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Shi X, Zhang J, Wang Q, Wang K, Han J, Hui Y, Jin X, Jin P. The sewer advances: How to select eco-friendly pipe materials for environmental protection. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175853. [PMID: 39222807 DOI: 10.1016/j.scitotenv.2024.175853] [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: 06/25/2024] [Revised: 08/15/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Sewer pipe materials exhibit diverse inner-surface features, which can affect the attachment of biofilm and influence microbial metabolic processes. To investigate the role of the type of pipe material on the composition and metabolic capabilities of the adhering microorganisms, three sets of urban sewers (High-Density Polyethylene Pipe (HDPE), Ductile Iron Pipe (DIP), and Concrete Pipe (CP)) were constructed. Measurements of biofilm thickness and environmental factors revealed that the thickest biofilm in CP pipes reached 2000 μm, with ORP values as low as -325 mV, indicating a more suitable anaerobic microbial habitat. High-throughput sequencing showed similar relative abundances of genera related to carbon and sulfur metabolism in the DIP and CP pipes, whereas HDPE exhibited only half the relative abundance compared to that found in the other pipes. To explore the impact of pipe materials on the mechanisms of microbial response, a metagenomic approach was used to investigate the biological transformation of carbon and sulfur in wastewater. The annotations of the crucial enzyme-encoding genes related to methyl coenzyme M and sulfite reductase in DIP and CP were 50 and 110, respectively, whereas HDPE exhibited lower counts (25 and 70, respectively). This resulted in significantly lower carbon and sulfur metabolism capabilities in the HDPE biofilm than in the other two pipes. The stability of wastewater quality during the transmission process in HDPE pipes reduces the metabolic generation of toxic and harmful gases within the pipes, favoring the preservation of carbon sources for sewer systems. This study reveals the variations in carbon and sulfur metabolism in wastewater pipe systems influenced by pipe materials and provides insights for designing future sewers.
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Affiliation(s)
- Xuan Shi
- School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, China
| | - Jin Zhang
- School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, China; College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, Hebei Province 056038, China
| | - Qize Wang
- Future City Innovation Technology Co., Ltd., Shaanxi Construction Engineering Holding Group, Xi'an 710116, China; SCEGC-XJTU Joint Research Center for Future City Construction and Management Innovation, Xi'an Jiaotong University, Xi'an 710116, China
| | - Kai Wang
- Future City Innovation Technology Co., Ltd., Shaanxi Construction Engineering Holding Group, Xi'an 710116, China; SCEGC-XJTU Joint Research Center for Future City Construction and Management Innovation, Xi'an Jiaotong University, Xi'an 710116, China
| | - Jianshuang Han
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Yilian Hui
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Xin Jin
- School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, China
| | - Pengkang Jin
- School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, China.
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Hussain F, Kim LH, Kim H, Kim Y, Oh SE, Kim S. Enhanced bioremediation of acid mine-influenced groundwater with micro-sized emulsified corn oil droplets (MOD) and sulfate-reducing bacteria (Desulfovibrio vulgaris) in a microcosm assay. CHEMOSPHERE 2024; 352:141403. [PMID: 38368967 DOI: 10.1016/j.chemosphere.2024.141403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
High concentrations of metals and sulfates in acid mine drainage (AMD) are the cause of the severe environmental hazard that mining operations pose to the surrounding ecosystem. Little study has been conducted on the cost-effective biological process for treating high AMD. The current research investigated the potential of the proposed carbon source and sulfate reduction bacteria (SRB) culture in achieving the bioremediation of sulfate and heavy metals. This work uses individual and combinatorial bioaugmentation and bio-stimulation methods to bioremediate acid-mine-influenced groundwater in batch microcosm experiments. Bioaugmentation and bio-stimulation methods included pure culture SRB (Desulfovibrio vulgaris) and microsized oil droplet (MOD) by emulsifying corn oil. The research tested natural attenuation (T 1), bioaugmentation (T2), biostimulation (T3), and bioaugmentation plus biostimulation (T4) for AM-contaminated groundwater remediation. Bioaugmentation and bio-stimulation showed the greatest sulfate reduction (75.3%) and metal removal (95-99%). Due to carbon supply scarcity, T1 and T2 demonstrated 15.7% and 27.8% sulfate reduction activities. Acetate concentrations in T3 and T4 increased bacterial activity by providing carbon sources. Metal bio-precipitation was substantially linked with sulfate reduction and cell growth. SEM-EDS study of precipitates in T3 and T4 microcosm spectra indicated peaks for S, Cd, Mn, Cu, Zn, and Fe, indicating metal-sulfide association for metal removal precipitates. The MOD provided a constant carbon source for indigenous bacteria, while Desulfovibrio vulgaris increased biogenic sulfide synthesis for heavy metal removal.
