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Shahid M, Ahmed W, Khan AB, Shams ZI, Arif A. Identification of bacterial community in a rapid composting method using 16SrDNA genes sequencing. Biodegradation 2024; 35:361-370. [PMID: 37987937 DOI: 10.1007/s10532-023-10056-z] [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: 02/09/2023] [Accepted: 09/21/2023] [Indexed: 11/22/2023]
Abstract
Composting is a process of microbial degradation of organic waste and is commonly applied for waste management. This is a slow process and requires a lot of land and human resources. The present study investigated mechanical augmentation with required microbial culture for composting municipal solid waste (MSW). Thirty isolates were subjected to 16S rDNA PCR amplification and gene sequencing. The isolates' sequencing from the compost samples was processed on BLASTn. Fourteen strains were identified for further experiments. The results divulge that Empedobacter (04), Bacillus (02), Proteus (02), Lactiplantibacillus (01), Klebsiella (01), Citrobacter (01), Brevibacillus (01), E. coli (01) and one unidentified strain were growing during composting. Eleven combinations of bacterial consortium and respective additives were applied for the organic waste decomposition in the next stage, resulting in varied completion periods ranging from 3 to 14 days. Two combinations were completed within 3 days, which are considered ideal combinations for composting. The microbial consortium was significantly diverse, which is a reason for rapid biodegradation. The present study reveals that the technology will be highly feasible for municipal solid waste management in tropical/subtropical countries.
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Affiliation(s)
- Muhammad Shahid
- Institute of Environmental Studies, University of Karachi, Karachi, 75270, Pakistan
| | - Waqar Ahmed
- Institute of Environmental Studies, University of Karachi, Karachi, 75270, Pakistan.
| | | | - Zafar Iqbal Shams
- Institute of Environmental Studies, University of Karachi, Karachi, 75270, Pakistan
| | - Afsheen Arif
- The Karachi Institute of Biotechnology and Genetic Engineering [KIBGE], University of Karachi, Karachi, Pakistan
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2
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Luo C, Li S, Ren P, Yan F, Wang L, Guo B, Zhao Y, Yang Y, Sun J, Gao P, Ji P. Enhancing the carbon content of coal gangue for composting through sludge amendment: A feasibility study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 348:123439. [PMID: 38325505 DOI: 10.1016/j.envpol.2024.123439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/03/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024]
Abstract
Cocomposting coal gangue and sludge eliminates the challenge of utilizing coal gangue. However, there is limited understanding about the feasibility of cocomposting sludge and coal gangue, as well as the composting indicators, functional microorganisms, and safety risks involved. Therefore, this study evaluated the feasibility of enhancing carbon composting in coal gangue by incorporating sludge along with sawdust as a conditioner. Three laboratory-scale reactors were designed and labeled as T1 (20 % coal gangue, 60 % sludge, and 20 % sawdust), T2 (40 % coal gangue, 40 % sludge, and 20 % sawdust), and T3 (60 % coal gangue, 20 % sludge, and 20 % sawdust). Seed germination and plant growth assessments were conducted to ensure compost stability and assess phytotoxicity to cabbage (Brassica rapa chinensis L.) in terms of growth and biomass. The results indicated that the temperature, pH, EC and ammonia nitrogen of all three reactor conditions met the requirements for product decomposition. Composting was successfully achieved when the sludge proportion was 20 % (T3). However, when the sludge proportion was markedly high (T1), the harmlessness of the compost was reduced. The germination indices of T1, T2, and T3 reached 95 %, 122 %, and 119 % at maturity, respectively. This confirmed that the harmless cycle, which involved promoting condensation and aromatization, enhancing decay, and reducing composting time, was shorter in T2 and T3 than in T1. Coal gangue can also serve as a beneficial habitat for microorganisms, promoting an increase in their population and activity. Potting experiments in sandy soil revealed that the mechanism of action of compost products in soil included not only the enhancement of soil nutrients but also the improvement of soil texture. The results of this study suggest that using coal gangue as a raw material for composting is an efficient and environmentally friendly approach for producing organic fertilizers.
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Affiliation(s)
- Chi Luo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shaohua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Pengyu Ren
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fan Yan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lu Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Bin Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yimo Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yue Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jian Sun
- Institute of Agricultural Quality Standard and Testing Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Pengcheng Gao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Puhui Ji
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Kim HS, Noh MH, White EM, Kandefer MV, Wright AF, Datta D, Lim HG, Smiggs E, Locklin JJ, Rahman MA, Feist AM, Pokorski JK. Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration. Nat Commun 2024; 15:3338. [PMID: 38688899 PMCID: PMC11061138 DOI: 10.1038/s41467-024-47132-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
The field of hybrid engineered living materials seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. Engineered living materials have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication is demonstrated in which spores from polymer-degrading bacteria are incorporated into a thermoplastic polyurethane using high-temperature melt extrusion. Bacteria are engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 °C. Furthermore, the overall tensile properties of spore-filled thermoplastic polyurethanes are substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitate disintegration in compost in the absence of a microbe-rich environment. Finally, embedded spores demonstrate a rationally programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.
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Affiliation(s)
- Han Sol Kim
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Myung Hyun Noh
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30 Jongga-ro, Ulsan, 44429, Republic of Korea
| | - Evan M White
- New Materials Institute, University of Georgia, Athens, GA, 30602, USA
| | | | - Austin F Wright
- New Materials Institute, University of Georgia, Athens, GA, 30602, USA
| | - Debika Datta
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Ethan Smiggs
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Jason J Locklin
- New Materials Institute, University of Georgia, Athens, GA, 30602, USA
| | - Md Arifur Rahman
- Thermoplastic Polyurethane Research, BASF Corporation, 1609 Biddle Ave., Wyandotte, MI, 48192, USA.
| | - Adam M Feist
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs, Lyngby, Denmark.
| | - Jonathan K Pokorski
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
- Institute for Materials Discovery and Design, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
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Sun Y, Staley ZR, Woodbury B, Riethoven JJ, Li X. Composting reduces the risks of resistome in beef cattle manure at the transcriptional level. Appl Environ Microbiol 2024; 90:e0175223. [PMID: 38445903 PMCID: PMC11022583 DOI: 10.1128/aem.01752-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Transcriptomic evidence is needed to determine whether composting is more effective than conventional stockpiling in mitigating the risk of resistome in livestock manure. The objective of this study is to compare composting and stockpiling for their effectiveness in reducing the risk of antibiotic resistance in beef cattle manure. Samples collected from the center and the surface of full-size manure stockpiling and composting piles were subject to metagenomic and metatranscriptomic analyses. While the distinctions in resistome between stockpiled and composted manure were not evident at the DNA level, the advantages of composting over stockpiling were evident at the transcriptomic level in terms of the abundance of antibiotic resistance genes (ARGs), the number of ARG subtypes, and the prevalence of high-risk ARGs (i.e., mobile ARGs associated with zoonotic pathogens). DNA and transcript contigs show that the pathogen hosts of high-risk ARGs included Escherichia coli O157:H7 and O25b:H4, Klebsiella pneumoniae, and Salmonella enterica. Although the average daily temperatures for the entire composting pile exceeded 55°C throughout the field study, more ARG and ARG transcripts were removed at the center of the composting pile than at the surface. This work demonstrates the advantage of composting over stockpiling in reducing ARG risk in active populations in beef cattle manure.IMPORTANCEProper treatment of manure before land application is essential to mitigate the spread of antibiotic resistance in the environment. Stockpiling and composting are two commonly used methods for manure treatment. However, the effectiveness of composting in reducing antibiotic resistance in manure has been debated. This work compared the ability of these two methods to reduce the risk of antibiotic resistance in beef cattle manure. Our results demonstrate that composting reduced more high-risk resistance genes at the transcriptomic level in cattle manure than conventional stockpiling. This finding not only underscores the effectiveness of composting in reducing antibiotic resistance in manure but also highlights the importance of employing RNA analyses alongside DNA analyses.
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Affiliation(s)
- Yuepeng Sun
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Zachery R. Staley
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Bryan Woodbury
- USDA-ARS U.S. Meat Animal Research Center, Clay Center, Clay Center, Nebraska, USA
| | - Jean-Jack Riethoven
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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5
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Li L, Liu X, Li J, Chen Z, Song T, Jin S, Zhu C, Luo L, Geng B, Zhu J. Mitigating Tetracycline antibiotic contamination in chicken manure using ex situ fermentation system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120614. [PMID: 38513588 DOI: 10.1016/j.jenvman.2024.120614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/21/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
Excessive use of tetracycline antibiotics in poultry farming results in significant concentrations of these drugs and tetracycline resistance genes (TRGs) in chicken manure, impacting both environmental and human health. Our research represents the first investigation into the removal dynamics of chlortetracycline (CTC) and TRGs in different layers of an ex situ fermentation system (EFS) for chicken waste treatment. By pinpointing and analyzing dominant TRGs-harboring bacteria and their interactions with environmental variables, we've closed an existing knowledge gap. Findings revealed that CTC's degradation half-lives spanned 3.3-5.8 days across different EFS layers, and TRG removal efficiency ranged between 86.82% and 99.52%. Network analysis highlighted Proteobacteria and Actinobacteria's essential roles in TRGs elimination, whereas Chloroflexi broadened the potential TRG hosts in the lower layer. Physical and chemical conditions within the EFS influenced microbial community diversity, subsequently impacting TRGs and integrons. Importantly, our study reports that the middle EFS layer exhibited superior performance in eliminating CTC and key TRGs (tetW, tetG, and tetX) as well as intI2. Our work transcends immediate health and environmental remediation by offering insights that encourage sustainable agriculture practices.
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Affiliation(s)
- Luyao Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Xue Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jiabin Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Zhuobo Chen
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Tingting Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Shan Jin
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Liangguo Luo
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Bing Geng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
| | - Jie Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
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Bai Y, Wu D, Dolfing J, Zhang L, Xie B. Dynamics and functions of biomarker taxa determine substrate-specific organic waste composting. BIORESOURCE TECHNOLOGY 2024; 393:130118. [PMID: 38029801 DOI: 10.1016/j.biortech.2023.130118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 12/01/2023]
Abstract
Bacteria are an influential component of diverse composting microbiomes, but their structure and underlying dynamics are poorly understood. This study analyzed the bacterial communities of 577 compost datasets globally and constructed a substrate-dependent catalog with more than 15 million non-redundant 16S rRNA gene sequences. Using a random-forest machine-learning model, 30 biomarker taxa were identified that accurately distinguish between the food, sludge and manure waste composting microbiomes (accuracy >98 %). These biomarker taxa were closely associated with carbon and nitrogen metabolic processes, during which they contributed to the predominant stochastic process and are influenced by different factors in the substrate-specific composts. This is corroborated by the community topological characteristics, which feature the biomarkers as keystone taxa maintaining the bacterial network stability. These findings provide a theoretical basis to identify and enhance the biomarker-functional bacteria for optimizing the composting performance of different organic wastes.
