1
|
Zhao B, Dong W, Chen Z, Zhao X, Cai Z, Feng J, Li S, Sun X. Microbial inoculation accelerates rice straw decomposition by reshaping structure and function of lignocellulose-degrading microbial consortia in paddy fields. BIORESOURCE TECHNOLOGY 2024; 413:131545. [PMID: 39341423 DOI: 10.1016/j.biortech.2024.131545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/23/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024]
Abstract
Inoculating lignocellulose-degrading microorganisms can accelerate straw decomposition in paddy field; however, the relationship between indigenous and inoculated microorganisms remains unclear. This study explored the effects of microbial inoculation on straw decomposition, microbial community, lignocellulose-degrading consortia, and associated functional genes. After inoculation, straw degradation rate increased by up to 4.9 %, and the rice yield increased by 790 kg/ha. Microbial inoculation restructured soil microbial community, influencing key taxa and interactions within the microbial network. A lignocellulose-degrading consortia consisting 37 genera was established, with a notable increase in the relative abundance of lignocellulose-degrading bacteria following inoculation. Among them, Pseudarthrobacter, with high lignin-degrading enzyme activity, emerged as a key genus after inoculation. Additionally, the abundance of lignin-degrading enzyme genes also increased significantly after inoculation. These findings offer new insights into how microbial inoculation accelerates the in situ decomposition of rice straw by reshaping the structure and function of lignocellulose-degrading consortia within the soil ecosystem.
Collapse
Affiliation(s)
- Binhan Zhao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Wenjun Dong
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China
| | - Zhiling Chen
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xin Zhao
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zhanjun Cai
- Ordos Mengkangyuan Biotechnology Research Co., Ltd, Erdos 017299, China
| | - Junjian Feng
- Liaoning Junzhe Biotechnology Co., Ltd, Shenyang 110122, China
| | - Shaojie Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xianyun Sun
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China.
| |
Collapse
|
2
|
Ni S, Wu Y, Zhu N, Leng F, Wang Y. Bacillus licheniformisYB06: A Rhizosphere-Genome-Wide Analysis and Plant Growth-Promoting Analysis of a Plant Growth-Promoting Rhizobacterium Isolated from Codonopsis pilosula. Microorganisms 2024; 12:1861. [PMID: 39338535 PMCID: PMC11433706 DOI: 10.3390/microorganisms12091861] [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: 08/21/2024] [Revised: 09/01/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
Codonopsis pilosula, commonly known as Dangshen, is a valuable medicinal plant, but its slow growth and susceptibility to environmental stress pose challenges for its cultivation. In pursuit of sustainable agricultural practices to enhance the yield and quality of Dangshen, the present study isolated a bacterial strain exhibiting plant growth-promoting potential from the rhizosphere of C. pilosula. This strain was subsequently identified as Bacillus licheniformisYB06. Assessment of its plant growth-promoting attributes revealed the potential of B. licheniformis YB06 as a biofertilizer. Whole-genome sequencing of B. licheniformis YB06 revealed a genome size of 4,226,888 bp with a GC content of 46.22%, harboring 4325 predicted protein-coding sequences. Genomic analysis of B. licheniformis YB06 revealed a diverse array of genes linked to induced systemic resistance (ISR) and plant growth-promoting (PGP) traits, encompassing phytohormone production, nitrogen assimilation and reduction, siderophore biosynthesis, phosphate solubilization, biofilm formation, synthesis of PGP-related amino acids, and flagellar motility. Seed germination assays demonstrated the positive effects of B. licheniformis YB06 on the germination and growth of C. pilosula seedlings. Furthermore, we explored various fertilization regimes, particularly the B. licheniformis YB06-based biofertilizer, were investigated for their impact on the structure and diversity of the C. pilosula rhizosphere soil bacterial community. Our findings revealed that fertilization significantly impacted soil bacterial composition and diversity, with the combined application of B. licheniformis YB06-based biofertilizer and organic fertilizer exhibiting a particularly pronounced enhancement of rhizosphere bacterial community structure and diversity. This study represents the first report on the beneficial effects of B. licheniformis YB06 on both the growth of C. pilosula and the composition of its rhizosphere soil microbial community. These findings provide a theoretical foundation and practical guidance for the development of novel bio-organic compound fertilizers, thereby contributing to the sustainable cultivation of C. pilosula.
Collapse
Affiliation(s)
| | | | | | | | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China; (S.N.); (Y.W.); (N.Z.); (F.L.)
| |
Collapse
|
3
|
Wardman JF, Withers SG. Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening. RSC Chem Biol 2024; 5:595-616. [PMID: 38966674 PMCID: PMC11221537 DOI: 10.1039/d4cb00024b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.
Collapse
Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
| |
Collapse
|
4
|
Möller L, Vainshtein Y, Meyer B, Neidhardt J, Eren AM, Sohn K, Rabus R. Rich microbial and depolymerising diversity in Antarctic krill gut. Microbiol Spectr 2024; 12:e0403523. [PMID: 38466097 PMCID: PMC10986584 DOI: 10.1128/spectrum.04035-23] [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: 11/25/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter, also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire.IMPORTANCEThe Antarctic krill (Euphausia superba) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.
Collapse
Affiliation(s)
- Lars Möller
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Yevhen Vainshtein
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Bettina Meyer
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- Biosciences, Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - John Neidhardt
- Department of Human Medicine, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - A. Murat Eren
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- HIFMB-MPG Bridging Group for Marine Genomics, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute (AWI), Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Kai Sohn
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| |
Collapse
|
5
|
Subbaiyan R, Ganesan A. In vitro and in vivo assessment of antimicrobial, enzymatic, and antifouling properties of self-potent lichen symbiotic bacteria. Biotechnol Appl Biochem 2024; 71:446-459. [PMID: 38185532 DOI: 10.1002/bab.2551] [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: 08/21/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
This study aimed to comprehensively assess the antimicrobial, antifouling, and antibiofilm-forming potential of lichen symbiotic bacteria against marine fouling bacterial strains. A total of 50 lichen-associated bacteria (LAB) isolates were successfully characterized and evaluated for their effectiveness in mitigating biofouling caused by various marine biofoulers. Through a battery of biological assays encompassing enzymatic, antagonistic, antimicrobial, and antifouling assays, 15 LAB isolates were identified based on their antagonist activities. Notably, the strain LAB4 exhibited remarkable performance across all bioassays, demonstrating its proficiency as an antifouling agent. The production of crude LAB extracts was successfully scaled up using a large-scale fermentor and further optimized. Additionally, a phylogenetic analysis of the isolated strain Bacillus proteolyticus D65's 16S ribosomal RNA gene revealed a high query coverage and percentage identity of 92.62% (accession no. MK883171.1). In conclusion, the lichen bacterial symbiotic isolate B. proteolyticus exhibited significant in vitro and in vivo inhibition of foulants. This study highlights the potential of lichens as a valuable source of yet unexplored bacteria. The bacterial consortium associated with Parmotrema sp. holds promise in combatting biofouling, which poses a substantial threat to the maritime industries and their economic stability.
Collapse
Affiliation(s)
- Rubavathi Subbaiyan
- Department of Biotechnology, K. S. Rangasamy College of Technology, Namakkal, Tamil Nadu, India
| | - Ayyappadasan Ganesan
- Department of Biotechnology, K. S. Rangasamy College of Technology, Namakkal, Tamil Nadu, India
| |
Collapse
|
6
|
Yaşar Yildiz S. Exploring the Hot Springs of Golan: A Source of Thermophilic Bacteria and Enzymes with Industrial Promise. Curr Microbiol 2024; 81:101. [PMID: 38376803 DOI: 10.1007/s00284-024-03617-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/14/2024] [Indexed: 02/21/2024]
Abstract
In recent years, there has been a surge in research on extremophiles due to their remarkable ability to survive in harsh environments. Extremophile thermophilic bacteria provide thermostable enzymes for biotechnology and industry. Thermophilic bacteria live in extreme environments like hot springs at 45-80 °C. This study screens and isolates thermophilic bacteria and thermozymes from the Golan hot springs in Karakocan, Elazig, Turkey. The study also characterizes thermophilic bacteria and their thermozymes to understand their features and applications better. Golan hot spring water samples at 50 °C yielded 12 isolates. GKE 02, 07, 08, and 10 produce amylase, GKE 04, 08, and 11 cellulase, and GKE 06 xylanase. One isolate (GKE 08) displayed both amylolytic and cellulolytic activity on agar plates. GKE 02 had the highest plate assay amylolytic index (2.3) and amylase activity (67.87 U/ml). Plate assay indicates GKE 08 has 1.5 amylolytic index, 1.1 cellulolytic index, 38.57 U/ml amylase, and 6.81 U/ml cellulase. GKE 04 had the greatest cellulolytic index (1.7) and cellulase activity (27.46). GKE 06, the only xylanase producer, has 19.67 U/ml activity and 1.4 plate assay index. The investigation also included determining the optimal pH and temperature conditions for each enzyme. 16S rDNA gene sequencing revealed seven thermozyme-producing bacteria Bacillus, Geobacillus, and Thermomonas. Thermomonas hydrothermalis genome annotation showed glycosyl hydrolase genes for amylolytic and cellulolytic activity. The findings of this study on thermophilic bacteria and thermostable enzyme synthesis in the Golan hot springs are promising, particularly for T. hydrothermalis, which has limited research on its potential as a thermozyme producer.
Collapse
Affiliation(s)
- Songül Yaşar Yildiz
- Bioengineering Department, Faculty of Engineering and Natural Sciences, Istanbul Medeniyet University, Istanbul, 34700, Turkey.
| |
Collapse
|
7
|
Chen B, Zeng Y, Wang J, Lei M, Gan B, Wan Z, Wu L, Luo G, Cao S, An T, Zhang Q, Pan K, Jing B, Ni X, Zeng D. Targeted Screening of Fiber Degrading Bacteria with Probiotic Function in Herbivore Feces. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10215-5. [PMID: 38300451 DOI: 10.1007/s12602-024-10215-5] [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] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
Cellulolytic bacteria with probiotic functions play a crucial role in promoting the intestinal health in herbivores. In this study, we aimed to correlate the 16S rRNA gene amplicon sequencing and fiber-degrading enzyme activity data from six different herbivore feces samples. By utilizing the separation and screening steps of probiotics, we targeted and screened high-efficiency fiber-degrading bacteria with probiotic functions. The animals included Maiwa Yak (MY), Holstein cow (CC), Tibetan sheep (TS), Southern Sichuan black goat (SG), Sichuan white rex rabbit (CR), and New Zealand white rabbit (ZR). The results showed that the enzymes associated with fiber degradation were higher in goat and sheep feces compared to cattle and rabbit's feces. Correlation analysis revealed that Bacillus and Fibrobacter were positively correlated with five types of fiber-degrading related enzymes. Notably, the relative abundance of Bacillus in the feces of Tibetan sheep was significantly higher than that of other five herbivores. A strain TS5 with good cellulose decomposition ability from the feces of Tibetan sheep by Congored staining, filter paper decomposition test, and enzyme activity determination was isolated. The strain was identified as Bacillus velezensis by biological characteristics, biochemical analysis, and 16S rRNA gene sequencing. To test the probiotic properties of Bacillus velezensis TS5, we evaluated its tolerance to acid and bile salt, production of digestive enzymes, antioxidants, antibacterial activity, and adhesion ability. The results showed that the strain had good tolerance to pH 2.0 and 0.3% bile salts, as well as good potential to produce cellulase, protease, amylase, and lipase. This strain also had good antioxidant capacity and the ability to antagonistic Staphylococcus aureus BJ216, Salmonella SC06, Enterotoxigenic Escherichia coli CVCC196, and Escherichia coli ATCC25922. More importantly, the strain had good self-aggregation and Caco-2 cell adhesion rate. In addition, we tested the safety of Bacillus velezensis TS5 by hemolysis test, antimicrobial susceptibility test, and acute toxicity test in mice. The results showed that the strain had no hemolytic phenotype, did not develop resistance to 19 commonly used antibiotics, had no cytotoxicity to Caco-2, and did not have acute toxic harm to mice. In summary, this study targeted isolated and screened a strain of Bacillus velezensis TS5 with high fiber-degrading ability and probiotic potency. This strain can be used as a potential probiotic for feeding microbial preparations for ruminants.