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Affiliation(s)
- Fida Hussain
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city, 30019, Republic of Korea; Department of Environmental Science, University of Lahore, Lahore, 545590, Pakistan; Department of biological Environment, Kangwon National University, Chuncheon-si, 24341, Republic of Korea
| | - Lan Hee Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city, 30019, Republic of Korea
| | - Huiyun Kim
- Department of Environmental Engineering, Korea University, 2511 Sejong-ro, Sejong city, 30019, Republic of Korea
| | - Young Kim
- Department of Environmental Engineering, Korea University, 2511 Sejong-ro, Sejong city, 30019, Republic of Korea
| | - Sang-Eun Oh
- Department of biological Environment, Kangwon National University, Chuncheon-si, 24341, Republic of Korea
| | - Sungpyo Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city, 30019, Republic of Korea; Department of Environmental Engineering, Korea University, 2511 Sejong-ro, Sejong city, 30019, Republic of Korea.
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3
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Prem EM, Markt R, Wunderer M, Wagner AO. Meso- and thermophilic posttreatment of press water coming from a thermophilic municipal solid waste digester. Biotechnol Bioeng 2024; 121:266-280. [PMID: 37902646 PMCID: PMC10953027 DOI: 10.1002/bit.28577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/31/2023]
Abstract
An efficient biogas production out of organic (waste) materials is important to contribute to a carbon-neutral future. In this study, thermophilic press water (PW) coming from an organic fraction of the municipal solid waste digester was further digested in a thermo- and mesophilic posttreatment approach using two semicontinuous 14 L digesters. The results showed that the PW can still have considerable high biogas potential-at least during the touristic high season in central Europe. The change in temperature led to an increase in volatile fatty acid concentrations and a decrease in biogas production in the mesophilic approach in the first days. However, the losses in biogas production at the beginning could be compensated thus there were no considerable differences in biogas production between thermo- and mesophilic posttreatment at the end of incubation. This can most probably be contributed to a change in the microbial community, and potentially problematic intermediates like valerate could be better degraded in the mesophilic reactor. Especially the abundance of representatives of the phylum Bacteroidota, like Fermentimonas spp., increased during mesophilic anaerobic digestion.
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Affiliation(s)
- Eva Maria Prem
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| | - Rudolf Markt
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
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Kumari S, Das S. Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:79676-79705. [PMID: 37330441 DOI: 10.1007/s11356-023-28130-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/01/2023] [Indexed: 06/19/2023]
Abstract
Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.
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Affiliation(s)
- Swetambari Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Chai G, Wang D, Zhang Y, Wang H, Li J, Jing X, Meng H, Wang Z, Guo Y, Jiang C, Li H, Lin Y. Effects of organic substrates on sulfate-reducing microcosms treating acid mine drainage: Performance dynamics and microbial community comparison. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 330:117148. [PMID: 36584458 DOI: 10.1016/j.jenvman.2022.117148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Bioremediation techniques utilizing sulfate-reducing bacteria (SRB) for acid mine drainage (AMD) treatment have attracted growing attention in recent years, yet substrate bioavailability for SRB is a key factor influencing treatment effectiveness and long-term stability. This study investigated the effects of external organic substrates, including four complex organic wastes (i.e., sugarcane bagasse, straw compost, shrimp shell (SS), and crab shell (CS)) and a small-molecule organic acid (i.e., propionate), on AMD removal performance and associated microbial communities during the 30-day operation of sulfate-reducing microcosms. The results showed that the pH values increased in all five microcosms, while CS exhibited the highest neutralization ability and a maximum alkalinity generation of 1507 mg/L (as CaCO3). Sulfate reduction was more effective in SS and CS microcosms, with sulfate removal efficiencies of 95.6% and 86.0%, respectively. All sulfate-reducing microcosms could remove heavy metals to different degrees, with the highest removal rate of >99.0% observed for aluminum. The removal efficiency of manganese, the most recalcitrant metal, was the highest (96%) in the CS microcosm. Correspondingly, SRB was more abundant in the CS and SS microcosms as revealed by sequencing analysis, while Desulfotomaculum was the dominant SRB in the CS microcosm, accounting for 10.8% of total effective bacterial sequences. Higher abundances of functional genes involved in fermentation and sulfur cycle were identified in CS and SS microcosms. This study suggests that complex organic wastes such as CS and SS could create and maintain preferable micro-environments for active growth and metabolism of functional microorganisms, thus offering a cost-efficient, stable, and environmental-friendly solution for AMD treatment and management.