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Affiliation(s)
- Yudan Bai
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.
| | - Jan Dolfing
- Faculty Energy and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, United Kingdom
| | - Liangmao Zhang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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7
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Grenier V, Laur J, Gonzalez E, Pitre FE. Glyphosate has a negligible impact on bacterial diversity and dynamics during composting. Environ Microbiol 2023; 25:2897-2912. [PMID: 36975075 DOI: 10.1111/1462-2920.16374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
The herbicide glyphosate has several potential entry points into composting sites and its impact on composting processes has not yet been evaluated. To assess its impact on bacterial diversity and abundance as well as on community composition and dynamics, we conducted a mesocosm experiment at the Montreal Botanical Garden. Glyphosate had no effect on physicochemical property evolution during composting, while it was completely dissipated by the end of the experiment. Sampling at Days 0, 2, 28 and 112 of the process followed by 16S rRNA amplicon sequencing also found no effect of glyphosate on species richness and community composition. Differential abundance analyses revealed an increase of a few taxa in the presence of glyphosate, namely TRA3-20 (order Polyangiales), Pedosphaeraceae and BIrii41 (order Burkholderiales) after 28 days. In addition, five amplicon sequence variants (ASVs) had lower relative abundance in the glyphosate treatment compared to the control on Day 2, namely Comamonadaceae, Pseudomonas sp., Streptomyces sp., Thermoclostridium sp. and Actinomadura keratinilytica, while two ASVs were less abundant on Day 112, namely Pedomicrobium sp. and Pseudorhodoplanes sp. Most differences in abundance were measured between the different sampling points within each treatment. These results present glyphosate as a poor determinant of species recruitment during composting.
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Affiliation(s)
- Vanessa Grenier
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de recherche en biologie végétale, Montréal, Québec, Canada
| | - Joan Laur
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de recherche en biologie végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montreal, Québec, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill Genome Centre, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Frederic E Pitre
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de recherche en biologie végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montreal, Québec, Canada
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Andraskar J, Yadav S, Khan D, Kapley A. Treatment Options for Municipal Solid Waste by Composting and Its Challenges. Indian J Microbiol 2023; 63:235-243. [PMID: 37781005 PMCID: PMC10533440 DOI: 10.1007/s12088-023-01087-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 08/03/2023] [Indexed: 10/03/2023] Open
Abstract
Recovery and recycling of municipal solid waste biodegradable fraction (50-55%) are essential for attaining sustainability and a circular economy. Among organic waste treatment methods, composting is used to recycle organic fractions of waste. However, only 10-12% of municipal solid waste is utilized for composting treatment due to a lack of segregation practices and process challenges, including long process periods, odorous and greenhouse gas emissions, nitrogen loss, and low compost quality, which hinders large-scale practice. The current review paper discusses the challenges of composting treatment and its possible solutions. Various strategies were explored to address these challenges, such as utilizing microbial inoculum, additives, and optimization of physicochemical parameters. It also emphasizes the application of metagenomics for exploring key species. The knowledge about the microbial community and biochemical pathways (genome mining) can be exploited for the improvement of treatment efficiency. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01087-4.
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Affiliation(s)
- Jayanta Andraskar
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Shailendra Yadav
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020 India
| | - Debishree Khan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
- Chemical and Hazardous Waste Management Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020 India
| | - Atya Kapley
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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Santos-Pereira C, Sousa J, Costa ÂMA, Santos AO, Rito T, Soares P, Franco-Duarte R, Silvério SC, Rodrigues LR. Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12627-9. [PMID: 37417976 PMCID: PMC10390414 DOI: 10.1007/s00253-023-12627-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023]
Abstract
The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples' microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. KEY POINTS: • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.
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Affiliation(s)
- Cátia Santos-Pereira
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Joana Sousa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Ângela M A Costa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Andréia O Santos
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Teresa Rito
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro Soares
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sara C Silvério
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal.
| | - Lígia R Rodrigues
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
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10
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Moubareck CA, Alawlaqi B, Alhajeri S. Characterization of physicochemical parameters and bacterial diversity of composted organic food wastes in Dubai. Heliyon 2023; 9:e16426. [PMID: 37274727 PMCID: PMC10238688 DOI: 10.1016/j.heliyon.2023.e16426] [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: 12/27/2022] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 06/06/2023] Open
Abstract
Composting favours recycling organic waste and producing an end product with high bioenergy potential and significant nutritional value for the soil. Analysing composted organic waste prepared in Dubai, a region with a desertic climate and a unique environment is essential since environmental conditions can greatly affect the physicochemical and biological soil properties and no studies in the Gulf region have been published yet on that process. This study analysed twelve different compost samples prepared in well ventilated wooden chambers, using home-generated organic wastes following the hot aerobic composting method for a duration of three months. The physicochemical parameters, measured at the end of the study, revealed that organic matter, electrical conductivity and pH were within the standard ranges while moisture content was low. Concerning macronutrients, most of the samples were within the standard range for carbon, potassium and sodium, while they were poor in phosphorous and nitrogen. Metagenomic analysis with Illumina MiSeq revealed the abundance of Firmicutes (30.35%), followed by Bacteroidota (26.69%), Proteobacteria (21.47%), and Actinobacteriota (11.17%). The phylum Planctomycetota, solely detected in compost and known to have a significant impact on soil ecosystem and decomposition of organic matter, was reported at a relatively significant level (2.35%). The Clostridia class, efficient in degrading cellulose, was described at high levels compared to other studies. The composting project succeeded in generating a healthy soil but lengthening the duration will allow the samples to fully decompose and therefore increase the total available nitrogen and phosphorus to meet the criteria of a typical mature compost. Various microbial consortia helped in the decomposition process. The qualitative information collected in this study will help in improving the composting technology to favour its utilization by a larger public in the Gulf region.
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Affiliation(s)
| | - Buthaina Alawlaqi
- College of Natural and Health Sciences, Zayed University, Dubai, United Arab Emirates
| | - Salama Alhajeri
- Department of Corporate Environmental Health & Safety, Dubai Health Authority, Dubai, United Arab Emirates
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11
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Glushakova АМ, Kachalkin АV. Yeast community succession in cow dung composting process. Fungal Biol 2023; 127:1075-1083. [PMID: 37344009 DOI: 10.1016/j.funbio.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
Yeast complexes in the composting process of cow dung prepared to fertilize the soil for growing vegetables and fruits were studied. The average abundance of yeasts changed during the four temperature stages of the composting process. The highest abundance of yeasts, 1.38 × 104 cfu/g, was observed in the second stage of heating from 20 to 40 °C; the lowest was studied in the stage with the highest temperature (65 °C), 1.68 × 103 cfu/g. A total of 19 yeast species were observed and identified: 11 ascomycetes and 8 basidiomycetes, belonging to five subphyla of Fungi: Saccharomycotina (10), Pezizomycotina (1), Agaricomycotina (5), Pucciniomycotina (2), and Ustilaginomycotina (1). The greatest diversity of yeasts was found in the initial (20 °C) and second (heating up to 40 °C) temperature stages of composting (Aureobasidium pullulans (yeast-like fungus), Candida parapsilosis, Candida saitoana, Candida santamariae, Candida tropicalis, Curvibasidium cygneicollum, Cutaneotrichosporon moniliforme, Debaryomyces fabryi, Debaryomyces hansenii, Filobasidium magnum, Kazachstania sp., Moesziomyces bullatus, Naganishia globosa, Papiliotrema flavescens, Rhodotorula mucilaginosa, Scheffersomyces insectosa, Torulaspora delbrueckii, Vanrija musci), and the lowest in the stage of maximum heating (65 °C) (C. parapsilosis, C. tropicalis, Cyberlindnera jadinii).The opportunistic yeasts C. parapsilosis and C. tropicalis were obtained not only in the initial, second and third temperature stages of the composting process, but also in mature compost in the final stage prepared for soil application. This study shows that the cow dung, used in the farm studied did not meet the microbiological safety criteria. The reduction of opportunistic yeast species was not achieved with the composting method used. The likelihood of these species entering agricultural products via compost and soil and developing as endophytes in the internal tissues of fruits is very high. Since some strains of opportunistic Candida species from cow dung exhibited virulent characteristics (they produced hydrolytic enzymes and were resistant to antifungal compounds), additional phenotypic and genetic studies of the compost strains and their comparison with clinical isolates should be pursued.
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Affiliation(s)
- Аnna М Glushakova
- M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064, Russia.
| | - Аleksey V Kachalkin
- M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, 142290, Russia
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12
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Pottipati S, Jat N, Kalamdhad AS. Bioconversion of Eichhornia crassipes into vermicompost on a large scale through improving operational aspects of in-vessel biodegradation process: Microbial dynamics. BIORESOURCE TECHNOLOGY 2023; 374:128767. [PMID: 36822559 DOI: 10.1016/j.biortech.2023.128767] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/12/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Eichhornia crassipes is a common, abundant aquatic weed biomass found globally. The present study examined optimum biodegradation procedures through batch studies (550 L rotating drum composter) and the resulting best combination on a large scale (5000 L rotary drum composter). The pilot scale rotary drum reactor was commenced with cow manure and then treated for 3 months with 250 kg/day of homogenously mixed E. crassipes and dry leaves. The rotary drum's inlet and outlet temperatures were 60 °C and 39 °C, respectively, suggesting thermophilic conditions with a 7-day waste retention duration. Eisenia fetida was used for vermicomposting the outlet material for 20 days, raising the nitrogen content to 3.2%. Bacterial diversity (16S-rRNA) sequencing revealed that Proteobacteria and Euryarchaeota are the most predominant. After 27 days, the volume dropped by 71%, and the product was stable and soil-safe. Large-scale optimised biodegradation may be a better way to handle aquatic weed biomass.