Collapse
Affiliation(s)
- Benhao Chen
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jie Wang
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingxia Lei
- Neijiang Center for Animal and Plant Epidemic Disease Prevention and Control and Agricultural Products Quality Inspection, Neijiang, China
| | - Baoxing Gan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhiqiang Wan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Liqian Wu
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Guangrong Luo
- Sichuan Longri Breeding Stock Farm, Aba Autonomous Prefecture, China
| | - Suizhong Cao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Tianwu An
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Qibin Zhang
- Agricultural Comprehensive Service Center of Beimu Town, Neijiang, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bo Jing
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.
| |
Collapse
|
8
|
Thapa S, Zhou S, O'Hair J, Al Nasr K, Ropelewski A, Li H. Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach. BMC Biotechnol 2023; 23:51. [PMID: 38049781 PMCID: PMC10696843 DOI: 10.1186/s12896-023-00821-6] [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: 03/17/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Goat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities. RESULTS Bacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat's rumen metagenome are unique with only 56-59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity. CONCLUSIONS In summary, this study provided the database resources of bacterial metagenomes from goat's rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.
Collapse
Affiliation(s)
- Santosh Thapa
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
- Vanderbilt University Medical Center, 2215 Garland Ave, Nashville, TN, 37232, USA
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Joshua O'Hair
- Department of Biological Sciences, College of Life & Physical Sciences, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Kamal Al Nasr
- Department of Computer Sciences, College of Engineering, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Alexander Ropelewski
- Pittsburgh Supercomputing Center, 300 S. Craig Street, Pittsburgh, PA, 15213, USA
| | - Hui Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA.
| |
Collapse
|
9
|
Vardhan H, Sasamal S, Mohanty K. Xylitol Production by Candida tropicalis from Areca Nut Husk Enzymatic Hydrolysate and Crystallization. Appl Biochem Biotechnol 2023; 195:7298-7321. [PMID: 36995656 DOI: 10.1007/s12010-023-04469-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
Lignocellulosic biomasses are extensively used by researchers to produce a variety of renewable bioproducts. This research described an environment-friendly technique of xylitol production by an adapted strain of Candida tropicalis from areca nut hemicellulosic hydrolysate, produced through enzymatic hydrolysis. To enhance the activity of xylanase enzymes, lime and acid pretreatment was conducted to make biomass more amenable for saccharification. To improve the efficiency of enzymatic hydrolysis, saccharification parameters like xylanase enzyme loading were varied. Results exposed that the highest yield (g/g) of reducing sugar, about 90%, 83%, and 15%, were achieved for acid-treated husk (ATH), lime-treated husk (LTH), and raw husk (RH) at an enzyme loading of 15.0 IU/g. Hydrolysis was conducted at a substrate loading of 2% (w/V) at 30 °C, 100 rpm agitation, for 12 h hydrolysis time at pH 4.5 to 5.0. Subsequently, fermentation of xylose-rich hemicellulose hydrolysate was conducted with pentose utilizing the yeast Candida tropicalis to produce xylitol. The optimum concentration of xylitol was obtained at about 2.47 g/L, 3.83 g/L, and 5.88 g/L, with yields of approximately 71.02%, 76.78%, and 79.68% for raw fermentative hydrolysate (RFH), acid-treated fermentative hydrolysate (ATFH), and lime-treated fermentative gydrolysate (LTFH), respectively. Purification and crystallization were also conducted to separate xylitol crystals, followed by characterization like X-ray diffraction (XRD) and scanning electron microscopy (SEM) analysis. Results obtained from crystallization were auspicious, and about 85% pure xylitol crystal was obtained.
Collapse
Affiliation(s)
- Harsh Vardhan
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Soumya Sasamal
- Department of Biotechnology, Visva Bharati, Santiniketan, 731235, India.
| | - Kaustubha Mohanty
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India.
| |
Collapse
|
10
|
Woźniak M, Tyśkiewicz R, Siebielec S, Gałązka A, Jaroszuk-Ściseł J. Metabolic Profiling of Endophytic Bacteria in Relation to Their Potential Application as Components of Multi-Task Biopreparations. MICROBIAL ECOLOGY 2023; 86:2527-2540. [PMID: 37392205 PMCID: PMC10640448 DOI: 10.1007/s00248-023-02260-4] [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: 04/28/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
Agricultural crops are exposed to various abiotic and biotic stresses that can constrain crop productivity. Focusing on a limited subset of key groups of organisms has the potential to facilitate the monitoring of the functions of human-managed ecosystems. Endophytic bacteria can enhance plant stress resistance and can help plants to cope with the negative impacts of stress factors through the induction of different mechanisms, influencing plant biochemistry and physiology. In this study, we characterise endophytic bacteria isolated from different plants based on their metabolic activity and ability to synthesise 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD), the activity of hydrolytic exoenzymes, the total phenolic compounds (TPC) and iron-complexing compounds (ICC). Test GEN III MicroPlate indicated that the evaluated endophytes are highly metabolically active, and the best used substrates were amino acids, which may be important in selecting potential carrier components for bacteria in biopreparations. The ACCD activity of strain ES2 (Stenotrophomonas maltophilia) was the highest, whereas that of strain ZR5 (Delftia acidovorans) was the lowest. Overall, the obtained results indicated that ∼91.3% of the isolates were capable of producing at least one of the four hydrolytic enzymes. In addition, most of the tested strains produced ICC and TPC, which play a significant role in reducing stress in plants. The results of this study suggest that the tested endophytic bacterial strains can potentially be used to mitigate climate change-associated stresses in plants and to inhibit plant pathogens.
Collapse
Affiliation(s)
- Małgorzata Woźniak
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation-State Research Institute, Czartoryskich 8, 24-100, Pulawy, Poland.
| | - Renata Tyśkiewicz
- Analytical Laboratory, Łukasiewicz Research Network-New Chemical Syntheses Institute, Al. Tysiąclecia Państwa Polskiego 13a, 24-110, Pulawy, Poland
| | - Sylwia Siebielec
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation-State Research Institute, Czartoryskich 8, 24-100, Pulawy, Poland
| | - Anna Gałązka
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation-State Research Institute, Czartoryskich 8, 24-100, Pulawy, Poland
| | - Jolanta Jaroszuk-Ściseł
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| |
Collapse
|
11
|
Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
Collapse
Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
| |
Collapse
|
12
|
Zhao Y, Li S, Lessing DJ, Guo L, Chu W. Characterization of Cetobacterium somerae CPU-CS01 isolated from the intestine of healthy crucian carp (Carassius auratus) as potential probiotics against Aeromonas hydrophila infection. Microb Pathog 2023; 180:106148. [PMID: 37169311 DOI: 10.1016/j.micpath.2023.106148] [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: 04/14/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
Cetobacterium somerae is a commensal bacterium for many fish species. However, research on C. somerae has been limited so far, and its function and beneficial potential require to be further investigated. The objective of this study was to evaluate the probiotic properties of C. somerae CPU-CS01 isolated from the intestinal contents of crucian carp (Carassius auratus). Hemolytic activity, antibiotic susceptibility, acid tolerance, bile salt tolerance, free radical scavenging, and enzyme production properties were tested for in vitro. Caenorhabditis elegans and zebrafish (Danio rerio) model were used to evaluate the antioxidant and anti-infective effects of C. somerae CPU-CS01 in vivo. Our results showed that C. somerae CPU-CS01 had no hemolytic activity, it produced cellulase, amylase, and survived at low pH (2.0-3.0) and in the presence of bile salts. The cell-free culture supernatant (CFCS) of C. somerae CPU-CS01 possessed DPPH radical, hydroxyl radical, and superoxide anion scavenging activity. C. elegans fed with C. somerae CPU-CS01 were more resistant to hydrogen peroxide-induced oxidative stress and Aeromonas hydrophila infection. In addition, zebrafish-fed diets containing C. somerae CPU-CS01 showed improved survival after A.hydrophila infection. Based on these results, the positive probiotic properties of C. somerae CPU-CS01 isolated from the intestinal contents of crucian carp make it a potential candidate for probiotic.
Collapse
Affiliation(s)
- Yang Zhao
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Shipo Li
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Duncan James Lessing
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Liyun Guo
- Department of Microbiology, Nanjing Institute of Fisheries Science, Nanjing, 210036, China
| | - Weihua Chu
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.
| |
Collapse
|
13
|
Castaldi S, Valkov VT, Ricca E, Chiurazzi M, Isticato R. Use of halotolerant Bacillus amyloliquefaciens RHF6 as a bio-based strategy for alleviating salinity stress in Lotus japonicus cv Gifu. Microbiol Res 2023; 268:127274. [PMID: 36527786 DOI: 10.1016/j.micres.2022.127274] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Halotolerant (HT) bacteria are a group of microorganisms able to thrive in environments with relatively high salt concentrations. HT-microorganisms with plant growth-promoting (PGP) characteristics have been proposed to increase plant tolerance in salty soil. Here, we evaluated the PGP properties at increasing NaCl concentrations of HT-Bacillus strains, previously shown to have beneficial effects under physiological conditions. Most of the isolated showed indole acetic acid and ammonia production and were able to solubilize phosphate and suppress the proliferation of the phytopathogenic fungus Macrophomina phaseolina 2013-1 at high salt concentrations. One of the selected strains, Bacillus amyloliquefaciens RHF6, which retained its beneficial properties up to 400 mM NaCl in vitro, was tested on the legume model plant Lotus japonicus cv Gifu under salt stress. The inoculation with RHF6 significantly improved the survival of plants under high salinity conditions, as reflected in seedling root and shoot growth and total fresh weight (increased by 40%) when compared with non-inoculated plants. The ability of RHF6 to induce a plant antioxidant response, secrete the osmoprotectant proline and reduce ethylene level via the enzymatic ACC deaminase activity indicated this strain as a potentially helpful PGPB for the treatment of degraded soils.
Collapse
Affiliation(s)
- Stefany Castaldi
- Department of Biology, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Vladimir Totev Valkov
- Institute of Biosciences and Bioresources (IBBR), Italian National Research Council (CNR), Napoli, Italy
| | - Ezio Ricca
- Department of Biology, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy
| | - Maurizio Chiurazzi
- Institute of Biosciences and Bioresources (IBBR), Italian National Research Council (CNR), Napoli, Italy
| | - Rachele Isticato
- Department of Biology, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Naples, Italy; Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), Portici, NA, Italy; National Biodiversity Future Center (NBFC), Palermo 90133, Italy.
| |
Collapse
|
14
|
Huang R, Zhang F, Zhou H, Yu H, Shen L, Jiang J, Qin Y, Liu Y, Song Y. Characterization of Trichoderma reesei endoglucanase displayed on the Saccharomyces cerevisiae cell surface and its effect on wine flavor in combination with β-glucosidase. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
15
|
Shrestha S, Chio C, Khatiwada JR, Kognou ALM, Qin W. Optimization of multiple enzymes production by fermentation using lipid-producing Bacillus sp. Front Microbiol 2022; 13:1049692. [PMID: 36386650 PMCID: PMC9663924 DOI: 10.3389/fmicb.2022.1049692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
The present study identified the pectinase-producing bacterium isolated from the contaminated broth as Bacillus sp. on 16S rDNA sequence analysis. The bacterium illustrated water-like droplets on the colony grown on the Sabouraud dextrose agar plate. It also exhibited multi-enzymes activities, such as pectinase, polygalacturonase, xylanase, and cellulase by using various agro-wastes as low-cost substrates. The orange peel was observed to be the best substrate among the agro-wastes used for maximum multi-enzymes (pectinase, polygalacturonase, xylanase, and cellulase). However, the bacterium demonstrated its capability to produce different enzymes according to the different substrates/agro-wastes used. The Plackett-Burman design was used to determine the essential influencing factors, while the Box Behnken design response surface methodology was for optimizing cultural conditions. At their optimal conditions (40°C incubation temperature, 24 h of incubation period, 1% w/v orange peel, and 2% v/v inoculum volume), the bacterium exhibited the maximum pectinase (9.49 ± 1.25 U/ml) and xylanase (16.27 ± 0.52 U/ml) activities. Furthermore, the study explored the ability of the bacterium to produce bacterial lipids and observed about 25% bacterial lipid content on a dry weight basis. Therefore, the bacterium is a good candidate for producing important multi-enzymes and subsequent agro-waste degradation controlling the environment, and facilitating waste management. Also, the bacterium can be a potential feedstock in producing renewable biofuel.
