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Coelho LF, Couceiro JF, Keller-Costa T, Valente SM, Ramalho TP, Carneiro J, Comte J, Blais MA, Vincent WF, Martins Z, Canário J, Costa R. Structural shifts in sea ice prokaryotic communities across a salinity gradient in the subarctic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154286. [PMID: 35247410 DOI: 10.1016/j.scitotenv.2022.154286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Current knowledge of the processes that shape prokaryotic community assembly in sea ice across polar ecosystems is scarce. Here, we coupled culture-dependent (bacterial isolation on R2A medium) and culture-independent (high-throughput 16S rRNA gene sequencing) approaches to provide the first comprehensive assessment of prokaryotic communities in the late winter ice and its underlying water along a natural salinity gradient in coastal Hudson Bay, an iconic cryo-environment that marks the ecological transition between Canadian Subarctic and Arctic biomes. We found that prokaryotic community assembly processes in the ice were less selective at low salinity since typical freshwater taxa such as Frankiales, Burkholderiales, and Chitinophagales dominated both the ice and its underlying water. In contrast, there were sharp shifts in community structure between the ice and underlying water samples at sites with higher salinity, with the orders Alteromonadales and Flavobacteriales dominating the ice, while the abovementioned freshwater taxa dominated the underlying water communities. Moreover, primary producers including Cyanobium (Cyanobacteria, Synechococcales) may play a role in shaping the ice communities and were accompanied by known Planctomycetes and Verrucomicrobiae taxa. Culture-dependent analyses showed that the ice contained pigment-producing psychrotolerant or psychrophilic bacteria from the phyla Proteobacteria, Actinobacteriota, and Bacteroidota, likely favored by the combination of low temperatures and the seasonal increase in sunlight. Our findings suggest that salinity, photosynthesis and dissolved organic matter are the main drivers of prokaryotic community structure in the late winter ice of coastal Hudson Bay, the ecosystem with the fastest sea ice loss rate in the Canadian North.
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Affiliation(s)
- Lígia Fonseca Coelho
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Joana Fernandes Couceiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sara Martinez Valente
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Tiago Pereirinha Ramalho
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Joana Carneiro
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut National de la Recherche Scientifique, G1K 9A9 Quebec City, QC, Canada; Centre for Northern Studies (CEN), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Marie-Amélie Blais
- Centre for Northern Studies (CEN), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biologie & Takuvik Joint International Laboratory, Université Laval, Quebec City, Québec G1V 0A6, Canada
| | - Warwick F Vincent
- Centre for Northern Studies (CEN), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biologie & Takuvik Joint International Laboratory, Université Laval, Quebec City, Québec G1V 0A6, Canada
| | - Zita Martins
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - João Canário
- Centro de Química Estrutural, Institute of Molecular Sciences and Department of Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal; Department of Energy - Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Isolation of Chitinolytic Bacteria from European Sea Bass Gut Microbiota Fed Diets with Distinct Insect Meals. BIOLOGY 2022; 11:biology11070964. [PMID: 36101344 PMCID: PMC9312007 DOI: 10.3390/biology11070964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary The ever-growing human population is increasingly demanding more fish. As a response, aquaculture has become the fastest growing industry in its sector. Alternatives to fish meal, an unsustainable commodity used as the main protein source for carnivorous species, are urgently needed in aquafeeds. Recently, in Europe, seven insect species have been approved as potential ingredients for animal feeds, including fish feed. However, chitin, one of the components of an insect’s exoskeleton, is indigestible for several economically valuable fish species, decreasing fish performance upon inclusion. This work aimed to isolate, from the European sea bass gastrointestinal tract, probiotic bacteria capable of producing chitinases to improve the use of diets containing high levels of insect meal. Based on the enhanced adaptability of gut microbial communities and the selective pressure of chitin-enriched diets on fish gut microbiota, bacteria were first isolated from the gastrointestinal tract of European sea bass fed chitin-enriched diets. Isolates were then comprehensively screened in vitro for important traits such as their ability to utilize chitin, gut-survival aptitude, and biosafety-related issues required to be considered eligible as probiotics by the European Food Safety Authority (EFSA). Abstract Insect meal (IM), recently authorized for use in aquafeeds, positions itself as a promising commodity for aquafeed inclusion. However, insects are also rich in chitin, a structural polysaccharide present in the exoskeleton, which is not digested by fish, resulting in lower fish performance. Through the application of a dietary pressure, this study aimed to modulate European sea bass gut microbiota towards the enrichment of chitinolytic bacteria to allow the isolation of novel probiotics capable of improving the use of IM-containing diets, overcoming chitin drawbacks. Five isoproteic (44%) and isolipidic (18%) diets were used: a fish meal (FM)-based diet (diet CTR), a chitin-supplemented diet (diet CHIT5), and three diets with either 25% of Hermetia illucens and Tenebrio molitor larvae meals (HM25 and TM25, respectively) or H. illucens exuviae meal (diet HEM25) as partial FM substitutes. After an 8-week feeding trial, the results showed a clear modulatory effect towards spore-forming bacteria by HM25 and HEM25 diets, with the latter being responsible for the majority of the chitinolytic fish isolates (FIs) obtained. Sequential evaluation of the FI hemolytic activity, antibiotic resistance, total chitinolytic activity, sporulation, and survival in gastrointestinal-like conditions identified FI645 and FI658 as the most promising chitinolytic probiotics for in vivo application.