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Affiliation(s)
- Suryateja Pottipati
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Neeraj Jat
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ajay S Kalamdhad
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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13
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Composition, structure, and functional shifts of prokaryotic communities in response to co-composting of various nitrogenous green feedstocks. BMC Microbiol 2023; 23:50. [PMID: 36859170 PMCID: PMC9979578 DOI: 10.1186/s12866-023-02798-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 02/17/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Thermophilic composting is a promising method of sanitizing pathogens in manure and a source of agriculturally important thermostable enzymes and microorganisms from organic wastes. Despite the extensive studies on compost prokaryotes, shifts in microbial profiles under the influence of various green materials and composting days are still not well understood, considering the complexity of the green material sources. Here, the effect of regimens of green composting material on the diversity, abundance, and metabolic capacity of prokaryotic communities in a thermophilic compost environment was examined. METHODS Total community 16S rRNA was recovered from triplicate compost samples of Lantana-based, Tithonia-based, Grass-based, and mixed (Lantana + Tithonia + Grass)- based at 21, 42, 63, and 84 days of composting. The 16S rRNA was sequenced using the Illumina Miseq platform. Bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 (DADA2) R version 4.1 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States version 2 (PICRUSt2) pipelines for community structure and metabolic profiles, respectively. In DADA2, prokaryotic classification was done using the Refseq-ribosomal database project (RDP) and SILVA version 138 databases. RESULTS Our results showed apparent differences in prokaryotic community structure for total diversity and abundance within the four compost regimens and composting days. The study showed that the most prevalent phyla during composting included Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, and Proteobacteria. Additionally, there were differences in the overall diversity of metabolic pathways but no significant differences among the various compost treatments on major metabolic pathways like carbohydrate biosynthesis, carbohydrate degradation, and nitrogen biosynthesis. CONCLUSION Various sources of green material affect the succession of compost nutrients and prokaryotic communities. The similarity of amounts of nutrients, such as total Nitrogen, at the end of the composting process, despite differences in feedstock material, indicates a significant influence of composting days on the stability of nutrients during composting.
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14
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Grenier V, Gonzalez E, Brereton NJB, Pitre FE. Dynamics of bacterial and archaeal communities during horse bedding and green waste composting. PeerJ 2023; 11:e15239. [PMID: 37159830 PMCID: PMC10163874 DOI: 10.7717/peerj.15239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.
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Affiliation(s)
- Vanessa Grenier
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
| | - Emmanuel Gonzalez
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill Genome Centre, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Nicholas JB Brereton
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Frederic E. Pitre
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montréal, Québec, Canada
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15
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Zhan Y, Chang Y, Tao Y, Zhang H, Lin Y, Deng J, Ma T, Ding G, Wei Y, Li J. Insight into the dynamic microbial community and core bacteria in composting from different sources by advanced bioinformatics methods. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:8956-8966. [PMID: 35462586 DOI: 10.1007/s11356-022-20388-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/18/2022] [Indexed: 05/26/2023]
Abstract
Microbial communities are important for high composting efficiency and good quality composts. This study was conducted to compare the changes of physicochemical and bacterial characteristics in composting from different raw materials, including chicken manure (CM), duck manure (DM), sheep manure (SM), food waste (FW), and vegetable waste (VW). The role and interactions of core bacteria and their contribution to maturity in diverse composts were analyzed by advanced bioinformatics methods combined sequencing with co-occurrence network and structural equation modeling (SEM). Results indicated that there were obviously different bacterial composition and diversity in composting from diverse sources. FW had a low pH and different physiochemical characteristics compared to other composts but they all achieved similar maturity products. Redundancy analysis suggested total organic carbon, phosphorus, and temperature governed the composition of microbial species but key factors were different in diverse composts. Network analysis showed completely different interactions of core bacterial community from diverse composts but Thermobifida was the ubiquitous core bacteria in composting bacterial network. Sphaerobacter and Lactobacillus as core genus were presented in the starting mesophilic and thermophilic phases of composting from manure (CM, DM, SM) and municipal solid waste (FW, VW), respectively. SEM indicated core bacteria had the positive, direct, and the biggest (> 80%) effects on composting maturity. Therefore, this study presents theoretical basis to identify and enhance the core bacteria for improving full-scale composting efficiency facing more and more organic wastes.
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Affiliation(s)
- Yabin Zhan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Organic Recycling Research Institute (Suzhou) of China Agricultural University, Suzhou, 215100, China
| | - Yuan Chang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Organic Recycling Research Institute (Suzhou) of China Agricultural University, Suzhou, 215100, China
| | - Yueyue Tao
- Institute of Agricultural Sciences in Taihu Lake District, Suzhou Academy of Agricultural Sciences, Suzhou, 215155, China
| | - Hao Zhang
- Technical Center for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing, 100012, China
| | - Yongfeng Lin
- Organic Recycling Research Institute (Suzhou) of China Agricultural University, Suzhou, 215100, China
| | - Jie Deng
- Organic Recycling Research Institute (Suzhou) of China Agricultural University, Suzhou, 215100, China
- College of Resources and Environmental Science, Yunnan Agricultural University, Kunming, 650201, China
| | - Tiantian Ma
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Guochun Ding
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Organic Recycling Research Institute (Suzhou) of China Agricultural University, Suzhou, 215100, China
| | - Yuquan Wei
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
- Organic Recycling Research Institute (Suzhou) of China Agricultural University, Suzhou, 215100, China.
| | - Ji Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Organic Recycling Research Institute (Suzhou) of China Agricultural University, Suzhou, 215100, China
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16
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He Y, Liu D, He X, Wang Y, Liu J, Shi X, Chater CCC, Yu F. Characteristics of bacterial and fungal communities and their impact during cow manure and agroforestry biowaste co-composting. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 324:116377. [PMID: 36352711 DOI: 10.1016/j.jenvman.2022.116377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/17/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Microbial communities and environmental conditions are both of great importance for efficient utilization of agroforestry resources. Nevertheless, knowledge about the role of soluble nutrients and enzymatic properties, and their inner links with microbial communities remain limited. This is especially the case for the co-composting of agricultural and forestry biowaste. Here, we investigate the succession of key microbes during co-composting (sawdust + cow manure, SA; straw + cow manure, ST), employing amplicon sequencing, enzyme assays, and physicochemical analyses. N-fixing bacteria (Pseudomonas) and C-degrading fungi (Acaulium) have been identified as dominant taxa during such co-composting. Although eight antibiotic resistance genes were found to persist during composting, pathogenic microbes declined with composting time. NO3--N content was screened as a determinant structuring the bacterial and fungal communities, with importance also shown for C-degrading enzymes such as cellulose, laccase, and peroxidase activity. These results identify the key microbial taxa and their main interactive environmental factors, which are potentially valuable for the development of a mixed microbial inoculant to accelerate the maturation of agroforestry biowastes composting.
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Affiliation(s)
- Yan He
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Dong Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Xinhua He
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China; Department of Land, Air and Water Resources, University of California at Davis, Davis, CA, 95616, USA; School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Yanliang Wang
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jianwei Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China; Guizhou Kangqunyuan Biotechnology Co., LTD, Liupanshui, 553600, Guizhou, China
| | | | - Fuqiang Yu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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17
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Li Q, Zhang K, Yang Z, Guo H, Zheng X, Zhang Q, Xiong J, Lu X. Dynamic changes of microbial community and moisture ratio during bio-drying of sludge after electro-dewatering. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 324:116366. [PMID: 36183534 DOI: 10.1016/j.jenvman.2022.116366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Using electro-dewatering as the pretreatment process for sludge bio-drying can improve the dewatering performance. It was innovatively investigated including the microbial mechanism and the kinetics of moisture removal by bio-drying with electro-dewatered sludge in this study. Two bio-drying processes using electro-dewatered sludge (EDS) and sludge added cornstalk conditioner (CSS) were compared. Microbial community analysis showed that the abundance of Bacteroidetes increased from 4.21% to 16.67% after electro-dewatering. The dominant phyla were Bacteroidetes (36.79%), Proteobacteria (32.35%), and Actinobacteria (24.58%) at the end of EDS bio-drying. Network analysis revealed that the co-occurrence patterns in EDS included 40 nodes and 97 edges. The prediction results of the Kyoto Encyclopedia of Genes and Genomes demonstrated that the relative abundances of carbohydrate metabolism and metabolism of terpenoids and polyketides in sludge decreased, while the relative abundances of lipid metabolism, xenobiotic biodegradation and metabolism increased after electro-dewatering. Five thin layer drying kinetic models were analyzed to estimate the bio-drying kinetic parameters. The Page's model could be better fitted to the results and the highest R2 was 0.9570 in the EDS. The new coefficients k (0.1637) and n (1.2097) were obtained. The results provided mechanism and data support for exploring and applying bio-drying technology after sludge electro-dewatering.
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Affiliation(s)
- Qian Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; School of Environmental Science and Engineering, Tianjin University, Tianjin, 300354, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Zengjun Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Haigang Guo
- Hebei University of Engineering, Handan, 056038, China
| | - Xiangqun Zheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Qiangying Zhang
- Department of Chemistry & Environmental Science, School of Science, Tibet University, Lhasa, 850000, China
| | - Jian Xiong
- Department of Chemistry & Environmental Science, School of Science, Tibet University, Lhasa, 850000, China
| | - Xuebin Lu
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300354, China; Department of Chemistry & Environmental Science, School of Science, Tibet University, Lhasa, 850000, China.
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18
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Martínez-Yáñez MG, Silva-Ortega CO, Hernández-Aranda VA, Vallejo-Pérez MR, Alcalá-Briseño R, Vega-Manriquez DX, Aguilar-Benítez G, Jarquin-Gálvez R, Lara-Ávila JP. Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02156-9. [PMID: 36520176 DOI: 10.1007/s00248-022-02156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Mature composts and their water-based extracts, known as aerated compost teas (ACTs), are biofertilizers that share bioactive effects like soil restoration and plant health promotion, widely used for sustainable agriculture. Bioactive effects of compost and ACTs could be associated with their physicochemical and biological characteristics, like carbon/nitrogen (C/N) ratio and microbiota structure respectively. In our study, we elaborated ACTs using mature homemade compost, wheat bran, and grass clippings, following the C/N ratio criteria. Irrigation of tomato plantlets with ACT whose C/N ratio was close to the expected C/N ratio for mature compost evidenced plant growth promotion. Exploring the bacterial microbiota of elaborated ACTs and origin compost revealed significant structural differences, including phyla involved in N mineralization and free-living N-fixing bacteria. Therefore, ACTs harbor diverse bacterial microbiota involved in the N cycle, which would enrich plant and soil bacterial communities at the taxonomic and functional levels. Furthermore, ACTs are considered a part of agroecological and circular economy approaches.
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Affiliation(s)
| | | | | | - Moisés Roberto Vallejo-Pérez
- CONACYT, Universidad Autónoma de San Luis Potosí. Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACYT), San Luis Potosí, SLP, México
| | | | - Delia Xochil Vega-Manriquez
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Soledad de Graciano Sánchez, SLP, México
| | - Gisela Aguilar-Benítez
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Soledad de Graciano Sánchez, SLP, México
| | - Ramón Jarquin-Gálvez
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Soledad de Graciano Sánchez, SLP, México
| | - José Pablo Lara-Ávila
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Soledad de Graciano Sánchez, SLP, México.