Collapse
Affiliation(s)
| | | | | | | | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| |
Collapse
|
16
|
Plant Growth-Promoting Bacterial Consortia as a Strategy to Alleviate Drought Stress in Spinacia oleracea. Microorganisms 2022; 10:microorganisms10091798. [PMID: 36144400 PMCID: PMC9501077 DOI: 10.3390/microorganisms10091798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Drought stress is one of the most severe abiotic stresses affecting soil fertility and plant health, and due to climate change, it is destined to increase even further, becoming a serious threat to crop production. An efficient, eco-friendly alternative is the use of plant growth-promoting bacteria (PGPB), which can promote plant fitness through direct and indirect approaches, protecting plants from biotic and abiotic stresses. The present study aims to identify bacterial consortia to promote Spinacia oleracea L. cv Matador’s seed germination and protect its seedlings from drought stress. Eight PGPB strains belonging to the Bacillus, Azotobacter, and Pseudomonas genera, previously characterized in physiological conditions, were analyzed under water-shortage conditions, and a germination bioassay was carried out by biopriming S. oleracea seeds with either individual strains or consortia. The consortia of B. amyloliquefaciens RHF6, B. amyloliquefaciens LMG9814, and B. sp. AGS84 displayed the capacity to positively affect seed germination and seedlings’ radical development in both standard and drought conditions, ameliorating the plants’ growth rate compared to the untreated ones. These results sustain using PGPB consortia as a valid ameliorating water stress strategy in the agro-industrial field.
Collapse
|
17
|
Screening of Cellulolytic Bacteria from Various Ecosystems and Their Cellulases Production under Multi-Stress Conditions. Catalysts 2022. [DOI: 10.3390/catal12070769] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Cellulose represents the most abundant component of plant biomass on earth; it is degraded by cellulases, specific enzymes produced by microorganisms. However, cellulases of bacterial origin attract more interest due to their natural diversity and ability to inhabit a variety of niches, allowing the selection of cellulolytic strains resistant to environmental stresses. The screening of the cellulolytic activity of 398 bacteria isolated from various ecosystems in Algeria (cave, ruins, chott, thermal station, and rhizosphere of arid and semi-arid regions) was performed by the appearance of a hydrolysis zone on carboxymethylcellulose (CMC) medium. The cellulase activity on CMC (1%) broth allowed to select 26 strains among which 12 had the best activity (0.3 U/mL to 2.2 U/mL). Optimization of physicochemical parameters (salinity: 0–1 M NaCl; pH: 3, 4, 7, 9, and 11; temperature: 30, 45, and 50 °C; PEG8000: 0 and 30%) involved in growth and cellulose production showed that the majority of strains were mesophilic, neutrophilic, or alkali- tolerant and tolerant to 30% of PEG8000. The cellulase activity and stability under different stress allowed to retain five strains, which the most efficient. Based on the 16S-rRNA sequencing results, they belonged to the genus Bacillus. The physicochemical properties of cellulases (crude extract) showed a CMCase active over a wide range of pH (4 to 11), optimal at 50 °C and 60 °C. The inhibiting salinity effect on the activity was not detected and was negligible on the enzymatic stability. The residual CMCase activity remained between 40 and 70% in a temperature range between 40 and 70 °C, was stable over a wide range of saline concentrations (0–2000 mM), and was weakly affected at 30% of PEG8000. The crude enzyme extract was able to hydrolyze both soluble and insoluble cellulosic substrates. The evaluation of the hydrolysis capacity of lignocellulosic waste revealed the ability of tested strains to degrade wheat bran, barley bran, and corncob. In addition, the enzyme showed significant multi-stress resistance on solid and liquid media. By these characteristics, these cellulolytic bacteria could be attractive to be used in various industrial and biotechnology applications.
Collapse
|
18
|
Response-Surface Statistical Optimization of Submerged Fermentation for Pectinase and Cellulase Production by Mucor circinelloides and M. hiemalis. FERMENTATION 2022. [DOI: 10.3390/fermentation8050205] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cellulase and pectinase are degrading cellulosic and pectic substances that form plant cell walls and, thereby, they have a wide range of applications in the agro-industrial by-products recycling and food industries. In the current research, Mucor circinelloides and M. hiemalis strains were tested for their ability to produce cellulase and pectinase from tangerine peel by submerged fermentation. Experiments on five variables: temperature, pH, incubation period, inoculum size, and substrate concentration, were designed with a Box–Behnken design, as well as response surface methodology (RSM), and analysis of variance was performed. In addition, cellulase and pectinase were partially purified and characterized. At their optimum parameters, M. circinelloides and M. hiemalis afforded high cellulase production (37.20 U/mL and 33.82 U/mL, respectively) and pectinase (38.02 U/mL and 39.76 U/mL, respectively). The partial purification of M. circinelloides and M. hiemalis cellulase produced 1.73- and 2.03-fold purification with 31.12 and 32.02% recovery, respectively; meanwhile, 1.74- and 1.99-fold purification with 31.26 and 31.51% recovery, respectively, were obtained for pectinase. Partially purified cellulase and pectinase from M. circinelloides and M. hiemalis demonstrated the highest activity at neutral pH, and 70 and 50 °C, for cellulase and 50 and 60 °C, for pectinase, respectively. Moreover, 10 mM of K+ increased M. circinelloides enzymatic activity. The production of cellulase and pectinase from M. circinelloides and M. hiemalis utilizing RSM is deemed profitable for the decomposition of agro-industrial wastes.
Collapse
|
19
|
Harnessing Mucor spp. for Xylanase Production: Statistical Optimization in Submerged Fermentation Using Agro-Industrial Wastes. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3816010. [PMID: 35496057 PMCID: PMC9045992 DOI: 10.1155/2022/3816010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 04/01/2022] [Indexed: 11/18/2022]
Abstract
Xylan is the primary hemicellulosic polymer found in lignocellulosic agricultural wastes and can be degraded by xylanase. In the current research, Mucor circinelloides and M. hiemalis were tested for their ability to produce xylanase from tangerine peel by submerged fermentation. Experiments on five variables were designed with Box–Behnken design and response surface methodology. Analysis of variance was exercised, the xylanase output was demonstrated with a mathematical equation as a function of the five factors, and the quixotic states for xylanase biosynthesis was secured. In addition, xylanase was partially purified, characterized, and immobilized on calcium alginate beads. The optimum parameters for xylanase production by M. circinelloides and M. hiemalis were consisted of incubation temperature (30 and 20°C), pH value (9 and 7) incubation period (9 and 9 days), inoculum size (3 and 3 mL), and substrate concentration (3 and 3 g/100 mL), respectively. M. circinelloides and M. hiemalis demonstrated the highest xylanase activities after RSM optimization, with 42.23 and 35.88 U/mL, respectively. The influence of single, interchange, and quadratic factors on xylanase output was investigated using nonlinear regression equations with significant R2 and p values. The partial purification of M. circinelloides and M. hiemalis xylanase yielded 1.69- and 1.97-fold purification, and 30.74 and 31.34% recovery with 292.08 and 240.15 U/mg specific activity, respectively. Partially purified xylanase from M. circinelloides and M. hiemalis demonstrated the highest activity at neutral pH and 60 and 50°C, respectively. The immobilized M. circinelloides and M. hiemalis xylanase retained 84.02 and 79.43% activity, respectively. The production of xylanase from M. circinelloides and M. hiemalis utilizing RSM is deemed profitable for the decomposition of the agro-industrial wastes.
Collapse
|
20
|
Al-Askar AA, Rashad EM, Moussa Z, Ghoneem KM, Mostafa AA, Al-Otibi FO, Arishi AA, Saber WIA. A Novel Endophytic Trichoderma longibrachiatum WKA55 With Biologically Active Metabolites for Promoting Germination and Reducing Mycotoxinogenic Fungi of Peanut. Front Microbiol 2022; 13:772417. [PMID: 35401430 PMCID: PMC8993229 DOI: 10.3389/fmicb.2022.772417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Plant residuals comprise the natural habitat of the plant pathogen; therefore, attention is currently focusing on biological-based bioprocessing of biomass residuals into benefit substances. The current study focused on the biodegradation of peanut plant residual (PNR) into citric acid (CA) through a mathematical modeling strategy. Novel endophytic Trichoderma longibrachiatum WKA55 (GenBank accession number: MZ014020.1), having lytic (cellulase, protease, and polygalacturonase) activity, and tricalcium phosphate (TCP) solubilization ability were isolated from peanut seeds and used during the fermentation process. As reported by HPLC, the maximum CA (5505.1 μg/g PNR) was obtained after 9 days in the presence of 15.49 mg TCP, and 15.68 mg glucose. GC–MS analysis showed other bioactive metabolites in the filtrate of the fermented PNR. Practically, the crude product (40%) fully inhibited (100%) the growth and spore germination of three mycotoxinogenic fungi. On peanuts, it improved the seed germination (91%), seedling features, and vigor index (70.45%) with a reduction of abnormal seedlings (9.33%). The current study presents the fundamentals for large-scale production in the industry for the sustainable development of PNR biomass as a natural source of bioactive metabolites, and safe consumption of lignocellulosic-proteinaceous biomass, as well. T. longibrachiatum WKA55 was also introduced as a novel CA producer specified on PNR. Application of the resulting metabolite is encouraged on a large scale.
