 2023; 13:metabo13030429. [PMID: 36984869 PMCID: PMC10057020 DOI: 10.3390/metabo13030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
β-Chitin is an important carbon fixation product of diatoms, and is the most abundant nitrogen-containing polysaccharide in the ocean. It has potential for widespread application, but the characterization of chitin-related enzymes from β-chitin producers has rarely been reported. In this study, a chitin deacetylase (TwCDA) was retrieved from the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) database and was heterologously expressed in vitro for functional analysis. The results showed that both the full-length sequence (TwCDA) and the N-terminal truncated sequence (TwCDA-S) had chitin deacetylase and chitinolytic activities after expression in Escherichia coli. High-performance liquid chromatography (HPLC) and gas chromatography–mass spectrometry (GC-MS) indicated that TwCDA and TwCDA-S could catalyze the deacetylation of oligosaccharide (GlcNAc)5. TwCDA had higher deacetylase activity, and also catalyzed the deacetylation of the β-chitin polymer. A dinitrosalicylic acid (DNS) assay showed that TwCDA-S had high chitinolytic activity for (GlcNAc)5, and the optimal reaction temperature was 35 °C. Liquid chromatography combined with time-of-flight mass spectrometry (LC-coTOF-MS) detected the formation of a N-acetylglucosamine monomer (C8H15NO6) in the reaction mixture. Altogether, we isolated a chitin deacetylase from a marine diatom, which can catalyze the deacetylation and degradation of chitin and chitin oligosaccharides. The relevant results lay a foundation for the internal regulation mechanism of chitin metabolism in diatoms and provide a candidate enzyme for the green industrial preparation of chitosan and chitin oligosaccharides.
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Affiliation(s)
- Mengzhen Cheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xin Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang Lu
- Department of Biological Engineering, College of Life Science, Yantai University, Yantai 264005, China
| | - Shuang Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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18
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Spatiotemporal Dynamics of Coastal Viral Community Structure and Potential Biogeochemical Roles Affected by an Ulva prolifera Green Tide. mSystems 2023; 8:e0121122. [PMID: 36815859 PMCID: PMC10134843 DOI: 10.1128/msystems.01211-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The world's largest macroalgal green tide, caused by Ulva prolifera, has resulted in serious consequences for coastal waters of the Yellow Sea, China. Although viruses are considered to be one of the key factors in controlling microalgal bloom demise, understanding of the relationship between viral communities and the macroalgal green tide is still poor. Here, a Qingdao coastal virome (QDCV) time-series data set was constructed based on the metagenomic analysis of 17 DNA viromes along three coastal stations of the Yellow Sea, covering different stages of the green tide from Julian days 165 to 271. A total of 40,076 viral contigs were detected and clustered into 28,058 viral operational taxonomic units (vOTUs). About 84% of the vOTUs could not be classified, and 62% separated from vOTUs in other ecosystems. Green tides significantly influenced the spatiotemporal dynamics of the viral community structure, diversity, and potential functions. For the classified vOTUs, the relative abundance of Pelagibacter phages declined with the arrival of the bloom and rebounded after the bloom, while Synechococcus and Roseobacter phages increased, although with a time lag from the peak of their hosts. More than 80% of the vOTUs reached peaks in abundance at different specific stages, and the viral peaks were correlated with specific hosts at different stages of the green tide. Most of the viral auxiliary metabolic genes (AMGs) were associated with carbon and sulfur metabolism and showed spatiotemporal dynamics relating to the degradation of the large amount of organic matter released by the green tide. IMPORTANCE To the best of our knowledge, this study is the first to investigate the responses of viruses to the world's largest macroalgal green tide. It revealed the spatiotemporal dynamics of the unique viral assemblages and auxiliary metabolic genes (AMGs) following the variation and degradation of Ulva prolifera. These findings demonstrate a tight coupling between viral assemblages, and prokaryotic and eukaryotic abundances were influenced by the green tide.
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19
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Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches. mSystems 2023; 8:e0113122. [PMID: 36790195 PMCID: PMC10134812 DOI: 10.1128/msystems.01131-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
β-Chitin has important ecological and physiological roles and potential for widespread applications, but the characterization of chitin-related enzymes from β-chitin producers was rarely reported. Querying against the Tara Oceans Gene Atlas, 4,939 chitin-related unique sequences from 12 Pfam accessions were found in Bacillariophyta metatranscriptomes. Putative chitin synthase (CHS) sequences are decreasingly present in Crustacea (39%), Stramenopiles (16%) and Insecta (14%) from the Marine Atlas of Tara Oceans Unigenes version 1 Metatranscriptomes (MATOUv1+T) database. A CHS gene from the model diatom Thalassiosira pseudonana (Thaps3_J4413, designated TpCHS1) was identified. Homology analysis of TpCHS1 in Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), PhycoCosm, and the PLAZA diatom omics data set showed that Mediophyceae and Thalassionemales species were potential new β-chitin producers besides Thalassiosirales. TpCHS1 was overexpressed in Saccharomyces cerevisiae and Phaeodactylum tricornutum. In transgenic P. tricornutum lines, TpCHS1-eGFP localizes to the Golgi apparatus and plasma membrane and predominantly accumulates in the cleavage furrow during cell division. Enhanced TpCHS1 expression could induce abnormal cell morphology and reduce growth rates in P. tricornutum, which might be ascribed to the inhibition of the G2/M phase. S. cerevisiae was proved to be a better system for expressing large amounts of active TpCHS1, which effectively incorporates UDP-N-acetylglucosamine in radiometric in vitro assays. Our study expands the knowledge on chitin synthase taxonomic distribution in marine eukaryotic microbes, and is the first to collectively characterize an active marine diatom CHS which may play an important role during cell division. IMPORTANCE As the most abundant biopolymer in the oceans, the significance of chitin and its biosynthesis is rarely demonstrated in diatoms, which are the main contributors to the primary productivity of the oceans, ascribed to their huge biomass and efficient photosynthesis. We retrieved genes involved in chitin-based metabolism against the Tara Oceans Gene Atlas to expand our knowledge about their diversity and distribution in the marine environment. Potential new producers of chitin were found from the analysis of various algal transcriptome and genome databases. Heterologous expression confirms that Thalassiosira pseudonana contains an active chitin synthase (CHS) which may play an important role in the cell division process of diatoms. This study provides new insight into CHS geographic and taxonomic distribution in marine eukaryotic microbes, as well as into a new CHS functioning in the biosynthesis of β-chitin in diatoms.
