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Wang Z, Zhao Z, Wang H, Wu Q, Ke Q, Zhu L, Wu L, Chen L. Harvest residue recycling rather than slash-burning results in the enhancement of soil fertility and bacterial community stability in Eucalyptus plantations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173850. [PMID: 38901592 DOI: 10.1016/j.scitotenv.2024.173850] [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: 03/24/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/22/2024]
Abstract
Deforestation and slash combustion have substantial adverse impacts on the atmosphere, soil and microbe. Despite this awareness, numerous individuals persist in opting for high-intensity Eucalyptus planting through slash-burning in pursuit of immediate profits while disregarding the environmental significance and destroying the soil. Slash-unburnt agriculture can effectively safeguard the ecological environment, and compared with slash-burning, there remains a limited understanding of its regulatory mechanisms on soil fertility and microbial community. Also, large uncertainty persists regarding the utilization of harvest residues. Thoroughly investigating these questions from various perspectives encompassing physical soil characteristics, nutrient availability, bacterial community structures, and stability is crucial. To explore the ecological advantages of slash-unburnt techniques on microorganisms and their associated ecosystems, we used two slash-unburnt (Unburnt) planting techniques: Spread (naturally and evenly covering the forest floor after logging) and Stack (residues are piled along contour lines) as well as the traditional slash Burnt method (Burnt) in a Eucalyptus plantation. A comparative analysis was conducted between the two methods. We observed that over a span of 4 years, despite the initial lower application of fertilizer in the Unburnt treatments compared with the Burnt treatment during the first 2 years, the Unburnt treatment gradually caught up or even surpassed and attained similar nutrient levels as the Burnt treatment. Alphaproteobacteria was the main phyla that indicated the difference in soil bacterial communities between Burnt and Unburnt treatments. The microbial networks also highlighted the significance of the Unburnt method, as it contributed to the preservation of crucial network nodes and the stability of soil bacterial communities. Therefore, rational utilization of harvest residue may effectively avoid the vast damage caused by slash-burning to Eucalyptus trees and the soil environment but may also increase the potential for restoring soil fertility, improving fertilizer utilization efficiency, and maintaining microbial community stability over time.
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Affiliation(s)
- Zhengye Wang
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Ziqi Zhao
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; State-owned Gaofeng Forest Farm, Nanning, Guangxi 530002, China
| | - Huili Wang
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, Guangxi 530002, China
| | - Qinzhan Wu
- State-owned Daguishan Forest Farm, Hezhou, Guangxi 542800, China
| | - Qin Ke
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, Guangxi 530002, China
| | - Lingyue Zhu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Lichao Wu
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China; Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of National Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.
| | - Lijun Chen
- Key Laboratory of Soil and Water Conservation and Desertification Combating of Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China.
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Baev V, Iliev I, Apostolova E, Gozmanova M, Hristova Y, Ilieva Y, Yahubyan G, Gochev V. Genomic Exploration of a Chitinolytic Streptomyces albogriseolus PMB5 Strain from European mantis ( Mantis religiosa). Curr Issues Mol Biol 2024; 46:9359-9375. [PMID: 39329906 PMCID: PMC11430731 DOI: 10.3390/cimb46090554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/28/2024] Open
Abstract
The genus Streptomyces is renowned not only for its natural antibiotic production but also for its abundant chitinolytic enzymes, which break down stubborn chitin into chitooligosaccharides. Despite this, there have been limited studies utilizing whole-genome sequencing to explore the repertoire of chitin degradation and utilization genes in Streptomyces. A particularly compelling source of novel antimicrobials and enzymes lies in the microbiota of insects, where bacterial symbionts produce antimicrobials to protect against opportunistic pathogens and enzymes to adapt to the environment. In this study, we present the chitinolytic strain Streptomyces albogriseolus PMB5, isolated from the insectivorous Mantis religiosa (European mantis). Whole-genome sequencing revealed that PMB5 harbors a linear chromosome of 7,211,961 bp and a linear plasmid of 327,989 bp. The genome comprises 6683 genes, including 6592 protein-coding sequences and 91 RNA genes. Furthermore, genome analysis revealed 19 biosynthetic gene clusters covering polyketides, terpenes, and RiPPs, with 10 clusters showing significant gene similarity (>80%) to known clusters like antimycin, hopene, and geosmin. In the genome of S. albogriseolus PMB5, we were able to identify several antibiotic resistance genes; these included cml (resistance to phenicol), gimA (resistance to macrolides), parY (resistance to aminocoumarin), oleC/oleD (resistance to macrolides), novA (resistance to aminocoumarin) and bla/blc (resistance to beta-lactams). Additionally, three clusters displayed no similarity to known sequences, suggesting novel bioactive compound discovery potential. Remarkably, strain PMB5 is the first reported S. albogriseolus capable of thriving on a medium utilizing chitin as a carbon source, with over 50 chitin-utilizing genes identified, including five AA10 family LPMOs, five GH18 chitinases, and one GH19 chitinase. This study significantly enhances the genomic understanding of S. albogriseolus, a species previously underrepresented in research, paving the way to further exploration of the biotechnological potential of the species.
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Affiliation(s)
- Vesselin Baev
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Ivan Iliev
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Elena Apostolova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Mariyana Gozmanova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Yana Hristova
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Yanitsa Ilieva
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Galina Yahubyan
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Velizar Gochev
- Department of Biochemistry and Microbiology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
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de Matos JP, Ribeiro DF, da Silva AK, de Paula CH, Cordeiro IF, Lemes CGDC, Sanchez AB, Rocha LCM, Garcia CCM, Almeida NF, Alves RM, de Abreu VAC, Varani AM, Moreira LM. Diversity and potential functional role of phyllosphere-associated actinomycetota isolated from cupuassu (Theobroma grandiflorum) leaves: implications for ecosystem dynamics and plant defense strategies. Mol Genet Genomics 2024; 299:73. [PMID: 39066857 DOI: 10.1007/s00438-024-02162-1] [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: 11/07/2023] [Accepted: 06/25/2024] [Indexed: 07/30/2024]
Abstract
Exploring the intricate relationships between plants and their resident microorganisms is crucial not only for developing new methods to improve disease resistance and crop yields but also for understanding their co-evolutionary dynamics. Our research delves into the role of the phyllosphere-associated microbiome, especially Actinomycetota species, in enhancing pathogen resistance in Theobroma grandiflorum, or cupuassu, an agriculturally valuable Amazonian fruit tree vulnerable to witches' broom disease caused by Moniliophthora perniciosa. While breeding resistant cupuassu genotypes is a possible solution, the capacity of the Actinomycetota phylum to produce beneficial metabolites offers an alternative approach yet to be explored in this context. Utilizing advanced long-read sequencing and metagenomic analysis, we examined Actinomycetota from the phyllosphere of a disease-resistant cupuassu genotype, identifying 11 Metagenome-Assembled Genomes across eight genera. Our comparative genomic analysis uncovered 54 Biosynthetic Gene Clusters related to antitumor, antimicrobial, and plant growth-promoting activities, alongside cutinases and type VII secretion system-associated genes. These results indicate the potential of phyllosphere-associated Actinomycetota in cupuassu for inducing resistance or antagonism against pathogens. By integrating our genomic discoveries with the existing knowledge of cupuassu's defense mechanisms, we developed a model hypothesizing the synergistic or antagonistic interactions between plant and identified Actinomycetota during plant-pathogen interactions. This model offers a framework for understanding the intricate dynamics of microbial influence on plant health. In conclusion, this study underscores the significance of the phyllosphere microbiome, particularly Actinomycetota, in the broader context of harnessing microbial interactions for plant health. These findings offer valuable insights for enhancing agricultural productivity and sustainability.
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Affiliation(s)
- Jéssica Pereira de Matos
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Dilson Fagundes Ribeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Ana Karla da Silva
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Camila Henriques de Paula
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Isabella Ferreira Cordeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Angélica Bianchini Sanchez
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Camila Carrião Machado Garcia
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | | | | | - Alessandro M Varani
- Departamento de Biotecnologia Agropecuária e Ambiental, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil.
| | - Leandro Marcio Moreira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
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Pham VHT, Kim J, Chang S. A Valuable Source of Promising Extremophiles in Microbial Plastic Degradation. Polymers (Basel) 2024; 16:2109. [PMID: 39125136 PMCID: PMC11314448 DOI: 10.3390/polym16152109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Plastics have accumulated in open environments, such as oceans, rivers, and land, for centuries, but their effect has been of concern for only decades. Plastic pollution is a global challenge at the forefront of public awareness worldwide due to its negative effects on ecological systems, animals, human health, and national economies. Therefore, interest has increased regarding specific circular economies for the development of plastic production and the investigation of green technologies for plastic degradation after use on an appropriate timescale. Moreover, biodegradable plastics have been found to contain potential new hazards compared with conventional plastics due to the physicochemical properties of the polymers involved. Recently, plastic biodegradation was defined as microbial conversion using functional microorganisms and their enzymatic systems. This is a promising strategy for depolymerizing organic components into carbon dioxide, methane, water, new biomass, and other higher value bioproducts under both oxic and anoxic conditions. This study reviews microplastic pollution, the negative consequences of plastic use, and the current technologies used for plastic degradation and biodegradation mediated by microorganisms with their drawbacks; in particular, the important and questionable role of extremophilic multi-enzyme-producing bacteria in synergistic systems of plastic decomposition is discussed. This study emphasizes the key points for enhancing the plastic degradation process using extremophiles, such as cell hydrophobicity, amyloid protein, and other relevant factors. Bioprospecting for novel mechanisms with unknown information about the bioproducts produced during the plastic degradation process is also mentioned in this review with the significant goals of CO2 evolution and increasing H2/CH4 production in the future. Based on the potential factors that were analyzed, there may be new ideas for in vitro isolation techniques for unculturable/multiple-enzyme-producing bacteria and extremophiles from various polluted environments.
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Affiliation(s)
- Van Hong Thi Pham
- Department of Environmental Energy Engineering, College of Creative Engineering, Kyonggi University, Suwon 16227, Republic of Korea;
- Department of Life Science, College of Natural Science, Kyonggi University, Suwon 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Science, Kyonggi University, Suwon 16227, Republic of Korea
| | - Soonwoong Chang
- Department of Environmental Energy Engineering, College of Creative Engineering, Kyonggi University, Suwon 16227, Republic of Korea;
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Sui Y, Song P, Chen G, Zuo S, Liu H, Guo J, Chang Z, Dai H, Liu F, Dong H. Gut microbiota and Tritrichomonas foetus infection: A study of prevalence and risk factors based on pet cats. Prev Vet Med 2024; 226:106162. [PMID: 38518658 DOI: 10.1016/j.prevetmed.2024.106162] [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: 10/22/2023] [Revised: 01/16/2024] [Accepted: 02/23/2024] [Indexed: 03/24/2024]
Abstract
Tritrichomonas foetus (T. foetus) is a protozoal pathogen that infects cats and constitutes a significant cause of chronic colitis and diarrhea. Perturbations in the gut microbiota (GM) are affected by Trichomonas infection. Furthermore, dysregulation of the host GM enhances Trichomonas pathogenicity. However, it remains unclear whether the occurrence of diarrhea is associated with a dysregulation in GM following T. foetus infection in cats. Hence, the primary objective of this investigation was to explore the correlation between T. foetus infection and dysregulation in GM by analyzing fecal samples obtained from pet cats in Henan Province, central China. We randomly collected 898 fecal samples from pet cats living in 11 prefectural cities within Henan Province, and T. foetus was screened with polymerase chain reaction (PCR) amplification based on the 18 S rRNA gene. Subsequently, six T. foetus-positive and six T. foetus-negative samples underwent analysis through 16 S rRNA gene sequencing to evaluate the gut microbiota's composition. The overall prevalence of T. foetus infection among the collected samples was found to be 6.01% (54/898). Notably, a higher prevalence of infection was observed in young, undewormed, unimmunized, and diarrheic pet cats. T. foetus infection was found to significantly alter the composition of the pet cat fecal microbiota, leading to dysfunctions. Moreover, it resulted in a substantial increase in the abundance of Bacteroidetes, Proteobacteria, and Phascolarctobacterium spp., while decreasing the ratio of Firmicutes to Bacteroidetes (F/B) and the abundance of Actinobacteria, Clostridiaceae_Clostridium spp., Phascolarctobacterium spp., SMB53 spp., and Blautia spp. We constructed ROC curves to assess the diagnostic value of specific bacterial taxa in discriminating T. foetus infection. The analysis revealed that Proteobacteria and Clostridiaceae_Clostridium spp. were the most reliable single predictors for T. foetus infection. This finding suggests that alterations in the GM may be strongly associated with T. foetus infections.