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19
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Kong Y, Wang G, Chen W, Yang Y, Ma R, Li D, Shen Y, Li G, Yuan J. Phytotoxicity of farm livestock manures in facultative heap composting using the seed germination index as indicator. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114251. [PMID: 36327785 DOI: 10.1016/j.ecoenv.2022.114251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Static facultative heap composting of animal manure is widely used in China, but there is almost no systematic research on the phytotoxicity of the produced compost. Here, we evaluated the phytotoxic variation in compost produced by facultative heap composting of four types of animal manure (chicken manure, pig manure, sheep manure, and cattle manure) using different plant seeds (cucumber, radish, Chinese cabbage, and oilseed rape) to determine germination index (GI). The key factors that affected GI values were identified, including the dynamics of the phytotoxicity and microbial community during heap composting. Sensitivity to toxicity differed depending on the type of plant seed used. Phytotoxicity during facultative heap composting, evaluated by the GI, was in the order: chicken manure (0-6.6 %) < pig manure (14.4-90.5 %) < sheep manure (46.0-93.0 %) < cattle manure (50.2-105.8 %). Network analysis showed that the volatile fatty acid (VFA) concentration was positively correlated with Firmicutes abundance, and NH4+-N was correlated with Actinobacteria, Proteobacteria, and Bacteroidetes. More bacteria were stimulated to participate in conversions of dissolved organic carbon, dissolved nitrogen, VFA, and ammonia-nitrogen (NH4+-N) in sheep manure heap composting than that in other manure. The GI was most affected by VFA in chicken manure and cattle manure heap composting, while NH4+-N was the main factor affecting the GI in pig manure and sheep manure compost. The dissolved carbon and nitrogen content and composition, as well as the core and proprietary microbial communities, were the primary factors that affected the succession of phytotoxic substances in facultative heap composting, which in turn affected GI values. In this study, the key pathways of livestock manure composting that affected GI and phytotoxicity were found and evaluated, which provided new insights and theoretical support for the safe use of organic fertilizer.
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Affiliation(s)
- Yilin Kong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Guoying Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Wenjie Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Yan Yang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Ruonan Ma
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Danyang Li
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Yujun Shen
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Jing Yuan
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China.
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20
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Ma T, Zhan Y, Chen W, Xu S, Wang Z, Tao Y, Shi X, Sun B, Ding G, Li J, Wei Y. Impact of aeration rate on phosphorus conversion and bacterial community dynamics in phosphorus-enriched composting. BIORESOURCE TECHNOLOGY 2022; 364:128016. [PMID: 36162785 DOI: 10.1016/j.biortech.2022.128016] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
This study was to investigate the effects of different aeration rates on phosphorus (P) conversion and bacterial community dynamics in P-enriched composting by 16S rRNA gene sequencing, sequential P fractionation, network analysis and structural equation model (SEM). Results indicated that Olsen P content increased by 138 %, 150 %, 121 % after composting with aeration rate (L kg-1 DM min-1) at 0.2 (AR0.2), 0.4 (AR0.4) and 0.6 (AR0.6). AR0.4 was more conducive to enhance P solubilization efficacy and available P accumulation. Redundancy analysis indicated Lactobacillus, Spartobacteria and Pseudomonas were key bacteria associated with HCl-Pi especially in AR0.2 and AR0.4. Network analysis showed that increased aeration rate enhanced the connection and function homoplasy among modules and AR0.4 had more orderly community organization for key bacteria to solubilize P in directly and indirectly biotic way. SEM suggested indirectly biotic P-solubilization had more contribution than directly biotic way mainly by phosphate-solubilizing bacteria.
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Affiliation(s)
- Tiantian Ma
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193, Beijing, China
| | - Yabin Zhan
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Wenjie Chen
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Shaoqi Xu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China; DBN Agriculture Science and Technology Group CO, Ltd., DBN Pig Academy, Beijing 102629, China
| | - Zhigang Wang
- DBN Agriculture Science and Technology Group CO, Ltd., DBN Pig Academy, Beijing 102629, China
| | - Yueyue Tao
- Institute of Agricultural Sciences in Taihu Lake District, Suzhou Academy of Agricultural Sciences, Suzhou 215155, China
| | - Xiong Shi
- Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China
| | - Baoru Sun
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193, Beijing, China
| | - Guochun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China.
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21
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Fang C, Su Y, He X, Han L, Qu H, Zhou L, Huang G. Membrane-covered composting significantly decreases methane emissions and microbial pathogens: Insight into the succession of bacterial and fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157343. [PMID: 35842148 DOI: 10.1016/j.scitotenv.2022.157343] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
In this study, the effects of semipermeable membrane-covered on methane emissions and potential pathogens during industrial-scale composting of the solid fraction of dairy manure were investigated. The results showed that the oxygen concentration in the membrane-covered group (CT) was maintained above 10 %, and the cumulative methane emission in CT was >99 % lower than that in the control group (CK). Microbial analysis showed that the bacterial genus Thermus and the fungal genus Mycothermus were dominant in CT, and the richness and diversity of the bacterial community were greater than those of the fungal community. At the end of the composting, the relative abundance of potential bacterial pathogens in CT was 32.59 % lower than that in CK, and the relative abundance of potential fungal pathogens in each group was <2 %. Structural equation models revealed that oxygen concentration was a major factor influencing the bacterial diversity in CT, and the increase of oxygen concentration could limit methane emissions by inhibiting the growth of anaerobic bacteria. Therefore, membrane-covered composting could effectively improve compost safety and reduce methane emissions by regulating microbial community structure.
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Affiliation(s)
- Chen Fang
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Ya Su
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Xueqin He
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Lujia Han
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Huiwen Qu
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Ling Zhou
- Modern Agricultural Engineering Key Laboratory at Universities of Education Department of Xinjiang Uygur Autonomous Region, Tarim University, Alar, Xinjiang 843300, China
| | - Guangqun Huang
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China.
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22
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Kiruba N JM, Saeid A. An Insight into Microbial Inoculants for Bioconversion of Waste Biomass into Sustainable "Bio-Organic" Fertilizers: A Bibliometric Analysis and Systematic Literature Review. Int J Mol Sci 2022; 23:13049. [PMID: 36361844 PMCID: PMC9656562 DOI: 10.3390/ijms232113049] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/31/2023] Open
Abstract
The plant-microbe holobiont has garnered considerable attention in recent years, highlighting its importance as an ecological unit. Similarly, manipulation of the microbial entities involved in the rhizospheric microbiome for sustainable agriculture has also been in the limelight, generating several commercial bioformulations to enhance crop yield and pest resistance. These bioformulations were termed biofertilizers, with the consistent existence and evolution of different types. However, an emerging area of interest has recently focused on the application of these microorganisms for waste valorization and the production of "bio-organic" fertilizers as a result. In this study, we performed a bibliometric analysis and systematic review of the literature retrieved from Scopus and Web of Science to determine the type of microbial inoculants used for the bioconversion of waste into "bio-organic" fertilizers. The Bacillus, Acidothiobacillus species, cyanobacterial biomass species, Aspergillus sp. and Trichoderma sp. were identified to be consistently used for the recovery of nutrients and bioconversion of wastes used for the promotion of plant growth. Cyanobacterial strains were used predominantly for wastewater treatment, while Bacillus, Acidothiobacillus, and Aspergillus were used on a wide variety of wastes such as sawdust, agricultural waste, poultry bone meal, crustacean shell waste, food waste, and wastewater treatment plant (WWTP) sewage sludge ash. Several bioconversion strategies were observed such as submerged fermentation, solid-state fermentation, aerobic composting, granulation with microbiological activation, and biodegradation. Diverse groups of microorganisms (bacteria and fungi) with different enzymatic functionalities such as chitinolysis, lignocellulolytic, and proteolysis, in addition to their plant growth promoting properties being explored as a consortium for application as an inoculum waste bioconversion to fertilizers. Combining the efficiency of such functional and compatible microbial species for efficient bioconversion as well as higher plant growth and crop yield is an enticing opportunity for "bio-organic" fertilizer research.
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Affiliation(s)
- Jennifer Michellin Kiruba N
- Department of Engineering and Technology of Chemical Processes, Faculty of Chemistry, Wroclaw University Science and Technology, 50-373 Wroclaw, Poland
| | - Agnieszka Saeid
- Department of Engineering and Technology of Chemical Processes, Faculty of Chemistry, Wroclaw University Science and Technology, 50-373 Wroclaw, Poland
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23
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Tom LM, Aulitto M, Wu YW, Deng K, Gao Y, Xiao N, Rodriguez BG, Louime C, Northen TR, Eudes A, Mortimer JC, Adams PD, Scheller HV, Simmons BA, Ceja-Navarro JA, Singer SW. Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. MICROBIOME 2022; 10:183. [PMID: 36280858 PMCID: PMC9594917 DOI: 10.1186/s40168-022-01377-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/19/2022] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities. RESULTS To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted sorghum-degrading communities, including Actinotalea, Filomicrobium, and Gemmatimonadetes populations. Functional analysis demonstrated that the microbiomes proceeded through successive stages that are linked to enzymes that deconstruct plant cell wall polymers. The combination of network and functional analysis highlighted the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes. CONCLUSIONS The two-tier cultivation of compost-derived microbiomes on sorghum led to the establishment of microbiomes for which community structure and performance could be assessed. The work reinforces the observation that subtle differences in community composition and the genomic content of strains may lead to significant differences in community performance. Video Abstract.
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Affiliation(s)
- Lauren M Tom
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martina Aulitto
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu Gao
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Naijia Xiao
- Institute of Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | | | - Clifford Louime
- College of Natural Sciences, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Javier A Ceja-Navarro
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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24
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Lin WR, Li HY, Lin LC, Hsieh SY. Dynamics of Microbial Community during the Co-Composting of Swine and Poultry Manure with Spent Mushroom Substrates at an Industrial Scale. Microorganisms 2022; 10:microorganisms10102064. [PMID: 36296339 PMCID: PMC9608188 DOI: 10.3390/microorganisms10102064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Spent mushroom substrates (SMSs) can be developed as a biofertilizer through composting. Here, we investigated the dynamics of bacterial and fungal communities during commercial composting and the effect of swine and poultry manure on their communities through MiSeq pyrosequencing. Weissella paramesenteroides and Lactobacillus helveticus were dominant bacterial species in the composts with soy waste (SMS-SW), whereas Thermotogaceae sp. and Ureibacillus sp. were dominant in the composts with swine and poultry manure (SMS-PM). For the fungal community, Flammulina velutipes was dominant in SMS-SW, whereas Trichosporon asahii, Candida catenulate, Aspergillus fumigatus, and Candida tropicalis were dominant in SMS-PM. The addition of manure affected the bacterial community significantly. Redundancy analysis indicated that bacterial communities were affected by temperature, potassium, and potassium oxide and fungal communities by temperature, Kjeldahl nitrogen, organic matter, and ammonium nitrogen. Our findings can guide future research on composting microbiology.