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Affiliation(s)
- Guodong Chai
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Dongqi Wang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; Shaanxi Key Laboratory of Water Resources and Environment, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Yitong Zhang
- Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Hui Wang
- Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Jiake Li
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Xiaosheng Jing
- Zhongsheng Environmental Technology Development Co., Ltd., Xi'an, Shaanxi, 710054, China
| | - Haiyu Meng
- Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Zhe Wang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Yuan Guo
- Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Chunbo Jiang
- Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Huaien Li
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China.
| | - Yishan Lin
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China.
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6
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Yan G, Sun X, Dong Y, Gao W, Gao P, Li B, Yan W, Zhang H, Soleimani M, Yan B, Häggblom MM, Sun W. Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning. WATER RESEARCH 2022; 226:119247. [PMID: 36270146 DOI: 10.1016/j.watres.2022.119247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F420H2 dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.
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Affiliation(s)
- Geng Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Wenlong Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Wangwang Yan
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Haihan Zhang
- Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, 8415683111, Isfahan, Iran
| | - Bei Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, United States
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.
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Lu T, Zhang J, Su T, Liang X, Wei Y, He T. Coupled mechanism of enhanced and inhibitory effects of nanoscale zero-valent iron on methane production and antibiotic resistance genes in anaerobic digestion of swine manure. BIORESOURCE TECHNOLOGY 2022; 360:127635. [PMID: 35853593 DOI: 10.1016/j.biortech.2022.127635] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
In this study, the turning point for nanoscale zero-valent iron's (NZVI) promotion and inhibition effects of methane production coupled with the reduction of antibiotic resistance genes (ARGs) was investigated. Adding 150 mmol/L NZVI increased methane production by maximum of 23.8 %, which was due to the chemical reaction producing H2 and enhancement of direct interspecies electron transfer (DIET) by NZVI. NZVI350 dramatically repressed methane generation by 48.0 %, which might be associated with the large quantity of reactive oxygen species (ROS) and excessive H2 inhibiting the functioning of microorganisms. The fate of ARGs was significantly related to daily methane production, indicating that the more methane production finally generated, the less the abundance of ARGs at last left. The reduction of ARGs was enhanced by maximum of 61.0 %, which was attributed to the inhibition of vertical gene transfer (VGT) and horizontal gene transfer (HGT) caused by steric hindrance associated with NZVI corrosion.
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Affiliation(s)
- Tiedong Lu
- Agricultural Resources and Environment Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department ofIsotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig 04318, Germany; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Tianming Su
- Agricultural Resources and Environment Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Xuelian Liang
- Research Institute of Agro-products Quality Safety and Testing Technology, Guangxi Academy of Agriculture Sciences, Nanning 530007, Guangxi, China
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Tieguang He
- Agricultural Resources and Environment Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China.
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Tadmor AD, Phillips R. MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study. Bioinformatics 2022; 38:631-647. [PMID: 34636854 PMCID: PMC10060711 DOI: 10.1093/bioinformatics/btab703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Metagenomes offer a glimpse into the total genomic diversity contained within a sample. Currently, however, there is no straightforward way to obtain a non-redundant list of all putative homologs of a set of reference sequences present in a metagenome. RESULTS To address this problem, we developed a novel clustering approach called 'metagenomic clustering by reference library' (MCRL), where a reference library containing a set of reference genes is clustered with respect to an assembled metagenome. According to our proposed approach, reference genes homologous to similar sets of metagenomic sequences, termed 'signatures', are iteratively clustered in a greedy fashion, retaining at each step the reference genes yielding the lowest E values, and terminating when signatures of remaining reference genes have a minimal overlap. The outcome of this computation is a non-redundant list of reference genes homologous to minimally overlapping sets of contigs, representing potential candidates for gene families present in the metagenome. Unlike metagenomic clustering methods, there is no need for contigs to overlap to be associated with a cluster, enabling MCRL to draw on more information encoded in the metagenome when computing tentative gene families. We demonstrate how MCRL can be used to extract candidate viral gene families from an oral metagenome and an oral virome that otherwise could not be determined using standard approaches. We evaluate the sensitivity, accuracy and robustness of our proposed method for the viral case study and compare it with existing analysis approaches. AVAILABILITY AND IMPLEMENTATION https://github.com/a-tadmor/MCRL. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Arbel D Tadmor
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University, 55131 Mainz, Germany
- Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
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9
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Microbial Contamination of Photographic and Cinematographic Materials in Archival Funds in the Czech Republic. Microorganisms 2022; 10:microorganisms10010155. [PMID: 35056604 PMCID: PMC8782003 DOI: 10.3390/microorganisms10010155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
Abstract
In this study we investigated the microbial contamination of 126 samples of photographic and cinematographic materials from 10 archival funds in the Czech Republic. Microorganisms were isolated from the light-sensitive layer by swabbing it with a polyurethane sponge. Microbial isolates were identified by MALDI-TOF MS (bacteria) or by phenotype testing and microscopy (fungi). Bacterial contamination was more abundant and more diverse than fungal contamination, and both were significantly associated with archives. The most frequently isolated fungal genera were Cladosporium, Eurotium, Penicillium, Aspergillus and Alternaria. The most frequently isolated bacteria were Gram-positive genera such as Staphylococcus, Micrococcus, Kocuria, Streptococcus and Bacillus. This bacterial and fungal diversity suggests that air is the main vehicle of contamination. We also analysed the impact of the type of material used for the carrier (paper, baryta paper, cellulose acetate and nitrate or glass) or the light-sensitive layer (albumen, gelatine, collodion and other) on the level and diversity of microbial contamination. Carriers such as polyester and cellulose nitrate may have a negative impact on bacterial contamination, while paper and baryta paper may have a partially positive impact on both fungal and bacterial contamination.