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Affiliation(s)
- Yuzhen Sui
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Pengtao Song
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Guizhen Chen
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Shoujun Zuo
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Hu Liu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Jinjie Guo
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Zhihai Chang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China
| | - Hongyu Dai
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China.
| | - Fang Liu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China.
| | - Haiju Dong
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, People's Republic of China.
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Liu G, Zhang T, Liu X, Jia G, Zhao H, Chen X, Zhang R, Wang J. Effects of dietary N-carbamylglutamate supplementation on the modulation of microbiota and Th17/Treg balance-related immune signaling after lipopolysaccharide challenge. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:2429-2439. [PMID: 37961849 DOI: 10.1002/jsfa.13128] [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: 06/19/2023] [Revised: 10/10/2023] [Accepted: 11/14/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND This study aimed to evaluate the effects of N-carbamylglutamate (NCG) on piglets' growth performance and immune response, and to unravel the mechanisms of such effects. In a 2 × 2 factorial design including diet (with or without NCG) and immunological challenge (saline or lipopolysaccharide (LPS)), 24 piglets were randomly distributed into four groups. After being fed a basic diet or a NCG-supplemented diet for 21 days, piglets were administered LPS or saline intraperitoneally. RESULTS The results showed that NCG increased the average daily gain and average daily feed intake, and the feed conversion ratio of piglets, and alleviated the adverse effects of LPS stimulation on intestinal morphology. At the phylum level, NCG reversed the increase in the abundance of Firmicutes and the reduction in that of Actinomycete caused by LPS stimulation. At the genus level, NCG increased the abundance of Lactobacillus, Blautia, norank_Butyricicoccaceae, Subdoligranulum, and Ruminococcus_gauvreauii_group, and LPS decreased the abundance of Escherichia-Shigella and Ruminococcus_gauvreauii_group. The short-chain fatty acid content was increased by NCG, but LPS reduced its content. N-Carbamylglutamate also inhibited significantly the LPS-induced increase in the relative expression of signal transducer and activator of transcription (STAT) 3, related orphan receptor (RAR) c, and pro-inflammatory cytokines, and the decrease in the relative expression of STAT5, forkhead box P3, IL-10 and transforming growth factor beta 1 mRNA. A significant correlation was found between intestinal microbiota and inflammatory cytokines and short-chain fatty acids. CONCLUSION N-Carbamylglutamate can improve piglets' growth performance. It can also attenuate LPS-induced intestinal inflammation by modulating microbiota and Th17/Treg balance-related immune signaling pathways. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Guangmang Liu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu, China
| | - Ting Zhang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu, China
| | - Xinlian Liu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu, China
| | - Gang Jia
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu, China
| | - Hua Zhao
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu, China
| | - Xiaoling Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu, China
| | - Ruinan Zhang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Chengdu, China
| | - Jing Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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Vojnovic S, Aleksic I, Ilic-Tomic T, Stevanovic M, Nikodinovic-Runic J. Bacillus and Streptomyces spp. as hosts for production of industrially relevant enzymes. Appl Microbiol Biotechnol 2024; 108:185. [PMID: 38289383 PMCID: PMC10827964 DOI: 10.1007/s00253-023-12900-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: 07/04/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 02/01/2024]
Abstract
The application of enzymes is expanding across diverse industries due to their nontoxic and biodegradable characteristics. Another advantage is their cost-effectiveness, reflected in reduced processing time, water, and energy consumption. Although Gram-positive bacteria, Bacillus, and Streptomyces spp. are successfully used for production of industrially relevant enzymes, they still lag far behind Escherichia coli as hosts for recombinant protein production. Generally, proteins secreted by Bacillus and Streptomyces hosts are released into the culture medium; their native conformation is preserved and easier recovery process enabled. Given the resilience of both hosts in harsh environmental conditions and their spore-forming capability, a deeper understanding and broader use of Bacillus and Streptomyces as expression hosts could significantly enhance the robustness of industrial bioprocesses. This mini-review aims to compare two expression hosts, emphasizing their specific advantages in industrial surroundings such are chemical, detergent, textile, food, animal feed, leather, and paper industries. The homologous sources, heterologous hosts, and molecular tools used for the production of recombinant proteins in these hosts are discussed. The potential to use both hosts as biocatalysts is also evaluated. Undoubtedly, Bacillus and Streptomyces spp. as production hosts possess the potential to take on a more substantial role, providing superior (bio-based) process robustness and flexibility. KEY POINTS: • Bacillus and Streptomyces spp. as robust hosts for enzyme production. • Industrially relevant enzyme groups for production in alternative hosts highlighted. • Molecular biology techniques are enabling easier utilization of both hosts.
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Affiliation(s)
- Sandra Vojnovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia.
| | - Ivana Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia
| | - Tatjana Ilic-Tomic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia
| | - Jasmina Nikodinovic-Runic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia.
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Su B, Gao C, Ji J, Zhang H, Zhang Y, Mouazen AM, Shao S, Jiao H, Yi S, Li S. Soil bacterial succession with different land uses along a millennial chronosequence derived from the Yangtze River flood plain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168531. [PMID: 37963526 DOI: 10.1016/j.scitotenv.2023.168531] [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: 07/17/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/16/2023]
Abstract
Wetlands reclamation has been a traditional and effective practice for obtaining new land to alleviate the pressure induced by population growth. However, the evolution of soil-dwelling microorganisms along with reclamation and the potential influence of land-use patterns on them remain unclear. In this study, a soil chronosequence derived from Yangtze River sediments was established, comprising of circa 0, 60, 160, 280, 2000, and 3000 years, to examine the succession of soil bacterial communities across different land uses. Our analysis revealed obvious development in soil properties and orderly bacterial succession along reclamation gradients. Over time, reclaimed land suffered from varying degrees of abundance loss and biodiversity simplification, with dryland being the most sensitive to reclamation duration changes, whereas woodland and paddies showed slight reductions. Bacterial communities tended to shift from oligotrophs (K-strategist) to copiotrophs (r-strategist) at the phylum level as reclamation proceeded for all land use types. The relative abundance of certain bacterial functional groups associated with the carbon (C) and nitrogen (N) cycles were significantly increased, including those involved in Aerobic chemoheterotrophy, Chitinolysis, Nitrate reduction, Nitrate respiration, and Ureolysis, while other groups, such as those related to Fermentation, Methylotrophy, Nitrification, and Hydrocarbon degradation, exhibited decreased expression. Notably, prolonged reclamation can also trigger ecological issues in soil, including a continuous increase of predatory/exoparasitic bacteria in dryland and woodland, as well as a significant increase in pathogenic bacteria during the later stages in paddy fields. Overall, our study identified the impact of long-term reclamation on soil bacterial communities and functional groups, providing insight into the development of land-use-oriented ecological protection strategies.
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Affiliation(s)
- Baowei Su
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Chao Gao
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Jiachen Ji
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Huan Zhang
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - Yalu Zhang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Abdul M Mouazen
- Precision Soil and Crop Engineering Group (Precision SCoRing), Department of Environment, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Blok B, 1st Floor, 9000 Gent, Belgium
| | - Shuangshuang Shao
- School of resource and environment, Henan University of Engineering, Zhengzhou 451191, Henan, China
| | - He Jiao
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Shuangwen Yi
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Shengfeng Li
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
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Rajendran K, Krishnamoorthy M, Karuppiah K, Ethiraj K, Sekar S. Chitinase from Streptomyces mutabilis as an Effective Eco-friendly Biocontrol Agent. Appl Biochem Biotechnol 2024; 196:18-31. [PMID: 37097402 DOI: 10.1007/s12010-023-04489-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/26/2023]
Abstract
Blood sucking parasites not only cause economic loss but also transmit numerous diseases. Dermanyssus gallinae, an obligatory blood feeding ectoparasite causes huge production loss to the poultry industry. Mosquitoes act as vector for transmitting several viral and parasitic diseases in humans. Acaricide resistance limits the control of these parasites. The present study was aimed to control the parasites using chitinase that have selective degradation of chitin, an important component in exoskeleton development. Chitinase was induced in Streptomyces mutabilis IMA8 with chitin extracted from Charybdis smithii. The enzyme showed more than 50% activity at 30-50 °C and the optimum activity at 45 °C. The enzyme activity of chitinase was highest at pH 7.0. The kinetic parameters Km and Vmax values of chitinase were determined by non-linear regression using Michaelis-Menten equation and its derivative Hanes-Wolf plot. The larvicidal effect of different concentrations of chitinase was evaluated against all instar larvae (I-IV) and pupae of An. stephensi and Ae. aegypti after 24 h of exposure. The percentage of mortality was directly proportional to the chitinase concentration. Bioassay for miticidal activity showed that chitinase had excellent miticidal activity (LC50 = 24.2 ppm) against D. gallinae. The present study suggested the usage of Streptomyces mutabilis for preparation of chitinase in mosquito and mite control.
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Affiliation(s)
- Kumar Rajendran
- Aquatic Microbiology Lab, Department of Animal Health and Management, Alagappa University, Karaikudi, 630003, Tamil Nadu, India.
- Department of Fisheries Science, Alagappa University, Karaikudi, 630003, Tamil Nadu, India.
| | - Madhuri Krishnamoorthy
- Aquatic Microbiology Lab, Department of Animal Health and Management, Alagappa University, Karaikudi, 630003, Tamil Nadu, India
| | - Kannan Karuppiah
- Department of Zoology, Kongunadu Arts and Science College, Coimbatore, 641029, Tamil Nadu, India
| | - Kannapiran Ethiraj
- Aquatic Microbiology Lab, Department of Animal Health and Management, Alagappa University, Karaikudi, 630003, Tamil Nadu, India.
- Department of Fisheries Science, Alagappa University, Karaikudi, 630003, Tamil Nadu, India.
| | - Sivaranjani Sekar
- Aquatic Microbiology Lab, Department of Animal Health and Management, Alagappa University, Karaikudi, 630003, Tamil Nadu, India
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10
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D'Andrea R, Khattar G, Koffel T, Frans VF, Bittleston LS, Cuellar-Gempeler C. Reciprocal inhibition and competitive hierarchy cause negative biodiversity-ecosystem function relationships. Ecol Lett 2024; 27:e14356. [PMID: 38193391 DOI: 10.1111/ele.14356] [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: 09/13/2023] [Revised: 11/02/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
The relationship between biodiversity and ecosystem function (BEF) captivates ecologists, but the factors responsible for the direction of this relationship remain unclear. While higher ecosystem functioning at higher biodiversity levels ('positive BEF') is not universal in nature, negative BEF relationships seem puzzlingly rare. Here, we develop a dynamical consumer-resource model inspired by microbial decomposer communities in pitcher plant leaves to investigate BEF. We manipulate microbial diversity via controlled colonization and measure their function as total ammonia production. We test how niche partitioning among bacteria and other ecological processes influence BEF in the leaves. We find that a negative BEF can emerge from reciprocal interspecific inhibition in ammonia production causing a negative complementarity effect, or from competitive hierarchies causing a negative selection effect. Absent these factors, a positive BEF was the typical outcome. Our findings provide a potential explanation for the rarity of negative BEF in empirical data.