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Affiliation(s)
- Wan-Rou Lin
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
- Correspondence: or (W.-R.L.); (S.-Y.H.)
| | - Han-Yun Li
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Lei-Chen Lin
- Department of Forestry and Natural Resources, National Chiayi University, Chiayi 60004, Taiwan
| | - Sung-Yuan Hsieh
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
- Correspondence: or (W.-R.L.); (S.-Y.H.)
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25
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Wang P, Wang Z, Ren Z, Ding Y, Pan J, Wang Y, Jin D. Effects of di-n-butyl phthalate on aerobic composting process of agricultural waste: Mainly based on bacterial biomass and community dynamics analysis. ENVIRONMENTAL RESEARCH 2022; 212:113290. [PMID: 35427593 DOI: 10.1016/j.envres.2022.113290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/23/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Phthalic acid esters (PAEs) pollution has become a major environmental problem in agricultural waste composting. However, little information was available about the how the PAEs alter microbial processes during composting. This study investigated the effects of di-n-butyl phthalate (DBP) on bacterial biomass and community dynamics during composting. The results showed that a decreasing of DBP was observed from thermophilic phase and 43.26% of DBP was degraded after composting. The bacterial biomass and diversity during composting were reduced under DBP stress, so delaying the decomposition of organic matter. Moreover, the changes in bacterial community were observed since the thermophilic phase of DBP-contaminated composting. KEGG pathway analysis indicated that DBP stress decreased the relative abundance of the main metabolic pathways and inhibited compost maturation. Moreover, DBP stress had more significant correlation with the dominant bacteria. This work will expand the understanding of PAEs-contaminated organic waste composting and further control of PAEs pollutants.
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Affiliation(s)
- Ping Wang
- School of Chemistry and Chemical Engineering, Zhoukou Normal University, Zhoukou, 466001, China
| | - Zhen Wang
- School of Chemistry and Chemical Engineering, Zhoukou Normal University, Zhoukou, 466001, China
| | - Ziming Ren
- School of Chemistry and Chemical Engineering, Zhoukou Normal University, Zhoukou, 466001, China
| | - Yuejie Ding
- School of Chemistry and Chemical Engineering, Zhoukou Normal University, Zhoukou, 466001, China
| | - Jiangang Pan
- School of Life Science and Technology, Inner Mongolia University of Science & Technology, Baotou, 014010, China
| | - Yanhui Wang
- Guangxi Key Laboratory for Biology of Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Decai Jin
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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26
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Wang H, Shankar V, Jiang X. Compositional and Functional Changes in Microbial Communities of Composts Due to the Composting-Related Factors and the Presence of Listeria monocytogenes. Microbiol Spectr 2022; 10:e0184521. [PMID: 35703536 PMCID: PMC9430276 DOI: 10.1128/spectrum.01845-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/19/2022] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a leading foodborne pathogen that can contaminate fresh produce in farm environment, resulting in deadly outbreaks. Composts contain a diversity of microorganisms, and some of them may be compost-adapted competitive exclusion microorganisms against L. monocytogenes. To understand interactions between compost microflora and the pathogen, both dairy- and poultry-wastes based composts (n = 12) were inoculated with L. monocytogenes, and then analyzed by next-generation sequencing approaches along with culturing methods. DNA extraction and enumeration of L. monocytogenes were performed at 0 and 72 h post-incubation at room temperature. The major bacterial phyla were identified as Firmicutes (23%), Proteobacteria (23%), Actinobacteria (19%), Chloroflexi (13%), Bacteroidetes (12%), Gemmatimonadetes (2%), and Acidobacteria (2%). The top three indicator genera enriched in different compost types were identified by LEfSe with LDA score > 2. The interactions between L. monocytogenes and indigenous microflora were limited as no significant changes in the dominant microbial members in compost ecosystem, but some discriminatory species such as Bacillus, Geobacillus, and Brevibacterium were identified by Random Forest analysis. Besides, changes in metabolic pathways and the increased abundance of bacteriocins category in the compost samples containing L. monocytogenes after 72 h postinoculation were revealed by metatranscriptomic sequencing. Taken together, the compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbial compositions, and the analysis of compost metagenome implied that interactions between L. monocytogenes and compost microflora may include competition for nutrients and the presence of antimicrobials. IMPORTANCE Listeria monocytogenes has been recognized as the etiological agent causing foodborne disease outbreaks, with fresh produce as vulnerable for contamination at even preharvest stage. Owing to the richness in microbial community, compost may mediate suppression of pathogens. In this study, the impact of compost-related factors and L. monocytogenes intrusion on dynamic changes in compost microbiome was investigated by next generation sequencing techniques. The compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbiome. The interactions between L. monocytogenes and compost microflora may include the competition for nutrients and the presence of antimicrobials produced by native compost microorganisms as potential competitive exclusion microorganisms. Findings from this study are important for the composting industry to understand the composition and functionality of microbial community in their products and help developing organic fertilizers fortified with anti-L. monocytogenes competitive exclusion microorganisms.
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Affiliation(s)
- Hongye Wang
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
| | - Vijay Shankar
- Center for Human Genetics, Clemson University, Greenwood, South Carolina, USA
| | - Xiuping Jiang
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
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27
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Lu M, Schneider D, Daniel R. Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern. Front Microbiol 2022; 13:851969. [PMID: 35756004 PMCID: PMC9226776 DOI: 10.3389/fmicb.2022.851969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.
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Affiliation(s)
| | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
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28
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Grenier V, Moingt M, Lucotte M, Pitre FE. Dissipation and effect of glyphosate during composting of organic wastes. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:399-410. [PMID: 35147980 DOI: 10.1002/jeq2.20335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
The addition of organic matter (OM) containing glyphosate during compost production, through the introduction of contaminated plant residues or sewage sludge, presents a risk of hindering the proper OM breakdown carried out by microorganisms and causing the accumulation of glyphosate or aminomethylphosphonic acid (AMPA). To measure the effect of glyphosate and glyphosate-based herbicide (GBH) on OM decomposition as well as the dissipation of glyphosate to AMPA during composting, a controlled-environment experiment was conducted using mesocosm-scale vessels. Analytical-grade (AG) glyphosate (150 mg kg-1 ) and GBH (VisionMAX) equivalent to the amounts applied in agricultural areas (300 mg kg-1 ) were added to a mixture of green residues, which were then composted for 112 d. Sampling after 2, 7, 28, and 112 d showed a negligible effect of glyphosate and GBH on physicochemical properties of the mixture (temperature, OM%, pH, total carbon [C], total nitrogen [N], and C/N ratio), ammonification, nitrification, and phosphate content. No differences between AG glyphosate and GBH treatments were measured. Glyphosate levels decreased significantly after 2 d to reach 53.1 and 71.1% of the initial content for the AG glyphosate and GBH treatments, respectively, and glyphosate dissipation was almost complete after 112 d of composting. Aminomethylphosphonic acid could not be detected at any time during the experiment regardless of the treatment. Our results show that conditions for OM decomposition were maintained despite the addition of glyphosate and suggest that only trace amounts of glyphosate or AMPA are likely to be present in mature compost.
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Affiliation(s)
- Vanessa Grenier
- Institut de recherche en biologie végétale, Univ. de Montréal, 4101 Sherbrooke East, Montréal, Québec, H1×2B2, Canada
| | - Matthieu Moingt
- GEOTOP & Institut des Sciences de l'environnement, Univ. du Québec à Montréal, 201, Avenue du Président-Kennedy, Montréal, Québec, H2×3Y7, Canada
| | - Marc Lucotte
- GEOTOP & Institut des Sciences de l'environnement, Univ. du Québec à Montréal, 201, Avenue du Président-Kennedy, Montréal, Québec, H2×3Y7, Canada
| | - Frederic E Pitre
- Institut de recherche en biologie végétale, Univ. de Montréal, 4101 Sherbrooke East, Montréal, Québec, H1×2B2, Canada
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29
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Jin X, Ai W, Zhang Y, Dong W. Application of functional microbial agent in aerobic composting of wheat straw for waste recycling. LIFE SCIENCES IN SPACE RESEARCH 2022; 33:13-20. [PMID: 35491025 DOI: 10.1016/j.lssr.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/22/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Controlled Ecological Life Support System (CELSS) is a closed artificial ecosystem which can regenerate oxygen, food, water and other substances for crew survival in long-term space missions. Solid organic waste is a vital resource pool for material reuse and recycling in CELSS. In this study, solid wastes including wheat straw and food waste were disposed via aerobic composting under functional microbial agent inoculation. Compared to tests with a commercial microbial agent addition and without exogenous microorganisms, system performance was promoted by the self-developed microbial agent significantly which exhibited the highest composting temperature (67.4 ± 1.5 °C) and longest thermophilic period (7 days). And treatment with self-developed microbial agent showed the highest values in volatile solid reduction, C/N reduction, germination index (124.83 ± 13.25%) and total available nutrient content (47.45 ± 1.69 g/kg), which suggested the feasibility of compost product to be used for crop cultivation. Moreover, shifts of microbial community in phylum and genus levels were observed. Microbial agent augmentation led to high quality and safe compost product after a short composting period (30 days) without leaching, which suggested an efficient way to promote the recycling and recovery of solid waste in CELSS.
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Affiliation(s)
- Xiangdan Jin
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China; Space Science and Technology Institute (Shenzhen), Shenzhen, 518117, China.
| | - Weidang Ai
- Space Science and Technology Institute (Shenzhen), Shenzhen, 518117, China; National key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Yang Zhang
- Space Science and Technology Institute (Shenzhen), Shenzhen, 518117, China; National key Laboratory of Human Factors Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Wenyi Dong
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China; Public Platform for Technological Service in Urban Waste Reuse and Energy Regeneration, Shenzhen, 518055, China
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Pottipati S, Kundu A, Kalamdhad AS. Performance evaluation of a novel two-stage biodegradation technique through management of toxic lignocellulosic terrestrial weeds. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 144:191-202. [PMID: 35381446 DOI: 10.1016/j.wasman.2022.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/22/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
The present study investigates the biodegradation of two potentially toxic terrestrial weeds Parthenium hysterophorus and Lantana camara, implementing a novel two-stage biodegradation technique; Rotary drum composting followed by vermicomposting (RV). The RV approach was refined for a 7-day thermophilic degradation in an in-vessel rotary drum composter, followed by a 20-day mesophilic degradation utilizing Eisenia fetida and Eudrilus eugeniae vermi-monocultures. However, rotary drum composting (RDC) was performed for both the weeds (for 27 days), facilitating only initial thermophilic degradation to compare the efficacy of the RV technique. Lignocelluloses analysis revealed that cellulose degradation doubled during RV technique, indicating efficient biodegradation in reactors administered with E. fetida vermiculture compared to RDC (19.60 to 42.80% and 26.80 to 66.50% in P. hysterophorus and L. camara feedstocks). Further, these results also correlated with the X-Ray diffractograms of all trials showing the degradation of crystalline cellulose at 2θ: 20-50° for RV. Moreover, to ensure product safety, the analyzed total heavy metals content also unveiled the advantage of RV over RDC as validated by the accumulation of higher concentrations of zinc (45% and 33% in P. hysterophorus and L. camara feedstocks) and lead (55% and 45% in P. hysterophorus and L. camara feedstocks) in reactors with E. fetida. The material's seed germination index increased to 80% in the final product of all trials in the RV technique, indicating the diminishing of the phytotoxic nature. Subsequently, pot studies also indicated that the RV technique was coherent in managing noxious weeds.