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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: 13] [Impact Index Per Article: 4.3] [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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Paenibacillus lutrae sp. nov., A Chitinolytic Species Isolated from A River Otter in Castril Natural Park, Granada, Spain. Microorganisms 2019; 7:microorganisms7120637. [PMID: 31810255 PMCID: PMC6955709 DOI: 10.3390/microorganisms7120637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 11/16/2022] Open
Abstract
A highly chitinolytic facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive, rod-shaped bacterial strain N10T was isolated from the feces of a river otter in the Castril Natural Park (Granada, Spain). It is a slightly halophilic, motile, catalase-, oxidase-, ACC deaminase- and C4 and C8 lipase-positive strain. It is aerobic, respiratory and has a fermentative metabolism using oxygen as an electron acceptor, produces acids from glucose and can fix nitrogen. Phylogenetic analysis of the 16S rRNA gene sequence, multilocus sequence analysis (MLSA) of 16S rRNA, gyrB, recA and rpoB, as well as phylogenomic analyses indicate that strain N10T is a novel species of the genus Paenibacillus, with the highest 16S rRNA sequence similarity (95.4%) to P. chitinolyticus LMG 18047T and <95% similarity to other species of the genus Paenibacillus. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANIb) were 21.1% and <75%, respectively. Its major cellular fatty acids were anteiso-C15:0, C16:0, and iso-C15:0. G + C content ranged between 45%–50%. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with chemotaxonomic and phenotypic data, we demonstrate that type strain N10T (= CECT 9541T =LMG 30535T) is a novel species of genus Paenibacillus and the name Paenibacillus lutrae sp. nov. is proposed.
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Hettiarachchi SA, Kwon YK, Lee Y, Jo E, Eom TY, Kang YH, Kang DH, De Zoysa M, Marasinghe SD, Oh C. Characterization of an acetyl xylan esterase from the marine bacterium Ochrovirga pacifica and its synergism with xylanase on beechwood xylan. Microb Cell Fact 2019; 18:122. [PMID: 31286972 PMCID: PMC6615230 DOI: 10.1186/s12934-019-1169-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/26/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Acetyl xylan esterase plays an important role in the complete enzymatic hydrolysis of lignocellulosic materials. It hydrolyzes the ester linkages of acetic acid in xylan and supports and enhances the activity of xylanase. This study was conducted to identify and overexpress the acetyl xylan esterase (AXE) gene revealed by the genomic sequencing of the marine bacterium Ochrovirga pacifica. RESULTS The AXE gene has an 864-bp open reading frame that encodes 287 aa and consists of an AXE domain from aa 60 to 274. Gene was cloned to pET-16b vector and expressed the recombinant AXE (rAXE) in Escherichia coli BL21 (DE3). The predicted molecular mass was 31.75 kDa. The maximum specific activity (40.08 U/mg) was recorded at the optimal temperature and pH which were 50 °C and pH 8.0, respectively. The thermal stability assay showed that AXE maintains its residual activity almost constantly throughout and after incubation at 45 °C for 120 min. The synergism of AXE with xylanase on beechwood xylan, increased the relative activity 1.41-fold. CONCLUSION Resulted higher relative activity of rAXE with commercially available xylanase on beechwood xylan showed its potential for the use of rAXE in industrial purposes as a de-esterification enzyme to hydrolyze xylan and hemicellulose-like complex substrates.