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Affiliation(s)
- Rafael D'Andrea
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Gabriel Khattar
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Thomas Koffel
- Laboratoire de Biométrie et Biologie Evolutive UMR5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Veronica F Frans
- Department of Fisheries and Wildlife, Center for Systems Integration and Sustainability, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
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11
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Moran CL, Debowski A, Vrielink A, Stubbs K, Sarkar-Tyson M. N-acetyl-β-hexosaminidase activity is important for chitooligosaccharide metabolism and biofilm formation in Burkholderia pseudomallei. Environ Microbiol 2024; 26:e16571. [PMID: 38178319 DOI: 10.1111/1462-2920.16571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Burkholderia pseudomallei is a saprophytic Gram-negative bacillus that can cause the disease melioidosis. Although B. pseudomallei is a recognised member of terrestrial soil microbiomes, little is known about its contribution to the saprophytic degradation of polysaccharides within its niche. For example, while chitin is predicted to be abundant within terrestrial soils the chitinolytic capacity of B. pseudomallei is yet to be defined. This study identifies and characterises a putative glycoside hydrolase, bpsl0500, which is expressed by B. pseudomallei K96243. Recombinant BPSL0500 was found to exhibit activity against substrate analogues and GlcNAc disaccharides relevant to chitinolytic N-acetyl-β-d-hexosaminidases. In B. pseudomallei, bpsl0500 was found to be essential for both N-acetyl-β-d-hexosaminidase activity and chitooligosaccharide metabolism. Furthermore, bpsl0500 was also observed to significantly affect biofilm deposition. These observations led to the identification of BPSL0500 activity against model disaccharide linkages that are present in biofilm exopolysaccharides, a feature that has not yet been described for chitinolytic enzymes. The results in this study indicate that chitinolytic N-acetyl-β-d-hexosaminidases like bpsl0500 may facilitate biofilm disruption as well as chitin assimilation, providing dual functionality for saprophytic bacteria such as B. pseudomallei within the competitive soil microbiome.
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Affiliation(s)
- Clare L Moran
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Aleksandra Debowski
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
| | - Keith Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, University of Western Australia, Crawley, Australia
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
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12
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Rebollar EA. Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent. Microb Genom 2024; 10:001181. [PMID: 38240649 PMCID: PMC10868611 DOI: 10.1099/mgen.0.001181] [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: 09/13/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.
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Affiliation(s)
| | - Víctor Ávila-Akerberg
- Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | | | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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13
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Hegazy GE, Olama ZA, Abou-Elela GM, Ramadan HS, Ibrahim WM, El Badan DES. Biodiversity and biological applications of marine actinomycetes-Abu-Qir Bay, Mediterranean Sea, Egypt. J Genet Eng Biotechnol 2023; 21:150. [PMID: 38015326 PMCID: PMC10684441 DOI: 10.1186/s43141-023-00612-8] [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: 05/18/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND The ability of actinomycetes to produce bioactive secondary metabolites makes them one of the most important prokaryotes. Marine actinomycetes are one of the most important secondary metabolites producers used for pharmaceuticals and other different industries. RESULTS In this study, the promising actinomycetes were isolated from Abu-Qir Bay. Four different media named as starch nitrate, starch casein, glycerol asparagine, and glycerol glycine were used as a preliminary experimental media to study the role of the medium components on the counts of actinomycetes in sediment samples. The results indicated that starch casein medium reported the highest counts (30-63 CFU/g) in all the tested sites. Lower counts were detected on starch nitrate and glycerol asparagine. On the other hand, glycerol glycine medium gave the lowest counts (15-48 CFU/g). Abu-Qir8 harbored the highest average count of actinomycetes (63 CFU/g), followed by Abu-Qir1 (48 CFU/g). The lower counts were detected in Abu-Qir5 and Abu-Qir7 (26 and 29 CFU/g, respectively). A total of 12 pure obtained actinomycetes isolates were subjected to morphological, physiological, and biochemical characterization. The selected actinobacterial isolates were subjected to numerical analysis, and the majority of isolates were grouped into four main clusters (A, B, C, & D), and each of them harbored two isolates; additionally, four isolates did not cluster at this similarity level. Isolate W4 was carefully chosen as the most promising pigment and antimicrobial agent's producer; the produced pigment was extracted and optimized by statistical experiments (PBD & BBD) and was tested for its anti-inflammatory activity. The results showed anti-inflammatory effect and prevented the denaturation of BSA protein at a concentration much higher than the safe dose and increased with increasing the pigment concentration. CONCLUSION Marine actinomycetes play a vital role in the production of novel and important economic metabolites that have many industrial and pharmaceuticals applications. Streptomyces genera are the most important actinomycetes that produce important metabolites as previously reported.
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Affiliation(s)
- Ghada E Hegazy
- National Institute of Oceanography and Fisheries (NIOF), Qaitbay Sq, El-Anfousy, Alexandria, 11865, Egypt.
| | - Zakia A Olama
- Botany & Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - G M Abou-Elela
- National Institute of Oceanography and Fisheries (NIOF), Qaitbay Sq, El-Anfousy, Alexandria, 11865, Egypt
| | - Heba S Ramadan
- Botany & Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Walaa M Ibrahim
- Botany & Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Dalia El S El Badan
- Botany & Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, Lebanon
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14
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Rui J, Zhao Y, Cong N, Wang F, Li C, Liu X, Hu J, Ling N, Jing X. Elevational distribution and seasonal dynamics of alpine soil prokaryotic communities. Front Microbiol 2023; 14:1280011. [PMID: 37808282 PMCID: PMC10557256 DOI: 10.3389/fmicb.2023.1280011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
The alpine grassland ecosystem is a biodiversity hotspot of plants on the Qinghai-Tibetan Plateau, where rapid climate change is altering the patterns of plant biodiversity along elevational and seasonal gradients of environments. However, how belowground microbial biodiversity changes along elevational gradient during the growing season is not well understood yet. Here, we investigated the elevational distribution of soil prokaryotic communities by using 16S rRNA amplicon sequencing along an elevational gradient between 3,200 and 4,200 m, and a seasonal gradient between June and September in the Qinghai-Tibetan alpine grasslands. First, we found soil prokaryotic diversity and community composition significantly shifted along the elevational gradient, mainly driven by soil temperature and moisture. Species richness did not show consistent elevational trends, while those of evenness declined with elevation. Copiotrophs and symbiotic diazotrophs declined with elevation, while oligotrophs and AOB increased, affected by temperature. Anaerobic or facultatively anaerobic bacteria and AOA were hump-shaped, mainly influenced by moisture. Second, seasonal patterns of community composition were mainly driven by aboveground biomass, precipitation, and soil temperature. The seasonal dynamics of community composition indicated that soil prokaryotic community, particularly Actinobacteria, was sensitive to short-term climate change, such as the monthly precipitation variation. At last, dispersal limitation consistently dominated the assembly process of soil prokaryotic communities along both elevational and seasonal gradients, especially for those of rare species, while the deterministic process of abundant species was relatively higher at drier sites and in drier July. The balance between deterministic and stochastic processes in abundant subcommunities might be strongly influenced by water conditions (precipitation/moisture). Our findings suggest that both elevation and season can alter the patterns of soil prokaryotic biodiversity in alpine grassland ecosystem of Qinghai-Tibetan Plateau, which is a biodiversity hotspot and is experiencing rapid climate change. This work provides new insights into the response of soil prokaryotic communities to changes in elevation and season, and helps us understand the temporal and spatial variations in such climate change-sensitive regions.
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Affiliation(s)
- Junpeng Rui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuwei Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Nan Cong
- Lhasa Plateau Ecosystem Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Fuxin Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Chao Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jingjing Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ning Ling
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xin Jing
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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15
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Such N, Schermann K, Pál L, Menyhárt L, Farkas V, Csitári G, Kiss B, Tewelde KG, Dublecz K. The Hatching Time of Broiler Chickens Modifies Not Only the Production Traits but Also the Early Bacteriota Development of the Ceca. Animals (Basel) 2023; 13:2712. [PMID: 37684976 PMCID: PMC10487082 DOI: 10.3390/ani13172712] [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: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
This trial was carried out to find out the effects of the parent flock and hatching time of broiler chickens on the production traits and bacteriota development of animals. Two sets of 730 hatching eggs were collected from two different parent flocks with ages of 25 and 50 weeks. In the hatchery, both groups were divided into two subgroups: those hatched during the first 10 and the subsequent 10 h of the hatching window. A feeding trial was carried out afterwards, using the four treatments in six replicate floor pens and feeding commercial starter, grower, and finisher diets that contained all the nutrients according to the breeder's recommendations. The day-old chickens of the older parent flock and those hatched later were heavier, and this advantage remained until the end of the production period. The different ages and origins of the parent flocks failed to modify the microbiological parameters of the chicken's ceca; however, the hatching time significantly influenced the different bacteriota diversity indices: the late-hatched chickens showed higher Bacteroidetes and lower Firmicutes and Actinobacteria abundances at day 11. These treatments resulted in differences in the main families, Ruminococcaceae, Lactobacillaceae, and Bacteroidaceae. These differences could not be found at day 39.
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Affiliation(s)
- Nikoletta Such
- Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Deák Ferenc Street 16, 8360 Keszthely, Hungary; (N.S.); (K.S.); (L.P.); (V.F.); (G.C.); (B.K.); (K.G.T.)
| | - Kornél Schermann
- Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Deák Ferenc Street 16, 8360 Keszthely, Hungary; (N.S.); (K.S.); (L.P.); (V.F.); (G.C.); (B.K.); (K.G.T.)
| | - László Pál
- Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Deák Ferenc Street 16, 8360 Keszthely, Hungary; (N.S.); (K.S.); (L.P.); (V.F.); (G.C.); (B.K.); (K.G.T.)
| | - László Menyhárt
- Institute of Technology, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Deák Ferenc Street 16, 8360 Keszthely, Hungary;
| | - Valéria Farkas
- Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Deák Ferenc Street 16, 8360 Keszthely, Hungary; (N.S.); (K.S.); (L.P.); (V.F.); (G.C.); (B.K.); (K.G.T.)
| | - Gábor Csitári
- Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Deák Ferenc Street 16, 8360 Keszthely, Hungary; (N.S.); (K.S.); (L.P.); (V.F.); (G.C.); (B.K.); (K.G.T.)
| | - Brigitta Kiss
- Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Deák Ferenc Street 16, 8360 Keszthely, Hungary; (N.S.); (K.S.); (L.P.); (V.F.); (G.C.); (B.K.); (K.G.T.)
| | - Kesete Goitom Tewelde
- Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Deák Ferenc Street 16, 8360 Keszthely, Hungary; (N.S.); (K.S.); (L.P.); (V.F.); (G.C.); (B.K.); (K.G.T.)
| | - Károly Dublecz
- Institute of Physiology and Nutrition, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Deák Ferenc Street 16, 8360 Keszthely, Hungary; (N.S.); (K.S.); (L.P.); (V.F.); (G.C.); (B.K.); (K.G.T.)