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20
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Qian L, Zhang K, Guo X, Yu M. What happens when chitin becomes chitosan? A single-molecule study. RSC Adv 2023; 13:2294-2300. [PMID: 36741137 PMCID: PMC9841443 DOI: 10.1039/d2ra07303j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
Chitin and chitosan are important support structures for many organisms and are important renewable macromolecular biomass resources. Structurally, with the removal of acetyl group, the solubility of chitosan is improved. However, the specific mechanism of solubility enhancement from chitin to chitosan is still unclear. In this study, the atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS) was used to obtain the single-chain mechanical behavior of chitin and chitosan. The results show that the hydrogen (H)-bonds' state, which can be influenced by the solvent, determines the degree of binding water (solubility) of polysaccharides, and that the binding water energy of a single chitosan chain is 6 times higher than that of chitin in water. Thus, H-bonding is the key to solubility enhancement and can be used to modulate the solubility properties of chitosan. It is expected that our studies can help to understand the structural and functional properties of chitin and chitosan at the single molecule level.
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Affiliation(s)
- Lu Qian
- School of Materials Science and Engineering, South China University of TechnologyGuangzhou 510641China
| | - Kai Zhang
- School of Mechanical Engineering, Sichuan UniversityChengdu 610065China
| | - Xin Guo
- School of Mechanical Engineering, Sichuan UniversityChengdu 610065China
| | - Miao Yu
- School of Mechanical Engineering, Sichuan UniversityChengdu 610065China
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Tamburino R, Marcolongo L, Sannino L, Ionata E, Scotti N. Plastid Transformation: New Challenges in the Circular Economy Era. Int J Mol Sci 2022; 23:ijms232315254. [PMID: 36499577 PMCID: PMC9736159 DOI: 10.3390/ijms232315254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
In a circular economy era the transition towards renewable and sustainable materials is very urgent. The development of bio-based solutions, that can ensure technological circularity in many priority areas (e.g., agriculture, biotechnology, ecology, green industry, etc.), is very strategic. The agricultural and fishing industry wastes represent important feedstocks that require the development of sustainable and environmentally-friendly industrial processes to produce and recover biofuels, chemicals and bioactive molecules. In this context, the replacement, in industrial processes, of chemicals with enzyme-based catalysts assures great benefits to humans and the environment. In this review, we describe the potentiality of the plastid transformation technology as a sustainable and cheap platform for the production of recombinant industrial enzymes, summarize the current knowledge on the technology, and display examples of cellulolytic enzymes already produced. Further, we illustrate several types of bacterial auxiliary and chitinases/chitin deacetylases enzymes with high biotechnological value that could be manufactured by plastid transformation.
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Affiliation(s)
- Rachele Tamburino
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Naples, Italy
| | | | - Lorenza Sannino
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Naples, Italy
| | - Elena Ionata
- CNR-IRET, Research Institute on Terrestrial Ecosystems, 80131 Naples, Italy
| | - Nunzia Scotti
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Naples, Italy
- Correspondence:
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22
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Bacterial chitinases: genetics, engineering and applications. World J Microbiol Biotechnol 2022; 38:252. [DOI: 10.1007/s11274-022-03444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022]
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23
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Perera IU, Fujiyoshi S, Nishiuchi Y, Nakai T, Maruyama F. Zooplankton act as cruise ships promoting the survival and pathogenicity of pathogenic bacteria. Microbiol Immunol 2022; 66:564-578. [PMID: 36128640 PMCID: PMC10091822 DOI: 10.1111/1348-0421.13029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 08/12/2022] [Accepted: 09/12/2022] [Indexed: 12/13/2022]
Abstract
Bacteria in general interact with zooplankton in aquatic ecosystems. These zooplankton-bacterial interactions help to shape the bacterial community by regulating bacterial abundances. Such interactions are even more significant and crucially in need of investigation in the case of pathogenic bacteria, which cause severe diseases in humans and animals. Among the many associations between a host metazoan and pathogenic bacteria, zooplankton provide nutrition and protection from stressful conditions, promote the horizontal transfer of virulence genes, and act as a mode of pathogen transport. These interactions allow the pathogen to survive and proliferate in aquatic environments and to endure water treatment processes, thereby creating a potential risk to human health. This review highlights current knowledge on the contributions of zooplankton to the survival and pathogenicity of pathogenic bacteria. We also discuss the need to consider these interactions as a risk factor in water treatment processes.