Collapse
Affiliation(s)
- Abdulaziz A. Al-Askar
- Department of Botany and Microbiology, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
- *Correspondence: Abdulaziz A. Al-Askar,
| | - Ehsan M. Rashad
- Department of Seed Pathology Research, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Zeiad Moussa
- Microbial Activity Unit, Department of Microbiology, Soils, Water and Environment Research Institute, Agricultural Research Center, Giza, Egypt
| | - Khalid M. Ghoneem
- Department of Seed Pathology Research, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ashraf A. Mostafa
- Department of Botany and Microbiology, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fatimah O. Al-Otibi
- Department of Botany and Microbiology, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
| | - Amr Abker Arishi
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - WesamEldin I. A. Saber
- Microbial Activity Unit, Department of Microbiology, Soils, Water and Environment Research Institute, Agricultural Research Center, Giza, Egypt
- WesamEldin I. A. Saber,
| |
Collapse
|
21
|
Zeng J, Huang W, Tian X, Hu X, Wu Z. Brewer’s spent grain fermentation improves its soluble sugar and protein as well as enzymatic activities using Bacillus velezensis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
22
|
Hazarika SN, Saikia K, Borah A, Thakur D. Prospecting Endophytic Bacteria Endowed With Plant Growth Promoting Potential Isolated From Camellia sinensis. Front Microbiol 2021; 12:738058. [PMID: 34659169 PMCID: PMC8515050 DOI: 10.3389/fmicb.2021.738058] [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: 07/08/2021] [Accepted: 08/20/2021] [Indexed: 01/11/2023] Open
Abstract
Endophytes are well-acknowledged inoculants to promote plant growth, and extensive research has been done in different plants. However, there is a lacuna about the endophytes associated with tea clones and their benefit to promote plant growth. The present study focuses on isolating and characterizing the beneficial endophytic bacteria (EnB) prevalent in commercially important tea clones cultivated in North Eastern India as plant growth promoters. Diversity of culturable EnB microbiome, in vitro traits for plant growth promotion (PGP), and applicability of potent isolates as bioinoculant for in vivo PGP abilities have been assessed in the present study. A total of 106 EnB identified as members of phyla Proteobacteria, Firmicutes, and Actinobacteria were related to 22 different genera and six major clusters. Regarding PGP traits, the percentage of isolates positive for the production of indole acetic acid, phosphate solubilization, nitrogen fixation siderophore, ammonia, and 1-aminocyclopropane-1-carboxylic acid deaminase production were 86.8, 28.3, 78.3, 30.2, 95.3, and 87.7, respectively. In total, 34.0, 52.8, and 17.0% of EnB showed notable production of hydrolytic enzymes like cellulase, protease, and amylase, respectively. Additionally, based on the bonitur score, the top two isolates K96 identified as Stenotrophomonas sp. and M45 identified as Pseudomonas sp. were evaluated for biofilm formation, motility, and in vivo plant growth promoting activity. Results suggested strong biofilm formation and motility in K96 and M45 which may attribute to the colonization of the strains in the plants. Further in vivo plant growth promotion experiment suggested sturdy efficacy of the K96 and M45 as plant growth promoters in nursery condition in commercial tea clones Tocklai vegetative (TV) TV22 and TV26. Thus, this study emphasizes the opportunity of commercialization of the selected isolates for sustainable development of tea and other crops.
Collapse
Affiliation(s)
- Shabiha Nudrat Hazarika
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India.,Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | - Kangkon Saikia
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
| | - Atlanta Borah
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
| | - Debajit Thakur
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
| |
Collapse
|
23
|
Koteshwara A. Simple Methods for the Preparation of Colloidal Chitin, Cell Free Supernatant and Estimation of Laminarinase. Bio Protoc 2021; 11:e4176. [PMID: 34722823 DOI: 10.21769/bioprotoc.4176] [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: 03/22/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 11/02/2022] Open
Abstract
Colloidal chitin (CC) is a common substrate used in research work involving chitin-active enzymes (chitinases). Cell free supernatant (CFS) is prepared from fermented broth. Preparation of CC and CFS usually involve large amounts of liquid, which must be separated from the solids. This necessitates the use of a large volume centrifugation facility, which may not be accessible to everyone. Filtration is a viable alternative to centrifugation, and several filter elements are described in the literature. Each of those elements has its own set of disadvantages like non-availability, high cost, fragility, and non-reusability. Here we describe the use of lab coat clothing material (LCCM) for the preparation of CC and CFS. For filtration purposes, the LCCM was found to be functional, rugged, reusable, and cost-effective. Also described here is a new method for the estimation of laminarinase using a laminarin infused agarose gel plate. An easily available optical fabric brightener (OFB) was used as a stain for the agarose plate. The laminarin infused agarose plate assay is simple, inexpensive, and was found to be impervious to high amounts of ammonium sulfate (AS) in enzyme precipitates.
Collapse
Affiliation(s)
- Ananthamurthy Koteshwara
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences (MCOPS), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| |
Collapse
|
24
|
Rodrigues GR, Pinto OHB, Schroeder LF, Fernandes GDR, Costa OYA, Quirino BF, Kuramae EE, Barreto CC. Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils. FEMS Microbiol Lett 2021; 367:5902847. [PMID: 32897365 DOI: 10.1093/femsle/fnaa149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/02/2020] [Indexed: 11/13/2022] Open
Abstract
The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.
Collapse
Affiliation(s)
- Gisele Regina Rodrigues
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| | - Otávio Henrique Bezerra Pinto
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| | - Luís Felipe Schroeder
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| | | | - Ohana Yonara Assis Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
| | - Betania Ferraz Quirino
- Brazilian Agricultural Research Corporation - EMBRAPA/Agroenergy, Brasília, DF 70770-901, Brazil
| | - Eiko Eurya Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CS, Utrecht, The Netherlands
| | - Cristine Chaves Barreto
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| |
Collapse
|
25
|
Castaldi S, Petrillo C, Donadio G, Piaz FD, Cimmino A, Masi M, Evidente A, Isticato R. Plant Growth Promotion Function of Bacillus sp. Strains Isolated from Salt-Pan Rhizosphere and Their Biocontrol Potential against Macrophomina phaseolina. Int J Mol Sci 2021; 22:3324. [PMID: 33805133 PMCID: PMC8036593 DOI: 10.3390/ijms22073324] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/11/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022] Open
Abstract
In recent decades, intensive crop management has involved excessive use of pesticides or fertilizers, compromising environmental integrity and public health. Accordingly, there has been worldwide pressure to find an eco-friendly and safe strategy to ensure agricultural productivity. Among alternative approaches, Plant Growth-Promoting (PGP) rhizobacteria are receiving increasing attention as suitable biocontrol agents against agricultural pests. In the present study, 22 spore-forming bacteria were selected among a salt-pan rhizobacteria collection for their PGP traits and their antagonistic activity against the plant pathogen fungus Macrophomina phaseolina. Based on the higher antifungal activity, strain RHFS10, identified as Bacillus vallismortis, was further examined and cell-free supernatant assays, column purification, and tandem mass spectrometry were employed to purify and preliminarily identify the antifungal metabolites. Interestingly, the minimum inhibitory concentration assessed for the fractions active against M. phaseolina was 10 times lower and more stable than the one estimated for the commercial fungicide pentachloronitrobenzene. These results suggest the use of B. vallismortis strain RHFS10 as a potential plant growth-promoting rhizobacteria as an alternative to chemical pesticides to efficiently control the phytopathogenic fungus M. phaseolina.
Collapse
Affiliation(s)
- Stefany Castaldi
- Department of Biology, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126 Naples, Italy; (S.C.); (C.P.)
| | - Claudia Petrillo
- Department of Biology, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126 Naples, Italy; (S.C.); (C.P.)
| | - Giuliana Donadio
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy;
| | - Fabrizio Dal Piaz
- Department of Medicine, Surgery and Dentistry, University of Salerno, Via Giovanni Paolo II, 84084 Fisciano, Italy;
| | - Alessio Cimmino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126 Naples, Italy; (A.C.); (M.M.); (A.E.)
| | - Marco Masi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126 Naples, Italy; (A.C.); (M.M.); (A.E.)
| | - Antonio Evidente
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126 Naples, Italy; (A.C.); (M.M.); (A.E.)
| | - Rachele Isticato
- Department of Biology, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126 Naples, Italy; (S.C.); (C.P.)
| |
Collapse
|
26
|
Koteshwara A, Philip NV, Aranjani JM, Hariharapura RC, Volety Mallikarjuna S. A set of simple methods for detection and extraction of laminarinase. Sci Rep 2021; 11:2489. [PMID: 33510321 PMCID: PMC7844030 DOI: 10.1038/s41598-021-81807-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/04/2020] [Indexed: 11/08/2022] Open
Abstract
A carefully designed ammonium sulfate precipitation will simplify extraction of proteins and is considered to be a gold standard among various precipitation methods. Therefore, optimization of ammonium sulfate precipitation can be an important functional step in protein purification. The presence of high amounts of ammonium sulphate precludes direct detection of many enzymatically active proteins including reducing sugar assays (e.g. Nelson-Somogyi, Reissig and 3,5-dinitrosalicylic acid methods) for assessing carbohydrases (e.g. laminarinase (β (1-3)-glucanohydrolase), cellulases and chitinases). In this study, a simple method was developed using laminarin infused agarose plate for the direct analysis of the ammonium sulphate precipitates from Streptomyces rimosus AFM-1. The developed method is simple and convenient that can give accurate results even in presence of ammonium sulfate in the crude precipitates. Laminarin is a translucent substrate requiring the use of a stain to visualize the zones of hydrolysis in a plate assay. A very low-cost and locally available fluorescent optical fabric brightener Tinopal CBS-X has been used as a stain to detect the zones of hydrolysis. We also report simple methods to prepare colloidal chitin and cell free supernatant in this manuscript.
Collapse
Affiliation(s)
- Ananthamurthy Koteshwara
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Nancy V Philip
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Jesil Mathew Aranjani
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Raghu Chandrashekhar Hariharapura
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Subrahmanyam Volety Mallikarjuna
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India.
| |
Collapse
|
27
|
Al-Askar AA, Saber WIA, Ghoneem KM, Hafez EE, Ibrahim AA. Crude Citric Acid of Trichoderma asperellum: Tomato Growth Promotor and Suppressor of Fusarium oxysporum f. sp. lycopersici. PLANTS 2021; 10:plants10020222. [PMID: 33498925 PMCID: PMC7912305 DOI: 10.3390/plants10020222] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
Presently, the bioprocessing of agricultural residues to various bioactive compounds is of great concern, with the potential to be used as plant growth promoters and as a reductive of various diseases. Lycopersiconesculentum, one of the most consumed crops in the human diet, is attacked by Fusarium wilt disease, so the main aim is to biocontrol the pathogen. Several fungal species were isolated from decayed maize stover (MS). Trichodermaasperellum was chosen based on its organic acid productivity and was molecularly identified (GenBank accession number is MW195019). Citric acid (CA) was the major detected organic acid by HPLC. In vitro, CA of T.asperellum at 75% completely repressed the growth of Fusariumoxysporum f. sp. lycopersici (FOL). In vivo, soaking tomato seeds in CA enhanced the seed germination and vigor index. T. asperellum and/or its CA suppressed the wilt disease caused by FOL compared to control. There was a proportional increment of plant growth and yield, as well as improvements in the biochemical parameters (chlorophyll pigments, total phenolic contents and peroxidase, and polyphenol oxidase activities), suggesting targeting both the bioconversion of MS into CA and biological control of FOL.
Collapse
Affiliation(s)
- Abdulaziz A. Al-Askar
- Botany and Microbiology Department, Faculty of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - WesamEldin I. A. Saber
- Microbial Activity Unit,Microbiology Department, Soils, Water and Environment Research Institute, Agricultural Research Center (ID: 60019332), Giza 12112, Egypt
- Correspondence: (W.I.A.S.); (A.A.I.); Tel.: +020-111-173-1062 (W.I.A.S.); +020-106-667-7539 (A.A.I.)
| | - Khalid M. Ghoneem
- Seed Pathology Research Department, Plant Pathology Research Institute, Agricultural Research Center (ID: 60019332), Giza 12112, Egypt;
| | - Elsayed E. Hafez
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, New Borg El-Arab, Alexandria 21934, Egypt;
| | - Amira A. Ibrahim
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, New Borg El-Arab, Alexandria 21934, Egypt;
- Correspondence: (W.I.A.S.); (A.A.I.); Tel.: +020-111-173-1062 (W.I.A.S.); +020-106-667-7539 (A.A.I.)
| |
Collapse
|
28
|
Karnaouri A, Zerva A, Christakopoulos P, Topakas E. Screening of Recombinant Lignocellulolytic Enzymes Through Rapid Plate Assays. Methods Mol Biol 2021; 2178:479-503. [PMID: 33128767 DOI: 10.1007/978-1-0716-0775-6_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the search for novel biomass-degrading enzymes through mining microbial genomes, it is necessary to apply functional tests during high-throughput screenings, which are capable of detecting enzymatic activities directly by way of plate assay. Using the most efficient expression systems of Escherichia coli and Pichia pastoris, the production of a high amount of His-tagged recombinant proteins could be thrived, allowing the one-step isolation by affinity chromatography. Here, we describe simple and efficient assay techniques for the detection of various biomass-degrading enzymatic activities on agar plates, such as cellulolytic, hemicellulolytic, and ligninolytic activities and their isolation using immobilized-metal affinity chromatography.