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16
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Lu X, Jiao H, Shi Y, Li Y, Zhang H, Fu Y, Guo J, Wang Q, Liu X, Zhou M, Ullah MW, Sun J, Liu J. Fabrication of bio-inspired anisotropic structures from biopolymers for biomedical applications: A review. Carbohydr Polym 2023; 308:120669. [PMID: 36813347 DOI: 10.1016/j.carbpol.2023.120669] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
The anisotropic features play indispensable roles in regulating various life activities in different organisms. Increasing efforts have been made to learn and mimic various tissues' intrinsic anisotropic structure or functionality for broad applications in different areas, especially in biomedicine and pharmacy. This paper discusses the strategies for fabricating biomaterials using biopolymers for biomedical applications with the case study analysis. Biopolymers, including different polysaccharides, proteins, and their derivates, that have been confirmed with sound biocompatibility for different biomedical applications are summarized, with a special focus on nanocellulose. Advanced analytical techniques for understanding and characterizing the biopolymer-based anisotropic structures for various biomedical applications are also summarized. Challenges still exist in precisely constructing biopolymers-based biomaterials with anisotropic structures from molecular to macroscopic levels and fitting the dynamic processes in native tissue. It is foreseeable that with the advancement of biopolymers' molecular functionalization, biopolymer building block orientation manipulation strategies, and structural characterization techniques, developing anisotropic biopolymer-based biomaterials for different biomedical applications would significantly contribute to a friendly disease-curing and healthcare experience.
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Affiliation(s)
- Xuechu Lu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Haixin Jiao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Yifei Shi
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Yan Li
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Hongxing Zhang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Yinyi Fu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Jiaqi Guo
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Qianqian Wang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Xiang Liu
- Institute of Medicine & Chemical Engineering, Zhenjiang College, Zhenjiang 212028, China
| | - Mengbo Zhou
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Jun Liu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China; Key Laboratory of Pulp and Paper Science & Technology of Ministry of Education, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
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17
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Niu L, Zhao S, Chen Y, Li Y, Zou G, Tao Y, Zhang W, Wang L, Zhang H. Diversity and potential functional characteristics of phage communities colonizing microplastic biofilms. ENVIRONMENTAL RESEARCH 2023; 219:115103. [PMID: 36549484 DOI: 10.1016/j.envres.2022.115103] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/29/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
The multiple ecological influences and potential microbial degradation of microplastics are generally attributed to the microbial communities colonized on microplastics. Phages play an important role in the composition and function of their bacterial hosts, yet the occurrence and the potential functional characteristics of phages in the biofilms of microplastics have not been known. This study, for the first time, explored the diversity, composition, and potential function characteristics of phage communities living in the biofilms of PP, PE, and PET microplastics and stones, cultured in the same site, via the metagenome method. The results showed that a total of 240 non-redundant virus OTUs (vOTUs), distributed in at least four orders and seven families, were detected from biofilm metagenomes of microplastics. Compared to stones, some phages were selectively enriched by microplastic biofilms, with 13 vOTUs uniquely colonized on three microplastics, and these vOTUs mainly belong to the family Autographiviridae and Podoviridae. Except for the evenness of PP, the richness index, Chao 1 index, and abundance of phage communities of three microplastics were much higher than that of stone. At least 8 bacterial phyla and 72 genera were possibly infected by phages. Compared to the stones, both composition and abundance of the phages and hosts presented significant and strong correlations for three microplastics. Some of the bacterial hosts on microplastics were likely involved in the microplastic degradation, fermenters, nitrogen transformation processes, and so on. A total of 124 encoding auxiliary metabolic genes (AMGs) were detected from viral contigs. The abundance of AMGs in microplastics was much higher than that of stones, which may provide more direct or indirect support for the bacterial degradation of microplastics. This study provides a new perspective on the occurrence and potential functions of phages on microplastic biofilms, thus expanding our understanding of microbial communities on microplastic biofilms.
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Affiliation(s)
- Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Shiqin Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yamei Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Guanhua Zou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Ye Tao
- Shanghai BIOZERON Biotechnology Co., Ltd, Shanghai, 201800, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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18
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Thakur D, Chauhan A, Jhilta P, Kaushal R, Dipta B. Microbial chitinases and their relevance in various industries. Folia Microbiol (Praha) 2023; 68:29-53. [PMID: 35972681 DOI: 10.1007/s12223-022-00999-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/31/2022] [Indexed: 01/09/2023]
Abstract
Chitin, the second most abundant biopolymer on earth after cellulose, is composed of β-1,4-N-acetylglucosamine (GlcNAc) units. It is widely distributed in nature, especially as a structural polysaccharide in the cell walls of fungi, the exoskeletons of crustaceans, insects, and nematodes. However, the principal commercial source of chitin is the shells of marine or freshwater invertebrates. Microbial chitinases are largely responsible for chitin breakdown in nature, and they play an important role in the ecosystem's carbon and nitrogen balance. Several microbial chitinases have been characterized and are gaining prominence for their applications in various sectors. The current review focuses on chitinases of microbial origin, their diversity, and their characteristics. The applications of chitinases in several industries such as agriculture, food, the environment, and pharmaceutical sectors are also highlighted.
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Affiliation(s)
- Deepali Thakur
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Anjali Chauhan
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Prakriti Jhilta
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Rajesh Kaushal
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Bhawna Dipta
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India.
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19
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Chen L, Hua Y, Ji W, Wang J, Zhao H, Wang Z. Cloning, characterization, and expression analysis of the CHITINASE gene family in Helice tientsinensis. PeerJ 2023; 11:e15045. [PMID: 36935907 PMCID: PMC10022498 DOI: 10.7717/peerj.15045] [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: 12/11/2022] [Accepted: 02/21/2023] [Indexed: 03/15/2023] Open
Abstract
Chitinase is a kind of glycoside hydrolase which is widely distributed in nature and encoded by multiple genes to catalyze the decomposition of chitin, which plays an important role in the molting and pathogen defense of crustaceans. However, the research on chitinase in crustaceans is mainly focused on a few species with economic value. In this study, full-length cDNA sequences of the HtCHT1, HtCHT3 and HtCHT4 genes were cloned from the mudflat crab Helice tientsinensis by RACE, and the sequences were analyzed. The results showed that the full-length 2,229 bp of HtCHT1 gene encoded 627 amino acids, while the full-length 2,191 bp of HtCHT3 gene produced 489 amino acids, and the full-length 3,312 bp of HtCHT4 gene encoded 664 amino acids. Bioinformatics analysis showed that all the obtained chitinase proteins had the glycosyl hydrolase family 18 (GH18) catalytic domain and chitin-binding domain (ChtBD2), furthermore, HtCHT1 and HtCHT4 proteins had signal peptide domains at N-terminal. Phylogenetic analysis showed that different types of chitinase were clustered, and HtCHTs were closely related to chitinases in the Eriocheir sinensis. Expression profile analysis showed that the HtCHT1, HtCHT3 and HtCHT4 were significantly expressed in hepatopancreas. Furthermore, the expression of three genes was significantly up-regulated in hepatopancreas after the Vibrio parahaemolyticus challenge. These results suggested that HtCHT1, HtCHT3 and HtCHT4 were belonged to the CHITINASE gene family in H. tientsinensis and were potentially involved in the antibacterial immune response. This study provides essential information for further research of chitinase in H. tientsinensis and even crustaceans.
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Affiliation(s)
- Lulu Chen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Yuyan Hua
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Wenxuan Ji
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Jiayu Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Hua Zhao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, Jiangsu, China
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20
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Sherwell S, Kalra I, Li W, McKnight DM, Priscu JC, Morgan-Kiss RM. Antarctic lake phytoplankton and bacteria from near-surface waters exhibit high sensitivity to climate-driven disturbance. Environ Microbiol 2022; 24:6017-6032. [PMID: 35860854 PMCID: PMC10084183 DOI: 10.1111/1462-2920.16113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 01/12/2023]
Abstract
The McMurdo Dry Valleys (MDVs), Antarctica, represent a cold, desert ecosystem poised on the threshold of melting and freezing water. The MDVs have experienced dramatic signs of climatic change, most notably a warm austral summer in 2001-2002 that caused widespread flooding, partial ice cover loss and lake level rise. To understand the impact of these climatic disturbances on lake microbial communities, we simulated lake level rise and ice-cover loss by transplanting dialysis-bagged communities from selected depths to other locations in the water column or to an open water perimeter moat. Bacteria and eukaryote communities residing in the surface waters (5 m) exhibited shifts in community composition when exposed to either disturbance, while microbial communities from below the surface were largely unaffected by the transplant. We also observed an accumulation of labile dissolved organic carbon in the transplanted surface communities. In addition, there were taxa-specific sensitivities: cryptophytes and Actinobacteria were highly sensitive particularly to the moat transplant, while chlorophytes and several bacterial taxa increased in relative abundance or were unaffected. Our results reveal that future climate-driven disturbances will likely undermine the stability and productivity of MDV lake phytoplankton and bacterial communities in the surface waters of this extreme environment.
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Affiliation(s)
| | - Isha Kalra
- Department of Microbiology, Miami University, Oxford, Ohio, USA
| | - Wei Li
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Diane M McKnight
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
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21
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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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22
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Su H, Sun J, Jia Z, Zhao H, Mao X. Insights into promiscuous chitosanases: the known and the unknown. Appl Microbiol Biotechnol 2022; 106:6887-6898. [PMID: 36178516 DOI: 10.1007/s00253-022-12198-1] [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: 05/18/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022]
Abstract
Chitosanase, a glycoside hydrolase (GH), catalyzes the cleavage of β-1,4-glycosidic bonds in polysaccharides and is widely distributed in nature. Many organisms produce chitosanases, and numerous chitosanases in the GH families have been intensely studied. The reported chitosanases mainly cleaved the inter-glucosamine glycosidic bonds, while substrate specificity is not strictly unique due to the existence of bifunctional or multifunctional activity profiles. The promiscuity of chitosanases is essential for the different pathways of biomass polysaccharide conversion and understanding of the chitosanase evolutionary process. However, the reviews for this aspect are completely unknown. This review provides an overview of the promiscuous activities, also considering the substrate and product specificity of chitosanases observed to date. These contribute to important implications for the future discovery and research of promiscuous chitosanases and applications related to biomass conversion. KEY POINTS: • The promiscuity of chitosanases is reviewed for the first time. • The current review provides insights into the substrate specificity of chitosanases. • The mode-product relationship and prospect of promiscuous chitosanases are highlighted.
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Affiliation(s)
- Haipeng Su
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Zhenrong Jia
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Hongjun Zhao
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China. .,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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23
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dos Santos JDN, João SA, Martín J, Vicente F, Reyes F, Lage OM. iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments. Microorganisms 2022; 10:1471. [PMID: 35889190 PMCID: PMC9319460 DOI: 10.3390/microorganisms10071471] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from Memoria beach, Portugal. The isolates obtained were identified by 16S rRNA gene analysis, fingerprinted using BOX-PCR and ERIC-PCR, searched for the putative presence of secondary metabolism genes associated with polyketide synthase I (PKS-I) and non-ribosomal peptide synthetases (NRPS), screened for antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, and had bioactive extracts dereplicated by LC/HRMS. Of the 158 isolated strains, 96 were affiliated with the phylum Actinomycetota, PKS-I and NRPS genes were detected in 53 actinomycetotal strains, and 11 proved to be bioactive (10 against E. coli, 1 against S. aureus and 1 against both pathogens). Further bioactivities were explored using an "one strain many compounds" approach, with six strains showing continued bioactivity and one showing a novel one. Extract dereplication showed the presence of several known bioactive molecules and potential novel ones in the bioactive extracts. These results indicate the use of the bacteria isolated here as sources of new bioactive natural products.