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Affiliation(s)
- Ishara U Perera
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan.,Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - So Fujiyoshi
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan.,Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - Yukiko Nishiuchi
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
| | - Toshihiro Nakai
- Takehara Marine Science Station, Graduate School of Integrated Science for Life, Hiroshima University, Takehara City, Hiroshima, Japan
| | - Fumito Maruyama
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan.,Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
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24
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McReynolds C, Adrien A, Petitpas A, Rubatat L, Fernandes SCM. Double Valorization for a Discard-α-Chitin and Calcium Lactate Production from the Crab Polybius henslowii Using a Deep Eutectic Solvent Approach. Mar Drugs 2022; 20:717. [PMID: 36421995 PMCID: PMC9695577 DOI: 10.3390/md20110717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 04/25/2024] Open
Abstract
Polybius henslowii, an abundant yet unexploited species of swimming crab, was investigated as a potential source of α-chitin and calcium lactate using deep eutectic solvents (DES) as extracting solvents. Choline chloride-malonic acid (CCMA) and choline chloride-lactic acid (CCLA) were used to obtain high purity α-chitin from ball-milled P. henslowii exoskeleton in 2 h at 120 °C, with yields of 12.05 ± 2.54% and 12.8 ± 1.54%, respectively. The physical and chemical characteristics of the obtained chitins were assessed using CHN elemental analysis, attenuated total reflectance-Fourier transform infrared spectroscopy, thermogravimetric analysis, and scanning electron microscopy. Furthermore, the CCLA solvent was reusable three times with little effect on the extract purity, and calcium lactate was produced at the end of the recycling cycles. The ensuing calcium lactate was also characterized in terms of chemical and physical properties. The obtained chitin is a promising raw material for downstream processing and the double valorization pathway with the obtention of calcium salts may increase the viability of a DES-based approach for the processing of mineralized substrates.
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Affiliation(s)
- Colin McReynolds
- Universite de Pau et des Pays de l’Adour, E2S UPPA, IPREM, CNRS, 64 600 Anglet, France
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
| | - Amandine Adrien
- Universite de Pau et des Pays de l’Adour, E2S UPPA, IPREM, CNRS, 64 600 Anglet, France
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
| | - Arnaud Petitpas
- Universite de Pau et des Pays de l’Adour, E2S UPPA, IPREM, CNRS, 64 600 Anglet, France
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
| | - Laurent Rubatat
- Universite de Pau et des Pays de l’Adour, E2S UPPA, IPREM, CNRS, 64 600 Anglet, France
| | - Susana C. M. Fernandes
- Universite de Pau et des Pays de l’Adour, E2S UPPA, IPREM, CNRS, 64 600 Anglet, France
- MANTA—Marine Materials Research Group, Universite de Pau et des Pays de l’Adour, E2S UPPA, 64 600 Anglet, France
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25
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Wu YL, Wang S, Yang DF, Yang LY, Wang QY, Yu J, Li N, Pan LX. The Discovery, Enzymatic Characterization and Functional Analysis of a Newly Isolated Chitinase from Marine-Derived Fungus Aspergillus fumigatus df347. Mar Drugs 2022; 20:md20080520. [PMID: 36005523 PMCID: PMC9410337 DOI: 10.3390/md20080520] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 01/15/2023] Open
Abstract
In order to discover a broad-specificity and high stability chitinase, a marine fungus, Aspergillus fumigatus df347, was identified in the sediments of mangrove wetlands in Qinzhou Bay, China. The chitinase gene (AfChi28) from A. fumigatus df347 was cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme AfChi28 was purified and characterized. AfChi28 is an acido-halotolerant- and temperature-resistant bifunctional enzyme with both endo- and exo-cleavage functions. Its enzymatic products are mainly GlcNAc, (GlcNAc)2, (GlcNAc)3 and (GlcNAc)4. Na+, Mg2+, K+, Ca2+ and Tris at a concentration of 50 mM had a strong stimulatory effect on AfChi28. The crude enzyme and pure enzyme exhibited the highest specific activity of 0.737 mU/mg and 52.414 mU/mg towards colloidal chitin. The DxDxE motif at the end of strand β5 and with Glu154 as the catalytic residue was verified by the AlphaFold2 prediction and sequence alignment of homologous proteins. Moreover, the results of molecular docking showed that molecular modeling of chitohexaose was shown to bind to AfChi28 in subsites −4 to +2 in the deep groove substrate-binding pocket. This study demonstrates that AfChi28 is a promising chitinase for the preparation of desirable chitin oligosaccharides, and provides a foundation for elucidating the catalytic mechanism of chitinases from marine fungi.
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Affiliation(s)
- Ya-Li Wu
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Sheng Wang
- Nanning Pangbo Biological Engineering Co., Ltd., Nanning 530004, China
| | - Deng-Feng Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Li-Yan Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Qing-Yan Wang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Jun Yu
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
- College of Food and Quality Engineering, Nanning University, Nanning 530200, China
| | - Nan Li
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
- Correspondence: (N.L.); (L.-X.P.); Tel.: +86-1350-7868-042 (N.L.); +86-1376-8513-581 (L.-X.P.)
| | - Li-Xia Pan
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
- Correspondence: (N.L.); (L.-X.P.); Tel.: +86-1350-7868-042 (N.L.); +86-1376-8513-581 (L.-X.P.)