Collapse
Affiliation(s)
- Anthi Karnaouri
- Industrial Biotechnology and Biocatalysis Group, Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Anastasia Zerva
- Industrial Biotechnology and Biocatalysis Group, Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Paul Christakopoulos
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Evangelos Topakas
- Industrial Biotechnology and Biocatalysis Group, Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
| |
Collapse
|
29
|
Boonyapakron K, Chitnumsub P, Kanokratana P, Champreda V. Enhancement of catalytic performance of a metagenome-derived thermophilic oligosaccharide-specific xylanase by binding module removal and random mutagenesis. J Biosci Bioeng 2020; 131:13-19. [PMID: 33067124 DOI: 10.1016/j.jbiosc.2020.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
Xylo-oligosaccharide (XO) is a promising pre-biotic with applications in food, feed and healthcare products. XO can be produced by enzymatic digestion of xylan with xylanase. In this study, we aimed to improve the biochemical properties relevant to catalysis and kinetics of X11, a thermophilic glycosyl hydrolase (GH) family 11 endo-β-1,4-xylanase derived from a metagenomic library isolated from sugarcane bagasse, under high-temperature conditions preferred for XO synthesis. Removal of a carbohydrate-binding module (X11C) resulted in 6.5 fold greater catalytic efficiency. X11C was further improved by a Pro71Thr mutation in the X11P variant obtained from a random mutagenesis library, which exhibited 15.9 fold greater catalytic efficiency compared with wild-type X11 under the enzyme's optimal conditions of 80°C and pH 6.0. Homology modeling suggested that the improved performance of X11P could be attributed to formation of an extra H-bond between Thr71 and Ser75, which stabilizes the key catalytic residue Glu180 at the active pocket and β-sheet layers and agrees with the respective increase in melting temperature (Tm) where X11P >X11C >X11 as determined by differential scanning fluorimetry. The X11P variant was tested for hydrolysis of beechwood xylan, which showed X6 as the major product followed by X3 and X4 XOs. The highest yield of 5.5 g total XOs product/mg enzyme was observed for X11P, equivalent to 3.7 fold higher than that of wild-type with XO production of >800 mg/g xylan. The X11P enzyme could be developed as a thermophilic biocatalyst for XO synthesis in biorefineries.
Collapse
Affiliation(s)
- Katewadee Boonyapakron
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Pattanop Kanokratana
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand.
| |
Collapse
|
30
|
Kumari P, Sayas T, Bucki P, Brown-Miyara S, Kleiman M. Real-Time Visualization of Cellulase Activity by Microorganisms on Surface. Int J Mol Sci 2020; 21:ijms21186593. [PMID: 32916923 PMCID: PMC7555966 DOI: 10.3390/ijms21186593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 01/03/2023] Open
Abstract
A variety of methods to detect cellulase secretion by microorganisms has been developed over the years, none of which enables the real-time visualization of cellulase activity on a surface. This visualization is critical to study the interaction between soil-borne cellulase-secreting microorganisms and the surface of plant roots and specifically, the effect of surface features on this interaction. Here, we modified the known carboxymethyl cellulase (CMC) hydrolysis visualization method to enable the real-time tracking of cellulase activity of microorganisms on a surface. A surface was formed using pure CMC with acridine orange dye incorporated in it. The dye disassociated from the film when hydrolysis occurred, forming a halo surrounding the point of hydrolysis. This enabled real-time visualization, since the common need for post hydrolysis dyeing was negated. Using root-knot nematode (RKN) as a model organism that penetrates plant roots, we showed that it was possible to follow microorganism cellulase secretion on the surface. Furthermore, the addition of natural additives was also shown to be an option and resulted in an increased RKN response. This method will be implemented in the future, investigating different microorganisms on a root surface microstructure replica, which can open a new avenue of research in the field of plant root-microorganism interactions.
Collapse
Affiliation(s)
- Pallavi Kumari
- Institute of Plant Sciences, Agricultural Research Organization (Volcani Center), Rishon Lezion 7505101, Israel; (P.K.); (T.S.)
| | - Tali Sayas
- Institute of Plant Sciences, Agricultural Research Organization (Volcani Center), Rishon Lezion 7505101, Israel; (P.K.); (T.S.)
| | - Patricia Bucki
- Institute of Plant Protection, Agricultural Research Organization (Volcani Center), Rishon Lezion 7505101, Israel; (P.B.); (S.B.-M.)
| | - Sigal Brown-Miyara
- Institute of Plant Protection, Agricultural Research Organization (Volcani Center), Rishon Lezion 7505101, Israel; (P.B.); (S.B.-M.)
| | - Maya Kleiman
- Institute of Plant Sciences, Agricultural Research Organization (Volcani Center), Rishon Lezion 7505101, Israel; (P.K.); (T.S.)
- Agro-NanoTechnology and Advanced Materials Center, Agricultural Research Organization (Volcani Center), Rishon Lezion 7505101, Israel
- Correspondence:
| |
Collapse
|
31
|
Hossain TJ, Chowdhury SI, Mozumder HA, Chowdhury MNA, Ali F, Rahman N, Dey S. Hydrolytic Exoenzymes Produced by Bacteria Isolated and Identified From the Gastrointestinal Tract of Bombay Duck. Front Microbiol 2020; 11:2097. [PMID: 32983064 PMCID: PMC7479992 DOI: 10.3389/fmicb.2020.02097] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
Bacteria producing hydrolytic exoenzymes are of great importance considering their contribution to the host metabolism as well as for their various applications in industrial bioprocesses. In this work hydrolytic capacity of bacteria isolated from the gastrointestinal tract of Bombay duck (Harpadon nehereus) was analyzed and the enzyme-producing bacteria were genetically characterized. A total of twenty gut-associated bacteria, classified into seventeen different species, were isolated and screened for the production of protease, lipase, pectinase, cellulase and amylase enzymes. It was found that thirteen of the isolates could produce at least one of these hydrolytic enzymes among which protease was the most common enzyme detected in ten isolates; lipase in nine, pectinase in four, and cellulase and amylase in one isolate each. This enzymatic array strongly correlated to the previously reported eating behavior of Bombay duck. 16S rRNA gene sequence-based taxonomic classification of the enzyme-producing isolates revealed that the thirteen isolates were grouped into three different classes of bacteria consisting of eight different genera. Staphylococcus, representing ∼46% of the isolates, was the most dominant genus. Measurement of enzyme-production via agar diffusion technique revealed that one of the isolates which belonged to the genus Exiguobacterium, secreted the highest amount of lipolytic and pectinolytic enzymes, whereas a Staphylococcus species produced highest proteolytic activity. The Exiguobacterium sp. expressing a maximum of four hydrolases, appeared to be the most promising isolate of all.
Collapse
Affiliation(s)
- Tanim J. Hossain
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Sumaiya I. Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Halima A. Mozumder
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad N. A. Chowdhury
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
| | - Ferdausi Ali
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | - Nabila Rahman
- Department of Biology, Chittagong Sunshine College, Chattogram, Bangladesh
| | - Sujan Dey
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| |
Collapse
|
32
|
Castañeda-Cisneros YE, Mercado-Flores Y, Anducho-Reyes MA, Álvarez-Cervantes J, Ponce-Lira B, Evangelista-Martínez Z, Téllez-Jurado A. Isolation and Selection of Streptomyces Species from Semi-arid Agricultural Soils and Their Potential as Producers of Xylanases and Cellulases. Curr Microbiol 2020; 77:3460-3472. [PMID: 32797266 DOI: 10.1007/s00284-020-02160-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/06/2020] [Indexed: 11/25/2022]
Abstract
The Mezquital Valley (MV), Mexico, is a semi-arid region whose main economic activity is agriculture, this zone is characterized by the use of wastewater for crop irrigation. This condition has increased the amount nutrients in soils, organic carbon content and native microorganisms. The Streptomyces species are a group of saprophytic bacteria that represent between 20 and 60% of the total microbial population in soils, capable of producing metabolites of commercial importance. In this work, Streptomyces species were isolated from agricultural soils of the MV and was evaluated the production of endoglucanases (CMCase) and xylanases (Xyl) in Solid-State Cultivation (SSC). From soil samples, 73 possible strains of Streptomyces species were isolated for their ability to produce CMCase and Xyl in SSC. The study also included its characterization by morphological characteristics. Of the isolated microorganisms, 38 strains were selected as strong enzyme producers according to the measurement of the halo generated in plate and by growth on barley straw as only carbon source. Two different sizes of barley straw particle were tested, finding that the greatest enzymatic activity was observed in particle size 12. Three strains of Streptomyces species were chosen which presented the best catalytic capacities, a maximum of 100.69 AU Xyl/gram dry matter (gdm), 82 AU Xyl/gdm and 26.02 AU CMCase/gdm for strains 30, 28 and 12, respectively. The strains were identified by ribosomal gen16s sequence and identified as S. flavogriseus, S. virginiae and S. griseoaurantiacus. It is the first report of endogluconase and xylanolytic activity by S. virginiae isolated from a semi-arid soil.
Collapse
Affiliation(s)
- Y E Castañeda-Cisneros
- AgroBiotechnology Laboratory, Polytechnic University of Pachuca, Carr. Pachuca-Cd. Sahagún, km 20, Ex-Hacienda de Santa Bárbara, C.P. 43830, Zempoala, Hidalgo, Mexico
| | - Y Mercado-Flores
- AgroBiotechnology Laboratory, Polytechnic University of Pachuca, Carr. Pachuca-Cd. Sahagún, km 20, Ex-Hacienda de Santa Bárbara, C.P. 43830, Zempoala, Hidalgo, Mexico
| | - M A Anducho-Reyes
- AgroBiotechnology Laboratory, Polytechnic University of Pachuca, Carr. Pachuca-Cd. Sahagún, km 20, Ex-Hacienda de Santa Bárbara, C.P. 43830, Zempoala, Hidalgo, Mexico
| | - J Álvarez-Cervantes
- AgroBiotechnology Laboratory, Polytechnic University of Pachuca, Carr. Pachuca-Cd. Sahagún, km 20, Ex-Hacienda de Santa Bárbara, C.P. 43830, Zempoala, Hidalgo, Mexico
| | - B Ponce-Lira
- Department of Agrobiotechnology Engineering, Polytechnic University of Francisco I. Madero, Carretera Tepatepec-San Juan Tepa, C.P.42660, Francisco I. Madero, Hidalgo, Mexico
| | - Z Evangelista-Martínez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco. AC, Parque Científico Tecnológico de Yucatán, Sierra Papacal-Chuburná Puerto, C.P.97302, Mérida, Yucatán, Mexico
| | - A Téllez-Jurado
- AgroBiotechnology Laboratory, Polytechnic University of Pachuca, Carr. Pachuca-Cd. Sahagún, km 20, Ex-Hacienda de Santa Bárbara, C.P. 43830, Zempoala, Hidalgo, Mexico.
| |
Collapse
|
33
|
Kumla J, Suwannarach N, Sujarit K, Penkhrue W, Kakumyan P, Jatuwong K, Vadthanarat S, Lumyong S. Cultivation of Mushrooms and Their Lignocellulolytic Enzyme Production Through the Utilization of Agro-Industrial Waste. Molecules 2020; 25:molecules25122811. [PMID: 32570772 PMCID: PMC7355594 DOI: 10.3390/molecules25122811] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 12/18/2022] Open
Abstract
A large amount of agro-industrial waste is produced worldwide in various agricultural sectors and by different food industries. The disposal and burning of this waste have created major global environmental problems. Agro-industrial waste mainly consists of cellulose, hemicellulose and lignin, all of which are collectively defined as lignocellulosic materials. This waste can serve as a suitable substrate in the solid-state fermentation process involving mushrooms. Mushrooms degrade lignocellulosic substrates through lignocellulosic enzyme production and utilize the degraded products to produce their fruiting bodies. Therefore, mushroom cultivation can be considered a prominent biotechnological process for the reduction and valorization of agro-industrial waste. Such waste is generated as a result of the eco-friendly conversion of low-value by-products into new resources that can be used to produce value-added products. Here, we have produced a brief review of the current findings through an overview of recently published literature. This overview has focused on the use of agro-industrial waste as a growth substrate for mushroom cultivation and lignocellulolytic enzyme production.