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Affiliation(s)
- Suryateja Pottipati
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Ashmita Kundu
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ajay S Kalamdhad
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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Abstract
Noncoding RNAs with secondary structures play important roles in CRISPR-Cas systems. Many of these structures likely remain undiscovered. We used a large-scale comparative genomics approach to predict 156 novel candidate structured RNAs from 36,111 CRISPR-Cas systems. A number of these were found to overlap with coding genes, including palindromic candidates that overlapped with a variety of Cas genes in type I and III systems. Among these 156 candidates, we identified 46 new models of CRISPR direct repeats and 1 tracrRNA. This tracrRNA model occasionally overlapped with predicted cas9 coding regions, emphasizing the importance of expanding our search windows for novel structure RNAs in coding regions. We also demonstrated that the antirepeat sequence in this tracrRNA model can be used to accurately assign thousands of predicted CRISPR arrays to type II-C systems. This study highlights the importance of unbiased identification of candidate structured RNAs across CRISPR-Cas systems.
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Affiliation(s)
- Brayon J. Fremin
- Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Bello A, Ogundeji A, Yu S, Jiang X, Deng L, Zhao L, Jong C, Xu X. Dynamics of fungal species related to nitrogen transformation and their network patterns during cattle manure-corn straw with biochar composting. Arch Microbiol 2022; 204:236. [PMID: 35362815 DOI: 10.1007/s00203-022-02848-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 11/02/2022]
Abstract
Fungi are reputed to play a significant role in the composting matrix as decomposers of recalcitrant organic materials like cellulose and lignin. However, information on the fungi communities' roles in nitrogen transformation under a compost-biochar mixture is scarce. This study investigated shifts in fungal species mediating N transformation and their network patterns in cattle manure-corn straw (CMCS) and CMCS plus biochar (CMCB) composting using high-throughput sequencing data. The results revealed that the addition of biochar altered fungal richness and diversity and significantly influenced their compositions during composting. Biochar also altered the compost fungal network patterns; CMCS had a more complex network with higher positive links than CMCB, suggesting stable niche overlap. The consistent agreement of multivariate analyses (redundancy, network, regression, Mantel and path analyses) indicated that Ciliophora_sp in CMCS and unclassified_norank_Pleosporales in CMCB were the key fungal species mediating total N transformation, whereas Scedosporium_prolificans in CMCS and unclassified_Microascaceae in CMCB were identified as major predictive indices determining NO3--N transformation. Also, Coprinopsis cinerea and Penicillium oxalicum were the predictive factors for NH4+-N transformation in CMCS and CMCB during composting. These results indicated that the effects of biochar on N conversions in composting could be unraveled using multivariate analyses on fungi community evolution, network patterns, and metabolism.
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Affiliation(s)
- Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.,College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Abiola Ogundeji
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Sun Yu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xin Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Liyan Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Chol Jong
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.,College of Agriculture, Kimjewon Agricultural University, Haeju City, Hwanghae South Province, 999093, Republic of Korea
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
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Ma JJ, Jiang CL, Tao XH, Sheng JL, Sun XZ, Zhang TZ, Zhang ZJ. Insights on dissolved organic matter and bacterial community succession during secondary composting in residue after black soldier fly larvae (Hermetia illucens L.) bioconversion for food waste treatment. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 142:55-64. [PMID: 35176599 DOI: 10.1016/j.wasman.2022.01.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/20/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Black soldier fly larvae (Hermetia illucens L. BSFL) bioconversion is a promising biotechnology for food waste treatment. However, the separated residues still do not meet criteria for use as land application biofertilizers. In this work, we investigated a full-scale BSFL bioconversion project to explore features of dissolved organic matter (DOM) and its associated responses of bacterial community succession in residue during secondary composting. Data showed that the concentrations of total nitrogen and ammonium nitrogen decreased by 11.8% and 22.6% during the secondary composting, respectively, while the nitrate nitrogen concentration increased 18.7 times. The DOM concentration decreased by 69.1%, in which protein-like, alcohol-phenol, and biodegradable aliphatic substances were metabolized by bacteria during the thermophilic phase together with the accumulation of humus-like substances, resulting in an increase in the relative concentration of aromatic compounds. The structure of the bacterial community varied at different stages of the bioprocess, in which Bacteroidetes, Actinobacteria, Proteobacteria, and Firmicutes were the dominant bacterial phyla. Lysinibacillus, Pusillimonas, and Caldicoprobacter were found to be key contributors in the degradation and formation of DOM. The DOM concentration (33.4%) and temperature (17.7%) were the prime environmental factors that promoted succession of the bacterial community. Through bacterial metabolism, the structural stability of DOM components was improved during the composting process, and the degrees of humification and aromaticity were also increased. This study depicted the dynamic features of DOM and the associated bacterial community succession in residue during secondary composting, which is conducive with the reuse of BSFL residue as biofertilizer for agriculture.
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Affiliation(s)
- Jing-Jin Ma
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688, HangZhou, ZheJiang Province 310058, PR China
| | - Cheng-Liang Jiang
- HangZhou GuSheng Technology Company Limited, XiangWang Ave 1118, HangZhou 311121, PR China; ZheJiang FuMei Biotechnology Company Limited, PingYao Future Complex Park, PingYao Ave, HangZhou 311115, PR China
| | - Xing-Hua Tao
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688, HangZhou, ZheJiang Province 310058, PR China
| | - Jian-Lin Sheng
- HangZhou GuSheng Technology Company Limited, XiangWang Ave 1118, HangZhou 311121, PR China; ZheJiang FuMei Biotechnology Company Limited, PingYao Future Complex Park, PingYao Ave, HangZhou 311115, PR China
| | - Xin-Zhao Sun
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688, HangZhou, ZheJiang Province 310058, PR China
| | - Ting-Zhou Zhang
- ZheJiang Cofine Biotechnology Company Limited, HaiNing 314400, PR China
| | - Zhi-Jian Zhang
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688, HangZhou, ZheJiang Province 310058, PR China; China Academy of West Region Development, ZheJiang University, YuHangTang Ave 866, HangZhou 310058, PR China.
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Xie WY, Wang YT, Yuan J, Hong WD, Niu GQ, Zou X, Yang XP, Shen Q, Zhao FJ. Prevalent and highly mobile antibiotic resistance genes in commercial organic fertilizers. ENVIRONMENT INTERNATIONAL 2022; 162:107157. [PMID: 35219935 DOI: 10.1016/j.envint.2022.107157] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/19/2022] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
Compost-based organic fertilizers made from animal manures may contain high levels of antibiotic resistance genes (ARGs). However, the factors affecting the abundance and profile of ARGs in organic fertilizers remain unclear. We conducted a national-wide survey in China to investigate the effect of material type and composting process on ARG abundance in commercial organic fertilizers and quantified the contributions of bacterial composition and mobile genetic elements (MGEs) to the structuring of ARGs, using quantitative PCR and Illumina sequencing of 16S rRNA gene amplicons. The tetracycline, sulfonamide, aminoglycoside and macrolide resistance genes were present at high levels in all organic fertilizers. Seven ARGs that confer resistance to clinically important antibiotics, including three β-lactam resistance genes, three quinolone resistance genes and the colistin resistance gene mcr-1, were detected in 8 - 50% the compost samples, whereas the vancomycin resistance gene vanC was not detected. Raw material type had a significant (p < 0.001) effect on the ARG abundance, with composts made from animal feces except some cattle feces generally having higher loads of ARGs than those from non-animal raw materials. Composting process type showed no significant (p > 0.05) effect on ARG abundance in the organic fertilizers. MGEs exerted a greater influence on ARG composition than bacterial community, suggesting a strong mobility of ARGs in the organic fertilizers. Our study highlights the need to manage the risk of ARG dissemination from agricultural wastes.
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Affiliation(s)
- Wan-Ying Xie
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ya-Ting Wang
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Yuan
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen-Dan Hong
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guo-Qing Niu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Zou
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin-Ping Yang
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Biyada S, Merzouki M, Dėmčėnko T, Vasiliauskienė D, Marčiulaitienė E, Vasarevičius S, Urbonavičius J. The Effect of Feedstock Concentration on the Microbial Community Dynamics During Textile Waste Composting. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.813488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In this study, the effect of initial feedstock concentration on the microbial community structure and dynamics during textile waste composting processes was investigated using the next-generation sequencing approach. For this, three mixtures were prepared with different textile waste concentrations mixed with green waste and paper and cardboard waste for composting, to choose the proportion that will provide a mature final compost. A comprehensive characterization of the microbial communities associated with different textile waste concentrations during composting was achieved. It was noted that by increasing the concentration of textile waste, microbial communities (bacterial and fungal) change. Genera and species belonging to Actinobacteria, Firmicutes, Chloroflexia, Rozellomycota, Mortierellomycota, Aphelidiomycota, Ascomycota, and Mucoromycota were the most abundant in the mixtures containing either 40 or 60% of textile waste, whereas some of the species were absent at 80% of textile waste in the mix; this difference was also reflected by their enzymatic activities. Generally, these phyla are associated with composting, and they play a major role in recalcitrant molecular decaying. Ultimately, it can be concluded that the shift most likely occurred in microbial communities during composting probably owing to the interaction between changes in the nutrient concentration and microbial communities. This investigation proves that the concentration of textile waste significantly affects the microbial communities and demonstrates that a high concentration of textile waste is not suitable to grant a good maturity of compost.
