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Mandal M, Roy A, Das S, Rakwal R, Agrawal GK, Singh P, Awasthi A, Sarkar A. Food waste-based bio-fertilizers production by bio-based fermenters and their potential impact on the environment. Chemosphere 2024; 353:141539. [PMID: 38417498 DOI: 10.1016/j.chemosphere.2024.141539] [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: 07/27/2023] [Revised: 02/01/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Increasing food waste is creating a global waste (and management) crisis. Globally, ∼1.6 billion tons of food is wasted annually, worth ∼$1.2 trillion. By reducing this waste or by turning it into valuable products, numerous economic advantages can be realized, including improved food security, lower production costs, biodegradable products, environmental sustainability, and cleaner solutions to the growing world's waste and garbage management. The appropriate handling of these detrimental materials can significantly reduce the risks to human health. Food waste is available in biodegradable forms and, with the potential to speed up microbial metabolism effectively, has immense potential in improving bio-based fertilizer generation. Synthetic inorganic fertilizers severely affect human health, the environment, and soil fertility, thus requiring immediate consideration. To address these problems, agricultural farming is moving towards manufacturing bio-based fertilizers via utilizing natural bioresources. Food waste-based bio-fertilizers could help increase yields, nutrients, and organic matter and mitigate synthetic fertilizers' adverse effects. These are presented and discussed in the review.
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Affiliation(s)
- Mamun Mandal
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda, 732 103, West Bengal, India
| | - Anamika Roy
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda, 732 103, West Bengal, India
| | - Sujit Das
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda, 732 103, West Bengal, India
| | - Randeep Rakwal
- Institute of Health and Sport Sciences, Global Sport Innovation Bldg., Room 403, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8574, Japan; GRADE Academy (Pvt.) Ltd., Birgunj, Nepal
| | | | - Pardeep Singh
- Department of Environmental Studies, PGDAV College, University of Delhi, New Delhi, 110065, India
| | - Amit Awasthi
- Department of Applied Sciences, University of Petroleum and Energy Studies, Dehradun, India
| | - Abhijit Sarkar
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda, 732 103, West Bengal, India.
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Jiang M, Khunjar W, Li A, Chandran K. Divergent microbial structure still results in convergent microbial function during arrested anaerobic digestion of food waste at different hydraulic retention times. Bioresour Technol 2024; 393:130069. [PMID: 38000643 DOI: 10.1016/j.biortech.2023.130069] [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: 09/18/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
In this study, two arrested anaerobic digestion bioreactors, fed with food waste, operated under different hydraulic retention times (HRTs) exhibited similar total volatile fatty acid (VFA) yields (p = 0.09). 16S rRNA gene sequencing revealed distinct microbial structure (p = 0.02) at the two HRTs. However, between the two HRTs, there were no differences in potential (DNA) and extant (mRNA) functionality for the production of acetic (AA)-, propionic (PA)-, butyric (BA)- and valeric-acid (VA), as indicated by the metagenome and metatranscriptome data, respectively. The highest potential and extant functionality for PA production in the reactor microbiomes mirrored the highest abundance of PA in the reactor effluents. Meta-omics analysis of BA production indicated possible metabolite exchange across different community members. Notably, the basis for similar VFA production performance observed under the HRTs tested lies in the community-level redundancy in convergent acidification functions and pathways, rather than trends in community-level structure alone.
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Affiliation(s)
- Minxi Jiang
- Earth and Environmental Engineering, Columbia University, New York, NY 10027, USA
| | | | - Anjie Li
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Kartik Chandran
- Earth and Environmental Engineering, Columbia University, New York, NY 10027, USA.
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McLeish AG, Gong S, Greenfield P, Midgley DJ, Paulsen IT. Microbial Community Shifts on Organic Rocks of Different Maturities Reveal potential Catabolisers of Organic Matter in Coal. Microb Ecol 2022; 84:780-793. [PMID: 34686899 DOI: 10.1007/s00248-021-01857-x] [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: 04/13/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
The global trend of transiting to more renewable energy sources requires transition fuels, such as coal seam gas, to supplement and secure energy needs. In order to optimise strategies and technologies for enhancing gas production, an understanding of the fundamental microbial processes and interactions would be advantageous. Models have recently begun mapping the microbial roles and interactions in coal seam environments, from direct coal degradation to methanogenesis. This study seeks to expand those models by observing community compositional shifts in the presence of differing organic matter by conducting 16S rRNA microbial surveys using formation water from the Surat and Sydney Basins grown on varying types of organic matter (black and brown coal, oil shale, humic acid, and lignin). A total of 135 microbes were observed to become enriched in the presence of added organic matter in comparison to carbon-free treatments. These surveys allowed detailed analysis of microbial compositions in order to extrapolate which taxa favour growth in the presence of differing organic matter. This study has experimentally demonstrated shifts in the microbial community composition due to differing carbon sources and, for the first time, generated a conceptual model to map putative degradation pathways regarding subsurface microbial consortia.