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26
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Ding X, Zhao L, Khan IM, Yue L, Zhang Y, Wang Z. Emerging chitosan grafted essential oil components: A review on synthesis, characterization, and potential application. Carbohydr Polym 2022; 297:120011. [DOI: 10.1016/j.carbpol.2022.120011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/04/2022] [Accepted: 08/18/2022] [Indexed: 01/19/2023]
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27
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Tsudome M, Tachioka M, Miyazaki M, Uchimura K, Tsuda M, Takaki Y, Deguchi S. An ultrasensitive nanofiber-based assay for enzymatic hydrolysis and deep-sea microbial degradation of cellulose. iScience 2022; 25:104732. [PMID: 36039358 PMCID: PMC9418596 DOI: 10.1016/j.isci.2022.104732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/10/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mikiko Tsudome
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Mikako Tachioka
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masayuki Miyazaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kohsuke Uchimura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Miwako Tsuda
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Takaki
- SUGAR Program, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Corresponding author
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28
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Shi LD, Dong X, Liu Z, Yang Y, Lin JG, Li M, Gu JD, Zhu LZ, Zhao HP. A mixed blessing of viruses in wastewater treatment plants. WATER RESEARCH 2022; 215:118237. [PMID: 35245718 DOI: 10.1016/j.watres.2022.118237] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Activated sludge of wastewater treatment plants harbors a very high diversity of both microorganisms and viruses, wherein the latter control microbial dynamics and metabolisms by infection and lysis of cells. However, it remains poorly understood how viruses impact the biochemical processes of activated sludge, for example in terms of treatment efficiency and pollutant removal. Using metagenomic and metatranscriptomic deep sequencing, the present study recovered thousands of viral sequences from activated sludge samples of three conventional wastewater treatment plants. Gene-sharing network indicated that most of viruses could not be assigned to known viral genera, implying activated sludge as an underexplored reservoir for new viruses and viral diversity. In silico predictions of virus-host linkages demonstrated that infected microbial hosts, mostly belonging to bacteria, were transcriptionally active and able to hydrolyze polymers including starches, celluloses, and proteins. Some viruses encode auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and sulfur cycling, and antibiotic resistance genes (ARGs) for resistance to multiple drugs. The virus-encoded AMGs may enhance the biodegradation of contaminants like starches and celluloses, suggesting a positive role for viruses in strengthening the performance of activated sludge. However, ARGs would be disseminated to different microorganisms using viruses as gene shuttles, demonstrating the possibility for viruses to facilitate the spread of antibiotic resistance in the environment. Collectively, this study highlights the mixed blessing of viruses in wastewater treatment plants, and deciphers how they manipulate the biochemical processes in the activated sludge, with implications for both environmental protection and ecosystem security.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zongbao Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Ji-Dong Gu
- Environmental Science and Engineering Program, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Li-Zhong Zhu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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29
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Chen H, Liu L, Chen F, Fan Y, Yong Q. Re-dispersible chitin nanofibrils with improved stability in green solvents for fabricating hydrophobic aerogels. Carbohydr Polym 2022; 283:119138. [DOI: 10.1016/j.carbpol.2022.119138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/14/2021] [Accepted: 01/10/2022] [Indexed: 01/08/2023]
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30
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A review on super-wettable porous membranes and materials based on bio-polymeric chitosan for oil-water separation. Adv Colloid Interface Sci 2022; 303:102635. [PMID: 35325601 DOI: 10.1016/j.cis.2022.102635] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 12/21/2022]
Abstract
Appropriate surface wettability of membranes and materials are of an extreme importance for targeting separation of mixtures/emulsions such as oil from water or conversely water from oil. The development of super-wettable membranes and materials surfaces have shown remarkable potential for recovering water from oil-water emulsion while offering maximum resistance to fouling. The availability of clean and potable water has been regarded as an important global challenge for coming human generations. Oil and gas industry is continuously producing immense quantities of waste stream regarded as produced water which contains oil dispersed in water along with other several components. Treating such immense quantities of oily wastewater is of utmost need for recovering precious water for possible reuse or safe disposal. Various technologies have been developed for targeting the separation of oil-water emulsions or mixtures to harness useful potable water and oil as products. Membrane-based separations or use of porous materials such as mesh have been explored in literature for separation of oil-water mixtures/emulsions. Given the unique features of special hydrophilicity, ease of tunability, control of molecular weight, abundant availability, and potential for commercial scale up, chitosan has been extensively used for modifying membranes/meshes or preparing composites with other materials for oil-water separations. This review has described in detail the synthesis, methods of modification and application of chitosan-based super-wettable membranes/meshes and porous materials for oil-water separation. The special wettability features including super-hydrophobicity/superoleophilicity, super-oleophobicity/super-hydrophilicity and super-hydrophilicity/underwater super-oleophobicity of various chitosan-based membranes and materials have been discussed in detail in the review. The strategies for enhancing or developing special wettability for target specific applications have also been discussed. Finally, the challenges, their respective importance have been identified along with a discussion on possible solutions to these challenges.