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Yang X, Zhang Y, Liu Q, Guo J, Zhou Q. Progress in the interaction of dissolved organic matter and microbes (1991-2020): a bibliometric review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:16817-16829. [PMID: 34997929 DOI: 10.1007/s11356-022-18540-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Dissolved organic matter (DOM) and microbes are key in the planetary carbon cycle, and research on them can lead to a better understanding of the global carbon cycle and an improved ability to cope with environmental challenges. Several papers have reviewed one or several aspects of the interaction of DOM and microbes, but no overall review has been performed. Here, we bibliometrically analyzed all publications from the Web of Science on DOM and microbes (1991-2020). The results showed that studies on DOM and microbes grew exponentially during this period; the USA contributed the most to the total publications, and China has had the fastest increasing rate since 2010. Moreover, we used the Latent Dirichlet Allocation model to identify topics and determine their (cold or hot) trends by analyzing the abstracts of 9851 publications related to DOM and microbes. A total of 96 topics were extracted, and these topics that are related to the source, composition, and removal path of DOM and the temporal-spatial patterns of DOM and microbes consistently rose from 1991 to 2020. Most studies have used accurate and rapid methods combined with microbiological genetic approaches to study the interaction of DOM and microbes in terrestrial and aquatic ecosystems. The results also showed that the impacts of climate change and land use on the interaction of DOM and microbes, and topics related to human health have received considerable attention. In the future, the interaction mechanism of DOM and microbes and its response to environmental change should be further elucidated.
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Affiliation(s)
- Xuan Yang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China
| | - Yun Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
| | - Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
| | - Jishu Guo
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
| | - Qichao Zhou
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China.
- Yunnan Key Laboratory of Pollution Process and Management of Plateau Lake-Watershed, Yunnan Research Academy of Eco-Environmental Sciences, Kunming, 650034, China.
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Metatranscriptome Profiling of a Specialized Microbial Consortium during the Degradation of Nixtamalized Maize Pericarp. Microbiol Spectr 2022; 10:e0231821. [PMID: 34985337 PMCID: PMC8729791 DOI: 10.1128/spectrum.02318-21] [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] [Indexed: 12/13/2022] Open
Abstract
Lignocellulose degradation by microbial consortia is multifactorial; hence, it must be analyzed from a holistic perspective. In this study, the temporal transcriptional activity of consortium PM-06, a nixtamalized maize pericarp (NMP) degrader, was determined and related to structural and physicochemical data to give insights into the mechanism used to degrade this substrate. Transcripts were described in terms of metabolic profile, carbohydrate-active enzyme (CAZyme) annotation, and taxonomic affiliation. The PM-06 gene expression pattern was closely related to the differential rates of degradation. The environmental and physiological conditions preceding high-degradation periods were crucial for CAZyme expression. The onset of degradation preceded the period with the highest degradation rate in the whole process, and in this time, several CAZymes were upregulated. Functional analysis of expressed CAZymes indicated that PM-06 overcomes NMP recalcitrance through modular enzymes operating at the proximity of the insoluble substrate. Increments in the diversity of expressed modular CAZymes occurred in the last stages of degradation where the substrate is more recalcitrant and environmental conditions are stressing. Taxonomic affiliation of CAZyme transcripts indicated that Paenibacillus macerans was fundamental for degradation. This microorganism established synergistic relationships with Bacillus thuringiensis for the degradation of cellulose and hemicellulose and with Microbacterium, Leifsonia, and Nocardia for the saccharification of oligosaccharides. IMPORTANCE Nixtamalized maize pericarp is an abundant residue of the tortilla industry. Consortium PM-06 efficiently degraded this substrate in 192 h. In this work, the temporal transcriptional profile of PM-06 was determined. Findings indicated that differential degradation rates are important sample selection criteria since they were closely related to the expression of carbohydrate-active enzymes (CAZymes). The initial times of degradation were crucial for the consumption of nixtamalized pericarp. A transcriptional profile at the onset of degradation is reported for the first time. Diverse CAZyme genes were rapidly transcribed after inoculation to produce different enzymes that participated in the stage with the highest degradation rate in the whole process. This study provides information about the regulation of gene expression and mechanisms used by PM-06 to overcome recalcitrance. These findings are useful in the design of processes and enzyme cocktails for the degradation of this abundant substrate.
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Gopalakrishnappa C, Gowda K, Prabhakara KH, Kuehn S. An ensemble approach to the structure-function problem in microbial communities. iScience 2022; 25:103761. [PMID: 35141504 PMCID: PMC8810406 DOI: 10.1016/j.isci.2022.103761] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The metabolic activity of microbial communities plays a primary role in the flow of essential nutrients throughout the biosphere. Molecular genetics has revealed the metabolic pathways that model organisms utilize to generate energy and biomass, but we understand little about how the metabolism of diverse, natural communities emerges from the collective action of its constituents. We propose that quantifying and mapping metabolic fluxes to sequencing measurements of genomic, taxonomic, or transcriptional variation across an ensemble of diverse communities, either in the laboratory or in the wild, can reveal low-dimensional descriptions of community structure that can explain or predict their emergent metabolic activity. We survey the types of communities for which this approach might be best suited, review the analytical techniques available for quantifying metabolite fluxes in communities, and discuss what types of data analysis approaches might be lucrative for learning the structure-function mapping in communities from these data.
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Affiliation(s)
| | - Karna Gowda
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | - Kaumudi H. Prabhakara
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | - Seppe Kuehn
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
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Metagenomic Analysis of Bacterial Community Structure and Dynamics of a Digestate and a More Stabilized Digestate-Derived Compost from Agricultural Waste. Processes (Basel) 2022. [DOI: 10.3390/pr10020379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Recycling of different products and waste materials plays a crucial role in circular economy, where the anaerobic digestion (AD) constitutes an important pillar since it reuses nutrients in the form of organic fertilizers. Knowledge about the digestate and compost microbial community structure and its variations over time is important. The aim of the current study was to investigate the microbiome of a slurry cow digestate produced on a farm (ADG) and of a more stabilized digestate-derived compost (DdC) in order to ascertain their potential uses as organic amendments in agriculture. The results from this study, based on a partial fragment of 16S bacterial rRNA NGS sequencing, showed that there is a greater microbial diversity in the DdC originated from agricultural waste compared to the ADG. Overall, the existence of a higher microbial diversity in the DdC was confirmed by an elevated number (1115) of OTUs identified, compared with the ADG (494 OTUs identified). In the DdC, 74 bacterial orders and 125 families were identified, whereas 27 bacterial orders and 54 families were identified in the ADG. Shannon diversity and Chao1 richness indexes were higher in DdC samples compared to ADG ones (Shannon: 3.014 and 1.573, Chao1: 68 and 24.75; p < 0.001 in both cases). A possible association between the microbiome composition at different stages of composting process and the role that these microorganisms may have on the quality of the compost-like substrate and its future uses is also discussed.
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Sagarika MS, Parameswaran C, Senapati A, Barala J, Mitra D, Prabhukarthikeyan SR, Kumar A, Nayak AK, Panneerselvam P. Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150451. [PMID: 34607097 DOI: 10.1016/j.scitotenv.2021.150451] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.
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Affiliation(s)
- Mahapatra Smruthi Sagarika
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India; Indira Gandhi Agricultural University, Raipur, Chhattisgarh 492012, India
| | | | - Ansuman Senapati
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Jatiprasad Barala
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Debasis Mitra
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | | | - Anjani Kumar
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
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Hernández-Lara A, Ros M, Cuartero J, Bustamante MÁ, Moral R, Andreu-Rodríguez FJ, Fernández JA, Egea-Gilabert C, Pascual JA. Bacterial and fungal community dynamics during different stages of agro-industrial waste composting and its relationship with compost suppressiveness. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150330. [PMID: 34818753 DOI: 10.1016/j.scitotenv.2021.150330] [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: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 05/28/2023]
Abstract
Composting is an advantageous and efficient process for recycling organic waste and producing organic fertilizers, and many kinds of microorganisms are involved in obtaining quality compost with suppressive activity against soil-borne pathogens. The aim of this work was to evaluate the main differences in the effects of three composting piles on the whole bacterial and fungal communities of baby-leaf lettuce crops and to determine the specific communities by high-throughput sequencing related to suppressiveness against the soil-borne plant pathogen Pythium irregulare- (P. irregulare). Compost pile A was composed of 47% vineyard pruning waste, 34% tomato waste and 19% leek waste; pile B was composed of 54% vineyard pruning waste and 46% tomato waste; and pile C was composed of 42% vineyard pruning waste, 25% tomato waste and 33% olive mill cake. The temperature and the chemical properties of the piles were monitored throughout the composting process. In addition, the potential suppressive capacity of the three composts (C_A, C_B and C_C) against P. irregulare in baby-leaf lettuce was assessed. We found that the bacterial community changed according to the composting phases and composting pile and was sensitive to chemical changes throughout the composting process. The fungal community, on the other hand, did not change between the composting piles and proved to be less influenced by chemical properties, but it did change, principally, according to the composting phases. All composts obtained were considered stable and mature, while compost C_C showed higher maturity than composts C_A and C_B. During composting, the three piles contained a greater relative abundance of Bacterioidetes, Proteobacterias and Actinobacterias related to the suppression of soil-borne pathogens such as Pythium irregulare. Composts C_A and C_B, however, showed higher suppressiveness against P. irregulare than compost C_C. Deeper study showed that this observed suppressiveness was favored by a higher abundance of genera that have been described as potential suppressive against P. irregulare, such as Aspergillus, Penicillium, Truepera and Luteimonas.
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Affiliation(s)
- Alicia Hernández-Lara
- Centro de Edafología y Biología Aplicada del Segura (CSIC), Campus Universitario de Espinardo, 30100 Murcia, Spain.
| | - Margarita Ros
- Centro de Edafología y Biología Aplicada del Segura (CSIC), Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - Jessica Cuartero
- Centro de Edafología y Biología Aplicada del Segura (CSIC), Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - María Ángeles Bustamante
- Department of Agrochemistry and Environment, Miguel Hernández University, EPS-Orihuela, ctra. Beniel Km 3.2, 03312, Orihuela, Alicante, Spain
| | - Raul Moral
- Department of Agrochemistry and Environment, Miguel Hernández University, EPS-Orihuela, ctra. Beniel Km 3.2, 03312, Orihuela, Alicante, Spain
| | - Francisco Javier Andreu-Rodríguez
- Department of Agrochemistry and Environment, Miguel Hernández University, EPS-Orihuela, ctra. Beniel Km 3.2, 03312, Orihuela, Alicante, Spain
| | - Juan A Fernández
- Department of Agricultural Engineering, Technical University of Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain; Plant Biotechnology Institute, Edificio I + D + i, Campus Muralla del Mar, 30202 Cartagena, Spain
| | - Catalina Egea-Gilabert
- Department of Agricultural Engineering, Technical University of Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain; Plant Biotechnology Institute, Edificio I + D + i, Campus Muralla del Mar, 30202 Cartagena, Spain
| | - José Antonio Pascual
- Centro de Edafología y Biología Aplicada del Segura (CSIC), Campus Universitario de Espinardo, 30100 Murcia, Spain
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Wang N, Li H, Wang B, Ding J, Liu Y, Wei Y, Li J, Ding GC. Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost. Front Microbiol 2022; 12:798476. [PMID: 35095808 PMCID: PMC8792965 DOI: 10.3389/fmicb.2021.798476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.