Collapse
Affiliation(s)
- Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kanaporn Sujarit
- Division of Biology, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, Thanyaburi, Pathumthani 12110, Thailand;
| | - Watsana Penkhrue
- School of Preclinic, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
- Center of Excellence in Microbial Technology for Agricultural Industry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Pattana Kakumyan
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand;
| | - Kritsana Jatuwong
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Santhiti Vadthanarat
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
- Correspondence: ; Tel.: +668-1881-3658
| |
Collapse
|
34
|
Sahu PK, Singh S, Gupta A, Singh UB, Paul S, Paul D, Kuppusamy P, Singh HV, Saxena AK. A Simplified Protocol for Reversing Phenotypic Conversion of Ralstonia solanacearum during Experimentation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17124274. [PMID: 32549351 PMCID: PMC7344456 DOI: 10.3390/ijerph17124274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Ralstonia solanacearum has the problem of losing the virulence in laboratory conditions, during prolonged experimentation. Since pure colonies of R. solanacearum contain cell fractions differing in virulence, it was considered worthwhile to find a way of selecting the cells with lower attenuation. Therefore, a methodology for inducing virulent-type colonies occurrence in Ralstonia solanacearum was developed. METHODS Nutrient gradient was created by swabbing R. solanacearum culture in a slanted KMTTC medium, and Phyllanthus emblica extract was given by well diffusion. Live-dead cell imaging using BacLight, effects of ascorbic acid on cell viability, and production of virulence factors (exopolysaccharides, cellulase, and pectinase) supported this hypothesis. The tagging of R. solanacearum with green fluorescent protein and further confocal scanning laser microscopic visualization confirmed the colonization in vascular bundles of tomato. RESULTS P. emblica extract suppressed R. solanacearum initially in well diffusion, but further developed virulent-type colonies around the wells. Nutrient deprivation was found to have synergistic effects with P. emblica extract. The converted fluidal (virulent type) colonies could be able to colonize vascular bundles and cause wilting symptoms. CONCLUSION This method will be useful in the laboratories working on biocontrol of R. solanacearum for maintaining virulent-type colonies. Moreover, it could form the basis for studies on the stability of phenotypic conversion and cell fractions in R. solanacearum.
Collapse
Affiliation(s)
- Pramod Kumar Sahu
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan UP-275103, India; (S.S.); (A.G.); (U.B.S.); (S.P.); (H.V.S.); (A.K.S.)
- Corresponding author:
| | - Shailendra Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan UP-275103, India; (S.S.); (A.G.); (U.B.S.); (S.P.); (H.V.S.); (A.K.S.)
| | - Amrita Gupta
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan UP-275103, India; (S.S.); (A.G.); (U.B.S.); (S.P.); (H.V.S.); (A.K.S.)
| | - Udai B. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan UP-275103, India; (S.S.); (A.G.); (U.B.S.); (S.P.); (H.V.S.); (A.K.S.)
| | - Surinder Paul
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan UP-275103, India; (S.S.); (A.G.); (U.B.S.); (S.P.); (H.V.S.); (A.K.S.)
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr. Cleveland, GA 30528, USA;
| | - Pandiyan Kuppusamy
- ICAR-Central Institute for Research on Cotton Technology, Ginning Training Centre, Nagpur, Maharashtra 440023, India;
| | - Harsh V. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan UP-275103, India; (S.S.); (A.G.); (U.B.S.); (S.P.); (H.V.S.); (A.K.S.)
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan UP-275103, India; (S.S.); (A.G.); (U.B.S.); (S.P.); (H.V.S.); (A.K.S.)
| |
Collapse
|
35
|
Hughes KW, Matheny PB, Miller AN, Petersen RH, Iturriaga TM, Johnson KD, Methven AS, Raudabaugh DB, Swenie RA, Bruns TD. Pyrophilous fungi detected after wildfires in the Great Smoky Mountains National Park expand known species ranges and biodiversity estimates. Mycologia 2020; 112:677-698. [PMID: 32497465 DOI: 10.1080/00275514.2020.1740381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Following a late fall wildfire in 2016 in the Great Smoky Mountains National Park, pyrophilous fungi in burn zones were documented over a 2-y period with respect to burn severity and phenology. Nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) barcodes were obtained to confirm morphological evaluations. Forty-one taxa of Ascomycota and Basidiomycota were identified from burn sites and categorized as fruiting only in response to fire or fruiting enhanced by fire. Twenty-two species of Pezizales (Ascomycota) were among the earliest to form ascomata in severe burn zones, only one of which had previously been documented in the Great Smoky Mountains National Park. Nineteen species of Basidiomycota, primarily Agaricales, were also documented. Among these, only five species (Coprinellus angulatus, Gymnopilus decipiens, Lyophyllum anthracophilum, Pholiota carbonicola, and Psathyrella pennata) were considered to be obligate pyrophilous taxa, but fruiting of two additional taxa (Hygrocybe conica and Mycena galericulata) was clearly enhanced by fire. Laccaria trichodermophora was an early colonizer of severe burn sites and persisted through the winter of 2017 and into spring and summer of 2018, often appearing in close association with Pinus pungens seedlings. Fruiting of pyrophilous fungi peaked 4-6 mo post fire then diminished, but some continued to fruit up to 2.5 y after the fire. In all, a total of 27 previously unrecorded taxa were added to the All Taxa Biodiversity Inventory (ATBI) database (~0.9%). Most pyrophilous fungi identified in this study are either cosmopolitan or have a Northern Hemisphere distribution, but cryptic endemic lineages were detected in Anthracobia and Sphaerosporella. One new combination, Hygrocybe spadicea var. spadicea f. odora, is proposed.
Collapse
Affiliation(s)
- Karen W Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee , Knoxville, Tennessee 37996
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee , Knoxville, Tennessee 37996
| | - Andrew N Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign , 1816 South Oak Street, Champaign, Illinois 61820
| | - Ronald H Petersen
- Department of Ecology and Evolutionary Biology, University of Tennessee , Knoxville, Tennessee 37996
| | - Teresa M Iturriaga
- Illinois Natural History Survey, University of Illinois Urbana-Champaign , 1816 South Oak Street, Champaign, Illinois 61820.,School of Integrated Plant Science, Cornell University, 334 Plant Science Building , Ithaca, New York 14853-5904
| | - Kristine D Johnson
- Resource Management and Science Division, Great Smoky Mountains National Park, 107 Park Headquarters Road, Gatlinburg, Tennessee 37738
| | - Andrew S Methven
- Department of Biology, Savannah State University , 3219 College Street, Savannah, Georgia 31404
| | - Daniel B Raudabaugh
- Illinois Natural History Survey, University of Illinois Urbana-Champaign , 1816 South Oak Street, Champaign, Illinois 61820.,Department of Plant Biology, University of Illinois Urbana-Champaign , 606 Champaign, Illinois 61801
| | - Rachel A Swenie
- Department of Ecology and Evolutionary Biology, University of Tennessee , Knoxville, Tennessee 37996
| | - Thomas D Bruns
- Department of Plant and Microbial Biology, University of California , Berkeley, California 94520-3102
| |
Collapse
|
36
|
Singh S, Singh UB, Malviya D, Paul S, Sahu PK, Trivedi M, Paul D, Saxena AK. Seed Biopriming with Microbial Inoculant Triggers Local and Systemic Defense Responses against Rhizoctonia solani Causing Banded Leaf and Sheath Blight in Maize ( Zea mays L.). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E1396. [PMID: 32098185 PMCID: PMC7068308 DOI: 10.3390/ijerph17041396] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 11/17/2022]
Abstract
Plant growth promoting rhizobacteria Pseudomonas aeruginosa strain MF-30 isolated from maize rhizosphere was characterized for several plant growth stimulating attributes. The strain MF-30 was also evaluated for antifungal properties against Rhizoctonia solani causing banded leaf and sheath blight in maize (Zea mays L.) under in vitro conditions and was found to have higher mycelial growth suppression in the culture suspension (67.41%) followed by volatile organic compounds (62.66%) and crude extract (51.20%) in a dual plate assay. The endophytic and epiphytic colonization ability was tested using Green Fluorescent Protein (GFP)-tagging. Visualization through confocal scanning laser microscope clearly indicated that strain MF-30 colonizes the root and foliar parts of the plants. Further, the effects of seed bio-priming with P. aeruginosa MF-30 was evaluated in the induction and bioaccumulation of defense-related biomolecules, enzymes, natural antioxidants, and other changes in maize under pot trial. This not only provided protection from R. solani but also ensured growth promotion under pathogenic stress conditions in maize. The maximum concentration of hydrogen peroxide (H2O2) was reported in the root and shoot of the plants treated with R. solani alone (8.47 and 17.50 mmol mg-1 protein, respectively) compared to bioagent, P. aeruginosa MF-30 bio-primed plants (3.49 and 7.50 mmol mg-1 protein, respectively). Effects on total soluble sugar content, total protein, and total proline were also found to enhanced significantly due to inoculation of P. aeruginosa MF-30. The activities of anti-oxidative defense enzymes phenylalanine ammonia lyase (PAL), ascorbate peroxidase, peroxidase, superoxide dismutase, and catalase increased significantly in the plants bio-primed with P. aeruginosa MF-30 and subsequent foliar spray of culture suspension of MF-30 compared to pathogen alone inoculated plants. qRT-PCR analysis revealed that seed bio-priming and foliar application of P. aeruginosa MF-30 significantly increased the expression of PR-1 and PR-10 genes with the simultaneous decrease in the disease severity and lesion length in the maize plants under pathogenic stress conditions. A significant enhancement of shoot and root biomass was recorded in MF-30 bio-primed plants as compared to untreated control (p < 0.05). Significant increase in plant growth and antioxidant content, as well as decreased disease severity in the P. aeruginosa MF-30 bio-primed plants, suggested the possibility of an eco-friendly and economical means of achieving antioxidants-rich, healthier maize plants.
Collapse
Affiliation(s)
- Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow 227105, India
| | - Udai B. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| | - Pramod Kumar Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| | - Mala Trivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow 227105, India
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA;
| | - Anil Kumar Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan 275103, India; (S.S.); (U.B.S.); (D.M.); (S.P.); (P.K.S.); (A.K.S.)
| |
Collapse
|
37
|
Grujić M, Dojnov B, Potočnik I, Atanasova L, Duduk B, Srebotnik E, Druzhinina IS, Kubicek CP, Vujčić Z. Superior cellulolytic activity of Trichoderma guizhouense on raw wheat straw. World J Microbiol Biotechnol 2019; 35:194. [PMID: 31776792 DOI: 10.1007/s11274-019-2774-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/21/2019] [Indexed: 01/22/2023]
Abstract
Lignocellulosic plant biomass is the world's most abundant carbon source and has consequently attracted attention as a renewable resource for production of biofuels and commodity chemicals that could replace fossil resources. Due to its recalcitrant nature, it must be pretreated by chemical, physical or biological means prior to hydrolysis, introducing additional costs. In this paper, we tested the hypothesis that fungi which thrive on lignocellulosic material (straw, bark or soil) would be efficient in degrading untreated lignocellulose. Wheat straw was used as a model. We developed a fast and simple screening method for cellulase producers and tested one hundred Trichoderma strains isolated from wheat straw. The most potent strain-UB483FTG2/ TUCIM 4455, was isolated from substrate used for mushroom cultivation and was identified as T. guizhouense. After optimization of growth medium, high cellulase activity was already achieved after 72 h of fermentation on raw wheat straw, while the model cellulase overproducing strain T. reesei QM 9414 took 170 h and reached only 45% of the cellulase activity secreted by T. guizhouense. Maximum production levels were 1.1 U/mL (measured with CMC as cellulase substrate) and 0.7 U/mL (β-glucosidase assay). The T. guizhouense cellulase cocktail hydrolyzed raw wheat straw within 35 h. Our study shows that screening for fungi that successfully compete for special substrates in nature will lead to the isolation of strains with qualitatively and quantitatively superior enzymes needed for their digestion which could be used for industrial purposes.