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Khosravi F, Khaleghi M, Naghavi H. Screening and identification of cellulose-degrading bacteria from soil and leaves at Kerman province, Iran. Arch Microbiol 2021; 204:88. [PMID: 34961888 DOI: 10.1007/s00203-021-02713-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022]
Abstract
Cellulosic biomass is considered one of the most promising sources for the production of alternative renewable bioenergy and other valuable products. Identification and optimization of strains with high enzymatic activity that can overcome constraints imposed by the cellulosic structure is an essential step in the development of new biotechnologies. The aim of this study was to isolate and identify thermophilic (50 °C) and mesophilic (37 °C) cellulolytic bacteria from soil and leaves samples at Kerman, Iran. Degrader bacteria were isolated using serial dilution and pour plate method. Media contained carboxymethylcellulose (CMC), and filter paper was used as sources of carbon. Totally 22 mesophilic and 17 thermophilic bacterial strains which produced clear zones were further identified by morphological and biochemical tests. Screening of purified bacteria was performed to identify cellulase-producing bacteria by Congo red test. These bacteria were compared to each other based on cellulase activity, the percentage of growth, and extracellular protein amounts. The strains with the highest enzymatic activity were determined by the DNS method. The isolated US5 and US7 grew rapidly, and produced cellulase. The US5 created the largest clear zones (7 mm). Besides, these strains were selected for analysis of 16S rRNA sequence. The results showed that selected bacteria strains belong to Brevibacillus borstelensis. The B. borstelensis strains isolated in this study showed a suitable cellulase enzyme activity.
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Affiliation(s)
- Farshid Khosravi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Mouj Khaleghi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hormazd Naghavi
- Soil and Water Research, Kerman Agricultural and Natural Resources Research and Education Center, AREEO, Kerman, Iran
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11
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Zhang J, Lu T, Zhong H, Shen P, Wei Y. Zero valent iron improved methane production and specifically reduced aminoglycoside and tetracycline resistance genes in anaerobic digestion. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 136:122-131. [PMID: 34662788 DOI: 10.1016/j.wasman.2021.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
It is unadvisable to discuss the antibiotic resistance genes (ARGs) reduction in anaerobic digestion (AD) system neglecting its main purpose-methane production. The methane production improvement coupling with antibiotic resistance genes (ARGs) reduction in anaerobic digestion (AD) by zero valent iron (ZVI) were simultaneously investigated. Whether the role of ZVI on the ARGs fate was random or specific was clarified through the high-throughput qPCR (HT-qPCR). Results indicated that ZVI improved methane production and ARGs reduction by 23.9% and 25.0%, respectively. The improved methane production was associated with chemical reaction and variances of microbial community caused by ZVI, where DIET between Petrimonas, Clostridium and Syntrophomonas, Methanosarcina was established along with ACAS being enriched. ZVI specifically, not randomly, facilitated the reduction of aminoglycoside resistance genes of antibiotic inactivation and tetracycline resistance genes of ribosomal protection proteins. The specifical reduction could be attributed to enzyme activity inhibition and intracellular ionic disturbance caused by higher amounts of ZVI, although most of ARGs fate could be well explained by microbial community which contributed the most to ARGs dynamics as a whole. ZVI-based AD was a promising way for the improvement of methane production coupling ARGs reduction.