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Affiliation(s)
- Ning Wang
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Huixiu Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Tangshan Normal University, Tangshan, China
| | - Bo Wang
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Jia Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Yingjie Liu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Yuquan Wei
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Guo-Chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
- *Correspondence: Guo-Chun Ding,
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Oliveira VM, Andreote FD, Cortelo PC, Castro-Gamboa I, Costa-Lotufo LV, Polizeli MDLTM, Thiemann OH, Setubal JC. Microorganisms: the secret agents of the biosphere, and their key roles in biotechnology. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract We present a survey of projects that have been funded by FAPESP under the BIOTA-Microorganisms program. These projects generated a wide variety of results, including the identification of novel antibacterial-producing microorganisms, the characterization of novel microbial enzymes for industrial applications, taxonomic classification of novel microorganisms in several environments, investigation of the soil and mangrove microbial ecosystems and its influence on endangered plant species, and the sequencing of novel metagenome-assembled genomes. The results surveyed demonstrate the importance of microorganisms in environments that play important roles in human activities as well as the potential that many of these microorganisms have in contributing to biotechnological applications crucial for human survival in the 21st century.
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Biyada S, Merzouki M, Dėmčėnko T, Vasiliauskienė D, Ivanec-Goranina R, Urbonavičius J, Marčiulaitienė E, Vasarevičius S, Benlemlih M. Microbial community dynamics in the mesophilic and thermophilic phases of textile waste composting identified through next-generation sequencing. Sci Rep 2021; 11:23624. [PMID: 34880393 PMCID: PMC8654937 DOI: 10.1038/s41598-021-03191-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023] Open
Abstract
Composting is a promising source of mesophilic and thermophilic microorganisms directly involved in the decay of organic matter. However, there is a paucity of information related to bacterial and fungal diversity in compost and their enzymatic activities during the composting process. In this work, bacterial and fungal diversity during the mesophilic and thermophilic phases of textile waste composting was investigated as a way to explain the physical–chemical results obtained during the composting process. This was accomplished using a next-generation sequencing approach that targets either the 16S rRNA or ITS genomic regions of bacteria and fungi, respectively. It was observed that Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant bacterial phyla present at the mesophilic phase but not at the thermophilic one. Composting textile waste exhibits a sustained thermophilic profile (above 55 °C) that usually precludes fungal activity. Nonetheless, the presence of fungi at the thermophilic phase was observed. Rozellomycota, Basidiomycota, and Ascomycota were the most dominant phyla during both composting phases. Such thermophilic fungi with great ability to decay organic matter could be isolated as pure cultures and used for the bioaugmentation of textile waste composting to achieve an advanced maturity level of textile waste compost.
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Affiliation(s)
- Saloua Biyada
- Laboratory of Biotechnology, Environment, Agrifood, and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Atlas, BP: 1796, 30 000, Fez, Morocco.
| | - Mohammed Merzouki
- Laboratory of Biotechnology, Environment, Agrifood, and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Atlas, BP: 1796, 30 000, Fez, Morocco
| | - Taisija Dėmčėnko
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Dovilė Vasiliauskienė
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Rūta Ivanec-Goranina
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Jaunius Urbonavičius
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Eglė Marčiulaitienė
- Department of Environmental Protection and Water Engineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Saulius Vasarevičius
- Department of Environmental Protection and Water Engineering, Vilnius Gediminas Technical University, 10223, Vilnius, Lithuania
| | - Mohamed Benlemlih
- Laboratory of Biotechnology, Environment, Agrifood, and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Atlas, BP: 1796, 30 000, Fez, Morocco
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Araujo ASF, de Pereira APDA, Antunes JEL, Oliveira LMDS, de Melo WJ, Rocha SMB, do Amorim MR, Araujo FF, Melo VMM, Mendes LW. Dynamics of bacterial and archaeal communities along the composting of tannery sludge. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:64295-64306. [PMID: 34304356 DOI: 10.1007/s11356-021-15585-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The process of composting has been proposed as a biological alternative to improve the quality of tannery sludge (TS) by the action of microbial communities. However, there is limited knowledge about the dynamic of these microbial communities during the composting process. This study assessed the responses of bacterial and archaeal communities during TS composting using the 16S rRNA sequencing. The composting process occurred within 90 days, and samples of compost were collected on day 7 (d7; mesophilic stage), 30 (d30; thermophilic stage), 60 (d60; cooling stage), and 90 (d90; maturation stage). The results showed a succession of microbial phyla during the composting with enrichment of Synergistetes, WS1, and Euryarchaeota at the mesophilic stage, while at the thermophilic stage, there was an enrichment of Hydrogenedentes, WPS-2, Chloroflexi, and Deinococcus-Thermus. At the cooling stage, there was an enrichment of Kiritimatiellaeota, and at the maturation stage, there was an enrichment of Entotheonellaeota, Dadabacteria, Nitrospirae, Dependiatiae, and Fibrobacteres. When analyzing the drivers influencing microbial communities, Cr and pH presented more negative correlations with general phyla. In contrast, S, C, K, temperature, and N presented more positive correlations, while Ni, Cd, and P showed fewer correlations. According to niche occupancy, we observed a decreased proportion of generalists with a consequently increased proportion of specialists following the composting process. This study showed that different stages of the composting present a specific microbial community structure and dynamics, which are related to some specific composting characteristics.
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Affiliation(s)
| | | | | | | | - Wanderley José de Melo
- Technology Department, São Paulo State University, Jaboticabal, SP, Brazil
- Graduate Program in Environmental Science, Campus of Descalvado, Brazil University, Descalvado, SP, Brazil
| | | | | | | | - Vania Maria Maciel Melo
- Laboratory of Microbial Ecology and Biotechnology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Lucas William Mendes
- Cellular and Molecular Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
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Blagodatskaya E, Tarkka M, Knief C, Koller R, Peth S, Schmidt V, Spielvogel S, Uteau D, Weber M, Razavi BS. Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces. Front Microbiol 2021; 12:625697. [PMID: 34777265 PMCID: PMC8581545 DOI: 10.3389/fmicb.2021.625697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 09/01/2021] [Indexed: 12/30/2022] Open
Abstract
In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.
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Affiliation(s)
- Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research Halle–Jena–Leipzig, Leipzig, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stephan Peth
- Institute of Soil Science, University of Hannover, Hanover, Germany
| | | | - Sandra Spielvogel
- Department Soil Science, Institute for Plant Nutrition and Soil Science, Christian-Albrechts University Kiel, Kiel, Germany
| | - Daniel Uteau
- Department of Soil Science, Faculty of Organic Agricultural Sciences, University of Kassel, Kassel, Germany
| | | | - Bahar S. Razavi
- Department of Soil and Plant Microbiome, Institute of Phytopathology, Christian-Albrechts-University of Kiel, Kiel, Germany
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Loakasikarn T, Kubota Y, Koyama M, Nakasaki K. Effect of seeding materials on organic matter degradation and microbial community succession during model organic waste composting. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Yi Y, Xu S, Kovalevsky A, Zhang X, Liu D, Wan Q. Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome. Appl Microbiol Biotechnol 2021; 105:7757-7767. [PMID: 34553251 DOI: 10.1007/s00253-021-11587-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
Xylanase is efficient for xylan degradation and widely applied in industries. We found a GH11 family xylanase (Xyn11A) with high thermostability and catalytic activity from compost metatranscriptome. This xylanase has the optimal reaction temperature at 80 °C with the activity of 2907.3 U/mg. The X-ray crystallographic structure shows a typical "right hand" architecture, which is the characteristics of the GH11 family enzymes. Comparing it with the mesophilic XYN II, a well-studied GH11 xylanase from Trichoderma reesei, Xyn11A is more compact with more H-bonds. Our mutagenic results show that the electrostatic interactions in the thumb and palm region of Xyn11A could result in its high thermostability and activity. Introducing a disulfide bond at the N-terminus further increased its optimal reaction temperature to 90 °C with augmented activity. KEY POINTS: • A hyperthermophilic xylanase with high activity was discovered using the metatranscriptomic method. • The mechanisms of thermophilicity and high activity were revealed using X-ray crystallography, mutagenesis, and molecular dynamics simulations. • The thermostability and activity were further improved by introducing a disulfide bond.
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Affiliation(s)
- Yunlei Yi
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shenyuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Xia Zhang
- Department of Molecular Biology, Qingdao Vland Biotech Group Inc., Qingdao, Shandong, 266000, People's Republic of China
| | - Dongyang Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. .,Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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49
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Braga LPP, Pereira RV, Martins LF, Moura LMS, Sanchez FB, Patané JSL, da Silva AM, Setubal JC. Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. BMC Genomics 2021; 22:652. [PMID: 34507539 PMCID: PMC8434746 DOI: 10.1186/s12864-021-07957-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. RESULTS Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. CONCLUSIONS The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.
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Affiliation(s)
- Lucas Palma Perez Braga
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Livia Maria Silva Moura
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio Beltrame Sanchez
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
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50
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Mironov V, Vanteeva A, Sokolova D, Merkel A, Nikolaev Y. Microbiota Dynamics of Mechanically Separated Organic Fraction of Municipal Solid Waste during Composting. Microorganisms 2021; 9:1877. [PMID: 34576772 PMCID: PMC8468692 DOI: 10.3390/microorganisms9091877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/13/2021] [Accepted: 09/02/2021] [Indexed: 11/23/2022] Open
Abstract
Mechanical-biological treatment of municipal solid waste (MSW) facilitates reducing the landfill workload. The current research aimed to study general activity parameters, content, functions, and diversity of fungal and prokaryotic microbiota in mechanically separated organic fraction of MSW (ms-OFMSW) composting, without using bulking agents and process-promoting additives. During 35 days of composting, vigorous emission of CO2 (max. 129.4 mg CO2 kg-1 h-1), NH3 (max. 0.245 mg NH3 kg-1 h-1), and heat release (max. 4.28 kJ kg-1 h-1) occurred, indicating intense microbial activity. Immediately following the preparation of the composting mixture, eight genera of lactic acid bacteria and fungal genera Rhizopus, Aspergillus, Penicillium, Agaricus, and Candida were predominant. When the temperature increased to more than 60 °C, the microbial biodiversity decreased. Due to succession, the main decomposers of ms-OFMSW changed. The Bacillaceae family, the genera Planifilum, Thermobifida, and Streptomyces, and the fungal genera Thermomyces and Microascus were involved in the processes of organic matter mineralization at the high-temperature and later stages. The biodiversity of the microbiota increased at the stages of cooling and maturation under conditions of relatively high nitrogen content. Thus, the microbial community and its succession during ms-OFMSW composting were characterized for the first time in this work.
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Affiliation(s)
- Vladimir Mironov
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.); (D.S.); (A.M.); (Y.N.)
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