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Affiliation(s)
- Sachithra Amarin Hettiarachchi
- Korea Institute of Ocean Science & Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.,Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences & Technology, University of Ruhuna, Matara, Sri Lanka
| | - Young-Kyung Kwon
- Korea Institute of Ocean Science & Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Youngdeuk Lee
- Korea Institute of Ocean Science & Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Eunyoung Jo
- Korea Institute of Ocean Science & Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Tae-Yang Eom
- Korea Institute of Ocean Science & Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yoon-Hyeok Kang
- Korea Institute of Ocean Science & Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Do-Hyung Kang
- Korea Institute of Ocean Science & Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Mahanama De Zoysa
- College of Veterinary Medicine, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Svini Dileepa Marasinghe
- Korea Institute of Ocean Science & Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chulhong Oh
- Korea Institute of Ocean Science & Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea. .,Department of Ocean Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.
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Yildirim-Aksoy M, Beck BH, Zhang D. Examining the interplay between Streptococcus agalactiae, the biopolymer chitin and its derivative. Microbiologyopen 2018; 8:e00733. [PMID: 30272387 PMCID: PMC6528556 DOI: 10.1002/mbo3.733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/10/2018] [Accepted: 08/20/2018] [Indexed: 11/30/2022] Open
Abstract
Streptococcus agalactiae is a highly pathogenic bacterium of aquatic species and terrestrial animals worldwide, whereas chitin and its derivative chitosan are among the most abundant biopolymers found in nature, including the aquatic milieu. The present investigation focused on the capability of S. agalactiae to degrade and utilize these polymers. Growth of S. agalactiae in the presence of colloid chitin, chitosan, or N‐acetyl‐glucosamine (GlcNAc) was evaluated. Chitosanase production was measured daily over 7 days of growth period and degraded products were evaluated with thin later chorography. Chitin had no effect on the growth of S. agalactiae. Degraded chitin, however, stimulated the growth of S. agalactiae. S. agalactiae cells did not produce chitinase to degrade chitin; however, they readily utilize GlcNAc (product of degraded chitin) as sole source of carbon and nitrogen for growth. Chitosan at high concentrations had antibacterial activities against S. agalactiae, while in the presence of lower than the inhibitory level of chitosan in the medium, S. agalactiae secrets chitosanase to degrade chitosan, and utilizes it to a limited extent to benefit growth. The interaction of S. agalactiae with chitin hydrolytes and chitosan could play a role in the diverse habitat distribution and pathogenicity of S. agalactiae worldwide.
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Affiliation(s)
- Mediha Yildirim-Aksoy
- Aquatic Animal Health Research Unit, United States Department of Agriculture, Agricultural Research Service, Auburn, Alabama
| | - Benjamin H Beck
- Aquatic Animal Health Research Unit, United States Department of Agriculture, Agricultural Research Service, Auburn, Alabama
| | - Dunhua Zhang
- Aquatic Animal Health Research Unit, United States Department of Agriculture, Agricultural Research Service, Auburn, Alabama
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Thimoteo SS, Glogauer A, Faoro H, de Souza EM, Huergo LF, Moerschbacher BM, Pedrosa FO. A broad pH range and processive chitinase from a metagenome library. ACTA ACUST UNITED AC 2017; 50:e5658. [PMID: 28076454 PMCID: PMC5264535 DOI: 10.1590/1414-431x20165658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/25/2016] [Indexed: 01/14/2023]
Abstract
Chitinases are hydrolases that degrade chitin, a polymer of N-acetylglucosamine
linked β(1-4) present in the exoskeleton of crustaceans, insects, nematodes and
fungal cell walls. A metagenome fosmid library from a wastewater-contaminated soil
was functionally screened for chitinase activity leading to the isolation and
identification of a chitinase gene named metachi18A. The
metachi18A gene was subcloned and overexpressed in
Escherichia coli BL21 and the MetaChi18A chitinase was purified
by affinity chromatography as a 6xHis-tagged fusion protein. The MetaChi18A enzyme is
a 92-kDa protein with a conserved active site domain of glycosyl hydrolases family
18. It hydrolyses colloidal chitin with an optimum pH of 5 and temperature of 50°C.
Moreover, the enzyme retained at least 80% of its activity in the pH range from 4 to
9 and 98% at 600 mM NaCl. Thin layer chromatography analyses identified chitobiose as
the main product of MetaChi18A on chitin polymers as substrate. Kinetic analysis
showed inhibition of MetaChi18A activity at high concentrations of colloidal chitin
and 4-methylumbelliferyl N,N′-diacetylchitobiose and sigmoid kinetics at low
concentrations of colloidal chitin, indicating a possible conformational change to
lead the chitin chain from the chitin-binding to the catalytic domain. The observed
stability and activity of MetaChi18A over a wide range of conditions suggest that
this chitinase, now characterized, may be suitable for application in the industrial
processing of chitin.
