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Dong W, Zhou R, Li X, Yan H, Zheng J, Peng N, Zhao S. Effect of simplified inoculum agent on performance and microbiome during cow manure-composting at industrial-scale. Bioresour Technol 2024; 393:130097. [PMID: 38013035 DOI: 10.1016/j.biortech.2023.130097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023]
Abstract
A simplified inoculum agent, only comprising Bacillus subtilis and Aspergillus niger, was utilized for industrial-scale cow-manure composting to investigate its impact on composting performance and microbiome. Inoculants elevated the average and peak temperatures by up to 7 and 10 °C, respectively, during the thermophilic stage, reduced organic matter content, and raised germination index. Inoculation also extended the period of composting above 50 °C from 12 to 26 days. Sequencing unveiled significant shifts in microbial diversity, composition, and function. Aspergillus thrived during the mesophilic phase, potentially initiating composting, whereas Bacillus, Lysinibacillus, and Clostridium were enriched during the thermophilic stage. Metagenomic sequencing revealed an increased abundance of carbohydrate-active enzymes and glycometabolism-related genes responsible for lignocellulose degradation and heat generation after inoculation. These enriched microbes and functional genes contributed to organic matter degradation and temperature maintenance during thermophilic stage, expediting composting. This suggests the effectiveness of this simplified inoculum in industrial-level cow-manure composting.
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Affiliation(s)
- Weiwei Dong
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; College of Life Sciences, Hubei Normal University, Huangshi 435002, China
| | - Rui Zhou
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; BGI Genomics, Shenzhen 518083, China; Clin Lab, BGI Genomics, Wuhan 430074, China
| | - Xudong Li
- National Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hua Yan
- Jiangsu Sweeper Biotechnology, Nanjing 211800, China
| | - Jinshui Zheng
- National Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nan Peng
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shumiao Zhao
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Peña-Castro JM, Muñoz-Páez KM, Robledo-Narvaez PN, Vázquez-Núñez E. Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion. Microorganisms 2023; 11:2197. [PMID: 37764041 PMCID: PMC10535843 DOI: 10.3390/microorganisms11092197] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.
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Affiliation(s)
- Julián Mario Peña-Castro
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico;
| | - Karla M. Muñoz-Páez
- CONAHCYT—Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Queretaro 76230, Queretaro, Mexico;
| | | | - Edgar Vázquez-Núñez
- Grupo de Investigación Sobre Aplicaciones Nano y Bio Tecnológicas para la Sostenibilidad (NanoBioTS), Departamento de Ingenierías Química, Electrónica y Biomédica, División de Ciencias e Ingenierías, Universidad de Guanajuato, Lomas del Bosque 103, Lomas del Campestre, León 37150, Guanajuato, Mexico
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Song X, Lu C, Luo J, Gong X, Guo D, Ma Y. Matured compost amendment improves compost nutrient content by changing the bacterial community during the composting of Chinese herb residues. Front Microbiol 2023; 14:1146546. [PMID: 37007496 PMCID: PMC10060987 DOI: 10.3389/fmicb.2023.1146546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Composting is a sustainable strategy to deal with organic waste. Our research aimed to study the influence of an amendment of 10% matured compost (MC) during Chinese herb residue (CHR) compost. Here, a 60-day CHR compost was performed, and MC application was able to reduce the nitrogen loss and enhance the humic acid accumulation during the composting as compared with the non-inoculated control (NC), by 25 and 19%, respectively. Furthermore, the matured compost amendment improved the diversity of the bacterial community, increased the complexity of the co-occurrence network, and changed the keystone and module hub bacteria during composting. The increased abundance levels of Thermopolyspora, Thermobispora, and Thermosporomyces, which were significantly higher in MC than in NC, may contribute to the degradation of cellulose and the formation of humic acid. Overall, this study extends our understanding of the effects of matured compost reflux on compost quality and the bacterial community.