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Affiliation(s)
- Andrew G McLeish
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia.
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 11 Julius Ave, North Ryde, Sydney, NSW, 2113, Australia.
| | - Se Gong
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 11 Julius Ave, North Ryde, Sydney, NSW, 2113, Australia
| | - Paul Greenfield
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 11 Julius Ave, North Ryde, Sydney, NSW, 2113, Australia
- Department of Biological Sciences, Macquarie University, North Ryde, Sydney, Australia
| | - David J Midgley
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 11 Julius Ave, North Ryde, Sydney, NSW, 2113, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia
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Do TT, Nolan S, Hayes N, O'Flaherty V, Burgess C, Brennan F, Walsh F. Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion. Environ Pollut 2022; 305:119271. [PMID: 35398400 DOI: 10.1016/j.envpol.2022.119271] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 03/11/2022] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Direct application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment.
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Affiliation(s)
- Thi Thuy Do
- Maynooth University, Biology Department, Ireland
| | - Stephen Nolan
- National University of Ireland Galway, School of Natural Science and Ryan Institute, Galway, Ireland
| | - Nicky Hayes
- Teagasc, Department of Environment, Soils and Landuse, Johnstown Castle, Wexford, Ireland
| | - Vincent O'Flaherty
- National University of Ireland Galway, School of Natural Science and Ryan Institute, Galway, Ireland
| | - Catherine Burgess
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Fiona Brennan
- Teagasc, Department of Environment, Soils and Landuse, Johnstown Castle, Wexford, Ireland
| | - Fiona Walsh
- Maynooth University, Biology Department, Ireland.
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Kumar A, Verma LM, Sharma S, Singh N. Overview on agricultural potentials of biogas slurry (BGS): applications, challenges, and solutions. Biomass Convers Biorefin 2022; 13:1-41. [PMID: 35004124 PMCID: PMC8725965 DOI: 10.1007/s13399-021-02215-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 06/01/2023]
Abstract
The residual slurry obtained from the anaerobic digestion (AD) of biogas feed substrates such as livestock dung is known as BGS. BGS is a rich source of nutrients and bioactive compounds having an important role in establishing diverse microbial communities, accelerating nutrient use efficiency, and promoting overall soil and plant health management. However, challenges such as lower C/N transformation rates, ammonia volatilization, high pH, and bulkiness limit their extensive applications. Here we review the strategies of BGS valorization through microbial and organomineral amendments. Such cohesive approaches can serve dual purposes viz. green organic inputs for sustainable agriculture practices and value addition of biomass waste. The literature survey has been conducted to identify the knowledge gaps and critically analyze the latest technological interventions to upgrade the BGS for potential applications in agriculture fields. The major points are as follows: (1) Bio/nanotechnology-inspired approaches could serve as a constructive platform for integrating BGS with other organic materials to exploit microbial diversity dynamics through multi-substrate interactions. (2) Advancements in next-generation sequencing (NGS) pave an ideal pathway to study the complex microflora and translate the potential information into bioprospecting of BGS to ameliorate existing bio-fertilizer formulations. (3) Nanoparticles (NPs) have the potential to establish a link between syntrophic bacteria and methanogens through direct interspecies electron transfer and thereby contribute towards improved efficiency of AD. (4) Developments in techniques of nutrient recovery from the BGS facilities' negative GHGs emissions and energy-efficient models for nitrogen removal. (5) Possibilities of formulating low-cost substrates for mass-multiplication of beneficial microbes, bioprospecting of such microbes to produce bioactive compounds of anti-phytopathogenic activities, and developing BGS-inspired biofertilizer formulations integrating NPs, microbial inoculants, and deoiled seed cakes have been examined.
