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Ni R, Wang S, Lin X, Song L. Antibiotics inhibit methanogenesis during municipal solid waste decomposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167397. [PMID: 37758143 DOI: 10.1016/j.scitotenv.2023.167397] [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: 07/30/2023] [Revised: 09/23/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Municipal solid waste (MSW) landfills are significant sources of antibiotics. However, the effects of antibiotics on MSW decomposition process and methanogenesis during solid waste decomposition remain insufficiently characterized. This study investigated the effects of environmentally relevant concentrations (ERCs) of antibiotics (200 μg/kg for each antibiotic) on MSW decomposition and methanogenesis in bioreactors treated with and without eight antibiotics (three tetracyclines, three sulfonamides, and two macrolides). The key phases of MSW decomposition, namely the aerobic, anaerobic acid, and methanogenic phases, were determined by analyzing the key physiochemical parameters of the leachate, including pH, chemical oxygen demand, and biochemical oxygen demand. We assessed the bacterial and archaeal compositions, along with the abundance of the gene encoding the alpha subunit of methyl-coenzyme M reductase (mcrA), during MSW decomposition using high throughput 16S ribosomal RNA (rRNA) gene sequencing and quantitative polymerase chain reactions, respectively. Our results revealed that antibiotics significantly altered the compositions of bacteria and methanogens, leading to decreased mcrA abundance and methanogenesis. Specifically, antibiotics inhibited cellulose-degrading bacteria (Firmicutes) and archaea (E2) in the anaerobic acid phase and hydrolytic bacteria (Proteobacteria) in the methanogenic phase, resulting in lower degradation of biodegradable matter than that of the biodegradation without antibiotics treatment. However, the typical MSW decomposition process indicated by the key decomposition phases was successfully separated in both bioreactors, suggesting that antibiotics did not affect overall MSW decomposition process development or the associated individual decomposition phases establishment. These findings suggest that antibiotics at ERCs may inhibit methanogenesis during MSW decomposition, thereby providing fundamental information for methane management and climate change studies.
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Affiliation(s)
- Renjie Ni
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi 247230, China
| | - Shuijing Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi 247230, China
| | - Xiaoxing Lin
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi 247230, China
| | - Liyan Song
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi 247230, China.
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El Houari A, Carpenter M, Chaplin D, Golyshin P, McDonald JE. Lutispora saccharofermentans sp. nov., a mesophilic, non-spore-forming bacterium isolated from a lab-scale methanogenic landfill bioreactor digesting anaerobic sludge, and emendation of the genus Lutispora to include species which are non-spore-forming and mesophilic. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748601 DOI: 10.1099/ijsem.0.005683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A novel anaerobic, mesophilic, non-spore-forming bacterium (strain m25T) was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor containing anaerobic digester sludge. Cells were Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, and motile by means of a flagellum. The genomic DNA G+C content was 40.11 mol%. The optimal NaCl concentration, temperature and pH for growth were 2.5 g l-1, 35 °C and at pH 7.0, respectively. Strain m25T was able to grow in the absence of yeast extract on glycerol, pyruvate, arginine and cysteine. In the presence of 0.2 % yeast extract, strain m25T grew on carbohydrates and was able to use glucose, cellobiose, fructose, raffinose and galactose. The novel strain could utilize glycerol, urea, pyruvate, peptone and tryptone. The major fatty acids were iso-C15 : 0, C14 : 0, C16 : 0 DMA (dimethyl acetal) and iso-C15 : 0 DMA. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was closely related to Lutispora thermophila EBR46T (95.02 % 16S rRNA gene sequence similarity). Genome relatedness was determined using both average nucleotide identity and amino acid identity analyses, the results of which both strongly supported that strain m25T belongs to the genus Lutispora. Based on its unique phylogenetic features, strain m25T is considered to represent a novel species within the genus Lutispora. Moreover, based on its unique physiologic features, mainly the lack of spore formation, a proposal to amend the genus Lutispora is also provided to include the non-spore-forming and mesophilic species. Lutispora saccharofermentans sp. nov. is proposed. The type strain of the species is m25T (=DSM 112749T=ATCC TSD-268T).