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Affiliation(s)
- José Diogo Neves dos Santos
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal; (S.A.J.); (O.M.L.)
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Susana Afonso João
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal; (S.A.J.); (O.M.L.)
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain; (J.M.); (F.V.); (F.R.)
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain; (J.M.); (F.V.); (F.R.)
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain; (J.M.); (F.V.); (F.R.)
| | - Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal; (S.A.J.); (O.M.L.)
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
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24
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Kim J, Lee B, Chhetri G, Kim I, So Y, Jang W, Seo T. Identification of Mucilaginibacter conchicola sp. nov., Mucilaginibacter achroorhodeus sp. nov. and Mucilaginibacter pallidiroseus sp. nov. and emended description of the genus Mucilaginibacter. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005431] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three chitinolytic, Gram-negative, light pink, capsule-forming, rod-shaped bacterial strains with gliding motion (MYSH2T, MJ1aT and dk17T) were isolated from seashells, soil and foxtail, respectively. Phylogenetic analysis of the 16S rRNA gene sequences and concatenated alignment of 92 core genes indicated that strains MYSH2T, MJ1aT and dk17T were novel species of the genus
Mucilaginibacter
and exhibited a high 16S rRNA sequence similarity (i.e. more than 97.2 %) among each other. These novel strains contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6), iso-C15:0 and MK-7 as the predominant fatty acids and menaquinone. According to the CAZys coding gene of KAAS, MYSH2T and MJ1aT were interpreted as strains containing both GH18 and 19 family coding genes, except for dk17T, which shows only GH19 family genes. These strains likely degrade chitin to chitobiose or directly to N-acetyl-d-glucosamine, which may enhance their chitinolytic capacity, thus making these stains potentially useful for industrial chitin degradation. Based on distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains MYSH2T, MJ1aT and dk17T represent three novel species in the genus
Mucilaginibacter
, for which the names Mucilaginibacter conchicola sp. nov. (=KACC 19716T=JCM 32787T), Mucilaginibacter achroorhodeus sp. nov. (=KACC 19906T=NBRC 113667T) and Mucilaginibacter pallidiroseus sp. nov. (=KACC 19907T=NBRC 113666T) are proposed. An emended description of the genus
Mucilaginibacter
is proposed.
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Affiliation(s)
- Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Byungjo Lee
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Wonhee Jang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
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25
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Duhsaki L, Mukherjee S, Rani TS, Madhuprakash J. Genome analysis of Streptomyces sp. UH6 revealed the presence of potential chitinolytic machinery crucial for chitosan production. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:431-442. [PMID: 34192819 DOI: 10.1111/1758-2229.12986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Chitosan and its derivatives have numerous applications in wastewater treatment as bio-coagulants, flocculants and bio-adsorbents against both particulate and dissolved pollutants. Chitinolytic bacteria secrete an array of enzymes, which play crucial role in chitin to chitosan conversion. Consequently, there is a growing demand for identification and characterization of novel bacterial isolates with potential implications in chitosan production. We describe genomic features of the new isolate Streptomyces sp. UH6. Analysis of the 6.51 Mb genome revealed the GC content as 71.95% and presence of 6990 coding sequences of which 63% were functionally annotated. Further, we identified two possible chitin-utilization pathways, which employ secreted enzymes like lytic polysaccharide monooxygenases and family-18 glycoside hydrolases (GHs). More importantly, the genome has six family-4 polysaccharide deacetylases with probable role in chitin to chitosan conversion, as well as two chitosanases belonging to GH46 and GH75 families. In addition, the gene clusters, dasABC and ngcEFG coding for transporters, which mediate the uptake of N,N'-diacetylchitobiose and N-acetyl-d-glucosamine were identified. Several genes responsible for hydrolysis of other polysaccharides and fermentation of sugars were also identified. Taken together, the phylogenetic and genomic analyses suggest that the isolate Streptomyces sp. UH6 secretes potential chitin-active enzymes responsible for chitin to chitosan conversion.
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Affiliation(s)
- Lal Duhsaki
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
| | - Saumashish Mukherjee
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
| | | | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
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26
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Shen Y, Jiang Z, Zhong X, Wang H, Liu Y, Li X. Manipulation of cadmium and diethylhexyl phthalate on Rana chensinensis tadpoles affects the intestinal microbiota and fatty acid metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153455. [PMID: 35093358 DOI: 10.1016/j.scitotenv.2022.153455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Gastrointestinal tract and intestine microbiota can both have deep effects on the lipid metabolism and immune function of amphibians. Additionally, the composition and structure of the microbial community are influenced by environmental pollutions. It is noteworthy that environmental compounds such as Cd and DEHP are pervasive in the aquatic environment and do not exist in isolation, and single exposure experiments cannot well explain the effects of unpredictable interactions between co-existing compounds on amphibians. In this study, we calculated the parameters of morphological and histological indices of Rana chensinensis tadpoles after treated with Cd and/or DEHP. The 16S rRNA gene sequencing technology was used to assess the relative abundance of intestinal microbial community among tadpoles from each treatment groups. We also examined the mRNA expression levels of lipid digestion and absorption and SCFAs related-genes. Our results indicated that all morphological and histological indices were significantly declined in the Cd treatment group, while the mixed treatment group was similar to the control group. Compared with the control group, the relative abundances of Firmicutes, Proteobacteria and Verrucomicrobia exhibited distinctive differences in Cd and/or DEHP treatment groups. Further, RT-qPCR results revealed that the expression levels of lipid metabolism and SCFAs related-genes were also significantly altered among the treatment groups. Taken together, the present study highlighted a new evidence that the alterations in intestinal microbial community and mRNA expression levels of larval amphibians after exposure to Cd and/or DEHP may impair lipid storage and transport, as well as reduce anti-inflammatory capacity, which may ultimately lead to a decline in amphibian populations.
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Affiliation(s)
- Yujia Shen
- College of Life Science, Shaanxi Normal University, Xi'an 710119, China
| | - Zhaoyang Jiang
- College of Life Science, Shaanxi Normal University, Xi'an 710119, China
| | - Xinyi Zhong
- College of Life Science, Shaanxi Normal University, Xi'an 710119, China
| | - Hemei Wang
- College of Life Science, Shaanxi Normal University, Xi'an 710119, China
| | - Yutian Liu
- College of Life Science, Shaanxi Normal University, Xi'an 710119, China
| | - Xinyi Li
- College of Life Science, Shaanxi Normal University, Xi'an 710119, China.
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27
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Rangel F, Enes P, Gasco L, Gai F, Hausmann B, Berry D, Oliva-Teles A, Serra CR, Pereira FC. Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals. Front Microbiol 2022; 13:831034. [PMID: 35495644 PMCID: PMC9041418 DOI: 10.3389/fmicb.2022.831034] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/22/2022] [Indexed: 01/04/2023] Open
Abstract
The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (Dicentrarchus labrax). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (Hermetia illucens, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families Bacillaceae, Enterococcaceae, and Lachnospiraceae and the Actinobacteria family Actinomycetaceae, which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in Paenibacillus and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (Tenebrio molitor, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from Paenibacillus species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.
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Affiliation(s)
- Fábio Rangel
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIMAR/CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Paula Enes
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIMAR/CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Laura Gasco
- Department of Agricultural, Forest and Food Sciences, University of Turin, Torino, Italy
| | - Francesco Gai
- Institute of Science of Food Production, National Research Council, Torino, Italy
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - David Berry
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Aires Oliva-Teles
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIMAR/CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Claudia R. Serra
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- CIMAR/CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Fátima C. Pereira
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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28
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Li BY, Xia ZY, Gou M, Sun ZY, Huang YL, Jiao SB, Dai WY, Tang YQ. Production of volatile fatty acid from fruit waste by anaerobic digestion at high organic loading rates: Performance and microbial community characteristics. BIORESOURCE TECHNOLOGY 2022; 346:126648. [PMID: 34974105 DOI: 10.1016/j.biortech.2021.126648] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/23/2021] [Accepted: 12/25/2021] [Indexed: 05/23/2023]
Abstract
This study examined the performance and microbial community dynamics of an anaerobic volatile fatty acid (VFA) production reactor for treating fruit waste by stepwise increasing organic loading rates (OLRs) from 8 to 24 g volatile total solids (VTS)/(L·d). Results showed that higher VFA concentrations of 52.25-61.90 g chemical oxygen demand (COD)/L can be maintained at each OLR, thereby resulting to a production of 0.70-0.76 g chemical oxygen demand (COD)VFA/g VTS. Notably, an increase in OLR from 8 to 14 g VTS/(L·d) was beneficial for achieving higher VFA concentrations and yields. Moreover, an increase in OLR affected the VFA distribution significantly; acetate and butyrate became dominant in the fermentation liquid at OLRs ≥ 14 g VTS/(L·d). Microbial community dynamics analysis revealed that phyla Firmicutes and Actinobacteriota were predominant at each OLR, and the genera Lactobacillus, Clostridium_sensu_stricto_12, and Caproiciproducens were closely related to anaerobic VFA production.
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Affiliation(s)
- Ben-Yan Li
- College of Architecture and Environment, Sichuan University, Chengdu 610065, Sichuan, China
| | - Zi-Yuan Xia
- College of Architecture and Environment, Sichuan University, Chengdu 610065, Sichuan, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, Chengdu 610065, Sichuan, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Yu-Lian Huang
- Chengdu Environment Group, Chengdu 610041, Sichuan, China
| | - Shuo-Bo Jiao
- Chengdu Environmental Innovation Technology Co. LTD, Chengdu 610065, Sichuan, China
| | - Wen-Ying Dai
- Chengdu Environmental Innovation Technology Co. LTD, Chengdu 610065, Sichuan, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, Sichuan, China
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Yu M, Meng T, He W, Huang H, Liu C, Fu X, He J, Yin Y, Xiao D. Dietary Chito-oligosaccharides Improve Intestinal Immunity via Regulating Microbiota and Th17/Treg Balance-Related Immune Signaling in Piglets Challenged by Enterotoxigenic E. coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15195-15207. [PMID: 34881888 DOI: 10.1021/acs.jafc.1c06029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This study was conducted to investigate how chito-oligosaccharides (COSs) affect the growth performance and immune stress response and to further explain their mechanisms. A total of 32 boars that were 28 days old and three-way weaned were randomly allotted to four equal groups [CON (basal diet) group, enterotoxigenic Escherichia coli (ETEC) group, COS group, and COS*ETEC group]. The results showed that COS partially reversed the negative changes in the average daily gain and average daily feed intake caused by the ETEC challenge and thereby alleviated the increase in the feed conversion ratio. Dietary COS increased the villus length as compared with the CON group and improved the ileal morphological structure. Additionally, it increased the bacterial diversity and Bacteroidetes abundance and lowered the Firmicutes abundance and Firmicutes-to-Bacteroidetes ratio at the phylum level. COS treatment lowered the abundance of Lactobacillus, Streptococcus, and Anarovovrio in the intestines of piglets, while it increased Muribaculaceae_unclassified and Prevotella at the genus level. COS had a significant inhibitory effect on the increase in the relative expression abundance of STAT3 mRNA caused by ETEC. The IL-10 and FOXP3 mRNAs were found to be significantly lower in the COS, ETEC, and COS*ETEC groups as compared to the CON group. These results demonstrate that COS could be beneficial for improving the growth performance and attenuating ETEC-challenged intestinal inflammation via regulating microbiota and Th17/Treg balance-related immune signaling pathways.