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Affiliation(s)
- Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Tiedong Lu
- College of Life Science and Technology, Guangxi University, Nanning 530005, Guangxi, China
| | - Hui Zhong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peihong Shen
- College of Life Science and Technology, Guangxi University, Nanning 530005, Guangxi, China
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Lin Y, Grembi JA, Goots SS, Sebastian A, Albert I, Brennan RA. Advantageous microbial community development and improved performance of pilot-scale field systems treating high-risk acid mine drainage with crab shell. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126665. [PMID: 34351284 DOI: 10.1016/j.jhazmat.2021.126665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/25/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities are crucial to the effectiveness and stability of bioremediation systems treating acid mine drainage (AMD); however, little research has addressed how they correlate to system performance under changing environmental conditions. In this study, 16S rRNA gene sequencing and quantitative PCR (qPCR) were used to characterize microbial communities within different substrate combinations of crab shell (CS) and spent mushroom compost (SMC) and their association with chemical performance in pilot-scale vertical flow ponds (VFPs) treating high risk AMD in central Pennsylvania over 643 days of operation. As compared to a control containing SMC, VFPs containing CS sustained higher alkalinity, higher sulfate-reducing rates, and more thorough metals removal (>90% for Fe and Al, >50% for Mn and Zn). Correspondingly, CS VFPs supported the growth of microorganisms in key functional groups at increasing abundance and diversity over time, especially more diverse sulfate-reducing bacteria. Through changing seasonal and operational conditions over almost two years, the relative abundance of the core phyla shifted in all reactors, but the smallest changes in functional gene copies were observed in VFPs containing CS. These results suggest that the high diversity and stability of microbial communities associated with CS are consistent with effective AMD treatment.
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Affiliation(s)
- Yishan Lin
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA; State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Jessica A Grembi
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA; School of Medicine, Stanford University, Stanford, CA, USA
| | - Sara S Goots
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA; Calfee, Halter & Griswold, Cleveland, OH, USA
| | - Aswathy Sebastian
- Bioinformatics, Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - István Albert
- Bioinformatics, Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Rachel A Brennan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.
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13
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Duval E, Cravo-Laureau C, Poinel L, Duran R. Development of molecular driven screening for desulfurizing microorganisms targeting the dszB desulfinase gene. Res Microbiol 2021; 172:103872. [PMID: 34375709 DOI: 10.1016/j.resmic.2021.103872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022]
Abstract
COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP) were developed for the detection of the dszB desulfinase gene (2'-hydroxybiphenyl-2-sulfinate desulfinase; EC 3.13.1.3) by polymerase chain reaction (PCR), which allow to reveal larger diversity than traditional primers. The new developed primers were used as molecular monitoring tool to drive a procedure for the isolation of desulfurizing microorganisms. The primers revealed a large dszB gene diversity in environmental samples, particularly in diesel-contaminated soil that served as inoculum for enrichment cultures. The isolation procedure using the dibenzothiophene sulfone (DBTO2) as sole sulfur source reduced drastically the dszB gene diversity. A dszB gene closely related to that carried by Gordonia species was selected. The desulfurization activity was confirmed by the production of desulfurized 2-hydroxybiphenyl (2-HBP). Metagenomic 16S rRNA gene sequencing showed that the Gordonia genus was represented at low abundance in the initial bacterial community. Such observation highlighted that the culture medium and conditions represent the bottleneck for isolating novel desulfurizing microorganisms. The new developed primers constitute useful tool for the development of appropriate cultural-dependent procedures, including medium and culture conditions, to access novel desulfurizing microorganisms useful for the petroleum industry.
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Affiliation(s)
- Emmanuel Duval
- Université de Pau et des Pays de l'Adour, E2S UPPA, IPREM UMR, CNRS 5254, Bat. IBEAS, Pau, France; Segula Technologies, 71 rue Henri Gautier, 44550, Montoir de Bretagne, France.
| | - Cristiana Cravo-Laureau
- Université de Pau et des Pays de l'Adour, E2S UPPA, IPREM UMR, CNRS 5254, Bat. IBEAS, Pau, France.
| | - Line Poinel
- Segula Technologies, 71 rue Henri Gautier, 44550, Montoir de Bretagne, France.
| | - Robert Duran
- Université de Pau et des Pays de l'Adour, E2S UPPA, IPREM UMR, CNRS 5254, Bat. IBEAS, Pau, France.
