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Mu M, Yang F, Han B, Tian G, Zhang K. Vermicompost: In situ retardant of antibiotic resistome accumulation in cropland soils. J Environ Sci (China) 2024; 141:277-286. [PMID: 38408828 DOI: 10.1016/j.jes.2023.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 02/28/2024]
Abstract
The dissemination of antibiotic resistance genes (ARGs) in soil has become a global environmental issue. Vermicomposting is gaining prominence in agricultural practices as a soil amendment to improve soil quality. However, its impact on soil ARGs remains unclear when it occurs in farmland. We comprehensively explored the evolution and fate of ARGs and their hosts in the field soil profiles under vermicompost application for more than 3 years. Vermicompost application increased several ARG loads in soil environment but decreased the high-risk bla-ARGs (blaampC, blaNDM, and blaGES-1) by log(0.04 - 0.43). ARGs in soil amended with vermicompost primarily occurred in topsoil (approximately 1.04-fold of unfertilized soil), but it is worth noting that their levels in the 40-60 cm soil layer were the same or even less than in the unfertilized soil. The microbial community structure changed in soil profiles after vermicompost application. Vermicompost application altered the microbial community structure in soil profiles, showing that the dominant bacteria (i.e., Proteobacteria, Actinobacteriota, Firmicutes) were decreased 2.62%-5.48% with the increase of soil depth. A network analysis further revealed that most of ARG dominant host bacteria did not migrate from surface soil to deep soil. In particular, those host bacteria harboring high-risk bla-ARGs were primarily concentrated in the surface soil. This study highlights a lower risk of the propagation of ARGs caused by vermicompost application and provides a novel approach to reduce and relieve the dissemination of ARGs derived from animals in agricultural production.
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Affiliation(s)
- Meirui Mu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Guisheng Tian
- Wuxue City Agriculture and Rural Bureau, Wuhan 435400, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Key Laboratory of Low-carbon Green Agriculture in North China, Ministry of Agriculture and Rural Affairs P. R. China, Beijing 10083, China.
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Bacterial Community and Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates from the Environment of a Health Care Facility in the Western Region of Saudi Arabia. Pharmaceuticals (Basel) 2022; 15:ph15050611. [PMID: 35631436 PMCID: PMC9145440 DOI: 10.3390/ph15050611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022] Open
Abstract
The escalating transmission of hospital-acquired infections, especially those due to antimicrobial-resistant bacteria, is a major health challenge worldwide. In this study, a culturomic analysis of bacterial community in a tertiary care hospital in the western region of Saudi Arabia is performed using environmental samples. The genome sequencing of four Acinetobacter baumannii was performed on isolates recovered from an intensive care unit (ICU) environment and clinical samples. A total of 361 bacterial isolates from surface and air samples were identified by MALDI-TOF technique or 16S rRNA gene sequencing. The isolates were classified into 70 distinct species, including ESKAPE pathogens. Resistance in Gram-positive isolates was mainly found to be against benzylpenicillin, azithromycin, ampicillin, and trimethoprim/sulfamethoxazole. Carbapenem- and multidrug-resistant isolates of A. baumannii and Klebsiella pneumonia were found on the ICU surfaces. Genome sequencing revealed that the carbapenem-resistant A. baumannii isolate from ICU environment was linked with those of clinical origin. The isolate Ab133-HEnv was classified as a novel sequence type (ST2528) based on a new allele of Oxf_gdhB-286. Three beta-lactam-antibiotic-resistance genes, blaADC-25, blaOXA-23, and blaOXA-66, were found in most of the analyzed genomes. Collectively, the results of this study highlight the spread of antimicrobial-resistant nosocomial pathogens in a health care facility in Saudi Arabia.
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Vermicompost and Its Derivatives against Phytopathogenic Fungi in the Soil: A Review. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Synthetic chemicals, such as fertilizers and pesticides, are abundantly used in agriculture to enhance soil fertility and prevent the occurrence of diseases, respectively. Many studies have reported a negative influence of these chemicals on the soil environment. Natural sources from earthworms and their products, as a result of vermicomposting, may be considered better alternatives. The aim of this review was to reveal the source of antifungal efficiency of vermicompost and its derivatives, such as vermiwash, coelomic fluid, skin secretion of earthworms, and metabolites from decomposer bacteria in vermicompost, in order to highlight their application in agriculture. The synergistic activity of bioactive compounds present in coelomic fluid, mucus, skin secretion, and metabolites from associated bacteria (decomposer) assisted crop plants for effective action against various soil pathogenic fungi, such as Rhizoctoniasolani, Alternaria solani, Aspergillus niger, A.flavus, Fusariumoxysporum, and F. graminearum. Thus, these bioactive metabolites can be recommended to suppress plant fungal diseases. Vermicompost and its derivatives should be considered for use in agricultural fields to control harmful soil fungi and increase crop productivity.
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Yasir M, Khan R, Ullah R, Bibi F, Khan I, Mustafa Karim A, Al-Ghamdi AK, Azhar EI. Bacterial diversity and the antimicrobial resistome in the southwestern highlands of Saudi Arabia. Saudi J Biol Sci 2022; 29:2138-2147. [PMID: 35531257 PMCID: PMC9072880 DOI: 10.1016/j.sjbs.2021.11.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/06/2021] [Accepted: 11/17/2021] [Indexed: 11/24/2022] Open
Abstract
Soil is a reservoir of microbial diversity and the most supportive habitat for acquiring and transmitting antimicrobial resistance. Resistance transfer usually occurs from animal to soil and vice versa, and it may ultimately appear in clinical pathogens. In this study, the southwestern highlands of Saudi Arabia were studied to assess the bacterial diversity and antimicrobial resistance that could be affected by the continuous development of tourism in the region. Such effects could have a long-lasting impact on the local environment and community. Culture-dependent, quantitative polymerase chain reaction (qPCR), and shotgun sequencing-based metagenomic approaches were used to evaluate the diversity, functional capabilities, and antimicrobial resistance of bacteria isolated from collected soil samples. Bacterial communities in the southwestern highlands were mainly composed of Proteobacteria, Bacteroidetes, and Actinobacteria. A total of 102 antimicrobial resistance genes (ARGs) and variants were identified in the soil microbiota and were mainly associated with multidrug resistance, followed by macrolide, tetracycline, glycopeptide, bacitracin, and beta-lactam antibiotic resistance. The mechanisms of resistance included efflux, antibiotic target alteration, and antibiotic inactivation. qPCR confirmed the detection of 18 clinically important ARGs. In addition, half of the 49 identified isolates were phenotypically resistant to at least one of the 15 antibiotics tested. Overall, ARGs and indicator genes of anthropogenic activities (human-mitochondrial [hmt] gene and integron-integrase [int1]) were found in relatively lower abundance. Along with a high diversity of bacterial communities, variation was observed in the relative abundance of bacterial taxa among sampling sites in the southwestern highlands of Saudi Arabia.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Riaz Ullah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Imran Khan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau S.A.R
| | - Asad Mustafa Karim
- Department of Bioscience and Biotechnology, The University of Suwon, Hwaseong City, Gyeonggi-do, Republic of Korea
| | - Ahmed K Al-Ghamdi
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Krishnaswamy VG, Sridharan R, Kumar PS, Fathima MJ. Cellulase enzyme catalyst producing bacterial strains from vermicompost and its application in low-density polyethylene degradation. CHEMOSPHERE 2022; 288:132552. [PMID: 34648790 DOI: 10.1016/j.chemosphere.2021.132552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/13/2021] [Accepted: 10/10/2021] [Indexed: 06/13/2023]
Abstract
Cellulose is the main polysaccharide present abundantly in the earth, an important substrate for the cellulase enzyme. Cellulases have attracted considerable attention due to its diverse application in different textile, detergent, leather, food, feed and paper industries. Among the cellulase producing microbes, bacteria have a faster growth compared to other microbes. The present study focuses on isolating bacterial strains (Bacillus pacificus and Pseudomonas mucidolens) from vermicompost. The study focused on extracting cellulase enzyme and its molecular weight using SDS-PAGE, which was determined to be 32Kda. The maximum enzyme activity resulted to be 0.12 U/mL and 0.17 U/mL after dialysis. The LDPE degradation was reported up to 30 days. Further, the growth conditions of the bacterial strains were optimised at different pH and temperature. The degradation of LDPE was determined using FTIR analysis, resulting in the peak changes (formation and shifts). The bacterial strains were morphologically characterized using Scanning Electron Microscopy. The bacterial strains Bacillus pacificus and Pseudomonas mucidolens were identified using 16 S rRNA sequencing.
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Affiliation(s)
- Veena Gayathri Krishnaswamy
- Department of Biotechnology, Stella Maris College (Autonomous), Affiliated to University of Madras, Chennai, India.
| | - Rajalakshmi Sridharan
- Department of Biotechnology, Stella Maris College (Autonomous), Affiliated to University of Madras, Chennai, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, Chennai, 603 110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, Chennai, 603 110, India.
| | - Mariyam Jaffer Fathima
- Department of Biotechnology, Stella Maris College (Autonomous), Affiliated to University of Madras, Chennai, India
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Srivastava V, Squartini A, Masi A, Sarkar A, Singh RP. Metabarcoding analysis of the bacterial succession during vermicomposting of municipal solid waste employing the earthworm Eisenia fetida. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:144389. [PMID: 33429300 DOI: 10.1016/j.scitotenv.2020.144389] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
A culture-independent DNA metabarcoding analysis of the bacterial communities was carried out throughout a complete vermicomposting cycle of municipal solid waste material using the earthworm Eisenia fetida. 16S rRNA amplicons from the initial material (0 days), an intermediate (42 days), and a final stage (84 days) were sequenced in an Illumina NGS platform and compared. A steady increase in community diversity was observed corresponding to a 2.5-fold higher taxa richness and correspondingly risen values of the Shannon and Simpson ecological indexes and the evenness parameter. A total of 49,665 operational taxonomic units (OTUs) were counted. From the qualitative standpoint, a clear successional shift was observed with an initial community dominated by putatively plant-associated groups belonging to the Rhizobiales order within the Alphaproteobacteria class, regressively leaving the scores of relative abundance (RA) to the Firmicutes phylum and in particular to the Bacilli. Vermistabilization of municipal solid waste (MSW) increased (p < 0.001) the TKN and total P content in the final vermicompost, while pH, TOC, and C/N ratio declined (p < 0.001) in the process. Likewise, a progressive decrease was noticed in β-glucosidase, acid phosphatase, and urease activity while protease and dehydrogenase showed a slight increase, followed by a steep fall. A strong positive correlation was observed among the canonical functions of physico-chemical attributes and enzyme activities. The canonical correspondence analysis (CCA) revealed that significant families did not change on the temporal scale; however, their abundance was influenced by the abiotic environmental factors. In comparison to prior studies on vermicomposting that used different earthworm species (Eisenia andrei) and different substrates, results reflect a considerable degree of substrate specificity for the earthworm species used. The results offer clues to optimize the vermistabilization of MSW along with its potential use in agriculture, to foster improved levels of the circular economy.