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31
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Zhao L, Brugel S, Ramasamy KP, Andersson A. Response of Coastal Shewanella and Duganella Bacteria to Planktonic and Terrestrial Food Substrates. Front Microbiol 2022; 12:726844. [PMID: 35250896 PMCID: PMC8888917 DOI: 10.3389/fmicb.2021.726844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Global warming scenarios indicate that in subarctic regions, the precipitation will increase in the future. Coastal bacteria will thus receive increasing organic carbon sources from land runoff. How such changes will affect the function and taxonomic composition of coastal bacteria is poorly known. We performed a 10-day experiment with two isolated bacteria: Shewanella baltica from a seaside location and Duganella sp. from a river mouth, and provided them with a plankton and a river extract as food substrate. The bacterial growth and carbon consumption were monitored over the experimental period. Shewanella and Duganella consumed 40% and 30% of the plankton extract, respectively, while the consumption of the river extract was low for both bacteria, ∼1%. Shewanella showed the highest bacterial growth efficiency (BGE) (12%) when grown on plankton extract, while when grown on river extract, the BGE was only 1%. Duganella showed low BGE when grown on plankton extract (< 1%) and slightly higher BGE when grown on river extract (2%). The cell growth yield of Duganella was higher than that of Shewanella when grown on river extract. These results indicate that Duganella is more adapted to terrestrial organic substrates with low nutritional availability, while Shewanella is adapted to eutrophied conditions. The different growth performance of the bacteria could be traced to genomic variations. A closely related genome of Shewanella was shown to harbor genes for the sequestration of autochthonously produced carbon substrates, while Duganella contained genes for the degradation of relatively refractive terrestrial organic matter. The results may reflect the influence of environmental drivers on bacterial community composition in natural aquatic environments. Elevated inflows of terrestrial organic matter to coastal areas in subarctic regions would lead to increased occurrence of bacteria adapted to the degradation of complex terrestrial compounds with a low bioavailability.
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Affiliation(s)
- Li Zhao
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Sonia Brugel
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Kesava Priyan Ramasamy
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
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32
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Bartlau N, Wichels A, Krohne G, Adriaenssens EM, Heins A, Fuchs BM, Amann R, Moraru C. Highly diverse flavobacterial phages isolated from North Sea spring blooms. THE ISME JOURNAL 2022; 16:555-568. [PMID: 34475519 PMCID: PMC8776804 DOI: 10.1038/s41396-021-01097-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
It is generally recognized that phages are a mortality factor for their bacterial hosts. This could be particularly true in spring phytoplankton blooms, which are known to be closely followed by a highly specialized bacterial community. We hypothesized that phages modulate these dense heterotrophic bacteria successions following phytoplankton blooms. In this study, we focused on Flavobacteriia, because they are main responders during these blooms and have an important role in the degradation of polysaccharides. A cultivation-based approach was used, obtaining 44 lytic flavobacterial phages (flavophages), representing twelve new species from two viral realms. Taxonomic analysis allowed us to delineate ten new phage genera and ten new families, from which nine and four, respectively, had no previously cultivated representatives. Genomic analysis predicted various life styles and genomic replication strategies. A likely eukaryote-associated host habitat was reflected in the gene content of some of the flavophages. Detection in cellular metagenomes and by direct-plating showed that part of these phages were actively replicating in the environment during the 2018 spring bloom. Furthermore, CRISPR/Cas spacers and re-isolation during two consecutive years suggested that, at least part of the new flavophages are stable components of the microbial community in the North Sea. Together, our results indicate that these diverse flavophages have the potential to modulate their respective host populations.
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Affiliation(s)
- Nina Bartlau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Wichels
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Biologische Anstalt Helgoland, Heligoland, Germany
| | - Georg Krohne
- Imaging Core Facility, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Anneke Heins
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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Polyextremophilic Chitinolytic Activity by a Marine Strain (IG119) of Clonostachys rosea. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030688. [PMID: 35163952 PMCID: PMC8838608 DOI: 10.3390/molecules27030688] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/17/2022]
Abstract
The investigation for novel unique extremozymes is a valuable business for which the marine environment has been overlooked. The marine fungus Clonostachys rosea IG119 was tested for growth and chitinolytic enzyme production at different combinations of salinity and pH using response surface methodology. RSM modelling predicted best growth in-between pH 3.0 and 9.0 and at salinity of 0-40‱, and maximum enzyme activity (411.137 IU/L) at pH 6.4 and salinity 0‱; however, quite high production (>390 IU/L) was still predicted at pH 4.5-8.5. The highest growth and activity were obtained, respectively, at pH 4.0 and 8.0, in absence of salt. The crude enzyme was tested at different salinities (0-120‱) and pHs (2.0-13.0). The best activity was achieved at pH 4.0, but it was still high (in-between 3.0 and 12.0) at pH 2.0 and 13.0. Salinity did not affect the activity in all tested conditions. Overall, C. rosea IG119 was able to grow and produce chitinolytic enzymes under polyextremophilic conditions, and its crude enzyme solution showed more evident polyextremophilic features. The promising chitinolytic activity of IG119 and the peculiar characteristics of its chitinolytic enzymes could be suitable for several biotechnological applications (i.e., degradation of salty chitin-rich materials and biocontrol of spoiling organisms, possibly solving some relevant environmental issues).
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34
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Multiple bacterial partners in symbiosis with the nudibranch mollusk Rostanga alisae. Sci Rep 2022; 12:169. [PMID: 34997021 PMCID: PMC8742107 DOI: 10.1038/s41598-021-03973-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 01/23/2023] Open
Abstract
The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host’s ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations. A total of 74 clones belonging to the phyla α-, β-, γ-Proteobacteria, Actinobacteria, and Cyanobacteria were identified. FISH confirmed that bacteriocytes were packed with Bradyrhizobium, Maritalea, Labrenzia, Bulkholderia, Achromobacter, and Stenotrophomonas mainly in the foot and notum epidermis, and also an abundance of Synechococcus cyanobacteria in the intestinal epithelium. An ultrastructural analysis showed several bacterial morphotypes of bacteria in epidermal cells, intestine epithelium, and in mucus layer covering the mollusk body. The high proportion of typical bacterial fatty acids in R. alisae indicated that symbiotic bacteria make a substantial contribution to its nutrition. Thus, the nudibranch harbors a high diversity of specific endo- and extracellular bacteria, which previously unknown as symbionts of marine invertebrates that provide the mollusk with essential nutrients. They can provide chemical defense against predators.