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14
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Zheng T, Li W, Ma Y, Liu J. Time-based succession existed in rural sewer biofilms: Bacterial communities, sulfate-reducing bacteria and methanogenic archaea, and sulfide and methane generation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:144397. [PMID: 33385817 DOI: 10.1016/j.scitotenv.2020.144397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/29/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Rural sewers are applied widely to collect rural sewage and biofilm characteristics in rural sewers may be different with municipal sewers. The succession of bacteria communities, sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) need to be studied since rural sewers have a potential risk of sulfide and methane accumulation. In this study, lab-scale rural sewer facilities were established to analyze the characteristics of sewer biofilm and the generation of sulfide and methane. The results indicate that the variation tendency of biofilm thickness in rural sewers was different with municipal sewers. Time-based bacterial succession existed in rural sewer biofilms and the predominant genus was changed from Acinetobacter (approximately 19.10%) to Pseudomonas (approximately 12.61%). SRB (mean 1.49 × 106dsrA copies/cm2) were abundant than MA (mean 2.57 × 105mcrA copies/cm2) while MA were eliminated gradually in rural sewer biofilms. The tendency of sulfide and methane generation was similar with the number variation of SRB and MA, indicating sulfide accumulation might be more serious trouble than methane accumulation in a long-run rural sewer. Overall, this study deeply analyzed the succession of rural sewer biofilms and found that MA and methane were automatically inhibited in rural sewers.
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Affiliation(s)
- Tianlong Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, 19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China.
| | - Wenkai Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, 19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yingqun Ma
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China; Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Junxin Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, 19 (A) Yuquan Road, Shijingshan District, Beijing 100049, China
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15
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Liu J, He X, Xu Y, Zuo Z, Lei P, Zhang J, Yin Y, Wei Y. Fate of mercury and methylmercury in full-scale sludge anaerobic digestion combined with thermal hydrolysis. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124310. [PMID: 33525130 DOI: 10.1016/j.jhazmat.2020.124310] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 06/12/2023]
Abstract
Methylmercury (MeHg) is one of the highly toxic and bio-accumulated forms of mercury. Its presence in wastewater treatment processes has been evidenced in recent studies. Considering its enrichment in sewage sludge and the ecological risk associated with its land application, this study investigated the fate of mercury and MeHg in full-scale anaerobic digestion combined with Cambi thermal hydrolysis based on one-year sampling. Results showed that the advanced anaerobic digestion could increase the total mercury (THg) content from 4.35 ± 0.43 mg/kg in raw sludge to 6.37 ± 1.05 mg/kg in digested sludge, and the MeHg content decreased from 1.61 to 8.94 ng/g in raw sludge to 0.21-2.03 ng/g after anaerobic digestion. The demethylation of MeHg was dominant in both thermal hydrolysis and anaerobic digestion; it was mostly derived from the physico-chemical impacts such as chemical decomposition in thermal hydrolysis and precipitation in anaerobic digestion. Although the reported microbial methylators, such as Methanosarcina and Clostridia, were dominant in anaerobic digestion, the relative abundances of hgcA and merA were relatively low and did not correlate with the MeHg profiles. Thus, microbial methylation or demethylation seems negligible in terms of MeHg transformation.
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Affiliation(s)
- Jibao Liu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Xianglin He
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yufeng Xu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhuang Zuo
- Beijing Drainage Group CO., LTD, Beijing 100192, China
| | - Pei Lei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210046, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yongguang Yin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Zeng Z, Zheng P, Kang D, Li Y, Li W, Xu D, Chen W, Pan C. The removal of copper and zinc from swine wastewater by anaerobic biological-chemical process: Performance and mechanism. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123767. [PMID: 33113734 DOI: 10.1016/j.jhazmat.2020.123767] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Copper and zinc are often used as feed additives and frequently detected in swine wastewater. Anaerobic granular sludge (AnGS) plays an important role in high-rate anaerobic methanation biotechnologies which are widely applied to treat swine wastewater. The removal of Cu2+ and Zn2+ by AnGS was investigated in the batch and continuous systems. The results of batch experiments showed the adsorption by AnGS could be a significant method for Cu2+ and Zn2+ removal with efficiencies of 99 % and 49 % respectively. The sulfide precipitation mediated by AnGS could be another significant pathway for Zn2+ removal with efficiency of 18-27 % in Protein/M2+ experiments and 16-46 % in SO42-/M2+ experiments (M2+ represents the total concentration of Cu2+ and Zn2+). The results of continuous experiment showed, with SO42-/M2+ larger than 1.5, the influent Cu2+ and Zn2+ could be effectively removed in an anaerobic methanation bioreactor and its effluent Cu2+and Zn2+concentrations were below 1 mg/L and 2 mg/L separately. The main removal mechanism of Cu2+and Zn2+ in the anaerobic methanation system was that the biological production of sulfide from sulfate was followed by chemical precipitation and reduction. It is helpful for the removal of Cu2+ and Zn2+ with organic pollutants simultaneously to eliminate environmental risk of swine wastewater.