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Affiliation(s)
| | - Morgan Carpenter
- School of Natural Sciences, Environment Center Wales, Bangor University, UK
| | - Daniel Chaplin
- Centre for Environmental Biotechnology (CEB), Bangor University, UK
| | - Peter Golyshin
- Centre for Environmental Biotechnology (CEB), Bangor University, UK
| | - James E McDonald
- School of Natural Sciences, Environment Center Wales, Bangor University, UK.,Current address: School of Biosciences, University of Birmingham, Birmingham, UK
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Sauk AH, Hug LA. Substrate-restricted methanogenesis and limited volatile organic compound degradation in highly diverse and heterogeneous municipal landfill microbial communities. ISME COMMUNICATIONS 2022; 2:58. [PMID: 37938269 PMCID: PMC9723747 DOI: 10.1038/s43705-022-00141-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/26/2022] [Accepted: 06/14/2022] [Indexed: 06/17/2023]
Abstract
Microbial communities in landfills transform waste and generate methane in an environment unique from other built and natural environments. Landfill microbial diversity has predominantly been observed at the phylum level, without examining the extent of shared organismal diversity across space or time. We used 16S rRNA gene amplicon and shotgun metagenomic sequencing to examine the taxonomic and functional diversity of the microbial communities inhabiting a Southern Ontario landfill. The microbial capacity for volatile organic compound degradation in leachate and groundwater samples was correlated with geochemical conditions. Across the landfill, 25 bacterial and archaeal phyla were present at >1% relative abundance within at least one landfill sample, with Patescibacteria, Bacteroidota, Firmicutes, and Proteobacteria dominating. Methanogens were neither numerous nor particularly abundant, and were predominantly constrained to either acetoclastic or methylotrophic methanogenesis. The landfill microbial community was highly heterogeneous, with 90.7% of organisms present at only one or two sites within this interconnected system. Based on diversity measures, the landfill is a microbial system undergoing a constant state of disturbance and change, driving the extreme heterogeneity observed. Significant differences in geochemistry occurred across the leachate and groundwater wells sampled, with calcium, iron, magnesium, boron, meta and para xylenes, ortho xylenes, and ethylbenzene concentrations contributing most strongly to observed site differences. Predicted microbial degradation capacities indicated a heterogeneous community response to contaminants, including identification of novel proteins implicated in anaerobic degradation of key volatile organic compounds.
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Affiliation(s)
- Alexandra H Sauk
- Department of Biology, University of Waterloo, 200 University Ave, Waterloo, ON, N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, 200 University Ave, Waterloo, ON, N2L 3G1, Canada.
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Delineating the Drivers and Functionality of Methanogenic Niches within an Arid Landfill. Appl Environ Microbiol 2022; 88:e0243821. [PMID: 35404071 PMCID: PMC9088289 DOI: 10.1128/aem.02438-21] [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] [Indexed: 11/20/2022] Open
Abstract
Microbial communities mediate the transformation of organic matter within landfills into methane (CH4). Yet their ecological role in CH4 production is rarely evaluated. To characterize the microbiome associated with this biotransformation, the overall community and methanogenic Archaea were surveyed in an arid landfill using leachate collected from distinctly aged landfill cells (i.e., younger, intermediate, and older). We hypothesized that distinct methanogenic niches exist within an arid landfill, driven by geochemical gradients that developed under extended and age-dependent waste biodegradation stages. Using 16S rRNA and mcrA gene amplicon sequencing, we identified putative methanogenic niches as follows. The order Methanomicrobiales was the most abundant order in leachate from younger cells, where leachate temperature and propionate concentrations were measured at 41.8°C ± 1.7°C and 57.1 ± 10.7 mg L−1. In intermediate-aged cells, the family Methanocellaceae was identified as a putative specialist family under intermediate-temperature and -total dissolved solid (TDS) conditions, wherein samples had a higher alpha diversity index and near CH4 concentrations. In older-aged cells, accumulating metals and TDS supported Methanocorpusculaceae, “Candidatus Bathyarchaeota,” and “Candidatus Verstraetearchaeota” operational taxonomic units (OTUs). Consistent with the mcrA data, we assayed methanogenic activity across the age gradient through stable isotopic measurements of δ13C of CH4 and δ13C of CO2. The majority (80%) of the samples’ carbon fractionation was consistent with hydrogenotrophic methanogenesis. Together, we report age-dependent geochemical gradients detected through leachate in an arid landfill seemingly influencing CH4 production, niche partitioning, and methanogenic activity. IMPORTANCE Microbiome analysis is becoming common in select municipal and service ecosystems, including wastewater treatment and anaerobic digestion, but its potential as a microbial-status-informative tool to promote or mitigate CH4 production has not yet been evaluated in landfills. Methanogenesis mediated by Archaea is highly active in solid-waste microbiomes but is commonly neglected in studies employing next-generation sequencing techniques. Identifying methanogenic niches within a landfill offers detail into operations that positively or negatively impact the commercial production of methane known as biomethanation. We provide evidence that the geochemistry of leachate and its microbiome can be a variable accounting for ecosystem-level (coarse) variation of CH4 production, where we demonstrate through independent assessments of leachate and gas collection that the functional variability of an arid landfill is linked to the composition of methanogenic Archaea.