Collapse
Affiliation(s)
- Marica Grujić
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia
| | - Biljana Dojnov
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
| | - Ivana Potočnik
- Laboratory of Applied Phytopathology, Institute of Pesticides and Environmental Protection, Banatska 31b, PO Box 163, Belgrade, Serbia
| | - Lea Atanasova
- Microbiology and Applied Genomics Group, Research Division of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Gumpendorferstrasse 1a/E166-5, 1060, Vienna, Austria.,Institute of Food Technology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Bojan Duduk
- Laboratory of Applied Phytopathology, Institute of Pesticides and Environmental Protection, Banatska 31b, PO Box 163, Belgrade, Serbia
| | - Ewald Srebotnik
- Bioresource Technology Group, Research Division of Bioresources and Plant Science, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Getreidemarkt 9/E166-A, 1060, Vienna, Austria
| | - Irina S Druzhinina
- Microbiology and Applied Genomics Group, Research Division of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Gumpendorferstrasse 1a/E166-5, 1060, Vienna, Austria.,Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Christian P Kubicek
- Microbiology and Applied Genomics Group, Research Division of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Gumpendorferstrasse 1a/E166-5, 1060, Vienna, Austria.,, Steinschötelgasse 7, 1100, Vienna, Austria
| | - Zoran Vujčić
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia
| |
Collapse
|
38
|
Alves KJ, da Silva MCP, Cotta SR, Ottoni JR, van Elsas JD, de Oliveira VM, Andreote FD. Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods. Braz J Microbiol 2019; 51:217-228. [PMID: 31741310 DOI: 10.1007/s42770-019-00162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/19/2019] [Indexed: 11/25/2022] Open
Abstract
Xylanase and α-amylase enzymes participate in the degradation of organic matter, acting in hemicellulose and starch mineralization, respectively, and are in high demand for industrial use. Mangroves represent a promising source for bioprospecting enzymes due to their unique characteristics, such as fluctuations in oxic/anoxic conditions and salinity. In this context, the present work aimed to bioprospect xylanases from mangrove soil using cultivation-dependent and cultivation-independent methods. Through screening from a metagenomic library, three potentially xylanolytic clones were obtained and sequenced, and reads were assembled into contigs and annotated. The contig MgrBr135 was affiliated with the Planctomycetaceae family and was one of 30 ORFs selected for subcloning that demonstrated only amylase activity. Through the cultivation method, 38 bacterial isolates with xylanolytic activity were isolated. Isolate 11 showed an enzymatic index of 10.9 using the plate assay method. Isolate 39 achieved an enzyme activity of 0.43 U/mL using the colorimetric method with 3,5-dinitrosalicylic acid. Isolate 39 produced xylanase on culture medium with salinity ranging from 1.25 to 5%. Partial 16S rRNA gene sequencing identified isolates in the Bacillus and Paenibacillus genera. The results of this study highlight the importance of mangroves as an enzyme source and show that bacterial groups can be used for starch and hemicellulose degradation.
Collapse
Affiliation(s)
- Kelly Jaqueline Alves
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil.
| | - Mylenne Calciolari Pinheiro da Silva
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
| | - Simone Raposo Cotta
- Center for Nuclear Energy in Agriculture, University of São Paulo, Centenario Avenue, 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Júlia Ronzella Ottoni
- University Center Dinâmica das Cataratas, Castelo Branco Street, 349, Foz do Iguaçu, Paraná, 85852-010, Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
| | - Valeria Maia de Oliveira
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Alexandre Cazellato Avenue, 999, Paulínia, São Paulo, 13140-000, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
| |
Collapse
|
39
|
Kalinina AN, Borshchevskaya LN, Gordeeva TL, Sineoky SP. Screening and Taxonomic Characterization of Xylanase Bacterial Producers. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683818070037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
40
|
Wang J, Chen X, Chio C, Yang C, Su E, Jin Y, Cao F, Qin W. Delignification overmatches hemicellulose removal for improving hydrolysis of wheat straw using the enzyme cocktail from Aspergillus niger. BIORESOURCE TECHNOLOGY 2019; 274:459-467. [PMID: 30553086 DOI: 10.1016/j.biortech.2018.12.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/07/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
Based on a general understanding that hemicellulose removal is more efficient than delignification for biomass deconstruction, an Aspergillus niger strain producing high xylanase activity was screened out from seventeen strains by clear halo experiments. Low-cost enzyme cocktail with high xylanase activity was produced from wheat straw medium fermented by the Gyx086 strain. The enzyme cocktail with high xylanase activity could more effectively hydrolyze wheat straw than other biomasses. However, only 30% of total carbohydrates could be hydrolyzed to reducing sugar in untreated wheat straw. Further enzymatic hydrolysis and pretreated trials were carried out, the results indicated that hemicellulose removal was less effective than delignification for de-recalcitrance of wheat straw and the crystallinity is little interference with the hydrolysis process. Delignified wheat straw was near-completely hydrolyzed by the enzyme cocktail in 60 h. This study advanced the knowledge in promoting wheat straw as feedstock for bio-based industry.
Collapse
Affiliation(s)
- Jiahong Wang
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China; Department of Biology, Lakehead University, Ontario P7B 5E1, Canada; Co-innovation Center for the Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Xuntong Chen
- Department of Biology, Lakehead University, Ontario P7B 5E1, Canada
| | - Chonlong Chio
- Department of Biology, Lakehead University, Ontario P7B 5E1, Canada
| | - Chun Yang
- Department of Biology, Lakehead University, Ontario P7B 5E1, Canada; Institute of Agricultural Products Processing, Shanxi Academy of Agricultural Science, Tianyuan 030031, China
| | - Erzheng Su
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yongcan Jin
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Fuliang Cao
- Co-innovation Center for the Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Wensheng Qin
- Department of Biology, Lakehead University, Ontario P7B 5E1, Canada.
| |
Collapse
|
41
|
Kumar B, Bhardwaj N, Alam A, Agrawal K, Prasad H, Verma P. Production, purification and characterization of an acid/alkali and thermo tolerant cellulase from Schizophyllum commune NAIMCC-F-03379 and its application in hydrolysis of lignocellulosic wastes. AMB Express 2018; 8:173. [PMID: 30334113 PMCID: PMC6192944 DOI: 10.1186/s13568-018-0696-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022] Open
Abstract
A cellulase producing fungus Schizophyllum commune NAIMCC-F-03379 was isolated from decomposed leaf sample of Lantana camera. The nutritional components (wheat bran, magnesium sulphate and calcium chloride concentrations) and physical parameters (temperature and pH) were optimised by response surface methodology for enhanced cellulase production by S. commune NAIMCC-F-03379. The optimized medium contained: 1% (w/v) wheat bran, 0.3 g/L MgSO4, 0.8–1.0 g/L CaCl2, optimum temperature and pH were 25 °C and 5 respectively. Under optimum condition, 5.35-fold increase in CMCase and 6.62-fold increase in FPase activity was obtained as compared to un-optimized condition. Crude cellulase enzyme was subjected to different purification techniques and comparative evaluation of their efficiency was performed. The aqueous two-phase system using polyethylene glycol 8000/MnSO4 system showed maximum purification with 10.4-fold increase in activity, 79.5% yield and 0.5 partition coefficient. The cellulase enzyme obtained from S. commune NAIMCC-F-03379 has shown high stability i.e. more than 55% relative activity after 12 h of incubation over wide range of temperature (25–65 °C) and pH (3–10). The molecular weight of the cellulase enzyme was estimated as ~ 60 kDa by using sodium dodecyl sulphate-polyacrylamide electrophoresis (SDS-PAGE) and zymography. Km and Vmax value of cellulase on carboxy-methyl cellulose were obtained as 0.0909 mg/mL and 45.45 μmol/min mg respectively. Rice straw and wheat bran were subjected to hydrolysis using cellulase and cellulase–xylanase cocktail and analysed by thin layer chromatography and high performance liquid chromatography (HPLC). The HPLC analysis showed glucose concentration of 1.162 mg/mL after enzymatic hydrolysis of rice straw.
Collapse
|
42
|
Lin JD, Lemay MA, Parfrey LW. Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera. Front Microbiol 2018; 9:1914. [PMID: 30177919 PMCID: PMC6110156 DOI: 10.3389/fmicb.2018.01914] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
Bacteria are integral to marine carbon cycling. They transfer organic carbon to higher trophic levels and remineralise it into inorganic forms. Kelp forests are among the most productive ecosystems within the global oceans, yet the diversity and metabolic capacity of bacteria that transform kelp carbon is poorly understood. Here, we use 16S amplicon and metagenomic shotgun sequencing to survey bacterial communities associated with the surfaces of the giant kelp Macrocystis pyrifera and assess the capacity of these bacteria for carbohydrate metabolism. We find that Macrocystis-associated communities are distinct from the water column, and that they become more diverse and shift in composition with blade depth, which is a proxy for tissue age. These patterns are also observed in metagenomic functional profiles, though the broader functional groups—carbohydrate active enzyme families—are largely consistent across samples and depths. Additionally, we assayed more than 250 isolates cultured from Macrocystis blades and the surrounding water column for the ability to utilize alginate, the primary polysaccharide in Macrocystis tissue. The majority of cultured bacteria (66%) demonstrated this capacity; we find that alginate utilization is patchily distributed across diverse genera in the Bacteroidetes and Proteobacteria, yet can also vary between isolates with identical 16S rRNA sequences. The genes encoding enzymes involved in alginate metabolism were detected in metagenomic data across taxonomically diverse bacterial communities, further indicating this capacity is likely widespread amongst bacteria in kelp forests. Overall, the M. pyrifera epibiota shifts across a depth gradient, demonstrating a connection between bacterial assemblage and host tissue state.
Collapse
Affiliation(s)
- Jordan D Lin
- Department of Botany, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada
| | - Matthew A Lemay
- Department of Botany, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada
| | - Laura W Parfrey
- Department of Botany, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
43
|
Takenaka M, Lee JM, Kahar P, Ogino C, Kondo A. Efficient and Supplementary Enzyme Cocktail from Actinobacteria and Plant Biomass Induction. Biotechnol J 2018; 14:e1700744. [PMID: 29981210 DOI: 10.1002/biot.201700744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 06/28/2018] [Indexed: 11/08/2022]
Abstract
Actinobacteria plays a key role in the cycling of organic matter in soils. They secret biomass-degrading enzymes that allow it to produce the unique metabolites that originate in plant biomass. Although past studies have focused on these unique metabolites, a large-scale screening of Actinobacteria is yet to be reported to focus on their biomass-degrading ability. In the present study, a rapid and simple method is constructed for a large-scale screening, and the novel resources that form the plant biomass-degrading enzyme cocktail are identified from 850 isolates of Actinobacteria. As a result, Nonomuraea fastidiosa secretes a biomass degrading enzyme cocktail with the highest enzyme titer, although cellulase activities are lower than a commercially available enzyme. So the rich accessory enzymes are suggested to contribute to the high enzyme titer for a pretreated bagasse with a synergistic effect. Additionally, an optimized cultivation method of biomass induction caused to produce the improved enzyme cocktail indicated strong enzyme titers and a strong synergistic effect. Therefore, the novel enzyme cocktails are selected via the optimized method for large-scale screening, and then the enzyme cocktail can be improved via the optimized production with biomass-induction.