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Affiliation(s)
- Zhuo Zeng
- Department of Environmental Science & Engineering, Faculty of Geosciences & Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, Sichuan, People's Republic of China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, People's Republic of China.
| | - Da Kang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, People's Republic of China
| | - Yiyu Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, People's Republic of China
| | - Wenji Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, People's Republic of China
| | - Dongdong Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, People's Republic of China
| | - Wenda Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, People's Republic of China
| | - Chao Pan
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, People's Republic of China
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17
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Jin P, Ren B, Wang XC, Jin X, Shi X. Mechanism of microbial metabolic responses and ecological system conversion under different nitrogen conditions in sewers. WATER RESEARCH 2020; 186:116312. [PMID: 32846381 DOI: 10.1016/j.watres.2020.116312] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Nitrogen plays a central role in the sewer ecosystem, and the bioconversion of nitrogen can significantly affect bioreactions in sewers. However, the mechanisms underlying the involvement of nitrogen-associated pollutants in sewer ecosystems remain unknown. In this study, the effects of two typical nitrogen ratios (organic/inorganic nitrogen: 7/3 (Group A) and 3/7 (Group B)) on carbon, nitrogen, and sulfur bioconversions were investigated in a pilot sewer. The distribution of amino acids, such as proline, glycine and methionine, was significantly different between Groups A and B, and carbon-associated communities (based on 16S rRNA gene copies) were more prevalent in Group A, while sulfur and nitrogen-associated communities were more prevalent in Group B. To explore the effect of nitrogen on microbial response mechanisms, metagenomics-based methods were used to investigate the roles of amino acids involved in carbon, nitrogen, and sulfur bioconversion in sewers. Proline, glycine, and tyrosine in Group A promoted the expression of genes associated with cell membrane transport and increased the rate of protein synthesis, which stimulated the enrichment of carbon-associated communities. The transmembrane transport of higher concentrations of alanine and methionine in Group B was essential for cell metabolism and nutrient transport, thereby enriching nitrogen and sulfur-associated communities. In this investigation, insights into carbon, nitrogen and sulfur bioconversions in sewer ecosystems were revealed, significantly improving the understanding of the sewer ecosystem within a community context.
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Affiliation(s)
- Pengkang Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Bo Ren
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Xiaochang C Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Xin Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China; Northwest China Key Laboratory of Water Resources and Environment Ecology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Xuan Shi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China; Northwest China Key Laboratory of Water Resources and Environment Ecology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China.
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18
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Shi X, Gao G, Tian J, Wang XC, Jin X, Jin P. Symbiosis of sulfate-reducing bacteria and methanogenic archaea in sewer systems. ENVIRONMENT INTERNATIONAL 2020; 143:105923. [PMID: 32634668 DOI: 10.1016/j.envint.2020.105923] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/20/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
Sulfide and methane emissions always simultaneously exist in natural environment and constitute a major topic of societal concern. However, the metabolic environments between sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) exist a great difference, which seems to be opposite to the coexisting phenomenon. To explore this issue, the comprehensive biofilm structures, substrate consuming and metabolism pathways of SRB and MA were investigated in a case study of urban sewers. The results showed that, due to the stricter environmental requirements of MA than SRB, SRB became the preponderant microorganism which promoted the rapid generation of sulfide in the initial period of biofilm formation. According to a metagenomic analysis, the SRB appeared to be more preferential than MA in sewers, and the preponderant SRB could provide a key medium (Methyl-coenzyme M) for methane metabolism. Therefore, the diversity of MA gradually increased, and the symbiosis system formed preliminarily. In addition, via L-cysteine, methane metabolism also participated in sulfide consumption which was involved in cysteine and methionine metabolism. This phenomenon of sulfide consumption led to the forward reaction of sulfide metabolism, which could promote sulfide generation while stabilizing the pH value (H+ concentration) and S2- concentrations which should have inhibited SRB and MA production. Therefore, the heavily intertwined interactions between sulfide and methane metabolism provided environmental security for SRB and MA, and completely formed the symbiosis between SRB and MA. Based on these findings, an ecological model involving synergistic mechanism between sulfide and methane generation is proposed and this model can also improve understanding on the symbiosis of SRB and MA in the natural environment.
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Affiliation(s)
- Xuan Shi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Ge Gao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Jiameng Tian
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Xiaochang C Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China; Northwest China Key Laboratory of Water Resources and Environment Ecology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Xin Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China
| | - Pengkang Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China; Northwest China Key Laboratory of Water Resources and Environment Ecology, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province 710055, China.