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Eukaryotic community composition and dynamics during solid waste decomposition. Appl Microbiol Biotechnol 2022; 106:3307-3317. [PMID: 35403856 DOI: 10.1007/s00253-022-11912-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/25/2022] [Accepted: 04/02/2022] [Indexed: 11/27/2022]
Abstract
Consortia of microbial community are involved in organic waste decomposition in municipal solid waste (MSW) landfill via competition, syntropy, and predation. Bacterial and archaeal community structure and function have been extensively studied in this process, whereas the eukaryotic community structure and function are largely unidentified. This gap stands for one of the fundamental researches of microbial ecology, that is, "what is the importance of variation in eukaryotic community structure and function to solid waste decomposition? The main idea of this work is to characterize changes in eukaryotic community composition and the associated driver during solid waste decomposition. Using high throughput sequencing targeting 18S rRNA genes, community composition and dynamics of eukaryotic during solid wasted decomposition were studied, as well as the differences with solid waste and leachate physiochemical parameters. Concomitant to the expected changes in physiochemical factors, eukaryotic community composition and diversity changed along solid waste decomposition indicated by aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) and the structure was shaped by the nutrients (BOD5, total phosphorus, and nitrate) in leachate. Ascomycota, the predominant eukaryote, showed significant (p < 0.05) different structure among AP, ACP, and MP in phylum, genera, and species levels. Abundant Freshwater Opisthokonta was present in MP, suggesting a methane carbon cycling via grazing methane oxidation microorganism. Amoebozoa, Alveolata, Rhizaria, and Stramenopiles showed successional pattern during solid waste decomposition, indicating a short food chain establishment. Characterization on eukaryotic community composition and dynamics during solid waste decomposition are crucial for understanding of microbial consortia ecological function on solid waste decomposition and are also helpful for MSW management.Key points• Abundant Ascomycota significantly differed at AP, ACP, and MP.• Eukaryotic succession indicated a short food chain establishment.• Entire eukaryotic community structure was associated to nutrients in leachate.
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6
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Yang S, Li L, Peng X, Song L. Leachate microbiome profile reveals bacteria, archaea and eukaryote dynamics and methanogenic function during solid waste decomposition. BIORESOURCE TECHNOLOGY 2021; 320:124359. [PMID: 33157448 DOI: 10.1016/j.biortech.2020.124359] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Bacterial, archaeal, and eukaryotic community composition and dynamics in leachate during solid waste decomposition were investigated using Illumina MiSeq sequencing. The functional enzyme-encoding genes of methanogenic pathways were also predicted via PICRUSt. Succession of bacterial, archaeal, and eukaryotic community composition in aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) was observed. The main representatives of microbial phyla, genera, and species significantly (p < 0.05) differed at least two phases. Protist Ciliophora occurred at ACP and was prevalent in MP, suggesting a short food chain establishment in the methanogenesis. Bacterial, archaeal, fungi and eukaryotic community structure were all pH and biochemical oxygen demand (BOD5) dependent patter. Acetoclastic and hydrogenotrophic methanogenesis pathways with associated functional genes differed during solid waste decomposition and were inhibited in ACP.
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Affiliation(s)
- Shu Yang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Lei Li
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Xuya Peng
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Liyan Song
- Environmental Microbiology and Ecology Research Center, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 400714, China; School of Resources and Environmental Engineering, Anhui University, Anhui 230039, China.
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7
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Sekhohola-Dlamini L, Selvarajan R, Ogola HJO, Tekere M. Community diversity metrics, interactions, and metabolic functions of bacteria associated with municipal solid waste landfills at different maturation stages. Microbiologyopen 2020; 10:e1118. [PMID: 33314739 PMCID: PMC7818627 DOI: 10.1002/mbo3.1118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/13/2020] [Accepted: 08/20/2020] [Indexed: 01/26/2023] Open
Abstract
Municipal landfills are hot spots of dynamic bioprocesses facilitated by complex interactions of a multifaceted microbiome, whose functioning in municipal landfills at different maturing stages is poorly understood. This study determined bacterial community composition, interaction conetworks, metabolic functions, and controlling physicochemical properties in two landfills aged 14 and 36 years. High throughput sequencing revealed a similar distribution of bacterial diversity, evenness, and richness in the 14‐ and 36‐year‐old landfills in the 0–90 cm depth. At deeper layers (120–150 cm), the 14‐year‐old landfill had significantly greater bacterial diversity and richness indicating that it is a more active microcosm than the 36‐year‐old landfill, where phylum Epsilonbacteraeota was overwhelmingly dominant. The taxonomic and functional diversity in the 14‐year‐old landfill was further reflected by the abundant presence of indicator genera Pseudomonas,Lutispora,Hydrogenspora, and Sulfurimonas coupled with the presence of biomarker enzymes associated with carbon (C), nitrogen (N), and sulfur (S) metabolism. Furthermore, canonical correspondence analysis revealed that bacteria in the 14‐year‐old landfill were positively correlated with high C, N, S, and phosphorus resulting in positive cooccurrence interactions. In the 36‐year‐old landfill, negative coexclusion interactions populated by members of N fixing Rhizobiales were dominant, with metabolic functions and biomarker enzymes predicting significant N fixation that, as indicated by interaction network, potentially inhibited ammonia‐intolerant bacteria. Overall, our findings show that diverse bacterial community in the 14‐year‐old landfill was dominated by copiotrophs associated with positive conetworks, whereas the 36‐year‐old landfill was dominated by lithotrophs linked to coexclusion interactions that greatly reduced bacterial diversity and richness.