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Affiliation(s)
- Ajay Kumar
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 India
- Department of Biotechnology, Mewar Institute of Management, Vasundhara, Ghaziabad, UP 201012 India
| | - Lahur Mani Verma
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 India
| | - Satyawati Sharma
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 India
| | - Neetu Singh
- Department of Biotechnology, Mewar Institute of Management, Vasundhara, Ghaziabad, UP 201012 India
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da Silva GH, Barros NO, Santana LAR, Carneiro JDC, Otenio MH. Shifts of acidogenic bacterial group and biogas production by adding two industrial residues in anaerobic co-digestion with cattle manure. J Environ Sci Health A Tox Hazard Subst Environ Eng 2021; 56:1503-1511. [PMID: 34903145 DOI: 10.1080/10934529.2021.2015987] [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: 03/23/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Anaerobic biodigestion figures as a sustainable alternative to avoid discharge of cattle manure in the environment, which results in biogas and biofertilizer. The anaerobic bioconversion of biomass to methane via anaerobic biodigestion requires a multi-step biological process, including microorganisms with distinct roles. Here, the dynamics of acidogenic bacterial populations by classical microbiology, as well as biogas productivity by gasometer and chromatography, in the anaerobic co-digestion process were studied. This paper presents a performance evaluation of co-digestion systems for biogas production using cattle manure and wastes from the Sewage Treatment Station of a brewery and ricotta cheese whey. The search revealed that the type of substrate added in co-digestion with cattle manure, Carbon/Nitrogen ratio, and Ammonia Nitrogen were the most influential factors that explained many of the variations of the microbiota in the biodigesters fed. This study demonstrated a good potential for the use of ricotta cheese whey in the production of biogas and its further conversion into energy. These findings could provide some fundamental and technical information for the co-treatment of industrial derived wastes in centralized anaerobic biodigestion facilities in a sustainable manner with high process capacity and methane recovery.
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Affiliation(s)
- Guilherme Henrique da Silva
- Institute of Biological Sciences, Graduate Program in Ecology, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Nathan Oliveira Barros
- Institute of Biological Sciences, Graduate Program in Ecology, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Larice Aparecida Rezende Santana
- Faculty of Pharmacy, Graduate Program in Science and Technology of Milk and Derivatives, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
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Gurmessa B, Ashworth AJ, Yang Y, Savin M, Moore PA, Ricke SC, Corti G, Pedretti EF, Cocco S. Variations in bacterial community structure and antimicrobial resistance gene abundance in cattle manure and poultry litter. Environ Res 2021; 197:111011. [PMID: 33774017 DOI: 10.1016/j.envres.2021.111011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 11/18/2020] [Revised: 02/03/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Cattle manure and poultry litter are widely used as fertilizers as they are excellent sources of nutrients; however, potential adverse environmental effects exist during land applications, due to the release of zoonotic bacteria and antimicrobial resistance (AMR) genes. This study was conducted to understand linkages between physiochemical composition, bacterial diversity, and AMR gene presence of cattle manure and poultry litter using quantitative polymerase chain reaction to enumerate four AMR genes (ermB, sulI, intlI, and blactx-m-32), Illumina sequencing of the 16 S region, and analysis of physical and chemical properties. Principal coordinate analysis of Bray-Curtis distance revealed distinct bacterial community structures between the two manure sources. Greater alpha diversity occurred in cattle manure compared to poultry litter (P < 0.05). Redundancy analysis showed a strong relationship between manure physiochemical and composition and bacterial abundance, with positive relationships occurring among electrical conductivity and carbon/nitrogen, and negative associations for total solids and soluble fractions of heavy metals. Cattle manure exhibited greater abundance of macrolide (ermB) and sulfonamide (sulI) resistant genes. Consequently, fresh cattle manure applications may result in greater potential spread of AMR genes to the soil-water environment (relative to poultry litter) and novel best management strategies (such as composting) may reduce the release of AMR genes to the soil-water environment.
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Affiliation(s)
- Biyensa Gurmessa
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche 10, 60131, Ancona, Italy
| | - Amanda J Ashworth
- USDA-ARS, Poultry Production and Product Safety Research Unit, 1260 W. Maple St, Fayetteville, AR, 72701, USA.