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Affiliation(s)
- Xiuchao Song
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chao Lu
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jia Luo
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Nanjing, China
| | - Xin Gong
- Jiangsu Key Laboratory for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dejie Guo
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Ma
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Nanjing, China
- *Correspondence: Yan Ma,
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Zhang J, Yue Z, Ding C, Zhou Z, Zhang T, Wang X. Metagenomic binning analyses of pig manure composting reveal potential antibiotic-degrading bacteria and their risk of antibiotic resistance genes. Bioresour Technol 2023; 371:128540. [PMID: 36581234 DOI: 10.1016/j.biortech.2022.128540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Antibiotic-degrading bacteria are commonly used to treat antibiotic contamination, but the antibiotic resistance genes (ARGs) they carry are often overlooked. This study used metagenomic assembly and binning analyses to explore potential antibiotic-degrading bacteria and their ARGs during pig manure composting. The result showed that 35 metagenome-assembled genomes (MAGs) mainly containing alkyl-aryl transferase and decarboxylase genes involved in the removal of antibiotics. Multidrug (124), β-lactam (67), macrolide-lincosamide-streptogramin (MLS) (64), and tetracycline (43) were the central ARG types detected in the 35 MAGs. Furthermore, the risk of ARGs was evaluated using the arg_ranker framework, and 19 MAGs were found to contain intermediate-high-risk ARGs with human-associated-enrichment, gene transferability, and host pathogenicity. Bin 34 of the genus of Geofilum had the highest ARG risk. Bin 6, Bin 11 and Bin 14 of the genus of Limnochorda, Chelatococcus and Niabella, had a lower ARG risk and were considered as potential antibiotic-degrading bacteria.
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Affiliation(s)
- Jing Zhang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengfu Yue
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Key Laboratory of Low-carbon Green Agriculture in Tropical region of China, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China
| | - Changfeng Ding
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan 335211, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigao Zhou
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Taolin Zhang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingxiang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan 335211, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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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. Environ Sci Pollut Res Int 2023; 30:8956-8966. [PMID: 35462586 DOI: 10.1007/s11356-022-20388-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Marghoob MU, Rodriguez-Sanchez A, Imran A, Mubeen F, Hoagland L. Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan. Front Microbiol 2022; 13:1020175. [PMID: 36419426 PMCID: PMC9676371 DOI: 10.3389/fmicb.2022.1020175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/10/2022] [Indexed: 08/27/2023] Open
Abstract
Soil salinization and heavy metal (HM) contamination are major challenges facing agricultural systems worldwide. Determining how soil microbial communities respond to these stress factors and identifying individual phylotypes with potential to tolerate these conditions while promoting plant growth could help prevent negative impacts on crop productivity. This study used amplicon sequencing and several bioinformatic programs to characterize differences in the composition and potential functional capabilities of soil bacterial, fungal, and archaeal communities in five agricultural fields that varied in salinity and HM concentrations within the Indus basin region of Pakistan. The composition of bacteria with the potential to fix atmospheric nitrogen (N) and produce the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase were also determined. Microbial communities were dominated by: Euryarchaeota (archaea), Actinobacteria, Proteobacteria, Planctomycetota, Firimicutes, Patescibacteria and Acidobacteria (bacteria), and Ascomycota (fungi), and all soils contained phylotypes capable of N-fixation and ACC-deaminase production. Salinity influenced bacterial, but not archaeal or fungal communities. Both salinity and HM altered the relative abundance of many phylotypes that could potentially promote or harm plant growth. These stress factors also appeared to influence the potential functional capabilities of the microbial communities, especially in their capacity to cycle phosphorous, produce siderophores, and act as symbiotrophs or pathotrophs. Results of this study confirm that farms in this region are at risk due to salinization and excessive levels of some toxic heavy metals, which could negatively impact crop and human health. Changes in soil microbial communities and their potential functional capabilities are also likely to affect several critical agroecosystem services related to nutrient cycling, pathogen suppression, and plant stress tolerance. Many potentially beneficial phylotypes were identified that appear to be salt and HM tolerant and could possibly be exploited to promote these services within this agroecosystem. Future efforts to isolate these phylotypes and determine whether they can indeed promote plant growth and/or carry out other important soil processes are recommended. At the same time, identifying ways to promote the abundance of these unique phylotypes either through modifying soil and crop management practices, or developing and applying them as inoculants, would be helpful for improving crop productivity in this region.