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Affiliation(s)
- S S Thimoteo
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - A Glogauer
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil.,Agência de Inovação, Instituto de Tecnologia do Paraná - Tecpar, Curitiba, PR, Brasil
| | - H Faoro
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil.,Instituto Carlos Chagas, Fiocruz, Curitiba, PR, Brasil
| | - E M de Souza
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - L F Huergo
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - B M Moerschbacher
- Institute for Biology and Biotechnology of Plants, WWU Münster University, Münster, Germany
| | - F O Pedrosa
- Departmento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Paulsen SS, Andersen B, Gram L, Machado H. Biological Potential of Chitinolytic Marine Bacteria. Mar Drugs 2016; 14:md14120230. [PMID: 27999269 PMCID: PMC5192467 DOI: 10.3390/md14120230] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 12/26/2022] Open
Abstract
Chitinolytic microorganisms secrete a range of chitin modifying enzymes, which can be exploited for production of chitin derived products or as fungal or pest control agents. Here, we explored the potential of 11 marine bacteria (Pseudoalteromonadaceae, Vibrionaceae) for chitin degradation using in silico and phenotypic assays. Of 10 chitinolytic strains, three strains, Photobacterium galatheae S2753, Pseudoalteromonas piscicida S2040 and S2724, produced large clearing zones on chitin plates. All strains were antifungal, but against different fungal targets. One strain, Pseudoalteromonas piscicida S2040, had a pronounced antifungal activity against all seven fungal strains. There was no correlation between the number of chitin modifying enzymes as found by genome mining and the chitin degrading activity as measured by size of clearing zones on chitin agar. Based on in silico and in vitro analyses, we cloned and expressed two ChiA-like chitinases from the two most potent candidates to exemplify the industrial potential.
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Affiliation(s)
- Sara Skøtt Paulsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Birgitte Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Henrique Machado
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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Matos MN, Lozada M, Anselmino LE, Musumeci MA, Henrissat B, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lundgren L, Dionisi HM. Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments. Environ Microbiol 2016; 18:4471-4484. [PMID: 27348213 DOI: 10.1111/1462-2920.13433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/23/2016] [Indexed: 12/20/2022]
Abstract
Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.
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Affiliation(s)
- Marina N Matos
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Luciano E Anselmino
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Matías A Musumeci
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France.,INRA, USC 1408 AFMB, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Walter P Mac Cormack
- Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, C1064ABR, Argentina.,Instituto Nanobiotec, CONICET - Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1113AAC, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram - High North Research Centre for Climate and the Environment, Tromsø, NO-9296, Norway.,CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, UiT The Arctic University of Norway, Tromsø, N-9037, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, 141 89, Sweden
| | | | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
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10
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A cold-adapted, solvent and salt tolerant esterase from marine bacterium Psychrobacter pacificensis. Int J Biol Macromol 2015; 81:180-7. [DOI: 10.1016/j.ijbiomac.2015.07.045] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 11/20/2022]
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11
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Lau MCY, Cameron C, Magnabosco C, Brown CT, Schilkey F, Grim S, Hendrickson S, Pullin M, Sherwood Lollar B, van Heerden E, Kieft TL, Onstott TC. Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships. Front Microbiol 2014; 5:531. [PMID: 25400621 PMCID: PMC4215791 DOI: 10.3389/fmicb.2014.00531] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 09/24/2014] [Indexed: 11/30/2022] Open
Abstract
Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes.