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Affiliation(s)
- Vaibhav Srivastava
- Department of Environment & Sustainable Development, Institute of Environment & Sustainable Development, Banaras Hindu University, Varanasi 221005, India
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Università, 16, 35020 Legnaro, PD, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Università, 16, 35020 Legnaro, PD, Italy
| | - Abhijit Sarkar
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732103, West Bengal, India.
| | - Rajeev Pratap Singh
- Department of Environment & Sustainable Development, Institute of Environment & Sustainable Development, Banaras Hindu University, Varanasi 221005, India.
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Yasir M, Qureshi AK, Azhar EI. 16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients. PeerJ 2021; 9:e10995. [PMID: 33859871 PMCID: PMC8020870 DOI: 10.7717/peerj.10995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/02/2021] [Indexed: 12/05/2022] Open
Abstract
Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from the non-enriched Tatta Pani hot spring sediment samples, and 33 distinct bacterial phyla and 890 genera from the enriched sediment samples. Unique phyla specimens from the enriched samples included Candidatus Cloacimonetes, Caldiserica, and Korarchaeota archaea. The enriched samples yielded specific microbiota including 805 bacteria and 42 archaea operational taxonomic units with 97% similarity, though decreased thermophilic microbiota were observed in the enriched samples. Microbial diversity increased as temperature decreased. Candidate novel species were isolated from the culture-dependent screening, along with several genera that were not found in the 16S amplicon sequencing data. Overall, the enriched sediments showed high microbial diversity but with adverse changes in the composition of relatively dominant bacteria. Metagenomic analyses are needed to study the diversity, phylogeny, and functional investigation of hot spring microbiota.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arooj K Qureshi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Singh R, D'Alessio M, Meneses Y, Bartelt-Hunt S, Ray C. Nitrogen removal in vermifiltration: Mechanisms, influencing factors, and future research needs. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 281:111868. [PMID: 33387734 DOI: 10.1016/j.jenvman.2020.111868] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
To meet global health and sanitation goals, there is a continued need for sustainable wastewater treatment alternatives that require minimal energy and investment. Vermifiltration, a technology gaining relevance in Africa and Asia, may be an alternative to traditional wastewater treatment systems due to its cost-effectiveness, ease of application and maintenance, and sustainability. However, nitrogen removal in vermifiltration is not well understood since most of the prior research focuses on organics removal. Thus, a state of the art review is necessary to separately focus on the mechanisms associated with nitrogen removal in vermifiltration, along with the factors affecting nitrogen removal. For the first time, this review attempts to present the types of vermifilter based on their flow pattern. The review further discusses the current status of the application of vermifiltration, along with the benefits and limitations associated with the adoption of this technology. It also explores possible strategies that could be adopted to maximize the nitrogen removal potential of vermifilters as optimizing nitrogen removal is critical for improving the performance of vermifiltration based treatment systems.
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Affiliation(s)
- Rajneesh Singh
- Nebraska Water Center, University of Nebraska-Lincoln, NE, USA
| | - Matteo D'Alessio
- Department of Civil Engineering, University of Mississippi, MS, USA
| | - Yulie Meneses
- Daugherty Water for Food Global Institute, University of Nebraska-Lincoln, NE, USA
| | - Shannon Bartelt-Hunt
- Daugherty Water for Food Global Institute, University of Nebraska-Lincoln, NE, USA; Dept. of Civil and Environmental Engineering, University of Nebraska-Lincoln, NE, USA
| | - Chittaranjan Ray
- Nebraska Water Center, University of Nebraska-Lincoln, NE, USA; Daugherty Water for Food Global Institute, University of Nebraska-Lincoln, NE, USA; Dept. of Civil and Environmental Engineering, University of Nebraska-Lincoln, NE, USA.
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Przemieniecki SW, Zapałowska A, Skwiercz A, Damszel M, Telesiński A, Sierota Z, Gorczyca A. An evaluation of selected chemical, biochemical, and biological parameters of soil enriched with vermicompost. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:8117-8127. [PMID: 33051843 PMCID: PMC7854409 DOI: 10.1007/s11356-020-10981-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
The aim of this study was to assess the changes in chemical and microbial properties and enzymatic activity of soil enriched with vermicompost derived from household waste. The vermicompost was tested in the rhizosphere of Larix decidua seedlings cultivated in 10-L pots in: (i) nursery soil (as the control), (ii) soil with 10% v/v vermicompost, and (iii) with 20% v/v vermicompost. The impact of vermicompost was assessed in terms of soil C/N ratio; bacterial, fungal, and nematode counts; and enzymatic activity. It was found that vermicompost increased the C/N ratio from 21 to 32, as well as the content of nitrate from 78 to 134 mg kg-1, of ammonium from 14 to 139 mg kg-1, of phosphorus from 92 to 521 mg kg-1, and of potassium from 142 to 1912 mg kg-1, compared with the control soil. The abundance of beneficial bacteria was increased (from 8.61 × 107 to 37.9 × 107), along with decreases in microbiological ratios of fungi and bacteria (e.g. fungi/Bacillus from 0.18818 to 0.00425). A significant 2- to 4-fold increase was observed compared with the control in the number of beneficial nematodes belonging to bacterivorous, fungivorous, and predatory groups with no change in the abundance of plant-parasitic nematodes. Addition of vermicompost brought about a change in soil enzyme activity. Vermicompost reduced the activity of alkaline phosphatase only. Both doses of vermicompost led to an increase in the activity of acid phosphatase, inorganic pyrophosphatase, dehydrogenases, β-glucosidase, and urease. Only the higher dose had an effect on increasing the activity of o-diphenol oxidase and proteases. No significant change was observed for nitrate reductase. Also, the presence of antibiotics produced by bacteria was detected depending on the dose of vermicompost, e.g. iturin (ituC) and bacillomycin (bmyB) were found in soil with a dose of 20% v/v vermicompost. Overall, vermicompost produced from household waste can be an excellent organic fertilizer for larch forest nurseries.
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Affiliation(s)
- Sebastian Wojciech Przemieniecki
- Faculty of Environmental Management and Agriculture, Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-720, Olsztyn, Poland.
| | - Anita Zapałowska
- College of Natural Sciences, Institute of Agricultural Sciences, Land Management and Environmental Protection, University of Rzeszów, Cwiklinskiej 1a, 35-601, Rzeszów, Poland
| | - Andrzej Skwiercz
- Faculty of Environmental Management and Agriculture, Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-720, Olsztyn, Poland
- Department of Pests Management, Research Institute of Horticulture in Skierniewice, Pomologiczna 18, 96-100, Skierniewice, Poland
| | - Marta Damszel
- Faculty of Environmental Management and Agriculture, Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-720, Olsztyn, Poland
| | - Arkadiusz Telesiński
- Faculty of Environmental Management and Agriculture, Department of Bioengineering, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Zbigniew Sierota
- Faculty of Environmental Management and Agriculture, Department of Forestry and Forest Ecology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 2, 10-727, Olsztyn, Poland
| | - Anna Gorczyca
- Faculty of Agriculture and Economics, Department of Microbiology and Biomonitoring, University of Agriculture in Krakow, Mickiewicza 21, 31-120, Krakow, Poland
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Mahmood S, Kumar M, Kumari P, Mahapatro GK, Banerjee N, Sarin NB. Novel insecticidal chitinase from the insect pathogen Xenorhabdus nematophila. Int J Biol Macromol 2020; 159:394-401. [PMID: 32422264 DOI: 10.1016/j.ijbiomac.2020.05.078] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/18/2020] [Accepted: 05/04/2020] [Indexed: 12/28/2022]
Abstract
Xenorhabdus nematophila strain ATCC 19061 is an insect pathogen that produces various protein toxins which intoxicate and kill its larval host. In the present study, we have described the cloning, expression and characterization of a 76-kDa chitinase protein of X. nematophila. A 1.9 kb DNA sequence encoding the chitinase gene was PCR amplified and cloned. Further, the chitinase protein was expressed in Escherichia coli and purified by using affinity chromatography. Two highly conserved domains were identified GH18 and ChiA. The purified chitinase protein showed chitobiosidase activity, β-N-acetylglucosaminidase and endochitinase activity, when enzyme activity was measured using respective substrates. The purified chitinase protein was found to be orally toxic to the larvae of a major crop pest, Helicoverpa armigera when fed to the larvae mixed with artificial diet. It also had adverse effect on the growth and development of the surviving larvae. Surviving larvae showed 9-fold reduction in weight, as a result the transformation of larvae into pupae was adversely affected. Our results demonstrated that the chitinase protein of X. nematophila has insecticidal property and can prove to be a potent candidate for pest control in plants.