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Affiliation(s)
- Lerato Sekhohola-Dlamini
- Department of Environmental Sciences, University of South Africa (UNISA), Johannesburg, South Africa
| | - Ramganesh Selvarajan
- Department of Environmental Sciences, University of South Africa (UNISA), Johannesburg, South Africa
| | - Henry Joseph Odour Ogola
- Department of Environmental Sciences, University of South Africa (UNISA), Johannesburg, South Africa.,School of Food and Agricultural Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Memory Tekere
- Department of Environmental Sciences, University of South Africa (UNISA), Johannesburg, South Africa
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Frank BP, Goodwin DG, Bohutskyi P, Phan DC, Lu X, Kuwama L, Bouwer EJ, Fairbrother DH. Influence of polymer type and carbon nanotube properties on carbon nanotube/polymer nanocomposite biodegradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140512. [PMID: 32721719 DOI: 10.1016/j.scitotenv.2020.140512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The interaction of anaerobic microorganisms with carbon nanotube/polymer nanocomposites (CNT/PNC) will play a major role in determining their persistence and environmental fate at the end of consumer use when these nano-enabled materials enter landfills and encounter wastewater. Motivated by the need to understand how different parameters (i.e., polymer type, microbial phenotype, CNT characteristics) influence CNT/PNC biodegradation rates, we have used volumetric biogas measurements and kinetic modeling to study biodegradation as a function of polymer type and CNT properties. In one set of experiments, oxidized multiwall carbon nanotubes (O-MWCNTs) with a range of CNT loadings 0-5% w/w were incorporated into poly-ε-caprolactone (PCL) and polyhydroxyalkanoates (PHA) matrices and subjected to biodegradation by an anaerobic microbial community. For each CNT/PNC, complete polymer biodegradation was ultimately observed, although the rate of biodegradation was inhibited above certain critical CNT loadings dependent upon the polymer type. Higher loadings of pristine MWCNTs were needed to decrease the rate of polymer biodegradation compared to O-MWCNTs, an effect ascribed principally to differences in CNT dispersion within the polymer matrices. Above certain CNT loadings, a CNT mat of similar shape to the initial PNC was formed after polymer biodegradation, while below this threshold, CNT aggregates fragmented in the media. In situations where biodegradation was rapid, methanogen growth was disproportionately inhibited compared to the overall microbial community. Analysis of the results obtained from this study indicates that the inhibitory effect of CNTs on polymer biodegradation rate is greatest under conditions (i.e., polymer type, microbial phenotype, CNT dispersion) where biodegradation of the neat polymer is slowest. This new insight provides a means to predict the environmental fate, persistence, and transformations of CNT-enabled polymer materials.
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Affiliation(s)
- Benjamin P Frank
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - David G Goodwin
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - Pavlo Bohutskyi
- Biological Sciences Division, Pacific Northwest National Laboratory, 3300 Stevens Dr., Richland, Washington 99354, United States
| | - Duc C Phan
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States; Department of Civil and Environmental Engineering, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, United States
| | - Xier Lu
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - Leo Kuwama
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - Edward J Bouwer
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - D Howard Fairbrother
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States.
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Xu Q, Qin J, Yuan T, Ko JH. Extracellular enzyme and microbial activity in MSW landfills with different gas collection and leachate management practices. CHEMOSPHERE 2020; 250:126264. [PMID: 32105861 DOI: 10.1016/j.chemosphere.2020.126264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/04/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
The performance of simulated municipal solid waste (MSW) landfills with two different biogas collection practices - (1) upward and upward-downward biogas flow collection (LT-TB) in sequence and (2) simultaneous upward-downward biogas flow collection (LTB) from the beginning of the anaerobic degradation process - was investigated in terms of landfill gas and leachate, enzyme activity, and microbial community structure associated with MSW compression and leachate recirculation. The cumulative methane volume in LTB was 1.5 times higher than that in LT-TB. With MSW compression and leachate recirculation, amylase and lipase activity were enhanced in LTB. In LT-TB, the activities gradually decreased after reaching a peak with compression. The two biogas collection strategies influenced the community structure and activity of bacteria and archaea. The upward and downward gas collection flow with waste compression and leachate recirculation improved the environment for enriching bacterial phyla Firmicutes, Proteobacteria, and Synergistetes and genus Methanosarcina in Archaea.
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Affiliation(s)
- Qiyong Xu
- Key Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, 518055, China
| | - Jie Qin
- Key Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, 518055, China
| | - Tugui Yuan
- Key Laboratory for Eco-efficient Recycled Materials, School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, 518055, China
| | - Jae Hac Ko
- Department of Environmental Engineering, College of Ocean Sciences, Jeju National University, Jeju Special Self-Governing Province, 63243, Republic of Korea.