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Kumawat TK, Kumawat V, Sharma S, Sharma V, Pandit A, Kandwani N, Biyani M. Sustainable Green Methods for the Extraction of Biopolymers. Biopolymers 2022. [DOI: 10.1007/978-3-030-98392-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sharma S, Kaur N, Kaur R, Kaur R. A review on valorization of chitinous waste. JOURNAL OF POLYMER RESEARCH 2021. [DOI: 10.1007/s10965-021-02759-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Xu CQ, Zhang XC, Wu Q, Chen LJ, Qu PH, Zhang YZ, Zhou TL, Zhou C. Skin and soft tissue infection caused by Cysteiniphilum litorale in an immunocompetent patient: A case report. Indian J Med Microbiol 2021; 39:545-547. [PMID: 34493415 DOI: 10.1016/j.ijmmb.2021.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/17/2021] [Accepted: 08/04/2021] [Indexed: 11/25/2022]
Abstract
Cysteiniphilum litorale is a Gram-negative coccobacillus first isolated from the seawater of Wailingding Island near the estuary of Pearl River in southern China. This organism was previously not considered to cause disease in animals or humans. We report a case of a 19-year-old female patient infected with abscess caused by C. litorale in the middle digit of her right hand after minor trauma during the handling of estuarine shrimps at home. C. litorale was cultured from the wound exudate of the patient and identified by 16S rRNA gene sequencing. Whether C. litorale may be transmitted to humans via other channels requires further exploration.
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Affiliation(s)
- Chun-Quan Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, PR China
| | - Xiu-Cai Zhang
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310003, PR China
| | - Qing Wu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, PR China
| | - Li-Jiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, PR China
| | - Ping-Hua Qu
- Department of Laboratory Medical Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, PR China
| | - Yi-Zhi Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, PR China
| | - Tie-Li Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, PR China.
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, PR China.
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Xie XH, Fu X, Yan XY, Peng WF, Kang LX. A Broad-Specificity Chitinase from Penicillium oxalicum k10 Exhibits Antifungal Activity and Biodegradation Properties of Chitin. Mar Drugs 2021; 19:md19070356. [PMID: 34201595 PMCID: PMC8307900 DOI: 10.3390/md19070356] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
Penicillium oxalicum k10 isolated from soil revealed the hydrolyzing ability of shrimp chitin and antifungal activity against Sclerotinia sclerotiorum. The k10 chitinase was produced from a powder chitin-containing medium and purified by ammonium sulfate precipitation and column chromatography. The purified chitinase showed maximal activity toward colloidal chitin at pH 5 and 40 °C. The enzymatic activity was enhanced by potassium and zinc, and it was inhibited by silver, iron, and copper. The chitinase could convert colloidal chitin to N-acetylglucosamine (GlcNAc), (GlcNAc)2, and (GlcNAc)3, showing that this enzyme had endocleavage and exocleavage activities. In addition, the chitinase prevented the mycelial growth of the phytopathogenic fungi S. sclerotiorum and Mucor circinelloides. These results indicate that k10 is a potential candidate for producing chitinase that could be useful for generating chitooligosaccharides from chitinous waste and functions as a fungicide.
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Affiliation(s)
| | | | | | | | - Li-Xin Kang
- Correspondence: ; Tel.: +86-27-88661237-8024
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Raimundo I, Silva R, Meunier L, Valente SM, Lago-Lestón A, Keller-Costa T, Costa R. Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes. MICROBIOME 2021; 9:43. [PMID: 33583433 PMCID: PMC7883442 DOI: 10.1186/s40168-020-00970-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/18/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater. RESULTS We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates. CONCLUSIONS Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.
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Affiliation(s)
- I. Raimundo
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - R. Silva
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - L. Meunier
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
- Laboratory of Aquatic Systems Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - S. M. Valente
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - A. Lago-Lestón
- Department of Medical Innovation, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico
| | - T. Keller-Costa
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
| | - R. Costa
- Instituto de Bioengenharia e Biociências, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, Torre Sul, Piso 11, 11.6.11b, 1049-001 Lisbon, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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Cheng H, Shao Z, Lu C, Duan D. Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses. BMC PLANT BIOLOGY 2021; 21:87. [PMID: 33568068 PMCID: PMC7874618 DOI: 10.1186/s12870-021-02849-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. RESULTS Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. CONCLUSIONS Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.
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Affiliation(s)
- Haomiao Cheng
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhanru Shao
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
| | - Chang Lu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co Ltd, Qingdao, 266400, P. R. China.
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Gregory GJ, Boyd EF. Stressed out: Bacterial response to high salinity using compatible solute biosynthesis and uptake systems, lessons from Vibrionaceae. Comput Struct Biotechnol J 2021; 19:1014-1027. [PMID: 33613867 PMCID: PMC7876524 DOI: 10.1016/j.csbj.2021.01.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteria have evolved mechanisms that allow them to adapt to changes in osmolarity and some species have adapted to live optimally in high salinity environments such as in the marine ecosystem. Most bacteria that live in high salinity do so by the biosynthesis and/or uptake of compatible solutes, small organic molecules that maintain the turgor pressure of the cell. Osmotic stress response mechanisms and their regulation among marine heterotrophic bacteria are poorly understood. In this review, we discuss what is known about compatible solute metabolism and transport and new insights gained from studying marine bacteria belonging to the family Vibrionaceae.
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Affiliation(s)
| | - E. Fidelma Boyd
- Corresponding author at: Department of Biological Sciences, 341 Wolf Hall, University of Delaware, Newark, DE 19716, United States.