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Affiliation(s)
- Saquib Mahmood
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Mukesh Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Punam Kumari
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Gagan Kumar Mahapatro
- Division of Entomology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Nirupama Banerjee
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Neera Bhalla Sarin
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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11
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Composition and functional profiling of the microbiota in the casts of Eisenia fetida during vermicomposting of brewers' spent grains. ACTA ACUST UNITED AC 2020; 25:e00439. [PMID: 32140444 PMCID: PMC7047135 DOI: 10.1016/j.btre.2020.e00439] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 01/08/2023]
Abstract
E. fetida microbiota is affected by pH and carbon content of rearing substrates. This is the first report of the microbiota of E. fetida fed with brewers’ spent grains. Brewers’ spent grains induced proliferation of bacterial taxa involved in cellulose degradation and nitrogen cycle. Ammonia and nitrates were assimilated at high rates by the microbiota of E. fetida fed with brewers’ spent grains.
Vermicomposting is a cost-effective biotechnology for the management of organic wastes that relies on the activity of earthworms and their associated microbiota. Here, the microbiotas of the earthworm Eisenia fetida fed with brewers’ spent grains (FBSG), cow manure (FCM) and a mix of brewers’ spent grains/cow manure (FMIX), were identified by high-throughput DNA sequencing (16S rRNA). Bacterial community variance was correlated with the pH and the organic carbon content of the rearing substrates. FBSG microbiota was enriched in Paenibacillaceae, Enterobacteriaceae, Chitinophagaceae and Comamonadaceae. In addition, FBSG microbiota had a predicted higher abundance of genes involved in cellulose degradation as well as in the nitrogen cycle and showed higher utilization of ammonia and nitrate. Results obtained will allow to optimize the vermicomposting of brewers’ spent grains and to evaluate the effect of vermicompost addition on nutrient dynamics in soil.
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Huang K, Xia H, Zhang Y, Li J, Cui G, Li F, Bai W, Jiang Y, Wu N. Elimination of antibiotic resistance genes and human pathogenic bacteria by earthworms during vermicomposting of dewatered sludge by metagenomic analysis. BIORESOURCE TECHNOLOGY 2020; 297:122451. [PMID: 31787516 DOI: 10.1016/j.biortech.2019.122451] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/15/2019] [Accepted: 11/17/2019] [Indexed: 05/15/2023]
Abstract
This study used a metagenomic approach to investigate the effects of earthworms on ARGs and HPB during the vermicomposting of dewatered sludge. Results showed that 139 types of ARGs were found in sludge vermicompost, affiliated to 30 classes. Compared with the control, the total abundance of ARGs in sludge vermicompost decreased by 41.5%. Moreover, the types and sequences of plasmids and integrons were also decreased by vermicomposting. Proteobacteria and Actinobacteria were the most dominant hosts of ARGs in sludge vermicompost. In addition, earthworms reduced the total HPB abundance and modified their diversity, thus leading to higher abundance of Enterobacteriaceae in sludge vermicompost. However, the sludge vermicompost was still ARG and HPB enriched, indicating a remaining environmental risk for agricultural purpose. The observed change of microbial community and the reduction of mobile genetic elements caused by earthworm activity are the main reasons for the alleviation of ARG pollution during vermicomposting.
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Affiliation(s)
- Kui Huang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China.
| | - Hui Xia
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Yingying Zhang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Jianhui Li
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Guangyu Cui
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Fusheng Li
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Wei Bai
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Yufeng Jiang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Nan Wu
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
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Paenibacillus lutrae sp. nov., A Chitinolytic Species Isolated from A River Otter in Castril Natural Park, Granada, Spain. Microorganisms 2019; 7:microorganisms7120637. [PMID: 31810255 PMCID: PMC6955709 DOI: 10.3390/microorganisms7120637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 11/16/2022] Open
Abstract
A highly chitinolytic facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive, rod-shaped bacterial strain N10T was isolated from the feces of a river otter in the Castril Natural Park (Granada, Spain). It is a slightly halophilic, motile, catalase-, oxidase-, ACC deaminase- and C4 and C8 lipase-positive strain. It is aerobic, respiratory and has a fermentative metabolism using oxygen as an electron acceptor, produces acids from glucose and can fix nitrogen. Phylogenetic analysis of the 16S rRNA gene sequence, multilocus sequence analysis (MLSA) of 16S rRNA, gyrB, recA and rpoB, as well as phylogenomic analyses indicate that strain N10T is a novel species of the genus Paenibacillus, with the highest 16S rRNA sequence similarity (95.4%) to P. chitinolyticus LMG 18047T and <95% similarity to other species of the genus Paenibacillus. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANIb) were 21.1% and <75%, respectively. Its major cellular fatty acids were anteiso-C15:0, C16:0, and iso-C15:0. G + C content ranged between 45%–50%. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with chemotaxonomic and phenotypic data, we demonstrate that type strain N10T (= CECT 9541T =LMG 30535T) is a novel species of genus Paenibacillus and the name Paenibacillus lutrae sp. nov. is proposed.
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14
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Zhong H, Liu X, Zhu L, Yang Y, Yan S, Zhang X. Bioelectrochemically-assisted vermibiofilter process enhancing stabilization of sewage sludge with synchronous electricity generation. BIORESOURCE TECHNOLOGY 2019; 289:121740. [PMID: 31323716 DOI: 10.1016/j.biortech.2019.121740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 06/10/2023]
Abstract
Bioelectrochemically-assisted vermifilter (VBFBE) with sewage sludge as the anode fuel was constructed to accelerate composting of sewage sludge, which could increase the quality of the compost and harvest electric energy in comparison with vermicomposting and electrochemical only. Results revealed that the sludge stabilization with a higher soluble chemical oxygen demand (SCOD) and lower NH4+-H during 40 days of composting. At the composting, pH, C/N, electrical conductivity (EC) and germination index (GI) results demonstrated that the maturity degree of VBFBE4 was higher than that of other VBFBE. The VBFBE4 yielded a voltage of 1.024 V and maximum power density of 105.28 mW/m2 on 3th day. The bacteria in VBFBE4 were richer and higher in terms of diversity than those in other VBFBE, that was demonstrated that combination vermicomposting and electrochemistry could improve the sludge stabilization degree, accelerate sludge composting process and enhance composting maturity.
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Affiliation(s)
- Huiyuan Zhong
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan 063000, PR China.
| | - Xiao Liu
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan 063000, PR China
| | - Li Zhu
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan 063000, PR China
| | - Yong Yang
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan 063000, PR China
| | - Shan Yan
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan 063000, PR China
| | - Xinyuan Zhang
- College of Civil and Architectural Engineering, North China University of Science and Technology, Tangshan 063000, PR China
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15
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Ullah R, Yasir M, Bibi F, Abujamel TS, Hashem AM, Sohrab SS, Al-Ansari A, Al-Sofyani AA, Al-Ghamdi AK, Al-Sieni A, Azhar EI. Taxonomic diversity of antimicrobial-resistant bacteria and genes in the Red Sea coast. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 677:474-483. [PMID: 31063890 DOI: 10.1016/j.scitotenv.2019.04.283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/26/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Despite development of a record number of recreational sites and industrial zones on the Red Sea coast in the last decade, antibiotic-resistant bacteria in this environment remain largely unexplored. In this study, 16S rDNA sequencing was used to identify bacteria isolated from 12 sediment samples collected from the Red Sea coastal, offshore, and mangroves sites. Quantitative PCR was used to estimate the quantity of antimicrobial resistance genes (ARGs) in genomic DNA in the samples. A total of 470 bacteria were isolated and classified into 137 distinct species, including 10 candidate novel species. Site-specific bacterial communities inhabiting the Red Sea were apparent. Relatively, more resistant isolates were recovered from the coast, and samples from offshore locations contained the most multidrug-resistant bacteria. Eighteen ARGs were detected in this study encoding resistance to aminoglycoside, beta-lactam, sulfonamide, macrolide, quinolone, and tetracycline antibiotics. The qnrS, aacC2, ermC, and blaTEM-1 genes were commonly found in coastal and offshore sites. Relatively higher abundance of ARGs, including aacC2 and aacC3, were found in the apparently anthropogenically contaminated (beach) samples from coast compared to other collected samples. In conclusion, a relative increase in antimicrobial-resistant isolates was found in sediment samples from the Red Sea, compared to other studies. Anthropogenic activities likely contribute to this increase in bacterial diversity and ARGs.
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Affiliation(s)
- Riaz Ullah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Turki S Abujamel
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Al-Ansari
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulmohsin A Al-Sofyani
- Marine Biology Department, Faculty of Marine Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed K Al-Ghamdi
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulbasit Al-Sieni
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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16
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Khan I, Yasir M, Farman M, Kumosani T, AlBasri SF, Bajouh OS, Azhar EI. Evaluation of gut bacterial community composition and antimicrobial resistome in pregnant and non-pregnant women from Saudi population. Infect Drug Resist 2019; 12:1749-1761. [PMID: 31417292 PMCID: PMC6593780 DOI: 10.2147/idr.s200213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/01/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Gut microbiota (GM) has recently been described as a functional reservoir of antimicrobial resistant genes (ARGs). However, the ARG-carrying bacterial species in the human gut has been poorly studied. This study, for the first time, is reporting bacterial communities' composition and antimicrobial resistome in the stool samples of pregnant and non-pregnant (NP) Saudi females. Methods: Gut bacterial community composition was analyzed by 16S amplicon sequencing and culturomics. High throughput MALDI-TOF technique was used for identification of the isolates from stool samples and evaluated for resistance against 13 antibiotics using the agar dilution method. Clinically important ARGs were PCR amplified from genomic DNA of the stool samples using gene-specific primers. Results: 16S amplicon sequencing revealed that GM of pregnant and NP women were predominantly comprised of phyla Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Bacterial diversity decreased in pregnant groups, whereas phylum Bacteroidetes declined significantly (p<0.05) in the first trimester. We noticed a relatively high abundance of butyrate-producing bacteria (eg, Faecalibacterium spp. and Eubacterium spp.) in the gut of pregnant women, whereas Prevotella copri was found at significantly (p<0.01) higher abundance in NP women. Moreover, about 14,694 isolates were identified and classified into 132 distinct species. The majority of the species belonged to phyla Firmicutes and Proteobacteria. About 8,125 isolates exhibited resistance against antibiotics. Out of 73 resistant-species, Enterococcus was the most diverse genus and Escherichia coli was the highly prevalent bacterium. The majority of the isolates were resistant to antibiotics; trimethoprim/sulfamethoxazole, cycloserine, and cefixime. ARGs encoding resistance against aminoglycoside, macrolide, quinolone, β-lactam, and tetracycline antibiotics were predominantly found in genomic DNA of the stool samples. Conclusion: We conclude that pregnancy-associated GM modulations may help to sustain a healthy pregnancy, but a higher proportion of antibiotic resistance could be deleterious for both maternal and fetal health.