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Sekhohola-Dlamini L, Tekere M. Microbiology of municipal solid waste landfills: a review of microbial dynamics and ecological influences in waste bioprocessing. Biodegradation 2019; 31:1-21. [PMID: 31512011 DOI: 10.1007/s10532-019-09890-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/26/2019] [Indexed: 12/21/2022]
Abstract
Municipal solid waste landfills are widely used as a waste management tool and landfill microbiology is at the core of waste degradation in these ecosystems. This review investigates the microbiology of municipal solid waste landfills, focusing on the current state of knowledge pertaining to microbial diversity and functions facilitating in situ waste bioprocessing, as well as ecological factors influencing microbial dynamics in landfills. Bioprocessing of waste in municipal landfills emanates from substrate metabolism and co-metabolism by several syntrophic microorganisms, resulting in partial transformation of complex substrates into simpler polymeric compounds and complete mineralisation into inorganic salts, water and gases including the biofuel gas methane. The substrate decomposition is characterised by evolution and interactions of different bacterial, archaeal and fungal groups due to prevailing biotic and abiotic conditions in the landfills, allowing for hydrolytic, fermentative, acetogenic and methanogenic processes to occur. Application of metagenomics studies based on high throughput Next Generation Sequencing technique has advanced research on profiling of the microbial communities in municipal solid waste landfills. However, functional diversity and bioprocess dynamics, as well as key factors influencing the in situ bioprocesses involved in landfill waste degradation; the very elements that are key in determining the efficiency of municipal landfills as tools of waste management, remain ambiguous. Such gaps also hinder progressive understanding of fundamentals that underlie technology development based on waste biodegradation, and exploration of municipal waste as a bioresource.
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Affiliation(s)
- Lerato Sekhohola-Dlamini
- Department of Environmental Sciences, University of South Africa (UNISA), Florida, P.O. Box X6, Johannesburg, 1710, South Africa.
| | - Memory Tekere
- Department of Environmental Sciences, University of South Africa (UNISA), Florida, P.O. Box X6, Johannesburg, 1710, South Africa
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Liu X, Yang S, Wang Y, Zhao HP, Song L. Metagenomic analysis of antibiotic resistance genes (ARGs) during refuse decomposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:1231-1237. [PMID: 29660875 DOI: 10.1016/j.scitotenv.2018.04.048] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/30/2018] [Accepted: 04/04/2018] [Indexed: 05/26/2023]
Abstract
Landfill is important reservoirs of residual antibiotics and antibiotic resistance genes (ARGs), but the mechanism of landfill application influence on antibiotic resistance remains unclear. Although refuse decomposition plays a crucial role in landfill stabilization, its impact on the antibiotic resistance has not been well characterized. To better understand the impact, we studied the dynamics of ARGs and the bacterial community composition during refuse decomposition in a bench-scale bioreactor after long term operation (265d) based on metagenomics analysis. The total abundances of ARGs increased from 431.0ppm in the initial aerobic phase (AP) to 643.9ppm in the later methanogenic phase (MP) during refuse decomposition, suggesting that application of landfill for municipal solid waste (MSW) treatment may elevate the level of ARGs. A shift from drug-specific (bacitracin, tetracycline and sulfonamide) resistance to multidrug resistance was observed during the refuse decomposition and was driven by a shift of potential bacteria hosts. The elevated abundance of Pseudomonas mainly contributed to the increasing abundance of multidrug ARGs (mexF and mexW). Accordingly, the percentage of ARGs encoding an efflux pump increased during refuse decomposition, suggesting that potential bacteria hosts developed this mechanism to adapt to the carbon and energy shortage when biodegradable substances were depleted. Overall, our findings indicate that the use of landfill for MSW treatment increased antibiotic resistance, and demonstrate the need for a comprehensive investigation of antibiotic resistance in landfill.
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Affiliation(s)
- Xi Liu
- Environmental Microbiology and Ecology Research Center, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 101407, China
| | - Shu Yang
- Departments of Geology & Geophysics, University of Utah, Salt Lake City, UT 84112, USA
| | - Yangqing Wang
- Environmental Microbiology and Ecology Research Center, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 400714, China
| | - He-Ping Zhao
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Liyan Song
- Environmental Microbiology and Ecology Research Center, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 400714, China.