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Affiliation(s)
- Muhammad Usama Marghoob
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | | | - Asma Imran
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Fathia Mubeen
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Lori Hoagland
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
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Shi F, Xu C, Liu J, Sun F, Yu H, Wang S, Li P, Yu Q, Li D, Zuo X, Liu L, Pei Z. Static composting of cow manure and corn stalk covered with a membrane in cold regions. Front Bioeng Biotechnol 2022; 10:969137. [PMID: 36172023 PMCID: PMC9510635 DOI: 10.3389/fbioe.2022.969137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
The disposal of livestock wastes is an urgent task in China. Compost is highly regarded for its ability to treat livestock wastes and protect arable land. In particular, some problems of livestock manure in cold regions, such as low efficiency because of low environmental temperature in winter, urgently need to be solved. In order to provide valuable composting information in the cold area at low environmental temperatures, the composting experiments were carried out with cow manure and corn stalk as substrates. The properties and bacterial community of compost samples in different stages were investigated. The electrical conductivity (EC), total nitrogen (TN), total phosphorus (TP), and organic matter (OM) of the final compost were 551 μS/cm, 1.12, 0.77, and 63.5%, respectively. No E. coli or Ascaris eggs were detected. The temperature was the key factor to affect the physical-co-chemical and biological properties. The absolutely dominant genera were Sporosarcina, Virgibacillus, Flavobacterium, and Steroidobacter in heating, high temperature, cooling, and maturing stages, respectively. Also, these bacteria could act as biological indicators during the composting process. Cryobacterium, Caldicoprobacter, Virgibacillus, and Sporosarcina were relatively novel genera in the compost piles in a cold environment. The biodegradation of exogenous substances mainly occurs in the initial and maturing stages. It is proven that composting can be carried out successfully in early spring or later autumn after a harvest.
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Affiliation(s)
- Fengmei Shi
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry Ministry of Agriculture, Harbin, China
- Key Laboratory of Energy Utilization of Main Crop Stalk Resources, Harbin, China
| | - Chengjiao Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Jie Liu
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry Ministry of Agriculture, Harbin, China
- Key Laboratory of Energy Utilization of Main Crop Stalk Resources, Harbin, China
| | - Fang Sun
- Animal Husbandry Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hongjiu Yu
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry Ministry of Agriculture, Harbin, China
- Key Laboratory of Energy Utilization of Main Crop Stalk Resources, Harbin, China
| | - Su Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry Ministry of Agriculture, Harbin, China
- Key Laboratory of Energy Utilization of Main Crop Stalk Resources, Harbin, China
| | - Pengfei Li
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry Ministry of Agriculture, Harbin, China
- Key Laboratory of Energy Utilization of Main Crop Stalk Resources, Harbin, China
| | - Qiuyue Yu
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry Ministry of Agriculture, Harbin, China
- Key Laboratory of Energy Utilization of Main Crop Stalk Resources, Harbin, China
| | - Dan Li
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry Ministry of Agriculture, Harbin, China
- Key Laboratory of Energy Utilization of Main Crop Stalk Resources, Harbin, China
| | - Xin Zuo
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry Ministry of Agriculture, Harbin, China
- Key Laboratory of Energy Utilization of Main Crop Stalk Resources, Harbin, China
| | - Li Liu
- Animal Husbandry Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhanjiang Pei
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry Ministry of Agriculture, Harbin, China
- Key Laboratory of Energy Utilization of Main Crop Stalk Resources, Harbin, China
- *Correspondence: Zhanjiang Pei,
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Abstract
Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenome data. In the last few years, many thousands of MAGs have been reported in the literature, for a variety of environments and host-associated microbiota, including humans. MAGs have helped us better understand microbial populations and their interactions with the environment where they live; moreover most MAGs belong to novel species, therefore helping to decrease the so-called microbial dark matter. However, questions about the biological reality of MAGs have not, in general, been properly addressed. In this review, I define the notions of hypothetical MAGs and conserved hypothetical MAGs. These notions should help with the understanding of the biological reality of MAGs, their worldwide occurrence, and the efforts to improve MAG recovery processes.
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Affiliation(s)
- João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP 05508-000 São Paulo, Brazil
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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 Neotrop 2022. [DOI: 10.1590/1676-0611-bn-2022-1343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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