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Affiliation(s)
- Imran Khan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Biochemistry Department, Faculty of Science; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology Taipa, Macau, People's Republic of China
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Farman
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Biology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Taha Kumosani
- Biochemistry Department, Faculty of Science; Production of Bio-products for Industrial Applications Research Group, and Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Samera F AlBasri
- Department of Obstetrics & Gynecology, King Abdul Aziz University Hospital, Jeddah, Saudi Arabia
| | - Osama S Bajouh
- Department of Obstetrics & Gynecology, King Abdul Aziz University Hospital, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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17
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Gómez-Brandón M, Lores M, Insam H, Domínguez J. Strategies for recycling and valorization of grape marc. Crit Rev Biotechnol 2019; 39:437-450. [PMID: 30939940 DOI: 10.1080/07388551.2018.1555514] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Grapes are one of the most cultivated fruit crops worldwide. Either for wine or juice production, grape processing generates a large amount of residues that must be treated, disposed of or reused properly to reduce their pollution load before being applied to the soil. In this review, a special focus is given to the treatment and valorization of the winemaking by-product like grape marc via anaerobic digestion, composting and vermicomposting at laboratory, pilot, and industrial scales. The impact of the final products (digestates, composts, and vermicomposts) on soil properties is briefly addressed. Moreover, the role of grape marc and seeds as a valuable source of natural phytochemicals that include polyphenols and other bioactive compounds of interest for pharmaceutical, cosmetic, and food industries is also discussed. This is of paramount importance given the fact that sustainability requires the use of management and valorization strategies that allow the recovery of valuable compounds (e.g. antioxidants) with minimum disposal of waste streams.
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Affiliation(s)
- María Gómez-Brandón
- a Departamento de Ecoloxía e Bioloxía Animal , Universidade de Vigo , Vigo , Spain
| | - Marta Lores
- b Departamento de Química Analítica, Laboratorio de Investigación y Desarrollo de Soluciones Analíticas (LIDSA) , Nutrición y Bromatología, Universidade de Santiago de Compostela, Facultad de Quimica, Avda das Ciencias s/n , Santiago de Compostela , Spain
| | - Heribert Insam
- c Institute of Microbiology , University of Innsbruck , Innsbruck , Austria
| | - Jorge Domínguez
- a Departamento de Ecoloxía e Bioloxía Animal , Universidade de Vigo , Vigo , Spain
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18
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Yasir M, Qureshi AK, Khan I, Bibi F, Rehan M, Khan SB, Azhar EI. Culturomics-Based Taxonomic Diversity of Bacterial Communities in the Hot Springs of Saudi Arabia. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 23:17-27. [PMID: 30589606 DOI: 10.1089/omi.2018.0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hot springs are natural habitats for thermophilic microorganisms and provide a significant opportunity for bioprospecting thermostable biomolecules. However, the scientific community has only a fragmented understanding of the microbial diversity and composition in these biotopes. In this study, bacterial diversity in sediment samples from six hot springs of Saudi Arabia was investigated using an improved culture-dependent approach. High-throughput MALDI-TOF MS (matrix assisted laser desorption/ionization mass spectrometry) and 16S rRNA genes sequencing were used for the identification of purified isolates. Most of the hot springs had a neutral pH and a temperature range of 45-89°C. Relatively higher colony-forming units (1.9 ± 0.45 × 104) were observed with 60°C incubation of an 89°C sediment sample from the hot spring at Ain al Harra1. Among the 536 purified isolates, 6 novel candidate species were found, and the remaining isolates represented 139 distinct species. Several species, such as Bacillus cereus, Bacillus subtilis, and Bacillus schlegelii, were ubiquitous in the hot springs sampled, but 102 of the identified species were uniquely distributed among the hot springs. Sixteen of the isolated thermophilic bacteria, including Geobacillus kaustophilus, Thermus oshimai, and Brevibacillus thermoruber, grew at ≥60°C. In addition, 21 species exhibited hydrolytic enzymatic activity. Most of these species belonged to Bacillus and Brevibacillus. Overall, this study contributes to global knowledgebase on bacterial communities by comprehensively profiling culture-based bacterial diversity in the hot springs of Saudi Arabia. Further studies are required for investigating bacteria from hot springs by a metagenomic approach.
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Affiliation(s)
- Muhammad Yasir
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arooj K Qureshi
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Imran Khan
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,2 State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology Taipa, Macau, China
| | - Fehmida Bibi
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Rehan
- 3 King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sher Bahadar Khan
- 4 Department of Chemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,5 Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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19
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Ganguly RK, Chakraborty SK. Assessment of microbial roles in the bioconversion of paper mill sludge through vermicomposting. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2018; 16:205-212. [PMID: 30728992 PMCID: PMC6277328 DOI: 10.1007/s40201-018-0308-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/22/2018] [Indexed: 06/09/2023]
Abstract
PURPOSE Main thrust of the present study is to determine the role of microbes in changing the proportion and turnover of nutrients such as carbon and nitrogen during vermicomposting of paper mill sludge through the assessment of β-glucosidase and Leucine arylamidase activities. METHODS The change in the ratio of Total Organic Carbon (TOC) and Total Kjeldahl Nitrogen (TKN) during sludge composting using paper mill sludge, cow dung, straw in the ratio of 5:4:1 have been determined alongside observing β-glucosidase and Leucine arylamidase activities in different phases (0th, 30th and 60th days) of vermicomposting. The present study also assessed the bacterial assemblages in order to predict their role as major producers of these enzymes as estimated by Vitek 2 system. RESULTS A declining trend of C/N ratio was observed which exhibited significant negative and positive correlations with the activity of β-glucosidase and Leucine arylamidase respectively. Twenty-four strains were isolated under two genus Bacillus spp. and Lysinibacillus spp. which revealed differential sensitivity towards major carbon and nitrogen turnover mediating enzymes. CONCLUSION Change in the activities of carbon and nitrogen turnover enzymes due to microbial growth and proliferation are the mediator for the change in C/N ratio.
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Affiliation(s)
- Ram Kumar Ganguly
- Department of Zoology, Vidyasagar University, Midnapore, West Bengal 721102 India
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20
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Zhang M, Wang J, Bai SH, Teng Y, Xu Z. Evaluating the effects of phytoremediation with biochar additions on soil nitrogen mineralization enzymes and fungi. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:23106-23116. [PMID: 29860689 DOI: 10.1007/s11356-018-2425-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
Phytoremediation with biochar addition might alleviate pollutant toxicity to soil microorganism. It is uncertain to what extent biochar addition rate could affect activities of enzymes related to soil nitrogen (N) mineralization and alter fungal community under the phytoremediation. This study aimed to reveal the effects of Medicago sativa L. (alfalfa) phytoremediation, alone or with biochar additions, on soil protease and chitinase and fungal community and link the responses of microbial parameters with biochar addition rates. The alfalfa phytoremediation enhanced soil protease activities, and relative to the phytoremediation alone, biochar additions had inconsistent impacts on the corresponding functional gene abundances. Compared with the blank control, alfalfa phytoremediation, alone or with biochar additions, increased fungal biomass and community richness estimators. Moreover, relative to the phytoremediation alone, the relative abundances of phylum Zygomycota were also increased by biochar additions. The whole soil fungal community was not significantly changed by the alfalfa phytoremediation alone, but was indeed changed by alfalfa phytoremediation with 3.0% (w/w) or 6.0% biochar addition. This study suggested that alfalfa phytoremediation could enhance N mineralization enzyme activities and that biochar addition rates affected the responses of fungal community to the alfalfa phytoremediation.
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Affiliation(s)
- Manyun Zhang
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, Queensland, 4111, Australia.
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Jun Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Chongqing Research Academy of Environmental Sciences, Chongqing, 401147, China
| | - Shahla Hosseini Bai
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, Queensland, 4111, Australia
- GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Zhihong Xu
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, Queensland, 4111, Australia.
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21
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Lv B, Xing M, Yang J. Exploring the effects of earthworms on bacterial profiles during vermicomposting process of sewage sludge and cattle dung with high-throughput sequencing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:12528-12537. [PMID: 29464602 DOI: 10.1007/s11356-018-1520-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/08/2018] [Indexed: 05/15/2023]
Abstract
This study aims to reveal the effects of earthworms (Eisenia fetida) on bacterial profiles during the vermicomposting process of sewage sludge and cattle dung with the high-throughput sequencing technology. The earthworms could accelerate organic degradation and improve the stabilization process. Moreover, the addition of earthworms not only affected the bacterial numbers, but also increased the bacterial community diversity. The activity of earthworms had significant effects on the bacterial community structure as the bacterial community was clearly different between the vermicomposting and the control treatment. Furthermore, the earthworms affected the physical and chemical properties of substrates, thus promoting the growth of some microorganisms, such as Flavobacteria, Acidbacteria, and Planctomycetes. Earthworms largely inhibited the growth of various human pathogenic bacteria. In summary, earthworms significantly affected the bacterial community in vermicomposting and it could be applied as an authentically effective technique for the stabilization of organic wastes.