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Affiliation(s)
- Manrong Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Tiantian Meng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Wenxiang He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Hui Huang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Chunming Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xiaoqin Fu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central China, Ministry of Agriculture, Hunan Provincial Engineering Research Center of Healthy Livestock Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410128, China
| | - Dingfu Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
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Rodríguez-Fonseca MF, Sánchez-Suárez J, Valero MF, Ruiz-Balaguera S, Díaz LE. Streptomyces as Potential Synthetic Polymer Degraders: A Systematic Review. Bioengineering (Basel) 2021; 8:bioengineering8110154. [PMID: 34821720 PMCID: PMC8614672 DOI: 10.3390/bioengineering8110154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
The inherent resistance of synthetic plastics to degradation has led to an increasing challenge of waste accumulation problem and created a pollution issue that can only be addressed with novel complementary methods such as biodegradation. Since biocontrol is a promising eco-friendly option to address this challenge, the identification of suitable biological agents is a crucial requirement. Among the existing options, organisms of the Streptomyces genus have been reported to biodegrade several complex polymeric macromolecules such as chitin, lignin, and cellulose. Therefore, this systematic review aimed to evaluate the potential of Streptomyces strains for the biodegradation of synthetic plastics. The results showed that although Streptomyces strains are widely distributed in different ecosystems in nature, few studies have explored their capacity as degraders of synthetic polymers. Moreover, most of the research in this field has focused on Streptomyces strains with promising biotransforming potential against polyethylene-like polymers. Our findings suggest that this field of study is still in the early stages of development. Moreover, considering the diverse ecological niches associated with Streptomyces, these actinobacteria could serve as complementary agents for plastic waste management and thereby enhance carbon cycle dynamics.
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Affiliation(s)
- Maria Fernanda Rodríguez-Fonseca
- Master in Process Design and Management, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
| | - Jeysson Sánchez-Suárez
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
| | - Manuel Fernando Valero
- Energy, Materials and Environment Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
| | - Sonia Ruiz-Balaguera
- Conservation, Bioprospecting and Sustainable Development Group, Environmental Engineering Program, Universidad Nacional Abierta y a Distancia (UNAD), Bogotá 110911, Colombia;
| | - Luis Eduardo Díaz
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
- Correspondence: ; Tel.: +57-861-5555 (ext. 25208)
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31
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Plewniak F, Crognale S, Bruneel O, Sismeiro O, Coppée JY, Rossetti S, Bertin P. Metatranscriptomic outlook on green and brown food webs in acid mine drainage. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:606-615. [PMID: 33973709 DOI: 10.1111/1758-2229.12958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/15/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Acid mine drainages (AMDs), metal-rich acidic effluents generated by mining activities, are colonized by prokaryotic and eukaryotic microorganisms widely distributed among different phyla. We compared metatranscriptomic data from two sampling stations in the Carnoulès AMD and from a third station in the nearby Amous River, focussing on processes involved in primary production and litter decomposition. A synergistic relationship between the green and brown food webs was favoured in the AMD sediments by the low carbon content and the availability of mineral nutrients: primary production of organic matter would benefit C-limited decomposers whose activity of organic matter mineralization would in turn profit primary producers. This balance could be locally disturbed by heterogeneous factors such as an input of plant debris from the riparian vegetation, strongly boosting the growth of Tremellales which would then outcompete primary producers. In the unpolluted Amous River on the contrary, the competition for limited mineral nutrients was dominated by the green food web, fish and bacterivorous protists having a positive effect on phytoplankton. These results suggest that in addition to direct effects of low pH and metal contamination, trophic conditions like carbon or mineral nutrient limitations also have a strong impact on assembly and activities of AMDs' microbial communities.
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Affiliation(s)
- Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS - University of Strasbourg, Strasbourg, France
| | - Simona Crognale
- Istituto di Ricerca Sulle Acque, Consiglio Nazionale Delle Ricerche, Rome, Italy
| | - Odile Bruneel
- HydroSciences Montpellier, University of Montpellier - CNRS - IRD, Montpellier, France
| | - Odile Sismeiro
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
- Unité de Biologie des Bactéries Pathogènes à Gram Positif, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
- Biologie des ARN des Pathogènes Fongiques, Institut Pasteur, Paris, France
| | - Simona Rossetti
- Istituto di Ricerca Sulle Acque, Consiglio Nazionale Delle Ricerche, Rome, Italy
| | - Philippe Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS - University of Strasbourg, Strasbourg, France
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32
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Jabeen F, Younis T, Sidra S, Muneer B, Nasreen Z, Saleh F, Mumtaz S, Saeed RF, Abbas AS. Extraction of chitin from edible crab shells of Callinectes sapidus and comparison with market purchased chitin. BRAZ J BIOL 2021; 83:e246520. [PMID: 34468518 DOI: 10.1590/1519-6984.246520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/18/2021] [Indexed: 11/21/2022] Open
Abstract
Chitin and its derived products have immense economic value due to their vital role in various biological activities as well as biomedical and industrial application. Insects, microorganism and crustaceans are the main supply of chitin but the crustaceans shell like shrimp, krill, lobsters and crabs are the main commercial sources. Chitin content of an individual varies depending on the structures possessing the polymer and the species. In this study edible crabs' shells (Callinectes sapidus) were demineralized and deproteinized resulting in 13.8% (dry weight) chitin recovery from chitin wastes. FTIR and XRD analyses of the experimental crude as well as purified chitins revealed that both were much comparable to the commercially purchased controls. The acid pretreatment ceded 54g of colloidal chitin that resulted in 1080% of the crude chitin. The colloidal chitin was exploited for isolation of eighty five chitinolytic bacterial isolates from different sources. Zone of clearance was displayed by the thirty five isolates (41.17%) succeeding their growth at pH 7 on colloidal chitin agar medium. Maximum chitinolytic activity i.e. 301.55 U/ml was exhibited by isolate JF70 when cultivated in extracted chitin containing both carbon and nitrogen. The study showed wastes of blue crabs can be utilized for extraction of chitin and isolation of chitinolytic bacteria that can be used to degrade chitin waste, resolve environmental pollution as well as industrial purpose.
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Affiliation(s)
- F Jabeen
- University of Education, Department of Zoology, Lahore, Pakistan
| | - T Younis
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan
| | - S Sidra
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - B Muneer
- Government College University, Institute of Industrial Biotechnology, Lahore, Pakistan
| | - Z Nasreen
- University of Mianwali, Mianwali, Pakistan
| | - F Saleh
- Government College University Faisalabad, Department of Zoology, Punjab, Pakistan
| | - S Mumtaz
- National University Of Medical Sciences Rawalpindi, Department of biological sciences, Punjab, Pakistan
| | - R F Saeed
- National University Of Medical Sciences Rawalpindi, Department of biological sciences, Punjab, Pakistan
| | - A S Abbas
- University of Education, Department of Zoology, Lahore, Pakistan
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33
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Kumari K, Naskar M, Aftabuddin M, Das Sarkar S, Ghosh BD, Sarkar UK, Nag SK, Jana C, Das BK. Evaluation of Three Prokaryote Primers for Identification of Prokaryote Community Structure and Their Abode Preference in Three Distinct Wetland Ecosystems. Front Microbiol 2021; 12:643945. [PMID: 34335488 PMCID: PMC8317468 DOI: 10.3389/fmicb.2021.643945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/10/2021] [Indexed: 01/04/2023] Open
Abstract
The ultimate role of prokaryote (bacteria and archaea), the decomposer of the wetland ecosystem, depends on its community structure and its interaction with the environment. The present study has used three universal prokaryote primers to compare prokaryote community structure and diversity of three distinctly different wetlands. The study results revealed that α-diversity indices and phylogenetic differential abundance patterns did not differ significantly among primers, but they did differ significantly across wetlands. Microbial community composition revealed a distinct pattern for each primer in each wetland. Overall comparison of prokaryote communities in sediments of three wetlands revealed the highest prokaryote richness and diversity in Bhomra (freshwater wetland) followed by Malencho (brackish-water wetland) and East Kolkata wetland (EKW) (sewage-fed wetland). Indicator genus analysis identified 21, 4, and 29 unique indicator genera, having preferential abode for Bhomra, EKW, and Malencho, respectively. Prediction of potential roles of these microbes revealed a preference for sulfate-reducing microbes in Malencho and methanogens in Bhomra. The distinct phylogenetic differential abundance pattern, microbial abode preference, and their potential functional role predict ecosystem variables shaping microbial diversity. The variation in community composition of prokaryotes in response to ecosystem variables can serve as the most sensitive bioindicator of wetland ecosystem assessment and management.
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Affiliation(s)
- Kavita Kumari
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Malay Naskar
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Md Aftabuddin
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Soma Das Sarkar
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Bandana Das Ghosh
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Uttam Kumar Sarkar
- Reservoir and Wetland Fisheries Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Subir Kumar Nag
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Chayna Jana
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
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34
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Marasinghe SD, Jo E, Hettiarachchi SA, Lee Y, Eom TY, Gang Y, Kang YH, Oh C. Characterization of glycoside hydrolase family 11 xylanase from Streptomyces sp. strain J103; its synergetic effect with acetyl xylan esterase and enhancement of enzymatic hydrolysis of lignocellulosic biomass. Microb Cell Fact 2021; 20:129. [PMID: 34238305 PMCID: PMC8265113 DOI: 10.1186/s12934-021-01619-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/25/2021] [Indexed: 11/18/2022] Open
Abstract
Background Xylanase-containing enzyme cocktails are used on an industrial scale to convert xylan into value-added products, as they hydrolyse the β-1,4-glycosidic linkages between xylopyranosyl residues. In the present study, we focused on xynS1, the glycoside hydrolase (GH) 11 xylanase gene derived from the Streptomyces sp. strain J103, which can mediate XynS1 protein synthesis and lignocellulosic material hydrolysis. Results xynS1 has an open reading frame with 693 base pairs that encodes a protein with 230 amino acids. The predicted molecular weight and isoelectric point of the protein were 24.47 kDa and 7.92, respectively. The gene was cloned into the pET-11a expression vector and expressed in Escherichia coli BL21(DE3). Recombinant XynS1 (rXynS1) was purified via His-tag affinity column chromatography. rXynS1 exhibited optimal activity at a pH of 5.0 and temperature of 55 °C. Thermal stability was in the temperature range of 50–55 °C. The estimated Km and Vmax values were 51.4 mg/mL and 898.2 U/mg, respectively. One millimolar of Mn2+ and Na+ ions stimulated the activity of rXynS1 by up to 209% and 122.4%, respectively, and 1 mM Co2+ and Ni2+ acted as inhibitors of the enzyme. The mixture of rXynS1, originates from Streptomyces sp. strain J103 and acetyl xylan esterase (AXE), originating from the marine bacterium Ochrovirga pacifica, enhanced the xylan degradation by 2.27-fold, compared to the activity of rXynS1 alone when Mn2+ was used in the reaction mixture; this reflected the ability of both enzymes to hydrolyse the xylan structure. The use of an enzyme cocktail of rXynS1, AXE, and commercial cellulase (Celluclast® 1.5 L) for the hydrolysis of lignocellulosic biomass was more effective than that of commercial cellulase alone, thereby increasing the relative activity 2.3 fold. Conclusion The supplementation of rXynS1 with AXE enhanced the xylan degradation process via the de-esterification of acetyl groups in the xylan structure. Synergetic action of rXynS1 with commercial cellulase improved the hydrolysis of pre-treated lignocellulosic biomass; thus, rXynS1 could potentially be used in several industrial applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01619-x.
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Affiliation(s)
- Svini Dileepa Marasinghe
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Eunyoung Jo
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Sachithra Amarin Hettiarachchi
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.,Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences and Technology, University of Ruhuna, Matara, Sri Lanka
| | - Youngdeuk Lee
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Tae-Yang Eom
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yehui Gang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yoon-Hyeok Kang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chulhong Oh
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea. .,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.