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Affiliation(s)
- Maggie C Y Lau
- Department of Geosciences, Princeton University Princeton, NJ, USA
| | | | - Cara Magnabosco
- Department of Geosciences, Princeton University Princeton, NJ, USA
| | - C Titus Brown
- Department of Computer Science and Engineering and Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Faye Schilkey
- National Center for Genome Resources Santa Fe, NM, USA
| | - Sharon Grim
- The Marine Biological Laboratory Woods Hole, MA, USA
| | | | - Michael Pullin
- Department of Chemistry, New Mexico Tech Socorro, NM, USA
| | | | - Esta van Heerden
- Department of Biotechnology, University of Free State Bloemfontein, South Africa
| | | | - Tullis C Onstott
- Department of Geosciences, Princeton University Princeton, NJ, USA
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12
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Patterns of Microbially Driven Carbon Cycling in the Ocean: Links between Extracellular Enzymes and Microbial Communities. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/706082] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Heterotrophic microbial communities play a central role in the marine carbon cycle. They are active in nearly all known environments, from the surface to the deep ocean, in the sediments, and from the equator to the Poles. In order to process complex organic matter, these communities produce extracellular enzymes of the correct structural specificity to hydrolyze substrates to sizes sufficiently small for uptake. Extracellular enzymatic hydrolysis thus initiates heterotrophic carbon cycling. Our knowledge of the enzymatic capabilities of microbial communities in the ocean is still underdeveloped. Recent studies, however, suggest that there may be large-scale patterns of enzymatic function in the ocean, patterns of community function that may be connected to emerging patterns of microbial community composition. Here I review some of these large-scale contrasts in microbial enzyme activities, between high-latitude and temperate surface ocean waters, contrasts between inshore and offshore waters, changes with depth gradients in the ocean, and contrasts between the water column and underlying sediments. These contrasting patterns are set in the context of recent studies of microbial communities and patterns of microbial biogeography. Focusing on microbial community function as well as composition and potential should yield clearer understanding of the factors driving carbon cycling in the ocean.
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13
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Dworkin J. The medium is the message: interspecies and interkingdom signaling by peptidoglycan and related bacterial glycans. Annu Rev Microbiol 2014; 68:137-54. [PMID: 24847956 DOI: 10.1146/annurev-micro-091213-112844] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptidoglycan serves as a key structure of the bacterial cell by determining cell shape and providing resistance to internal turgor pressure. However, in addition to these essential and well-studied functions, bacterial signaling by peptidoglycan fragments, or muropeptides, has been demonstrated by recent work. Actively growing bacteria release muropeptides as a consequence of cell wall remodeling during elongation and division. Therefore, the presence of muropeptide synthesis is indicative of growth-promoting conditions and may serve as a broadly conserved signal for nongrowing cells to reinitiate growth. In addition, muropeptides serve as signals between bacteria and eukaryotic organisms during both pathogenic and symbiotic interactions. The increasingly appreciated role of the microbiota in metazoan organisms suggests that muropeptide signaling likely has important implications for homeostatic mammalian physiology.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032;
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14
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Beier S, Bertilsson S. Bacterial chitin degradation-mechanisms and ecophysiological strategies. Front Microbiol 2013; 4:149. [PMID: 23785358 PMCID: PMC3682446 DOI: 10.3389/fmicb.2013.00149] [Citation(s) in RCA: 227] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/28/2013] [Indexed: 11/13/2022] Open
Abstract
Chitin is one the most abundant polymers in nature and interacts with both carbon and nitrogen cycles. Processes controlling chitin degradation are summarized in reviews published some 20 years ago, but the recent use of culture-independent molecular methods has led to a revised understanding of the ecology and biochemistry of this process and the organisms involved. This review summarizes different mechanisms and the principal steps involved in chitin degradation at a molecular level while also discussing the coupling of community composition to measured chitin hydrolysis activities and substrate uptake. Ecological consequences are then highlighted and discussed with a focus on the cross feeding associated with the different habitats that arise because of the need for extracellular hydrolysis of the chitin polymer prior to metabolic use. Principal environmental drivers of chitin degradation are identified which are likely to influence both community composition of chitin degrading bacteria and measured chitin hydrolysis activities.