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Affiliation(s)
- Baoyi Lv
- Institute of Biofilm Technology, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai, 201306, China.
| | - Meiyan Xing
- Institute of Biofilm Technology, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
| | - Jian Yang
- Institute of Biofilm Technology, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
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22
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Identification of Chitin Degrading Bacterial Strains Isolated from Bulk and Rhizospheric Soil. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.1.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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23
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Singh A, Singh GS. Vermicomposting: A sustainable tool for environmental equilibria. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/tqem.21509] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Archana Singh
- Institute of Environment and Sustainable Development; Banaras Hindu University; Varanasi, Uttar Pradesh India
| | - Gopal Shankar Singh
- Institute of Environment and Sustainable Development; Banaras Hindu University; Varanasi, Uttar Pradesh India
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24
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Awasthi MK, Li J, Kumar S, Awasthi SK, Wang Q, Chen H, Wang M, Ren X, Zhang Z. Effects of biochar amendment on bacterial and fungal diversity for co-composting of gelatin industry sludge mixed with organic fraction of municipal solid waste. BIORESOURCE TECHNOLOGY 2017; 246:214-223. [PMID: 28747259 DOI: 10.1016/j.biortech.2017.07.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
The aim of the study was to evaluate the bacterial and fungal diversities of 18contrastivecomposts applied with 17 different sources mad biochars applied treatments using 16S rRNA and 18S rDNA technology, while T-1 used as a control. The results showed that bacterial species of the phyla Actinobacteria, Proteobacteria and Chloroflexi, and fungi of the phylum Ascomycota and Basidiomycota were pre-dominant among the all treatments. The bacterial genus Subgroup_6_norank, Nocardioides, Pseudonocardia, Sphingomonas, Solirubrobacter and RB41_norank are first time identified in composting ecosystem. In addition, the fungal genus Ascomycota_unclassified, Aspergillus, Penicillium, Pleosporales_unclassified and Herpotrichlellacease_unclassified ubiquitous among the all compost. The Shannon and refraction-curve biodiversity indices showed a clear heterogeneity among all the treatments, which could be due to isolation of new genera in this system. Finally, the principal component analysis of the relative number of sequences also confirmed that bacterial and fungal population indiscriminate in different sources mad biochar applied treatments.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Department of Biotechnology, Amicable Knowledge Solution University, Satna, India
| | - Jiao Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Solid and Hazardous Waste Management Division, Nagpur 440 020, Maharashtra, India
| | | | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Hongyu Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Meijing Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xiuna Ren
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China.
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25
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Yasir M. Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota. Braz J Microbiol 2017; 49:248-257. [PMID: 29108974 PMCID: PMC5913830 DOI: 10.1016/j.bjm.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 05/29/2017] [Accepted: 08/15/2017] [Indexed: 02/01/2023] Open
Abstract
In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.
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Affiliation(s)
- Muhammad Yasir
- King Abdulaziz University, King Fahd Medical Research Center, Special Infectious Agents Unit, Jeddah, Saudi Arabia.
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26
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Soobhany N, Mohee R, Garg VK. Inactivation of bacterial pathogenic load in compost against vermicompost of organic solid waste aiming to achieve sanitation goals: A review. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 64:51-62. [PMID: 28302524 DOI: 10.1016/j.wasman.2017.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 03/02/2017] [Accepted: 03/02/2017] [Indexed: 05/15/2023]
Abstract
Waste management strategies for organic residues, such as composting and vermicomposting, have been implemented in some developed and developing countries to solve the problem of organic solid waste (OSW). Yet, these biological treatment technologies do not always result in good quality compost or vermicompost with regards to sanitation capacity owing to the presence of bacterial pathogenic substances in objectionable concentrations. The presence of pathogens in soil conditioners poses a potential health hazard and their occurrence is of particular significance in composts and/or vermicomposts produced from organic materials. Past and present researches demonstrated a high-degree of agreement that various pathogens survive after the composting of certain OSW but whether similar changes in bacterial pathogenic loads arise during vermitechnology has not been thoroughly elucidated. This review garners information regarding the status of various pathogenic bacteria which survived or diffused after the composting process compared to the status of these pathogens after the vermicomposting of OSW with the aim of achieving sanitation goals. This work is also indispensable for the specification of compost quality guidelines concerning pathogen loads which would be specific to treatment technology. It was hypothesized that vermicomposting process for OSW can be efficacious in sustaining the existence of pathogenic organisms most specifically; human pathogens under safety levels. In summary, earthworms can be regarded as a way of obliterating pathogenic bacteria from OSW in a manner equivalent to earthworm gut transit mechanism which classifies vermicomposting as a promising sanitation technique in comparison to composting processes.
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Affiliation(s)
- Nuhaa Soobhany
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Mauritius, Reduit 80837, Mauritius.
| | - Romeela Mohee
- Office of Vice Chancellor, University of Mauritius, Reduit 80837, Mauritius
| | - Vinod Kumar Garg
- Centre for Environmental Science and Technology, Central University of Punjab, Bathinda 155001, Punjab, India
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27
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Blomström AL, Lalander C, Komakech AJ, Vinnerås B, Boqvist S. A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda. Infect Ecol Epidemiol 2016; 6:32453. [PMID: 27834174 PMCID: PMC5103666 DOI: 10.3402/iee.v6.32453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 11/14/2022] Open
Abstract
Background Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteria while reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system. Material and methods The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste. On Day 172, the compost was terminated and compost samples were collected from three layers of the unit: the top, the middle and the bottom layer. A metagenomic approach was then applied to characterise the viral and bacterial composition of the vermicomposting system. Results and discussion A high abundance and diversity of bacteria were identified. Proteobacteria was the largest phyla in the compost (mainly Alpha-, Gamma- and Betaproteobacteria), constituting almost 65% of the bacterial reads in the data sets. DNA samples from several possible pathogenic bacteria, such as Salmonella spp., Escherichia coli, Enterobacter spp., Enterococcus spp. and Clostridium spp, were detected in the vermicompost, suggesting that there might still be harmful bacteria in the vermicast. Phages constituted the main viral group; apart from phages, mainly insect viruses were identified. The only animal or human virus identified was kobuvirus. In summary, metagenomic analysis was shown to be an efficient technology to characterise the microbial composition of vermicast. The data from this study contribute to a better understanding of the microbes present in this kind of composting system and can help determine measures necessary for safe manure handling.
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Affiliation(s)
- Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden;
| | - Cecilia Lalander
- Department of Energy and Technology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Allan John Komakech
- Department of Energy and Technology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Agricultural and Bio-systems Engineering, Makerere University, Kampala, Uganda
| | - Björn Vinnerås
- Department of Energy and Technology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sofia Boqvist
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Mahmood S, Daur I, Al-Solaimani SG, Ahmad S, Madkour MH, Yasir M, Hirt H, Ali S, Ali Z. Plant Growth Promoting Rhizobacteria and Silicon Synergistically Enhance Salinity Tolerance of Mung Bean. FRONTIERS IN PLANT SCIENCE 2016; 7:876. [PMID: 27379151 PMCID: PMC4911404 DOI: 10.3389/fpls.2016.00876] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/03/2016] [Indexed: 05/05/2023]
Abstract
The present study explored the eco-friendly approach of utilizing plant-growth-promoting rhizobacteria (PGPR) inoculation and foliar application of silicon (Si) to improve the physiology, growth, and yield of mung bean under saline conditions. We isolated 18 promising PGPR from natural saline soil in Saudi Arabia, and screened them for plant-growth-promoting activities. Two effective strains were selected from the screening trial, and were identified as Enterobacter cloacae and Bacillus drentensis using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and 16S rRNA gene sequencing techniques, respectively. Subsequently, in a 2-year mung bean field trial, using a randomized complete block design with a split-split plot arrangement, we evaluated the two PGPR strains and two Si levels (1 and 2 kg ha(-1)), in comparison with control treatments, under three different saline irrigation conditions (3.12, 5.46, and 7.81 dS m(-1)). The results indicated that salt stress substantially reduced stomatal conductance, transpiration rate, relative water content (RWC), total chlorophyll content, chlorophyll a, chlorophyll b, carotenoid content, plant height, leaf area, dry biomass, seed yield, and salt tolerance index. The PGPR strains and Si levels independently improved all the aforementioned parameters. Furthermore, the combined application of the B. drentensis strain with 2 kg Si ha(-1) resulted in the greatest enhancement of mung bean physiology, growth, and yield. Overall, the results of this study provide important information for the benefit of the agricultural industry.
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Affiliation(s)
- Sajid Mahmood
- Department of Arid Land Agriculture, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Ihsanullah Daur
- Department of Arid Land Agriculture, King Abdulaziz UniversityJeddah, Saudi Arabia
| | | | - Shakeel Ahmad
- Department of Arid Land Agriculture, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Mohamed H. Madkour
- Department of Environmental Sciences, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Muhammad Yasir
- King Fahd Medical Research Center, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Heribert Hirt
- Center for Desert Agriculture, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Shawkat Ali
- Center for Desert Agriculture, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Zahir Ali
- Center for Desert Agriculture, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
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29
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Chen Y, Zhang Y, Zhang Q, Xu L, Li R, Luo X, Zhang X, Tong J. Earthworms modify microbial community structure and accelerate maize stover decomposition during vermicomposting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:17161-17170. [PMID: 26139410 DOI: 10.1007/s11356-015-4955-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 06/24/2015] [Indexed: 06/04/2023]
Abstract
In the present study, maize stover was vermicomposted with the epigeic earthworm Eisenia fetida. The results showed that, during vermicomposting process, the earthworms promoted decomposition of maize stover. Analysis of microbial communities of the vermicompost by high-throughput pyrosequencing showed more complex bacterial community structure in the substrate treated by the earthworms than that in the control group. The dominant microbial genera in the treatment with the earthworms were Pseudoxanthomonas, Pseudomonas, Arthrobacter, Streptomyces, Cryptococcus, Guehomyces, and Mucor. Compared to the control group, the relative abundance of lignocellulose degradation microorganisms increased. The results indicated that the earthworms modified the structure of microbial communities during vermicomposting process, activated the growth of lignocellulose degradation microorganisms, and triggered the lignocellulose decomposition.