Collapse
Affiliation(s)
- Musashi Takenaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
| | - Jae M Lee
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
| | - Prihardi Kahar
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho 1-1, 657-8501 Kobe, Japan
| |
Collapse
|
44
|
Saroj P, P M, Narasimhulu K. Characterization of thermophilic fungi producing extracellular lignocellulolytic enzymes for lignocellulosic hydrolysis under solid-state fermentation. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0216-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
45
|
Nie H, Wang Z, You J, Zhu G, Wang H, Wang F. Comparison of in vitro digestibility and chemical composition among four crop straws treated by Pleurotus ostreatus. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 33:24-34. [PMID: 29879812 PMCID: PMC6946984 DOI: 10.5713/ajas.18.0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/03/2018] [Indexed: 11/27/2022]
Abstract
Objective The effects of Pleurotus ostreatus on the feed utilization of broad bean stalks (BBS), rape straw (RS), paddy straw (PS), and corn stalk (CS) was examined. Methods The four roughages were co-cultured with Pleurotus ostreatus. The chemical composition; enzyme activities of laccase, carboxymethylcellulase (CMCase) and xylanase; carbohydrate and protein fractions (based on The Cornell Net Carbohydrate and Protein System [CNCPS]) were assessed at different days after inoculation (7, 14, 21, 28 d) and un-inoculated roughages (control, 0 d). The digestibility of nutrient components and the gas production of roughage with various incubation times were monitored at 0, 2, 4, 6, 9, 12, 24, 36, 48, 60, and 72 h using an in vitro ruminal fermentation method. Results A higher CMCase activity (0.1039 U/mL) and earlier time to peak (14 d) were detected in Pleurotus ostreatus cultured with CS (p<0.05). Significantly, the incubation length-dependent responses of cumulative gas production were observed from 24 to 72 hours post fermentation (p<0.05), and these incubation length-dependent effects on cumulative gas production of PS and CS appeared earlier (24 h) for PS and CS than those (48 h) for BBS and RS (p<0.05). The fast-degradable carbohydrate (CA) content for all four roughages significantly increased over time (p<0.05). Nonetheless, increased degradation efficiency for CA treated with Pleurotus ostreatus was detected at both 21 and 28 days of incubation (p<0.05). With the exception of PS (p<0.05), there were no significant difference among the roughages (p>0.05) in slowly-degradable carbohydrate (CB2) at different incubation times (p<0.05). Conclusion Assessment of the alterations in chemical composition, CNCPS system fractions, and the fermentation kinetics after biological pretreatment may yield a valuable database for evaluating the biological pretreatment of Pleurotus ostreatus in ruminant feed.
Collapse
Affiliation(s)
- Haitao Nie
- Deparment of Jiangsu Engineering Technology Research Center of Meat Sheep & Goat Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziyu Wang
- Deparment of Jiangsu Engineering Technology Research Center of Meat Sheep & Goat Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Jihao You
- Deparment of Jiangsu Engineering Technology Research Center of Meat Sheep & Goat Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Zhu
- Animal Husbandry and Veterinary Station of Guannan, Lianyungang 222500, China
| | - Hengchang Wang
- Animal Husbandry and Veterinary Station of Guannan, Lianyungang 222500, China
| | - Feng Wang
- Deparment of Jiangsu Engineering Technology Research Center of Meat Sheep & Goat Industry, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
46
|
Coronado-Ruiz C, Avendaño R, Escudero-Leyva E, Conejo-Barboza G, Chaverri P, Chavarría M. Two new cellulolytic fungal species isolated from a 19 th-century art collection. Sci Rep 2018; 8:7492. [PMID: 29748544 PMCID: PMC5945893 DOI: 10.1038/s41598-018-24934-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 04/12/2018] [Indexed: 11/08/2022] Open
Abstract
The archive of the Universidad de Costa Rica maintains a nineteenth-century French collection of drawings and lithographs in which the biodeterioration by fungi is rampant. Because of nutritional conditions in which these fungi grew, we suspected that they possessed an ability to degrade cellulose. In this work our goal was to isolate and identify the fungal species responsible for the biodegradation of a nineteenth-century art collection and determine their cellulolytic activity. Fungi were isolated using potato-dextrose-agar (PDA) and water-agar with carboxymethyl cellulose (CMC). The identification of the fungi was assessed through DNA sequencing (nrDNA ITS and α-actin regions) complemented with morphological analyses. Assays for cellulolytic activity were conducted with Gram's iodine as dye. Nineteen isolates were obtained, of which seventeen were identified through DNA sequencing to species level, belonging mainly to genera Arthrinium, Aspergillus, Chaetomium, Cladosporium, Colletotrichum, Penicillium and Trichoderma. For two samples that could not be identified through their ITS and α-actin sequences, a morphological analysis was conducted; they were identified as new species, named Periconia epilithographicola sp. nov. and Coniochaeta cipronana sp. nov. Qualitative tests showed that the fungal collection presents important cellulolytic activity.
Collapse
Affiliation(s)
- Carolina Coronado-Ruiz
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica
| | - Efraín Escudero-Leyva
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
| | - Geraldine Conejo-Barboza
- Escuela de Química, Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
- Instituto de Investigaciones en Arte (II Arte), 11501-2060, San Jose, Costa Rica
| | - Priscila Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, Maryland, USA
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica.
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica.
- Escuela de Química, Universidad de Costa Rica, 11501-2060, San Jose, Costa Rica.
| |
Collapse
|
47
|
Cao SN, Yuan Y, Qin YH, Zhang MZ, de Figueiredo P, Li GH, Qin QM. The pre-rRNA processing factor Nop53 regulates fungal development and pathogenesis via mediating production of reactive oxygen species. Environ Microbiol 2018; 20:1531-1549. [PMID: 29488307 DOI: 10.1111/1462-2920.14082] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 11/28/2022]
Abstract
Botrytis cinerea is a necrotrophic plant fungal pathogen that annually causes enormous economic losses worldwide. The ribosome is an organelle for cellular protein biosynthesis. However, little is known about how the ribosome operates as a machine to mediate microbial pathogenesis. Here, we demonstrate that Nop53, a late-acting factor for 60S ribosomal subunit maturation, is crucial for the pathogen's development and virulence. BcNop53 is functionally equivalent to yeast nop53p. Complementation of BcNOP53 completely restored the growth defect of the yeast Δnop53 mutant. BcNop53 is located in nuclei and disruption of BcNOP53 also dramatically impaired pathogen growth. Deletion of BcNOP53 blocked infection structure formation and abolished virulence of the pathogen, possibly due to reduced production of reactive oxygen species. Moreover, loss of BcNOP53 impaired pathogen conidiation and stress adaptation, altered conidial and sclerotial morphology, retarded conidium and sclerotium germination as well as reduced the activities of cell-wall degradation-associated enzymes. Sclerotium production was, however, increased. Complementation with the wild-type BcNOP53 allele rescued defects found in the ΔBcnop53 mutant. Our work establishes a systematic elucidation of Nop53 in regulating microbial development and pathogenesis, provides novel insights into ribosomal processes that regulate fungal pathogenesis, and may open up new targets for addressing fungal diseases.
Collapse
Affiliation(s)
- Sheng-Nan Cao
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Ye Yuan
- College of Plant Sciences, Jilin University, Changchun 130062, China.,Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun 130062, China
| | - Yu Haity Qin
- College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ming-Zhe Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, TX 77843, USA.,Norman Borlaug Center, Texas A&M University, College Station, TX 77843, USA.,Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Gui-Hua Li
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Qing-Ming Qin
- College of Plant Sciences, Jilin University, Changchun 130062, China.,Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun 130062, China
| |
Collapse
|
48
|
Rahmani N, Kahar P, Lisdiyanti P, Hermiati E, Lee J, Yopi, Prasetya B, Ogino C, Kondo A. Xylanase and feruloyl esterase from actinomycetes cultures could enhance sugarcane bagasse hydrolysis in the production of fermentable sugars. Biosci Biotechnol Biochem 2018; 82:1-12. [PMID: 29475403 DOI: 10.1080/09168451.2018.1438169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/30/2018] [Indexed: 10/18/2022]
Abstract
The addition of enzymes that are capable of degrading hemicellulose has a potential to reduce the need for commercial enzymes during biomass hydrolysis in the production of fermentable sugars. In this study, a high xylanase producing actinomycete strain (Kitasatospora sp. ID06-480) and the first ethyl ferulate producing actinomycete strain (Nonomuraea sp. ID06-094) were selected from 797 rare actinomycetes, respectively, which were isolated in Indonesia. The addition (30%, v/v) of a crude enzyme supernatant from the selected strains in sugarcane bagasse hydrolysis with low-level loading (1 FPU/g-biomass) of Cellic® CTec2 enhanced both the released amount of glucose and reducing sugars. When the reaction with Ctec2 was combined with crude enzymes containing either xylanase or feruloyl esterase, high conversion yield of glucose from cellulose at 60.5% could be achieved after 72 h-saccharification.
Collapse
Affiliation(s)
- Nanik Rahmani
- a Research Center for Biotechnology , Indonesian Institute of Sciences, Cibinong Science Center , Cibinong , Indonesia
| | - Prihardi Kahar
- b Department of Chemical and Engineering, Graduate School of Engineering , Kobe University , Kobe , Japan
| | - Puspita Lisdiyanti
- a Research Center for Biotechnology , Indonesian Institute of Sciences, Cibinong Science Center , Cibinong , Indonesia
| | - Euis Hermiati
- c Research Center for Biomaterial , Indonesian Institute of Sciences, Cibinong Science Center , Cibinong , Indonesia
| | - Jaemin Lee
- b Department of Chemical and Engineering, Graduate School of Engineering , Kobe University , Kobe , Japan
| | - Yopi
- a Research Center for Biotechnology , Indonesian Institute of Sciences, Cibinong Science Center , Cibinong , Indonesia
| | - Bambang Prasetya
- a Research Center for Biotechnology , Indonesian Institute of Sciences, Cibinong Science Center , Cibinong , Indonesia
- d National Standardization Agency of Indonesia, Gedung I BPPT , Jakarta , Indonesia
| | - Chiaki Ogino
- b Department of Chemical and Engineering, Graduate School of Engineering , Kobe University , Kobe , Japan
| | - Akihiko Kondo
- b Department of Chemical and Engineering, Graduate School of Engineering , Kobe University , Kobe , Japan
- e Graduate School of Science, Technology and Innovation , Kobe University , Kobe , Japan
| |
Collapse
|
49
|
Schückel J, Kračun SK. Two-Dimensional High-Throughput Endo-Enzyme Screening Assays Based on Chromogenic Polysaccharide Hydrogel and Complex Biomass Substrates. Methods Mol Biol 2018; 1796:201-217. [PMID: 29856056 DOI: 10.1007/978-1-4939-7877-9_15] [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] [Indexed: 06/08/2023]
Abstract
In this chapter, we present a two-dimensional approach for high-throughput screening of endo-cellulases as well as other endo-acting enzymes. The method is based on chromogenic substrates, produced either from purified or complex material, providing valuable information about enzyme activity toward its target as well as that same target in a context of complex natural material normally encountered in bioindustrial settings. The enzymes that can be tested using this assay can be from virtually any source: in purified form, directly from microbial cultures or even from raw materials, enabling study of the interplay between enzyme mixtures such as synergistic or inhibitory effects. By using the method of analysis described in this chapter, enzymes can be screened and evaluated quickly and information pertinent to both the inherent properties of the enzyme itself as well as predictions about its performance on complex biomass samples can be obtained.
Collapse
|
50
|
Gagoski D, Shi Z, Nielsen LK, Vickers CE, Mahler S, Speight R, Johnston WA, Alexandrov K. Cell-free pipeline for discovery of thermotolerant xylanases and endo -1,4-β-glucanases. J Biotechnol 2017; 259:191-198. [DOI: 10.1016/j.jbiotec.2017.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/04/2017] [Accepted: 07/12/2017] [Indexed: 11/29/2022]
|