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12
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Spina F, Tigini V, Romagnolo A, Varese GC. Bioremediation of Landfill Leachate with Fungi: Autochthonous vs. Allochthonous Strains. Life (Basel) 2018; 8:E27. [PMID: 29973501 PMCID: PMC6161071 DOI: 10.3390/life8030027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 12/05/2022] Open
Abstract
Autochthonous fungi from contaminated wastewater are potential successful agents bioremediation thanks to their adaptation to pollutant toxicity and to competition with other microorganisms present in wastewater treatment plant. Biological treatment by means of selected fungal strains could be a potential tool to integrate the leachate depuration process, thanks to their fungal extracellular enzymes with non-selective catalytical activity. In the present work, the treatability of two real samples (a crude landfill leachate and the effluent coming from a traditional wastewater treatment plant) was investigated in decolorization experiments with fungal biomasses. Five autochthonous fungi, Penicillium brevicompactum MUT 793, Pseudallescheria boydii MUT 721, P. boydii MUT 1269, Phanerochaete sanguinea MUT 1284, and Flammulina velutipes MUT 1275, were selected in a previous miniaturized decolorization screening. Their effectiveness in terms of decolorization, enzymatic activity (laccases and peroxidases), biomass growth and ecotoxicity removal was compared with that of five allochthonous fungal strains, Pleurotus ostreatus MUT 2976, Porostereum spadiceum MUT 1585, Trametespubescens MUT 2400, Bjerkanderaadusta MUT 3060 and B. adusta MUT 2295, selected for their well known capability to degrade recalcitrant pollutants. Moreover, the effect of biomass immobilization on polyurethane foam (PUF) cube was assessed. The best decolorization (60%) was achieved by P. spadiceum MUT 1585, P. boydii MUT 721 and MUT 1269. In the first case, the DP was achieved gradually, suggesting a biodegradation process with the involvement of peroxidases. On the contrary, the two autochthonous fungi seem to bioremediate the effluent mainly by biosorption, with the abatement of the toxicity (up to 100%). The biomass immobilization enhanced enzymatic activity, but not the DP. Moreover, it limited the biomass growth for the fast growing fungi, MUT 721 and MUT 1269. In conclusion, robust and versatile strains coming from well-characterized collections of microorganisms can obtain excellent results comparing and even exceeding the bioremediation yields of strains already adapted to pollutants.
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Affiliation(s)
- Federica Spina
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Turin, Italy.
| | - Valeria Tigini
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Turin, Italy.
| | - Alice Romagnolo
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Turin, Italy.
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Turin, Italy.
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Awasthi AK, Pandey AK, Khan J. A preliminary report of indigenous fungal isolates from contaminated municipal solid waste site in India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8880-8888. [PMID: 28204952 DOI: 10.1007/s11356-017-8472-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/16/2017] [Indexed: 04/15/2023]
Abstract
Municipal solid waste (MSW) containing harmful substances is a major concern in waste management and can cause adverse effects on diversity of fungi in soil. The main objective was to evaluate the fungal diversity inhabiting in the soil nearby MSW disposal site. The fungal strains were isolated in potato dextrose agar (PDA), media at temperatures 28 ± 1 °C by using standard serial dilution pour plate method, and appeared fungal colonies identified based on morphological characteristics. The overall most fungal diversity was found in soil sample collected from S5, followed by S4, S3, S1, and least in S2 site. A total of 24 fungal isolates recovered from the different MSW sites and Aspergillus sp., Fusarium sp., and Curvularia sp. genus has isolated from all the samples. In addition, the metal tolerance index performed because it needs to classify the fungus for their best use as potential agent for environmental protection. The metal tolerance outcomes revealed that both metals (cadmium and chromium) has appeared as the highest growth inhibitor for most strains and even fungal colonies did not propagate very well on the surface of media. Therefore, these findings suggest that the pre-adapted indigenous fungal isolates have proven remarkable tolerance ability to both metals. Furthermore, these highly metal-tolerant fungal strains are recommended for detail research or can use in pilot-scale bioremediation application to treat contaminated site.
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Affiliation(s)
- Abhishek Kumar Awasthi
- Mycological Research Laboratory, Department of Biological Sciences, Rani Durgavati University, Jabalpur, (M.P.), India.
- Department of Microbiology and Biotechnology, Veerangna Awanti Bai P.G. College, Chhatarpur, (M.P.), India.
- School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China.
| | - Akhilesh Kumar Pandey
- Mycological Research Laboratory, Department of Biological Sciences, Rani Durgavati University, Jabalpur, (M.P.), India
- Madhya Pradesh Private University Regulatory Commission, Bhopal, (M.P.), India
| | - Jamaluddin Khan
- Mycological Research Laboratory, Department of Biological Sciences, Rani Durgavati University, Jabalpur, (M.P.), India
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14
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Geographic and environmental sources of variation in bacterial community composition in a large-scale municipal landfill site in China. Appl Microbiol Biotechnol 2016; 101:761-769. [DOI: 10.1007/s00253-016-7917-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/25/2016] [Accepted: 10/04/2016] [Indexed: 01/07/2023]
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15
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Stamps BW, Lyles CN, Suflita JM, Masoner JR, Cozzarelli IM, Kolpin DW, Stevenson BS. Municipal Solid Waste Landfills Harbor Distinct Microbiomes. Front Microbiol 2016; 7:534. [PMID: 27148222 PMCID: PMC4837139 DOI: 10.3389/fmicb.2016.00534] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/31/2016] [Indexed: 11/16/2022] Open
Abstract
Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.