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Affiliation(s)
- Yuxiang Chen
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130025, China
- Key Laboratory of Biomimetic Engineering (Jilin University), Ministry of Education, Changchun, 130025, China
| | - Yufen Zhang
- Key Laboratory of Biodiversity Science and Ecological Engineering (Beijing Normal University), Ministry of Education, Beijing, 100875, China
| | - Quanguo Zhang
- Key Laboratory of Biodiversity Science and Ecological Engineering (Beijing Normal University), Ministry of Education, Beijing, 100875, China
| | - Lixin Xu
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130025, China
| | - Ran Li
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130025, China
| | - Xiaopei Luo
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130025, China
| | - Xin Zhang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130025, China
| | - Jin Tong
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130025, China.
- Key Laboratory of Biomimetic Engineering (Jilin University), Ministry of Education, Changchun, 130025, China.
- Collaborative Innovation Center of Grain Production Capacity Improvement in Heilongjiang Province, Harbin, China.
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30
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Lv B, Xing M, Yang J, Zhang L. Pyrosequencing reveals bacterial community differences in composting and vermicomposting on the stabilization of mixed sewage sludge and cattle dung. Appl Microbiol Biotechnol 2015; 99:10703-12. [PMID: 26318447 DOI: 10.1007/s00253-015-6884-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 07/22/2015] [Accepted: 07/26/2015] [Indexed: 10/23/2022]
Abstract
This study aimed to compare the microbial community structures and compositions in composting and vermicomposting processes. We applied 454 high-throughput pyrosequencing to analyze the 16S rRNA gene of bacteria obtained from bio-stabilization of sewage sludge and cattle dung. Results demonstrated that vermicomposting process presented higher operational taxonomic units and bacterial diversity than the composting. Analysis using weighted UniFrac indicated that composting exhibited higher effects on shaping microbial community structure than the vermicomposting. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting and shifted to Actinomycetes in the maturing stage. By contrast, Proteobacteria accounted for the highest proportions in the whole process of the vermicomposting. Furthermore, vermicomposting contained more uncultured and unidentified bacteria at the taxonomy level of genus than the composting. In summary, the bacterial community during composting significantly differed from that during vermicomposting. These two techniques played different roles in changing the diversity and composition of microbial communities.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai, 201306, China.,Institute of Biofilm Technology, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Meiyan Xing
- Institute of Biofilm Technology, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
| | - Jian Yang
- Institute of Biofilm Technology, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Liangbo Zhang
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, 450001, China
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31
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Purification and characterization of antifungal chitinase from Bacillus safensis MBCU6 and its application for production of chito-oligosaccharides. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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32
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Arumugam K, Ganesan S, Muthunarayanan V, Vivek S, Sugumar S, Munusamy V. Potentiality of Eisenia fetida to degrade disposable paper cups-an ecofriendly solution to solid waste pollution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:2868-2876. [PMID: 25220767 DOI: 10.1007/s11356-014-3456-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/14/2014] [Indexed: 06/03/2023]
Abstract
The aim of the present study was to subject the post-consumer waste, namely paper cups for vermicomposting along with cow dung in three different ratios for a period of 90-140 days employing Eisenia fetida. The post-consumer wastes are a menace in many developing countries including India. This waste was provided as feed for earthworms and was converted to vermicompost. Vermicompost prepared with paper cup waste was analyzed for their physicochemical properties. Based on the physicochemical properties, it was evident that the best manure is obtained from type A (paper cup/cow dung in the ratio 1:1) than type B (paper cup/cow dung in the ratio 1.5:0.5) and type C (paper cup/cow dung in the ratio 0.5:1.5). The results showed that earthworms accelerated the rate of mineralization and converted the wastes into compost with needed elements which could support the growth of crop plants. The predominant bacterial strains in the vermicompost were characterized biochemically as well as by 16S ribosomal RNA (rRNA) gene sequencing. The bacterial strains like Bacillus anthracis (KM289159), Bacillus endophyticus (KM289167), Bacillus funiculus (KM289165), Virigibacillius chiquenigi (KM289163), Bacillus thuringiensis (KM289164), Bacillus cereus (KM289160), Bacillus toyonensis (KM289161), Acinetobacter baumanni (KM289162), and Lactobacillus pantheries (KM289166) were isolated and identified from the final compost. The total protein content of E. fetida involved in vermicomposting was extracted, and the banding pattern was analyzed. During final stages of vermicomposting, it was observed that the earthworm did not act on the plastic material coated inside the paper cups and stagnated it around the rim of the tub. Further, the degradation of paper cup waste was confirmed by Fourier transform infrared spectroscopy analysis. Hence, vermicomposting was found to be an effective technology for the conversion of the paper cup waste material into a nutrient-rich manure, a value-added product.
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Affiliation(s)
- Karthika Arumugam
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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Huang K, Li F, Wei Y, Fu X, Chen X. Effects of earthworms on physicochemical properties and microbial profiles during vermicomposting of fresh fruit and vegetable wastes. BIORESOURCE TECHNOLOGY 2014; 170:45-52. [PMID: 25118152 DOI: 10.1016/j.biortech.2014.07.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/09/2014] [Accepted: 07/15/2014] [Indexed: 06/03/2023]
Abstract
This study aimed to investigate the effect of earthworms on physicochemical and microbial properties during vermicomposting of fresh fruit and vegetable wastes (FVW) by contrasting two decomposing systems of FVW with and without earthworms for 5weeks. Compared to control treatment (without earthworms), vermicomposting treatment resulted in a rapid decrease of electrical conductivity and losses of total carbon and nitrogen from the 2nd week. Quantitative PCR displayed that earthworms markedly enhanced bacterial and fungal densities, showing the higher values than control, during the whole decomposition process. In addition, denaturing gradient gel electrophoresis combined with sequencing analysis revealed that earthworms pronouncedly modified bacterial and fungal community structures, through broadening the community diversities of Actinobacteria, Bacteroidetes, Proteobacteria, and Ascomycotina. These results suggest that the presence of earthworms promoted the activity and population of bacteria and fungi, and modified their communities, thus altering the decomposition pathway of fresh FVW.
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Affiliation(s)
- Kui Huang
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Fusheng Li
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yongfen Wei
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Xiaoyong Fu
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Xuemin Chen
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
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34
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Romero-Tepal EM, Contreras-Blancas E, Navarro-Noya YE, Ruíz-Valdiviezo VM, Luna-Guido M, Gutiérrez-Miceli FA, Dendooven L. Changes in the bacterial community structure in stored wormbed leachate. J Mol Microbiol Biotechnol 2014; 24:105-13. [PMID: 24577291 DOI: 10.1159/000357915] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 12/11/2013] [Indexed: 11/19/2022] Open
Abstract
Organic wastes, such as cow manure, are often composted with earthworms (vermicomposting) while excess water is drained and collected. This wormbed leachate is nutrient-rich and it has been extensively used to fertilize plants. However, it is derived partially from a not yet finished compost process and could exhibit phytotoxicity or contain potentially hazardous microorganisms. The bacterial community in wormbed leachate derived from vermicomposting of cow manure was studied by pyrosequencing the 16S rRNA gene. The fresh wormbed leachate was rich in Mollicutes, particularly the genus Acholeplasma which contain phytopathogen species. The abundance of the Mollicutes decreased when the leachate was stored, while that of the Rhizobiales and the genus Pseudomonas increased. The bacterial communities changed rapidly in the leachate during storage. The changes in ammonium, nitrate and inorganic carbon content of the wormbed leachate when stored were correlated to changes in the bacterial community structure. It was found that storage of the wormbed leachate might be required before it can be applied to crops as large proportions of potentially plant pathogens were found in the fresh leachate.
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35
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Huang K, Li F, Wei Y, Chen X, Fu X. Changes of bacterial and fungal community compositions during vermicomposting of vegetable wastes by Eisenia foetida. BIORESOURCE TECHNOLOGY 2013; 150:235-241. [PMID: 24177156 DOI: 10.1016/j.biortech.2013.10.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/29/2013] [Accepted: 10/01/2013] [Indexed: 06/02/2023]
Abstract
Changes of bacterial and fungal community during vermicomposting of vegetable wastes by hatchling, juvenile and adult Eisenia foetida were investigated through analysis of the extracted bacterial 16S rDNA and fungal 18S rDNA with quantitative polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE) and sequencing. After 60days of composting, significantly lower values of microbial activity and bacterial and fungal densities were revealed in the products of composting with earthworms than in the control (without earthworms). PCR-DGGE images showed vermicomposting significantly enhanced the diversities of bacterial and fungal communities. However, for their structures, sequencing results revealed that, compared to the control where the bacterial Firmicutes were predominant, in the composts with earthworms, the bacterial Bacteroidetes and Actinomycetes, and the fungal Sordariomycetes were found dominant. In addition, some beneficial species of bacteria and fungi against pathogens were also isolated from the vermicomposting products.