| | - Yichao Yang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Mary Savin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Philip A Moore
- USDA-ARS, Poultry Production and Product Safety Research Unit, 1260 W. Maple St, Fayetteville, AR, 72701, USA
| | - Steven C Ricke
- Meat Science & Animal Biologics Discovery Program (MSABD), Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1933 Observatory Drive, Madison, WI, 53706, USA
| | - Giuseppe Corti
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche 10, 60131, Ancona, Italy
| | - Ester Foppa Pedretti
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche 10, 60131, Ancona, Italy
| | - Stefania Cocco
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche 10, 60131, Ancona, Italy
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Yue Y, Wang J, Wu X, Zhang J, Chen Z, Kang X, Lv Z. The fate of anaerobic syntrophy in anaerobic digestion facing propionate and acetate accumulation. Waste Manag 2021; 124:128-135. [PMID: 33611157 DOI: 10.1016/j.wasman.2021.01.038] [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: 07/09/2020] [Revised: 11/30/2020] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
How the acetate and propionate accumulation impact anaerobic syntrophy during methane formation is not well understood. To investigate such effect, continuous acetate (35 g/L), propionate (11.25 g/L) and bicarbonate (30 g/L) supplementation were used during mesophilic anaerobic digestion. The high throughput sequencing (16S rRNA and mcrA), Real-Time quantitative PCR, and stable carbon isotope fingerprinting were applied to investigate the structure and activity of microbial community members. The results demonstrated that the abundance of syntrophic acetate oxidizing bacteria exhibited a gradual decrease coupled with heavier stable carbon isotopic signature of methane (δ 13CH4) in the three reagents impacted reactors. The increased acetate and propionate concentrations exerted negative influence on biogas production but the relatively stable hydrogenotrophic methanogens together with syntrophic acetate/propionate oxidizing bacteria kept the stable methane formation facing acetate and propionate accumulation. The functional genes copy number of the hydrogenotrophic Methanocellaceae and Methanomicrobiaceae correlated significantly with δ 13CH4 (R2 > 0.74), but only the abundance of Methanocellaceae fitted well with δ 13CH4 (p < 0.05). The δ 13CH4 signatures can predict methanogenesis, as it directly reflects the main methanogenic pathway; yet, further investigation of isotope fractionation in acetate/propionate coupled with δ 13CH4 is needed. Collectively, these results provide deep insight into anaerobic syntrophy and reveal changes of synergistic relationships, both of which may contribute to the stability of biogas reactors.
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Affiliation(s)
- Yanan Yue
- School of Life, Jiangsu Normal University, Shanghai Road 101, 221116 Xuzhou, China
| | - Junyu Wang
- School of Life, Jiangsu Normal University, Shanghai Road 101, 221116 Xuzhou, China
| | - Xiayuan Wu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jianfeng Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhongbing Chen
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic.
| | - Xuejing Kang
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic
| | - Zuopeng Lv
- School of Life, Jiangsu Normal University, Shanghai Road 101, 221116 Xuzhou, China.
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Fernandez-Bayo JD, Simmons CW, VanderGheynst JS. Characterization of digestate microbial community structure following thermophilic anaerobic digestion with varying levels of green and food wastes. ACTA ACUST UNITED AC 2020; 47:1031-1044. [DOI: 10.1007/s10295-020-02326-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022]
Abstract
Abstract
The properties of digestates generated through anaerobic digestion are influenced by interactions between the digester microbial communities, feedstock properties and digester operating conditions. This study investigated the effect of varying initial feedstock carbon to nitrogen (C/N) ratios on digestate microbiota and predicted abundance of genes encoding lignocellulolytic activity. The C/N ratio had a significant impact on the digestate microbiome. Feedstocks with intermediate C/N ratio (20–27) (where higher biomethane potential was observed) showed higher relative abundance of archaea compared to feedstocks with C/N ratios at 17 and 34. Within microbial networks, four microbial clusters and eight connector microorganisms changed significantly with the C/N ratio (P < 0.05). Feedstocks with C/N < 23 were richer in organisms from the family Thermotogaceae and genus Caldicoprobacter and enhanced potential for degradation of maltose, galactomannans, melobiose and lactose. This study provides new insights into how anaerobic digestion conditions relate to the structure and functional potential of digester microbial communities, which may be relevant to both digester performance and subsequent utilization of digestates for composting or amending soil.
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Affiliation(s)
- Jesus D Fernandez-Bayo
- grid.27860.3b 0000 0004 1936 9684 Department of Biological and Agricultural Engineering University of California One Shields Ave. 95616 Davis CA USA
- grid.27860.3b 0000 0004 1936 9684 Department of Food Science and Technology University of California One Shields Ave. 95616 Davis CA USA
| | - Christopher W Simmons
- grid.27860.3b 0000 0004 1936 9684 Department of Food Science and Technology University of California One Shields Ave. 95616 Davis CA USA
| | - Jean S VanderGheynst
- grid.27860.3b 0000 0004 1936 9684 Department of Biological and Agricultural Engineering University of California One Shields Ave. 95616 Davis CA USA
- grid.266686.a 0000000102217463 Department of Bioengineering University of Massachusetts Dartmouth MA USA
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Mei R, Nobu MK, Narihiro T, Liu WT. Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters. Front Microbiol 2020; 11:593006. [PMID: 33193263 PMCID: PMC7661554 DOI: 10.3389/fmicb.2020.593006] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 10/13/2020] [Indexed: 01/22/2023] Open
Abstract
Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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