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Berger CA, Steinberg DK, Copley NJ, Tarrant AM. De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression. Mar Genomics 2021; 58:100835. [PMID: 33526377 DOI: 10.1016/j.margen.2021.100835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/30/2020] [Accepted: 12/30/2020] [Indexed: 11/18/2022]
Abstract
Copepods are small crustaceans that dominate most zooplankton communities in terms of both abundance and biomass. In the polar oceans, a subset of large lipid-storing copepods occupy central positions in the food web because of their important role in linking phytoplankton and microzooplankton with higher trophic levels. In this paper, we generated a high-quality de novo transcriptome for Rhincalanus gigas, the largest-and among the most abundant-of the Southern Ocean copepods. We then conducted transcriptional profiling to characterize the developmental transition between late-stage juveniles and adult females. We found that juvenile R. gigas substantially upregulate lipid synthesis and glycolysis pathways relative to females, as part of a developmental gene expression program that also implicates processes such as muscle growth, chitin formation, and ion transport. This study provides the first transcriptional profile of a developmental transition within Rhincalanus gigas or any endemic Southern Ocean copepod, thereby extending our understanding of copepod molecular physiology.
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Affiliation(s)
- Cory A Berger
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States; MIT-WHOI Joint Program in Oceanography/Applied Ocean Science & Engineering, Cambridge and Woods Hole, MA, USA
| | - Deborah K Steinberg
- Virginia Institute of Marine Science, William & Mary, Gloucester Pt, VA 23062, United States
| | - Nancy J Copley
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Ann M Tarrant
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States.
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Alexyuk M, Bogoyavlenskiy A, Alexyuk P, Moldakhanov Y, Berezin V, Digel I. Epipelagic microbiome of the Small Aral Sea: Metagenomic structure and ecological diversity. Microbiologyopen 2021; 10:e1142. [PMID: 33305509 PMCID: PMC7882900 DOI: 10.1002/mbo3.1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/04/2020] [Accepted: 11/07/2020] [Indexed: 11/11/2022] Open
Abstract
Microbial diversity studies regarding the aquatic communities that experienced or are experiencing environmental problems are essential for the comprehension of the remediation dynamics. In this pilot study, we present data on the phylogenetic and ecological structure of microorganisms from epipelagic water samples collected in the Small Aral Sea (SAS). The raw data were generated by massive parallel sequencing using the shotgun approach. As expected, most of the identified DNA sequences belonged to Terrabacteria and Actinobacteria (40% and 37% of the total reads, respectively). The occurrence of Deinococcus-Thermus, Armatimonadetes, Chloroflexi in the epipelagic SAS waters was less anticipated. Surprising was also the detection of sequences, which are characteristic for strict anaerobes-Ignavibacteria, hydrogen-oxidizing bacteria, and archaeal methanogenic species. We suppose that the observed very broad range of phylogenetic and ecological features displayed by the SAS reads demonstrates a more intensive mixing of water masses originating from diverse ecological niches of the Aral-Syr Darya River basin than presumed before.
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Affiliation(s)
- Madina Alexyuk
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | | | - Pavel Alexyuk
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Yergali Moldakhanov
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Vladimir Berezin
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Ilya Digel
- Institute for BioengineeringAachen University of Applied SciencesJülichGermany
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Identification and Characterization of a Newly Isolated Chitinase-Producing Strain Bacillus licheniformis SSCL-10 for Chitin Degradation. ARCHAEA (VANCOUVER, B.C.) 2020; 2020:8844811. [PMID: 33223963 PMCID: PMC7669355 DOI: 10.1155/2020/8844811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/09/2020] [Accepted: 10/15/2020] [Indexed: 11/21/2022]
Abstract
Chitinases or chitinolytic enzymes have different applications in the field of medicine, agriculture, and industry. The present study is aimed at developing an effective hyperchitinase-producing mutant strain of novel Bacillus licheniformis. A simple and rapid methodology was used for screening potential chitinolytic microbiota by chemical mutagenesis with ethylmethane sulfonate and irradiation with UV. There were 16 mutant strains exhibiting chitinase activity. Out of the chitinase-producing strains, the strain with maximum chitinase activity was selected, the protein was partially purified by SDS-PAGE, and the strain was identified as Bacillus licheniformis (SSCL-10) with the highest specific activity of 3.4 U/mL. The induced mutation model has been successfully implemented in the mutant EMS-13 (20.2 U/mL) that produces 5-6-fold higher yield of chitinase, whereas the mutant UV-11 (13.3 U/mL) has 3-4-fold greater chitinase activity compared to the wild strain. The partially purified chitinase has a molecular weight of 66 kDa. The wild strain (SSCL-10) was identified as Bacillus licheniformis using 16S rRNA sequence analysis. This study explores the potential applications of hyperchitinase-producing bacteria in recycling and processing chitin wastes from crustaceans and shrimp, thereby adding value to the crustacean industry.