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Affiliation(s)
- Kui Huang
- Graduate School of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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36
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Castillo JM, Romero E, Nogales R. Dynamics of microbial communities related to biochemical parameters during vermicomposting and maturation of agroindustrial lignocellulose wastes. BIORESOURCE TECHNOLOGY 2013; 146:345-354. [PMID: 23948272 DOI: 10.1016/j.biortech.2013.07.093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/20/2013] [Indexed: 06/02/2023]
Abstract
Scarce information is available on the changes in abundance of microbial taxa during vermicomposting. Quantitative PCR and DGGE analysis were used to monitor variations in the microbial structure, relative abundance of four bacterial classes and fungi over the vermicomposting and maturation period of wet olive cake (O) and vine shoots (W). Multivariate correlation analysis between microbial structure and abundance, earthworm biomass and enzyme activities revealed similar and divergent interactions in both processes. Although Eisenia fetida development was different, significant correlations were found with β-glucosidase activity and with bacterial and fungal structure. In the vermicomposting period of O and W, a decline was found in bacteria (94% and 77%), fungi (93% and 94%), and Gammaproteobacteria (56% and 71%) but an increase in Betaproteobacteria and Actinobacteria (62-79%). Alphaproteobacteria increased only in O (26%). Despite the different initial lignocellulose wastes, the mature vermicomposts were similar in microbial and biochemical properties.
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Affiliation(s)
- Jean Manuel Castillo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientificas (EEZ-CSIC), C/Profesor Albareda 1, 18008 Granada, Spain.
| | - Esperanza Romero
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientificas (EEZ-CSIC), C/Profesor Albareda 1, 18008 Granada, Spain
| | - Rogelio Nogales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientificas (EEZ-CSIC), C/Profesor Albareda 1, 18008 Granada, Spain
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Blaya J, López-Mondéjar R, Lloret E, Pascual JA, Ros M. Changes induced by Trichoderma harzianum in suppressive compost controlling Fusarium wilt. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2013; 107:112-119. [PMID: 25149244 DOI: 10.1016/j.pestbp.2013.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 05/28/2013] [Accepted: 06/03/2013] [Indexed: 06/03/2023]
Abstract
The addition of species of Trichoderma to compost is a widespread technique used to control different plant diseases. The biological control activity of these species is mainly attributable to a combination of several mechanisms of action, which may affect the microbiota involved in the suppressiveness of compost. This study was therefore performed to determine the effect of inoculation of Trichoderma harzianum (T. harzianum) on compost, focusing on bacterial community structure (16S rRNA) and chitinase gene diversity. In addition, the ability of vineyard pruning waste compost, amended (GCTh) or not (GC) with T. harzianum, to suppress Fusarium wilt was evaluated. The addition of T. harzianum resulted in a high relative abundance of certain chitinolytic bacteria as well as in remarkable protection against Fusarium oxysporum comparable to that induced by compost GC. Moreover, variations in the abiotic characteristics of the media, such as pH, C, N and iron levels, were observed. Despite the lower diversity of chitinolytic bacteria found in GCTh, the high relative abundance of Streptomyces spp. may be involved in the suppressiveness of this growing media. The higher degree of compost suppressiveness achieved after the addition of T. harzianum may be due not only to its biocontrol ability, but also to changes promoted in both abiotic and biotic characteristics of the growing media.
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Affiliation(s)
- Josefa Blaya
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus de Espinardo, P.O. Box 164, 30100 Espinardo, Murcia, Spain.
| | - Rubén López-Mondéjar
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus de Espinardo, P.O. Box 164, 30100 Espinardo, Murcia, Spain
| | - Eva Lloret
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus de Espinardo, P.O. Box 164, 30100 Espinardo, Murcia, Spain
| | - Jose Antonio Pascual
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus de Espinardo, P.O. Box 164, 30100 Espinardo, Murcia, Spain
| | - Margarita Ros
- Department of Soil and Water Conservation and Organic Waste Management, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Campus de Espinardo, P.O. Box 164, 30100 Espinardo, Murcia, Spain
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Yasir M, Khan H, Azam SS, Telke A, Kim SW, Chung YR. Cloning and functional characterization of endo-β-1,4-glucanase gene from metagenomic library of vermicompost. J Microbiol 2013; 51:329-35. [DOI: 10.1007/s12275-013-2697-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/19/2013] [Indexed: 10/26/2022]
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Beier S, Bertilsson S. Bacterial chitin degradation-mechanisms and ecophysiological strategies. Front Microbiol 2013; 4:149. [PMID: 23785358 PMCID: PMC3682446 DOI: 10.3389/fmicb.2013.00149] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/28/2013] [Indexed: 11/13/2022] Open
Abstract
Chitin is one the most abundant polymers in nature and interacts with both carbon and nitrogen cycles. Processes controlling chitin degradation are summarized in reviews published some 20 years ago, but the recent use of culture-independent molecular methods has led to a revised understanding of the ecology and biochemistry of this process and the organisms involved. This review summarizes different mechanisms and the principal steps involved in chitin degradation at a molecular level while also discussing the coupling of community composition to measured chitin hydrolysis activities and substrate uptake. Ecological consequences are then highlighted and discussed with a focus on the cross feeding associated with the different habitats that arise because of the need for extracellular hydrolysis of the chitin polymer prior to metabolic use. Principal environmental drivers of chitin degradation are identified which are likely to influence both community composition of chitin degrading bacteria and measured chitin hydrolysis activities.
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Affiliation(s)
- Sara Beier
- Department of Ecology and Genetics, Limnology, Uppsala University Uppsala, Sweden ; Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, UPMC Paris 06, UMR 7621 Banyuls sur mer, France ; Laboratoire d'Océanographie Microbienne, Observatoire Océanologique Centre National de la Recherche Scientifique, UMR 7621 Banyuls sur mer, France
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Pathma J, Sakthivel N. Microbial diversity of vermicompost bacteria that exhibit useful agricultural traits and waste management potential. SPRINGERPLUS 2012; 1:26. [PMID: 23961356 PMCID: PMC3725894 DOI: 10.1186/2193-1801-1-26] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/28/2012] [Indexed: 11/17/2022]
Abstract
Vermicomposting is a non-thermophilic, boioxidative process that involves earthworms and associated microbes. This biological organic waste decomposition process yields the biofertilizer namely the vermicompost. Vermicompost is a finely divided, peat like material with high porosity, good aeration, drainage, water holding capacity, microbial activity, excellent nutrient status and buffering capacity thereby resulting the required physiochemical characters congenial for soil fertility and plant growth. Vermicompost enhances soil biodiversity by promoting the beneficial microbes which inturn enhances plant growth directly by production of plant growth-regulating hormones and enzymes and indirectly by controlling plant pathogens, nematodes and other pests, thereby enhancing plant health and minimizing the yield loss. Due to its innate biological, biochemical and physiochemical properties, vermicompost may be used to promote sustainable agriculture and also for the safe management of agricultural, industrial, domestic and hospital wastes which may otherwise pose serious threat to life and environment.
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Affiliation(s)
- Jayakumar Pathma
- Department of Biotechnology School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014 India
| | - Natarajan Sakthivel
- Department of Biotechnology School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014 India
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41
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Isolation and purification of microbial community DNA from soil naturally enriched for chitin. Biologia (Bratisl) 2012. [DOI: 10.2478/s11756-012-0059-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Zhang Z, Wang H, Zhu J, Suneethi S, Zheng J. Swine manure vermicomposting via housefly larvae (Musca domestica): the dynamics of biochemical and microbial features. BIORESOURCE TECHNOLOGY 2012; 118:563-571. [PMID: 22728759 DOI: 10.1016/j.biortech.2012.05.048] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 05/06/2012] [Accepted: 05/11/2012] [Indexed: 06/01/2023]
Abstract
Improper handling of animal manure generated from concentrated swine operations greatly deteriorates water ecosystems. In this study, a full-scale vermireactor using housefly larvae (Musca domestica) was designed to investigate the effectiveness and efficiency of swine manure reduction, and to explore the associated biochemical-biological mechanisms. The one-week larvae vermireactor resulted in a total weight reduction rate of 106±17 kg/(m(3) d) and moisture reduction of 80.2%. Microbial activities in manure decreased by 45% after vermicomposting, while the activities of cellulose, proteases, and phosphatases in the vermicompost were significantly 69 times, 48%, and 82% lower than those in raw manure, respectively. The vermicompost was exclusively dominated by Entomoplasma somnilux, Proteobacterium, and Clostridiaceae bacterium where the microbial diversity was decreased from 2.57 in raw manure to 1.77. Correlation coefficients statistic showed that organic C might be a key indicator of the biochemical features and microbial functions of the larvae vermireactor.
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Affiliation(s)
- ZhiJian Zhang
- College of Natural Research and Environmental Sciences, Center of Water Ecosystem and Watershed Sustainability, ZheJiang University, YuHangTang Ave. 688, HangZhou, ZheJiang Province 310058, China.
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Fernández-Gómez MJ, Nogales R, Insam H, Romero E, Goberna M. Use of DGGE and COMPOCHIP for investigating bacterial communities of various vermicomposts produced from different wastes under dissimilar conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2012; 414:664-671. [PMID: 22154215 DOI: 10.1016/j.scitotenv.2011.11.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/20/2011] [Accepted: 11/14/2011] [Indexed: 05/31/2023]
Abstract
This study describes the use of denaturing gradient gel electrophoresis (DGGE) and COMPOCHIP (i.e. a microarray targeting typical bacteria of stabilized organic materials and pathogenic bacteria) for investigating the bacterial communities of four different vermicomposts. These included a commercial vermicompost produced from cattle manure (CM) and three vermicomposts produced at pilot-scale by recycling: damaged tomato fruits (DT); olive-mill waste mixed with biosolids (OB); and winery wastes (WW). DGGE provided distinctive fingerprints of each vermicompost, which were statistically related to their particular chemical features. The comparison of the various vermicompost fingerprints showed that they contained bacterial communities with an average similarity coefficient of close to 80%. COMPOCHIP detected the presence of Sphingobacterium, Streptomyces, Alpha-Proteobacteria, Delta-Proteobacteria, and Firmicutes in all the vermicomposts. COMPOCHIP showed differences in the abundance of particular bacterial taxa among the vermicomposts, giving an idea about the usefulness of each vermicompost in the search for bacteria valuable to biotechnology. The joint use of DGGE and COMPOCHIP is a useful tool to compare vermicompost bacterial communities and to assess the potential of different vermicomposts as bioactive organic materials.