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Affiliation(s)
- Blake W Stamps
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | - Christopher N Lyles
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | | | | | | | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
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16
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Emkes H, Coulon F, Wagland S. A decision support tool for landfill methane generation and gas collection. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 43:307-318. [PMID: 26168873 DOI: 10.1016/j.wasman.2015.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/24/2015] [Accepted: 07/02/2015] [Indexed: 06/04/2023]
Abstract
This study presents a decision support tool (DST) to enhance methane generation at individual landfill sites. To date there is no such tool available to provide landfill decision makers with clear and simplified information to evaluate biochemical processes within a landfill site, to assess performance of gas production and to identify potential remedies to any issues. The current lack in understanding stems from the complexity of the landfill waste degradation process. Two scoring sets for landfill gas production performance are calculated with the tool: (1) methane output score which measures the deviation of the actual methane output rate at each site which the prediction generated by the first order decay model LandGEM; and (2) landfill gas indicators' score, which measures the deviation of the landfill gas indicators from their ideal ranges for optimal methane generation conditions. Landfill gas indicators include moisture content, temperature, alkalinity, pH, BOD, COD, BOD/COD ratio, ammonia, chloride, iron and zinc. A total landfill gas indicator score is provided using multi-criteria analysis to calculate the sum of weighted scores for each indicator. The weights for each indicator are calculated using an analytical hierarchical process. The tool is tested against five real scenarios for landfill sites in UK with a range of good, average and poor landfill methane generation over a one year period (2012). An interpretation of the results is given for each scenario and recommendations are highlighted for methane output rate enhancement. Results demonstrate how the tool can help landfill managers and operators to enhance their understanding of methane generation at a site-specific level, track landfill methane generation over time, compare and rank sites, and identify problems areas within a landfill site.
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Affiliation(s)
- Harriet Emkes
- School of Energy, Environment and Agrifood, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Frédéric Coulon
- School of Energy, Environment and Agrifood, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Stuart Wagland
- School of Energy, Environment and Agrifood, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom.
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17
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Bacterial community diversity in municipal waste landfill sites. Appl Microbiol Biotechnol 2015; 99:7745-56. [DOI: 10.1007/s00253-015-6633-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 04/16/2015] [Accepted: 04/19/2015] [Indexed: 11/26/2022]
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18
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Song L, Wang Y, Zhao H, Long DT. Composition of bacterial and archaeal communities during landfill refuse decomposition processes. Microbiol Res 2015; 181:105-11. [PMID: 25991030 DOI: 10.1016/j.micres.2015.04.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/20/2015] [Accepted: 04/25/2015] [Indexed: 01/23/2023]
Abstract
Little is known about the archaeal and the bacterial diversities in a landfill during different phases of decomposition. In this study, the archaeal and the bacterial diversities of Laogang landfill (Shanghai, China) at two different decomposition phases (i.e., initial methanogenic phase (IMP) and stable methanogenic phase (SMP)), were culture-independently examined using PCR-based 454 pyrosequencing. A total of 47,753 sequences of 16S rRNA genes were retrieved from 69,954 reads and analyzed to evaluate the diversities of the archaeal and bacterial communities. The most predominant types of archaea were hydrogenotrophic Methanomicrobiales, and of bacteria were Proteobacteria, Firmicutes, and Bacteroidetes. As might be expected, their abundances varied at decomposition phases. Archaea Methanomicrobiales accounts for 97.6% of total archaeal population abundance in IMP and about 57.6% in SMP. The abundance of archaeal genus Halobacteriale was 0.1% in IMP and was 20.3% in the SMP. The abundance of Firmicutes was 21.3% in IMP and was 4.3% in SMP. The abundance of Bacteroidetes represented 11.5% of total bacterial in IMP and was dominant (49.4%) in SMP. Both the IMP and SMP had unique cellulolytic bacteria compositions. IMP consisted of members of Bacillus, Fibrobacter, and Eubacterium, while SMP harbored groups of Microbacterium. Both phases had Clostridium with different abundance, 4-5 folds higher in SMP.
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Affiliation(s)
- Liyan Song
- Research Center of Environmental Microbiology and Ecology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 401122, China.
| | - Yangqing Wang
- Research Center of Environmental Microbiology and Ecology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing 401122, China
| | - Heping Zhao
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China.
| | - David T Long
- Department of Geological Science, Michigan State University, East Lansing, MI 48824, USA
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19
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Song L, Wang Y, Tang W, Lei Y. Archaeal community diversity in municipal waste landfill sites. Appl Microbiol Biotechnol 2015; 99:6125-37. [DOI: 10.1007/s00253-015-6493-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 02/13/2015] [Accepted: 02/17/2015] [Indexed: 10/23/2022]
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20
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Gruninger RJ, Puniya AK, Callaghan TM, Edwards JE, Youssef N, Dagar SS, Fliegerova K, Griffith GW, Forster R, Tsang A, McAllister T, Elshahed MS. Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential. FEMS Microbiol Ecol 2014; 90:1-17. [PMID: 25046344 DOI: 10.1111/1574-6941.12383] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 02/05/2023] Open
Abstract
Anaerobic fungi (phylum Neocallimastigomycota) inhabit the gastrointestinal tract of mammalian herbivores, where they play an important role in the degradation of plant material. The Neocallimastigomycota represent the earliest diverging lineage of the zoosporic fungi; however, understanding of the relationships of the different taxa (both genera and species) within this phylum is in need of revision. Issues exist with the current approaches used for their identification and classification, and recent evidence suggests the presence of several novel taxa (potential candidate genera) that remain to be characterised. The life cycle and role of anaerobic fungi has been well characterised in the rumen, but not elsewhere in the ruminant alimentary tract. Greater understanding of the 'resistant' phase(s) of their life cycle is needed, as is study of their role and significance in other herbivores. Biotechnological application of anaerobic fungi, and their highly active cellulolytic and hemi-cellulolytic enzymes, has been a rapidly increasing area of research and development in the last decade. The move towards understanding of anaerobic fungi using -omics based (genomic, transcriptomic and proteomic) approaches is starting to yield valuable insights into the unique cellular processes, evolutionary history, metabolic capabilities and adaptations that exist within the Neocallimastigomycota.