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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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Doane M, Haggerty JM, da Silva Lopes CR, Yates P, Edwards R, Dinsdale E, Lopes FAC, Bruce T. Latitude and chlorophyll a density drive the distribution of carbohydrate-active enzymes in the planktonic microbial fraction of the epipelagic zone. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:473-485. [PMID: 32608067 DOI: 10.1111/1758-2229.12865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/08/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Microbes drive the majority of the global carbon cycle. The effect of environmental conditions on selecting microbial functional diversity is well established, and recent studies have revealed the effects of geographic distances on selecting the functional components of marine microbial communities. Our study is the first attempt at establishing the effects of environmental factors on driving the marine carbohydrate-active enzyme (CAZyme) distribution. We characterized the diversity of CAZyme genes and investigated the correlations between their distributions and biogeographic parameters (latitude, longitude, distance from the equator, site depth, water depth, chlorophyll density, salinity and temperature). Therefore, we accessed a subset of surface water samples (38 metagenomes) from the Global Ocean Sampling project. Only chlorophyll and latitude altered the distribution patterns of CAZymes, revealing the existence of two latitudinal gradients (positive and negative) of marine CAZyme abundance. Considering the importance of carbohydrates in microbial life, characterization of the spatial patterns of the genetic repertoire involved in carbohydrate metabolism represents an important step in improving our understanding of the metabolic strategies associated with the microbial marine carbon cycle and their effects on the productivity of marine ecosystems.
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Affiliation(s)
- Michael Doane
- Biology Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
- Sydney Institute of Marine Science, 19 Chowder Bay, Mosman, New South Wales, 2088, Australia
| | - John Matthew Haggerty
- Biology Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
| | | | - Peter Yates
- Sydney Institute of Marine Science, 19 Chowder Bay, Mosman, New South Wales, 2088, Australia
| | - Rob Edwards
- Computational Science Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
| | - Elizabeth Dinsdale
- Biology Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
| | | | - Thiago Bruce
- Biology Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
- Departamento de Biologia Celular, Laboratório de Enzimologia, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
- Departamento de Microbiologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Ondina, Salvador, BA, Brazil
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Ahmad SI, Ahmad R, Khan MS, Kant R, Shahid S, Gautam L, Hasan GM, Hassan MI. Chitin and its derivatives: Structural properties and biomedical applications. Int J Biol Macromol 2020; 164:526-539. [PMID: 32682975 DOI: 10.1016/j.ijbiomac.2020.07.098] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/19/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022]
Abstract
Chitin, a polysaccharide that occurs abundantly in nature after cellulose, has attracted the interest of the scientific community due to its plenty of availability and low cost. Mostly, it is derived from the exoskeleton of insects and marine crustaceans. Often, it is insoluble in common solvents that limit its applications but its deacetylated product, named chitosan is found to be soluble in protonated aqueous medium and used widely in various biomedical fields. Indeed, the existence of the primary amino group on the backbone of chitosan provides it an important feature to modify it chemically into other derivatives easily. In the present review, we present the structural properties of chitin, and its derivatives and highlighted their biomedical implications including, tissue engineering, drug delivery, diagnosis, molecular imaging, antimicrobial activity, and wound healing. We further discussed the limitations and prospects of this versatile natural polysaccharide.
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Affiliation(s)
- Syed Ishraque Ahmad
- Department of Chemistry, Zakir Husain Delhi College (University of Delhi), New Delhi 110002, India.
| | - Razi Ahmad
- Regional Center for Advanced Technologies and Materials, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Mohd Shoeb Khan
- Interdisciplinary Nanotechnology Centre, Aligarh Muslim University, Aligarh 202002, India
| | - Ravi Kant
- Department of Chemistry, Zakir Husain Delhi College (University of Delhi), New Delhi 110002, India
| | - Shumaila Shahid
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India
| | - Leela Gautam
- Department of Chemistry, Zakir Husain Delhi College (University of Delhi), New Delhi 110002, India
| | - Ghulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (Central University), New Delhi 110025, India.
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48
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He X, Yu M, Wu Y, Ran L, Liu W, Zhang XH. Two Highly Similar Chitinases from Marine Vibrio Species have Different Enzymatic Properties. Mar Drugs 2020; 18:E139. [PMID: 32120805 PMCID: PMC7143101 DOI: 10.3390/md18030139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
Chitinase, as one of the most important extracellular enzymes in the marine environment, has great ecological and applied values. In this study, two chitinases (Chi1557 and Chi4668) with 97.33% amino acid sequences identity were individually found in Vibrio rotiferianus and Vibrio harveyi. They both were encoding by 561 amino acids, but differed in 15 amino acids and showed different enzymatic properties. The optimal temperature and pH ranges were 45-50 °C and pH 5.0-7.0 for Chi1557, while ~50 °C and pH 3.0-6.0 for Chi4668. K+, Mg2+, and EDTA increased the enzymatic activity of Chi4668 significantly, yet these factors were inhibitory to Chi1557. Moreover, Chi1557 degraded colloidal chitin to produce (GlcNAc)2 and minor GlcNAc, whereas Chi4668 produce (GlcNAc)2 with minor (GlcNAc)3 and (GlcNAc)4. The Kcat/Km of Chi4668 was ~4.7 times higher than that of Chi1557, indicating that Chi4668 had stronger catalytic activity than Chi1557. Furthermore, site-directed mutagenesis was performed on Chi1557 focusing on seven conserved amino acid residues of family GH18 chitinases. Chi1557 was almost completely inactive after Glu154, Gln219, Tyr221, or Trp312 was individually mutated, retained ~50% activity after Tyr37 was mutated, and increased two times activity after Asp152 was mutated, indicating that these six amino acids were key sites for Chi1557.
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Affiliation(s)
- Xinxin He
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Min Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Yanhong Wu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Lingman Ran
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Weizhi Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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49
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Bioproduction of N-acetyl-glucosamine from colloidal α-chitin using an enzyme cocktail produced by Aeromonas caviae CHZ306. World J Microbiol Biotechnol 2019; 35:114. [DOI: 10.1007/s11274-019-2694-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/07/2019] [Indexed: 12/22/2022]
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50
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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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