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Affiliation(s)
- Sara Beier
- Department of Ecology and Genetics, Limnology, Uppsala University Uppsala, Sweden ; Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, UPMC Paris 06, UMR 7621 Banyuls sur mer, France ; Laboratoire d'Océanographie Microbienne, Observatoire Océanologique Centre National de la Recherche Scientifique, UMR 7621 Banyuls sur mer, France
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15
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Biochemical diversity of carboxyl esterases and lipases from Lake Arreo (Spain): a metagenomic approach. Appl Environ Microbiol 2013; 79:3553-62. [PMID: 23542620 DOI: 10.1128/aem.00240-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The esterases and lipases from the α/β hydrolase superfamily exhibit an enormous sequence diversity, fold plasticity, and activities. Here, we present the comprehensive sequence and biochemical analyses of seven distinct esterases and lipases from the metagenome of Lake Arreo, an evaporite karstic lake in Spain (42°46'N, 2°59'W; altitude, 655 m). Together with oligonucleotide usage patterns and BLASTP analysis, our study of esterases/lipases mined from Lake Arreo suggests that its sediment contains moderately halophilic and cold-adapted proteobacteria containing DNA fragments of distantly related plasmids or chromosomal genomic islands of plasmid and phage origins. This metagenome encodes esterases/lipases with broad substrate profiles (tested over a set of 101 structurally diverse esters) and habitat-specific characteristics, as they exhibit maximal activity at alkaline pH (8.0 to 8.5) and temperature of 16 to 40°C, and they are stimulated (1.5 to 2.2 times) by chloride ions (0.1 to 1.2 M), reflecting an adaptation to environmental conditions. Our work provides further insights into the potential significance of the Lake Arreo esterases/lipases for biotechnology processes (i.e., production of enantiomers and sugar esters), because these enzymes are salt tolerant and are active at low temperatures and against a broad range of substrates. As an example, the ability of a single protein to hydrolyze triacylglycerols, (non)halogenated alkyl and aryl esters, cinnamoyl and carbohydrate esters, lactones, and chiral epoxides to a similar extent was demonstrated.
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16
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Kielak AM, Cretoiu MS, Semenov AV, Sørensen SJ, van Elsas JD. Bacterial chitinolytic communities respond to chitin and pH alteration in soil. Appl Environ Microbiol 2013; 79:263-72. [PMID: 23104407 PMCID: PMC3536121 DOI: 10.1128/aem.02546-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/21/2012] [Indexed: 01/21/2023] Open
Abstract
Chitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA and chiA genes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity of chiA gene types in soil is enormous and (i) that different chiA gene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one of Actinobacteria in the immediate response to the added chitin (based on 16S rRNA gene abundance and chiA gene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes.
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Affiliation(s)
- Anna M. Kielak
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Mariana Silvia Cretoiu
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Alexander V. Semenov
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Søren J. Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
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17
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Beier S, Mohit V, Ettema TJG, Östman Ö, Tranvik LJ, Bertilsson S. Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing. Environ Microbiol 2012; 14:2467-79. [DOI: 10.1111/j.1462-2920.2012.02764.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Wang J, Yang D, Zhang Y, Shen J, van der Gast C, Hahn MW, Wu Q. Do patterns of bacterial diversity along salinity gradients differ from those observed for macroorganisms? PLoS One 2011; 6:e27597. [PMID: 22125616 PMCID: PMC3220692 DOI: 10.1371/journal.pone.0027597] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 10/20/2011] [Indexed: 11/18/2022] Open
Abstract
It is widely accepted that biodiversity is lower in more extreme environments. In this study, we sought to determine whether this trend, well documented for macroorganisms, also holds at the microbial level for bacteria. We used denaturing gradient gel electrophoresis (DGGE) with phylum-specific primers to quantify the taxon richness (i.e., the DGGE band numbers) of the bacterioplankton communities of 32 pristine Tibetan lakes that represent a broad salinity range (freshwater to hypersaline). For the lakes investigated, salinity was found to be the environmental variable with the strongest influence on the bacterial community composition. We found that the bacterial taxon richness in freshwater habitats increased with increasing salinity up to a value of 1‰. In saline systems (systems with >1‰ salinity), the expected decrease of taxon richness along a gradient of further increasing salinity was not observed. These patterns were consistently observed for two sets of samples taken in two different years. A comparison of 16S rRNA gene clone libraries revealed that the bacterial community of the lake with the highest salinity was characterized by a higher recent accelerated diversification than the community of a freshwater lake, whereas the phylogenetic diversity in the hypersaline lake was lower than that in the freshwater lake. These results suggest that different evolutionary forces may act on bacterial populations in freshwater and hypersaline lakes on the Tibetan Plateau, potentially resulting in different community structures and diversity patterns.
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Affiliation(s)
- Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Dongmei Yang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Yong Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- Life Sciences College, Anhui Normal University, Wuhu, China
| | - Ji Shen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Christopher van der Gast
- National Environment Research Council (NERC) Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Martin W. Hahn
- Institute for Limnology, Austrian Academy of Sciences, Mondsee, Austria
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- * E-mail:
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