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21
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Tigini V, Prigione V, Varese GC. Mycological and ecotoxicological characterisation of landfill leachate before and after traditional treatments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 487:335-341. [PMID: 24793330 DOI: 10.1016/j.scitotenv.2014.04.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/28/2014] [Accepted: 04/06/2014] [Indexed: 06/03/2023]
Abstract
Pollution caused by landfill leachates is one of the main problems of urbanised areas, on account of their chemical composition, which turn in an ineffective treatment. A characterisation of leachates, which takes into account chemical, ecotoxicological and mycological aspects, is basilar for the evaluation of environmental impact of leachate and the development of suitable treatment techniques. In this study, the toxicity of a raw leachate and an effluent coming from traditional wastewater treatment plant was assessed by means of 4 ecotoxicological assays. Both the samples exceed the legal threshold value according to all the tested organisms, indicating the ineffectiveness of activated sludge treatment in the reduction of toxicity. The autochthonous mycoflora of the two samples was evaluated by filtration. The fungal load was 73 CFU for leachate and 102 CFU for the effluent. Ascomycetes were the dominant fraction (81% and 61%, for leachate and effluent respectively), followed by basidiomycetes (19% and 39%, respectively). Most of them were potential emerging pathogens. A decolourisation screening with autochthonous fungi was set up towards both samples in the presence or absence of glucose. Eleven fungi (basidiomycetes and ascomycetes) achieved up to 38% decolourisation yields, showing to be promising fungi for the bioremediation of leachates. Further experiment will be aimed to the study of decolourisation mechanism and toxicity reduction.
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Affiliation(s)
- Valeria Tigini
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Turin, Italy.
| | - Valeria Prigione
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Turin, Italy
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli, 25, 10125 Turin, Italy
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22
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Krause DO, Nagaraja TG, Wright ADG, Callaway TR. Board-invited review: Rumen microbiology: leading the way in microbial ecology. J Anim Sci 2013; 91:331-41. [PMID: 23404990 DOI: 10.2527/jas.2012-5567] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal flora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were first described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques (such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were first made in the rumen, which have not been recognized in a broader sense.
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Affiliation(s)
- D O Krause
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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23
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McDonald JE, Houghton JNI, Rooks DJ, Allison HE, McCarthy AJ. The microbial ecology of anaerobic cellulose degradation in municipal waste landfill sites: evidence of a role for fibrobacters. Environ Microbiol 2012; 14:1077-87. [PMID: 22225785 DOI: 10.1111/j.1462-2920.2011.02688.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellulose is reputedly the most abundant organic polymer in the biosphere, yet despite the fundamental role of cellulolytic microorganisms in global carbon cycling and as potential sources of novel enzymes for biotechnology, their identity and ecology is not well established. Cellulose is a major component of landfill waste and its degradation is therefore a key feature of the anaerobic microbial decomposition process. Here, we targeted a number of taxa containing known cellulolytic anaerobes (members of the bacterial genus Fibrobacter, lineages of Clostridium clusters I, III, IV and XIV, and anaerobic fungi of the Neocallimastigales) in landfill leachate and colonized cellulose 'baits' via PCR and quantitative PCR (qPCR). Fibrobacter spp. and Clostridium clusters III, IV and XIV were detected in almost all leachate samples and cluster III and XIV clostridia were the most abundant (1-6% and 1-17% of total bacterial 16S rRNA gene copies respectively). Two landfill leachate microcosms were constructed to specifically assess those microbial communities that colonize and degrade cellulose substrates in situ. Scanning electron microscopy (SEM) of colonized cotton revealed extensive cellulose degradation in one microcosm, and Fibrobacter spp. and Clostridium cluster III represented 29% and 17%, respectively, of total bacterial 16S rRNA gene copies in the biofilm. Visible cellulose degradation was not observed in the second microcosm, and this correlated with negligible relative abundances of Clostridium cluster III and Fibrobacter spp. (≤ 0.1%), providing the first evidence that the novel fibrobacters recently detected in landfill sites and other non-gut environments colonize and degrade cellulose substrates in situ.
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Affiliation(s)
- James E McDonald
- School of Biological Sciences, University of Liverpool, Liverpool, UK
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