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Affiliation(s)
- Manuel J Fernández-Gómez
- Department of Environmental Protection, Estación Experimental del Zaidín, Profesor Albareda 1, 18008 Granada, Spain.
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Zarei M, Aminzadeh S, Zolgharnein H, Safahieh A, Daliri M, Noghabi KA, Ghoroghi A, Motallebi A. Characterization of a chitinase with antifungal activity from a native Serratia marcescens B4A. Braz J Microbiol 2011; 42:1017-29. [PMID: 24031719 PMCID: PMC3768790 DOI: 10.1590/s1517-838220110003000022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 01/13/2011] [Indexed: 11/22/2022] Open
Abstract
Chitinases have the ability of chitin digestion that constitutes a main compound of the cell wall in many of the phytopathogens such as fungi. In the following investigation, a novel chitinase with antifungal activity was characterized from a native Serratia marcescens B4A. Partially purified enzyme had an apparent molecular mass of 54 kDa. It indicated an optimum activity in pH 5 at 45°C. Enzyme was stable in 55°C for 20 min and at a pH range of 3-9 for 90 min at 25°C. When the temperature was raised to 60°C, it might affect the structure of enzymes lead to reduction of chitinase activity. Moreover, the Km and Vmax values for chitin were 8.3 mg/ml and 2.4 mmol/min, respectively. Additionally, the effect of some cations and chemical compounds were found to stimulate the chitinase activity. In addition, Iodoacetamide and Idoacetic acid did not inhibit enzyme activity, indicating that cysteine residues are not part of the catalytic site of chitinase. Finally, chitinase activity was further monitored by scanning electronic microscopy data in which progressive changes in chitin porosity appeared upon treatment with chitinase. This enzyme exhibited antifungal activity against Rhizoctonia solani, Bipolaris sp, Alternaria raphani, Alternaria brassicicola, revealing a potential application for the industry with potentially exploitable significance. Fungal chitin shows some special features, in particular with respect to chemical structure. Difference in chitinolytic ability must result from the subsite structure in the enzyme binding cleft. This implies that why the enzyme didn't have significant antifungal activity against other Fungi.
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Affiliation(s)
- Mandana Zarei
- Department of Animal and Marine Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB) , Shahrak-e Pajoohesh Km 15, Tehran-Karaj Highway, Tehran , Iran ; Faculty of Marine Sciences, Khorramshahr Marine Sciences and Technology University , Khorramshahr , Iran
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Pramanik P, Chung YR. Changes in fungal population of fly ash and vinasse mixture during vermicomposting by Eudrilus eugeniae and Eisenia fetida: documentation of cellulase isozymes in vermicompost. WASTE MANAGEMENT (NEW YORK, N.Y.) 2011; 31:1169-1175. [PMID: 21277188 DOI: 10.1016/j.wasman.2010.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 12/22/2010] [Accepted: 12/28/2010] [Indexed: 05/30/2023]
Abstract
Fly ash (FA) and vinasse (VN), two industrial wastes, are generated in huge amounts and cause serious hazards to the environment. In this experiment, different proportions of these two wastes were used as food for two epigeic earthworms (Eisenia fetida and Eudrilus eugeniae) to standardize the recycling technique of these two wastes and to study their effect on fungal especially cellulolytic fungal population, cellulase activity and their isozyme pattern, chitin content and microbial biomass of waste mixture during vermicomposting. Increasing VN proportion from 25% to 50% or even higher, counts of both fungi and cellulolytic fungi in waste mixtures were significantly (P ≤ 0.05) increased during vermicomposting. Higher cellulase activity in treatments having 50% or more vinasse might be attributed to the significantly (P ≤ 0.05) higher concentration of group I isozyme while concentrations of other isozymes (group II and III) of cellulase were statistically at par. Higher chitin content in vinasse-enriched treatments suggested that fungal biomass and fungi-to-microbial biomass ratio in these treatments were also increased due to vermicomposting. Results revealed that Eudrilus eugeniae and Eisenia fetida had comparable effect on FA and VN mixture during vermicomposting. Periodical analysis of above-mentioned biochemical and microbial properties and nutrient content of final vermicompost samples indicated that equal proportion (1:1, w/w) of FA and VN is probably the optimum composition to obtain best quality vermicompost.
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Affiliation(s)
- Prabhat Pramanik
- Division of Applied Life Sciences (BK21), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 900 Gazwa, Jinju 660-701, Republic of Korea.
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Neeraja C, Anil K, Purushotham P, Suma K, Sarma P, Moerschbacher BM, Podile AR. Biotechnological approaches to develop bacterial chitinases as a bioshield against fungal diseases of plants. Crit Rev Biotechnol 2010; 30:231-41. [PMID: 20572789 DOI: 10.3109/07388551.2010.487258] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Fungal diseases of plants continue to contribute to heavy crop losses in spite of the best control efforts of plant pathologists. Breeding for disease-resistant varieties and the application of synthetic chemical fungicides are the most widely accepted approaches in plant disease management. An alternative approach to avoid the undesired effects of chemical control could be biological control using antifungal bacteria that exhibit a direct action against fungal pathogens. Several biocontrol agents, with specific fungal targets, have been registered and released in the commercial market with different fungal pathogens as targets. However, these have not yet achieved their full commercial potential due to the inherent limitations in the use of living organisms, such as relatively short shelf life of the products and inconsistent performance in the field. Different mechanisms of action have been identified in microbial biocontrol of fungal plant diseases including competition for space or nutrients, production of antifungal metabolites, and secretion of hydrolytic enzymes such as chitinases and glucanases. This review focuses on the bacterial chitinases that hydrolyze the chitinous fungal cell wall, which is the most important targeted structural component of fungal pathogens. The application of the hydrolytic enzyme preparations, devoid of live bacteria, could be more efficacious in fungal control strategies. This approach, however, is still in its infancy, due to prohibitive production costs. Here, we critically examine available sources of bacterial chitinases and the approaches to improve enzymatic properties using biotechnological tools. We project that the combination of microbial and recombinant DNA technologies will yield more effective environment-friendly products of bacterial chitinases to control fungal diseases of crops.
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Affiliation(s)
- Chilukoti Neeraja
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Chen G, Zheng Z, Yang S, Fang C, Zou X, Luo Y. Experimental co-digestion of corn stalk and vermicompost to improve biogas production. WASTE MANAGEMENT (NEW YORK, N.Y.) 2010; 30:1834-1840. [PMID: 20378324 DOI: 10.1016/j.wasman.2010.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2009] [Revised: 03/05/2010] [Accepted: 03/14/2010] [Indexed: 05/29/2023]
Abstract
Anaerobic co-digestion of corn stalk and vermicompost (VC) as well as mono-digestion of corn stalk were investigated. Batch mono-digestion experiments were performed at 35+/-1 degrees C and initial total solid loading (TSL) ranged from 1.2% to 6.0%. Batch co-digestion experiments were performed at 35+/-1 degrees C and initial TSL of 6% with VC proportions ranged from 20% to 80% of total solid (TS). For mono-digestion of corn stalk, a maximum methane yield of 217.60+/-13.87 mL/g TS(added) was obtained at initial TSL of 4.8%, and acidification was found at initial TSL of 6.0% with the lowest pH value of 5.10 on day 4. Co-digestion improved the methane yields by 4.42-58.61% via enhancing volatile fatty acids (VFAs) concentration and pH value compared with mono-digestion of corn stalk. The maximum biogas yield of 410.30+/-11.01 mL/g TS(added) and methane yield of 259.35+/-13.85 mL/g TS(added) were obtained for 40% VC addition. Structure analysis by X-ray diffractometry (XRD) showed that the lowest crystallinity of 35.04 of digested corn stalk was obtained from co-digestion with 40% VC, which decreased 29.4% compared to 49.6 obtained from un-treated corn stalk. It is concluded that co-digestion with VC is beneficial for improving biodigestibility and methane yield from corn stalk.
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Affiliation(s)
- Guangyin Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
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Wang G, Wang Y, Yang P, Luo H, Huang H, Shi P, Meng K, Yao B. Molecular detection and diversity of xylanase genes in alpine tundra soil. Appl Microbiol Biotechnol 2010; 87:1383-93. [PMID: 20393704 DOI: 10.1007/s00253-010-2564-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 03/07/2010] [Accepted: 03/14/2010] [Indexed: 11/25/2022]
Abstract
Xylan is a major polysaccharide in plant cell walls, and its degradation is mainly conducted by microbial xylanases in nature. To explore the xylanase diversity in the environment, two sets of degenerate primers were designed based on the microbial xylanase sequences in Pfam database of glycosyl hydrolase (GH) family 10 and 11 and were used to amplify objective gene fragments directly from the alpine tundra soil DNA of the Tianshan Mountains, China. Ninety-six distinct GH 10 and 31 GH 11 xylanase gene fragments were retrieved, and most of them have low identities with known sequences in GenBank. Based on phylogenetic analysis, all of the GH 10 xylanase sequences fell into six clusters and were related to xylanases from Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, Firmicutes, and Acidobacteria. Three clusters of GH 11 xylanase sequences were established, and two of them were related with enzymes from fungi. These results indicated the diversity of xylanase genes in this cold environment. Four xylanolytic strains were isolated from the soil, and GH 10 xylanase gene fragments were cloned using the same primers. A full-length gene was obtained and expressed in Escherichia coli, and the recombinant enzyme showed some cold-related characteristics. Our study provides an efficient molecular approach to study xylanase in complex environments and casts an insight into the diversity and distribution of xylanases in a cold environment, which is very meaningful to understand their roles in xylan degradation in nature.
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Affiliation(s)
- Guozeng Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, People's Republic of China
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Das SN, Sarma PVSRN, Neeraja C, Malati N, Podile AR. Members of Gammaproteobacteria and Bacilli represent the culturable diversity of chitinolytic bacteria in chitin-enriched soils. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0369-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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