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35
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Pérez-Pascual D, Pérez-Cobas AE, Rigaudeau D, Rochat T, Bernardet JF, Skiba-Cassy S, Marchand Y, Duchaud E, Ghigo JM. Sustainable plant-based diets promote rainbow trout gut microbiota richness and do not alter resistance to bacterial infection. Anim Microbiome 2021; 3:47. [PMID: 34225826 PMCID: PMC8256591 DOI: 10.1186/s42523-021-00107-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/07/2021] [Indexed: 01/04/2023] Open
Abstract
Background Farmed fish food with reduced fish-derived products are gaining growing interest due to the ecological impact of fish-derived protein utilization and the necessity to increase aquaculture sustainability. Although different terrestrial plant proteins could replace fishmeal proteins, their use is associated with adverse effects. Here, we investigated how diets composed of terrestrial vegetal sources supplemented with proteins originating from insect, yeast or terrestrial animal by-products affect rainbow trout (Onchorynchus mykiss) gut microbiota composition, growth performance and resistance to bacterial infection by the fish pathogen Flavobacterium psychrophilum responsible for frequent outbreaks in aquaculture settings. Results We showed that the tested regimes significantly increased gut bacterial richness compared to full vegetal or commercial-like diets, and that vegetal diet supplemented with insect and yeast proteins improves growth performance compared to full vegetal diet without altering rainbow trout susceptibility to F. psychrophilum infection. Conclusion Our results demonstrate that the use of insect and yeast protein complements to vegetal fish feeds maintain microbiota functions, growth performance and fish health, therefore identifying promising alternative diets to improve aquaculture’s sustainability. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00107-2.
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Affiliation(s)
- David Pérez-Pascual
- Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS 2001, 75015, Paris, France
| | - Ana Elena Pérez-Cobas
- Biologie des Bactéries Intracellulaires Institut Pasteur, UMR CNRS 3525, 75015, Paris, France
| | - Dimitri Rigaudeau
- Unité Infectiologie Expérimentale Rongeurs et Poissons, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Tatiana Rochat
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | | | - Sandrine Skiba-Cassy
- INRAE, Univ Pau & Pays Adour, E2S UPPA, NUMEA, 64310, Saint-Pée-sur-Nivelle, France
| | | | - Eric Duchaud
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France.
| | - Jean-Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS 2001, 75015, Paris, France.
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Yan B, Liu N, Liu M, Du X, Shang F, Huang Y. Soil actinobacteria tend to have neutral interactions with other co-occurring microorganisms, especially under oligotrophic conditions. Environ Microbiol 2021; 23:4126-4140. [PMID: 33760351 DOI: 10.1111/1462-2920.15483] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/23/2021] [Indexed: 01/07/2023]
Abstract
Actinobacteria produce a variety of secondary metabolites that can influence the survival or behaviour of other organisms. The understanding of the ecological roles of actinobacteria has significantly improved in the past decades, but a systematic insight into the interactions between actinobacteria and other microbes in nature is warranted. Here, we studied the pairwise effects of actinobacteria on other microbes isolated from red soils under different nutritional conditions. We found that neutral effects dominated the interactions, accounting for 68.1% of the interactions in eutrophic conditions and for a significantly higher proportion (86.2%) in oligotrophic conditions. High nutrient levels boosted active metabolism of actinobacteria and generally made them more aggressive, supporting the stress gradient hypothesis. The secondary metabolites produced by actinobacteria played a pivotal role in interference competition with other microbes, of which the role of desferrioxamine siderophores could not be ignored. Niche overlap seemed to be another cause of competition, notably under oligotrophic conditions. Moreover, the large-scale phylogeny had a much greater impact on the interaction than the location origin of the microbes. These results provide an understanding of the coexistence of actinobacteria with other microbes in nature and suggest neutrality as a key mechanism for maintaining microbial diversity in soils.
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Affiliation(s)
- Bingfa Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Minghao Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xueyuan Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Shang
- Analytical and Testing Center, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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37
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Cold-adapted chitinases from Antarctic bacteria: Taxonomic assessment and enzyme production optimization. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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38
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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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40
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Bobadilla Alvarez MC, Palomino Cadenas EJ. CONTROL DE Aedes aegypti (DIPTERA: CULICIDAE) MEDIANTE ACTINOBACTERIAS FORMADORAS DE BIOPELÍCULAS. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v26n3.86966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El phylum Actinobacteria incluye miembros productores de compuestos bioinsecticidas. No obstante, la sobreexplotacion de metabolitos derivados de Streptomyces ha conllevado a explorar nuevas moléculas provenientes de bacterias no estreptomicetos para contrarrestar la resistencia a insecticidas químicos en Aedes aegypti. Concordantes con el uso de bioagentes ecológicos, esta investigación caracterizó actinobacterias formadoras de biopelículas con el fin de evaluar su dinámica de crecimiento, actividad larvicida y efectos subletales. La identificación, crecimiento de biopelículas y bioactividades se realizaron por cultivos, análisis de imágenes por fotomicrografía y bioensayos. Los resultados mostraron que las biopelículas pertenecen a Pseudonocardiaceae (PsA1TA) y Corynebacteriaceae (CoA2CA) característicamente dependientes del revestimiento cuticular. PsA1TA coloniza estructuras membranosas de tórax y abdomen con microcolonias aleatoriamente distribuidas que desarrollan a extensas biopelículas mono y biestratificadas, al cubrir cuatro veces la amplitud toracoabdominal (envergadura infectiva entre 1010 µm a 1036 µm). En contraste, CoA2CA envuelve radialmente estructuras esclerotizadas cefálica y anal al triplicar la amplitud de tales órganos (1820 a 2030 µm y 1650 a 1860 µm, respectivamente). Las biopelículas ejercieron mortalidad diferenciada a todos los estadios larvales, no obstante, PsA1TA resultó más mortal y virulento en el segundo estadio larval (58 %-96 horas, TL50: 3,4 días), mientras que CoA2CA lo fue en el cuarto estadio larval (85 %-96 horas, TL50: 2,5 días). CoA2CA indujo emergencia incompleta de adultos farados y despliegue de tarsos curvos en emergentes, además de revestir con robustas biopelículas cadáveres larvarios. Las biopelículas actinobacterianas revelaron ejercer función larvicida y respuestas subletales en A. aegypti.
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Processed Animal Proteins from Insect and Poultry By-Products in a Fish Meal-Free Diet for Rainbow Trout: Impact on Intestinal Microbiota and Inflammatory Markers. Int J Mol Sci 2021; 22:ijms22115454. [PMID: 34064267 PMCID: PMC8196822 DOI: 10.3390/ijms22115454] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
Sustainability of aquaculture is tied to the origin of feed ingredients. In search of sustainable fish meal-free formulations for rainbow trout, we evaluated the effect of Hermetia illucens meal (H) and poultry by-product meal (P), singly (10, 30, and 60% of either H or P) or in combination (10% H + 50% P, H10P50), as partial replacement of vegetable protein (VM) on gut microbiota (GM), inflammatory, and immune biomarkers. Fish fed the mixture H10P50 had the best growth performance. H, P, and especially the combination H10P50 partially restored α-diversity that was negatively affected by VM. Diets did not differ in the Firmicutes:Proteobacteria ratio, although the relative abundance of Gammaproteobacteria was reduced in H and was higher in P and in the fishmeal control. H had higher relative abundance of chitin-degrading Actinomyces and Bacillus, Dorea, and Enterococcus. Actinomyces was also higher in H feed, suggesting feed-chain microbiome transmission. P increased the relative abundance of protein degraders Paeniclostridium and Bacteroidales. IL-1β, IL-10, TGF-β, COX-2, and TCR-β gene expression in the midgut and head kidney and plasma lipopolysaccharide (LPS) revealed that the diets did not compromise the gut barrier function or induce inflammation. H, P, and H10P50 therefore appear valid protein sources in fishmeal-free aquafeeds.
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Genome Features of Asaia sp. W12 Isolated from the Mosquito Anopheles stephensi Reveal Symbiotic Traits. Genes (Basel) 2021; 12:genes12050752. [PMID: 34067621 PMCID: PMC8156966 DOI: 10.3390/genes12050752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/29/2023] Open
Abstract
Asaia bacteria commonly comprise part of the microbiome of many mosquito species in the genera Anopheles and Aedes, including important vectors of infectious agents. Their close association with multiple organs and tissues of their mosquito hosts enhances the potential for paratransgenesis for the delivery of antimalaria or antivirus effectors. The molecular mechanisms involved in the interactions between Asaia and mosquito hosts, as well as Asaia and other bacterial members of the mosquito microbiome, remain underexplored. Here, we determined the genome sequence of Asaia strain W12 isolated from Anopheles stephensi mosquitoes, compared it to other Asaia species associated with plants or insects, and investigated the properties of the bacteria relevant to their symbiosis with mosquitoes. The assembled genome of strain W12 had a size of 3.94 MB, the largest among Asaia spp. studied so far. At least 3585 coding sequences were predicted. Insect-associated Asaia carried more glycoside hydrolase (GH)-encoding genes than those isolated from plants, showing their high plant biomass-degrading capacity in the insect gut. W12 had the most predicted regulatory protein components comparatively among the selected Asaia, indicating its capacity to adapt to frequent environmental changes in the mosquito gut. Two complete operons encoding cytochrome bo3-type ubiquinol terminal oxidases (cyoABCD-1 and cyoABCD-2) were found in most Asaia genomes, possibly offering alternative terminal oxidases and allowing the flexible transition of respiratory pathways. Genes involved in the production of 2,3-butandiol and inositol have been found in Asaia sp. W12, possibly contributing to biofilm formation and stress tolerance.
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Vargas Hoyos HA, Chiaramonte JB, Barbosa-Casteliani AG, Fernandez Morais J, Perez-Jaramillo JE, Nobre Santos S, Nascimento Queiroz SC, Soares Melo I. An Actinobacterium Strain From Soil of Cerrado Promotes Phosphorus Solubilization and Plant Growth in Soybean Plants. Front Bioeng Biotechnol 2021; 9:579906. [PMID: 33968908 PMCID: PMC8100043 DOI: 10.3389/fbioe.2021.579906] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 03/03/2021] [Indexed: 11/28/2022] Open
Abstract
The huge biological diversity of the Brazilian Cerrado is an important source of economically interesting microbial agents. The phylum Actinobacteria plays an important role in nutrient cycling, potentially improving their availability to plants. In this study, we isolated an actinobacteria (strain 3AS4) from wheat rhizospheres of crops cultivated in the Cerrado biome. Strain 3AS4 was identified as belonging to the genus Streptomyces and had phosphorus mobilization ability, mineralizing approximately 410 μg ml–1 from phytate, 300 μg ml–1 from calcium phosphate, and 200 μg ml–1 from rock phosphate. The analysis of the actinobacteria crude extract by spectrometric techniques revealed the presence of gluconic and 2-ketogluconic acid, and a greenhouse experiment was carried out to evaluate its plant growth promotion activity in soybean. Soil in its natural condition (with no phosphorus addition), 40 kg ha–1 rock phosphate from Bayovar (RP) added to soil, and triple super phosphate (SPT) added to soil were used. Significant differences in plant height were observed at 6 weeks when the plants were inoculated with the 3AS4 strain. The growth of inoculated plants in natural condition was promoted in 17% compared with the RP and SPT non-inoculated conditions, suggesting that inoculation can enable plants to grow with lower chemical P fertilizers. In the plants that were inoculated with the 3AS4 strain in the RP condition, the plant height increased by approximately 80% and the shoot:root ratio was approximately 30% higher compared to control conditions (non-inoculated plants in natural conditions). 3AS4 has P-solubilizing potential and can be exploited as an inoculant for soybean cultivation. These results suggest that this actinobacterium is a valuable resource for sustainable agriculture and will allow the reduction of phosphate fertilization in the future.
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Affiliation(s)
- Harold Alexander Vargas Hoyos
- Program for the Study and Control of Tropical Diseases-PECET, School of Medicine, University of Antioquia, Medellín, Colombia.,Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, Brazil
| | | | | | | | - Juan Esteban Perez-Jaramillo
- Program for the Study and Control of Tropical Diseases-PECET, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | | | - Itamar Soares Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, Brazil
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Viotti C, Bach C, Maillard F, Ziegler-Devin I, Mieszkin S, Buée M. Sapwood and heartwood affect differentially bacterial and fungal community structure and successional dynamics during Quercus petraea decomposition. Environ Microbiol 2021; 23:6177-6193. [PMID: 33848050 DOI: 10.1111/1462-2920.15522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
In forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decomposition. Using Illumina metabarcoding, bacterial and fungal communities were monitored every 3 months for 3 years from Quercus petraea wood discs placed on forest soil. Wood density and microbial enzymes involved in biopolymer degradation were measured. We observed rapid changes in the bacterial and fungal communities and microbial ecological guilds associated with wood decomposition throughout the experiment. Bacterial and fungal succession dynamics were very contrasted between sapwood and heartwood. The initial microbial communities were quickly replaced by new bacterial and fungal assemblages in the sapwood. Conversely, some initial functional guilds (i.e. endophytes and yeasts) persisted all along the experiment in heartwood and finally became dominant, possibly limiting the development of saprotrophic fungi. Our data also suggested a significant role of bacteria in nitrogen cycle during wood decomposition.
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Affiliation(s)
- Chloé Viotti
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - Cyrille Bach
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - François Maillard
- Department of Plant and Microbial Biology University of Minnesota St. Paul, Saint Paul, Minnesota, 55108, USA
| | | | - Sophie Mieszkin
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
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Monge EC, Gardner JG. Efficient chito-oligosaccharide utilization requires two TonB-dependent transporters and one hexosaminidase in Cellvibrio japonicus. Mol Microbiol 2021; 116:366-380. [PMID: 33735458 DOI: 10.1111/mmi.14717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/13/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
Chitin utilization by microbes plays a significant role in biosphere carbon and nitrogen cycling, and studying the microbial approaches used to degrade chitin will facilitate our understanding of bacterial strategies to degrade a broad range of recalcitrant polysaccharides. The early stages of chitin depolymerization by the bacterium Cellvibrio japonicus have been characterized and are dependent on one chitin-specific lytic polysaccharide monooxygenase and nonredundant glycoside hydrolases from the family GH18 to generate chito-oligosaccharides for entry into metabolism. Here, we describe the mechanisms for the latter stages of chitin utilization by C. japonicus with an emphasis on the fate of chito-oligosaccharides. Our systems biology approach combined transcriptomics and bacterial genetics using ecologically relevant substrates to determine the essential mechanisms for chito-oligosaccharide transport and catabolism in C. japonicus. Using RNAseq analysis we found a coordinated expression of genes that encode polysaccharide-degrading enzymes. Mutational analysis determined that the hex20B gene product, predicted to encode a hexosaminidase, was required for efficient utilization of chito-oligosaccharides. Furthermore, two gene loci (CJA_0353 and CJA_1157), which encode putative TonB-dependent transporters, were also essential for chito-oligosaccharides utilization. This study further develops our model of C. japonicus chitin metabolism and may be predictive for other environmentally or industrially important bacteria.
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Affiliation(s)
- Estela C Monge
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
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Murphy R, Benndorf R, de Beer ZW, Vollmers J, Kaster AK, Beemelmanns C, Poulsen M. Comparative Genomics Reveals Prophylactic and Catabolic Capabilities of Actinobacteria within the Fungus-Farming Termite Symbiosis. mSphere 2021; 6:e01233-20. [PMID: 33658277 PMCID: PMC8546716 DOI: 10.1128/msphere.01233-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/01/2021] [Indexed: 11/20/2022] Open
Abstract
Actinobacteria, one of the largest bacterial phyla, are ubiquitous in many of Earth's ecosystems and often act as defensive symbionts with animal hosts. Members of the phylum have repeatedly been isolated from basidiomycete-cultivating fungus-farming termites that maintain a monoculture fungus crop on macerated dead plant substrate. The proclivity for antimicrobial and enzyme production of Actinobacteria make them likely contributors to plant decomposition and defense in the symbiosis. To test this, we analyzed the prophylactic (biosynthetic gene cluster [BGC]) and metabolic (carbohydrate-active enzyme [CAZy]) potential in 16 (10 existing and six new genomes) termite-associated Actinobacteria and compared these to the soil-dwelling close relatives. Using antiSMASH, we identified 435 BGCs, of which 329 (65 unique) were similar to known compound gene clusters, while 106 were putatively novel, suggesting ample prospects for novel compound discovery. BGCs were identified among all major compound categories, including 26 encoding the production of known antimicrobial compounds, which ranged in activity (antibacterial being most prevalent) and modes of action that might suggest broad defensive potential. Peptide pattern recognition analysis revealed 823 (43 unique) CAZymes coding for enzymes that target key plant and fungal cell wall components (predominantly chitin, cellulose, and hemicellulose), confirming a substantial degradative potential of these bacteria. Comparison of termite-associated and soil-dwelling bacteria indicated no significant difference in either BGC or CAZy potential, suggesting that the farming termite hosts may have coopted these soil-dwelling bacteria due to their metabolic potential but that they have not been subject to genome change associated with symbiosis.IMPORTANCEActinobacteria have repeatedly been isolated in fungus-farming termites, and our genome analyses provide insights into the potential roles they may serve in defense and for plant biomass breakdown. These insights, combined with their relatively higher abundances in fungus combs than in termite gut, suggest that they are more likely to play roles in fungus combs than in termite guts. Up to 25% of the BGCs we identify have no similarity to known clusters, indicating a large potential for novel chemistry to be discovered. Similarities in metabolic potential of soil-dwelling and termite-associated bacteria suggest that they have environmental origins, but their consistent presence with the termite system suggests their importance for the symbiosis.
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Affiliation(s)
- Robert Murphy
- University of Copenhagen, Department of Biology, Section for Ecology and Evolution, Copenhagen East, Denmark
| | - René Benndorf
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Z Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - John Vollmers
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Michael Poulsen
- University of Copenhagen, Department of Biology, Section for Ecology and Evolution, Copenhagen East, Denmark
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In Silico Studies of Lamiaceae Diterpenes with Bioinsecticide Potential against Aphis gossypii and Drosophila melanogaster. Molecules 2021; 26:molecules26030766. [PMID: 33540716 PMCID: PMC7867283 DOI: 10.3390/molecules26030766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 12/19/2022] Open
Abstract
Background: The growing demand for agricultural products has led to the misuse/overuse of insecticides; resulting in the use of higher concentrations and the need for ever more toxic products. Ecologically, bioinsecticides are considered better and safer than synthetic insecticides; they must be toxic to the target organism, yet with low or no toxicity to non-target organisms. Many plant extracts have seen their high insecticide potential confirmed under laboratory conditions, and in the search for plant compounds with bioinsecticidal activity, the Lamiaceae family has yielded satisfactory results. Objective: The aim of our study was to develop computer-assisted predictions for compounds with known insecticidal activity against Aphis gossypii and Drosophila melanogaster. Results and conclusion: Structure analysis revealed ent-kaurane, kaurene, and clerodane diterpenes as the most active, showing excellent results. We also found that the interactions formed by these compounds were more stable, or presented similar stability to the commercialized insecticides tested. Overall, we concluded that the compounds bistenuifolin L (1836) and bistenuifolin K (1931), were potentially active against A. gossypii enzymes; and salvisplendin C (1086) and salvixalapadiene (1195), are potentially active against D. melanogaster. We observed and highlight that the diterpenes bistenuifolin L (1836), bistenuifolin K (1931), salvisplendin C (1086), and salvixalapadiene (1195), present a high probability of activity and low toxicity against the species studied.
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Malik A, Kim YR, Kim SB. Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential. Genes (Basel) 2020; 11:genes11101166. [PMID: 33022985 PMCID: PMC7601586 DOI: 10.3390/genes11101166] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 12/23/2022] Open
Abstract
The genus Streptacidiphilus represents a group of acidophilic actinobacteria within the family Streptomycetaceae, and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely Streptomyces and Kitasatospora, these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 Streptacidiphilus species were subjected to the comparative analysis together with selected Streptomyces and Kitasatospora genomes. This study represents the first comprehensive comparative genomic analysis of the genus Streptacidiphilus. The results indicate that the genomes of Streptacidiphilus contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in Streptacidiphilus only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of Streptacidiphilus were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919T were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each Streptacidiphilus species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities.
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Affiliation(s)
- Adeel Malik
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea; (A.M.); (Y.R.K.)
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul 03016, Korea
| | - Yu Ri Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea; (A.M.); (Y.R.K.)
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea; (A.M.); (Y.R.K.)
- Correspondence:
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Cereijo AE, Kuhn ML, Hernández MA, Ballicora MA, Iglesias AA, Alvarez HM, Asencion Diez MD. Study of duplicated galU genes in Rhodococcus jostii and a putative new metabolic node for glucosamine-1P in rhodococci. Biochim Biophys Acta Gen Subj 2020; 1865:129727. [PMID: 32890704 DOI: 10.1016/j.bbagen.2020.129727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/11/2020] [Accepted: 08/30/2020] [Indexed: 01/10/2023]
Abstract
BACKGOUND Studying enzymes that determine glucose-1P fate in carbohydrate metabolism is important to better understand microorganisms as biotechnological tools. One example ripe for discovery is the UDP-glucose pyrophosphorylase enzyme from Rhodococcus spp. In the R. jostii genome, this gene is duplicated, whereas R. fascians contains only one copy. METHODS We report the molecular cloning of galU genes from R. jostii and R. fascians to produce recombinant proteins RjoGalU1, RjoGalU2, and RfaGalU. Substrate saturation curves were conducted, kinetic parameters were obtained and the catalytic efficiency (kcat/Km) was used to analyze enzyme promiscuity. We also investigated the response of R. jostii GlmU pyrophosphorylase activity with different sugar-1Ps, which may compete for substrates with RjoGalU2. RESULTS All enzymes were active as pyrophosphorylases and exhibited substrate promiscuity toward sugar-1Ps. Remarkably, RjoGalU2 exhibited one order of magnitude higher activity with glucosamine-1P than glucose-1P, the canonical substrate. Glucosamine-1P activity was also significant in RfaGalU. The efficient use of the phospho-amino-sugar suggests the feasibility of the reaction to occur in vivo. Also, RjoGalU2 and RfaGalU represent enzymatic tools for the production of (amino)glucosyl precursors for the putative synthesis of novel molecules. CONCLUSIONS Results support the hypothesis that partitioning of glucosamine-1P includes an uncharacterized metabolic node in Rhodococcus spp., which could be important for producing diverse alternatives for carbohydrate metabolism in biotechnological applications. GENERAL SIGNIFICANCE Results presented here provide a model to study evolutionary enzyme promiscuity, which could be used as a tool to expand an organism's metabolic repertoire by incorporating non-canonical substrates into novel metabolic pathways.
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Affiliation(s)
- A E Cereijo
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA, United States
| | - M A Hernández
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - M A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, IL 60660, United States
| | - A A Iglesias
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina
| | - H M Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina.
| | - M D Asencion Diez
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina.
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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