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19
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Rettenmaier R, Lo YK, Schmidt L, Munk B, Lagkouvardos I, Neuhaus K, Schwarz W, Liebl W, Zverlov V. A Novel Primer Mixture for GH48 Genes: Quantification and Identification of Truly Cellulolytic Bacteria in Biogas Fermenters. Microorganisms 2020; 8:E1297. [PMID: 32854333 PMCID: PMC7565076 DOI: 10.3390/microorganisms8091297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 12/22/2022] Open
Abstract
Genomic studies revealed the glycoside hydrolases of family 48 (GH48) as a powerful marker for the identification of truly cellulolytic bacteria. Here we report an improved method for detecting cellulolytic bacteria in lab-scale biogas fermenters by using GH48 genes as a molecular marker in DNA and RNA samples. We developed a mixture of primers for the specific amplification of a GH48 gene region in a broad range of bacteria. Additionally, we built a manually curated reference database containing GH48 gene sequences directly linked to the corresponding taxonomic information. Phylogenetic correlation analysis of GH48 to 16S rRNA gene sequences revealed that GH48 gene sequences with 94% identity belong with high confidence to the same genus. Applying this analysis, GH48 amplicon reads revealed that at mesophilic fermenter conditions, 50-99% of the OTUs appear to belong to novel taxa. In contrast, at thermophilic conditions, GH48 gene sequences from the genus Hungateiclostridium dominated with 60-91% relative abundance. The novel primer combinations enabled detection and relative quantification of a wide spectrum of GH48 genes in cellulolytic microbial communities. Deep phylogenetic correlation analysis and a simplified taxonomic identification with the novel database facilitate identification of cellulolytic organisms, including the detection of novel taxa in biogas fermenters.
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Affiliation(s)
- Regina Rettenmaier
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Yat Kei Lo
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Larissa Schmidt
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Bernhard Munk
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Lange Point 6, 85354 Freising, Germany;
| | - Ilias Lagkouvardos
- ZIEL—Core Facility Microbiome, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (I.L.); (K.N.)
| | - Klaus Neuhaus
- ZIEL—Core Facility Microbiome, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (I.L.); (K.N.)
| | - Wolfgang Schwarz
- Aspratis GmbH. Munich, Germany, Hübnerstr. 11, 80637 Munich, Germany;
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
- Institute of Molecular Genetics of National Research Centre (Kurchatov Institute), Kurchatov Sq. 2, 123182 Moscow, Russia
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20
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Lin Y, Newcombe CE, Brennan RA. Crab shell amendments enhance the abundance and diversity of key microbial groups in sulfate-reducing columns treating acid mine drainage. Appl Microbiol Biotechnol 2020; 104:8505-8516. [PMID: 32820375 DOI: 10.1007/s00253-020-10833-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/31/2020] [Accepted: 08/11/2020] [Indexed: 10/23/2022]
Abstract
Substrate amendments composed of crab shell (CS) waste materials have been shown to significantly improve the longevity and performance of acid mine drainage (AMD) treatment systems containing spent mushroom compost (SMC), yet the development of key microbial populations within these systems has not been investigated. To better understand the effects of CS on microbial dynamics in these systems, clone libraries and real-time quantitative PCR (qPCR) were performed on materials from a laboratory-scale AMD treatment system containing SMC and 0 to 100% CS substrate after receiving a continuous flow of AMD for 148 days (428 pore volumes). The proportion of CS in the substrate positively correlated with the diversity of sulfate-reducing bacteria (SRB) and archaeal clones, but negatively correlated with fungal diversity. CS also impacted microbial community structure, as revealed in Unifrac significance and principal coordinate analysis tests. The column containing 100% CS substrate supported 7 different genera of SRB-the most ever observed in an AMD treatment system. Moreover, the copy numbers of functional genes representing fermenters, sulfate reducers, and chitin degraders increased with increasing proportions of CS. These observations agree well with the chemical performance data, further validating that by supporting more abundant key microbial groups, chitinous substrates may provide benefits for improving both the longevity and performance of AMD treatment systems, and may provide similar benefits for the treatment of other environmental contaminants that are amenable to anaerobic bioremediation.Key points• Crab shell improves the longevity and performance of acid mine drainage treatment.• The diversity of sulfate-reducing bacteria is enhanced with crab shell amendments.• Crab shell supports more abundant key microbial groups than spent mushroom compost.
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Affiliation(s)
- Yishan Lin
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.,State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
| | - Caroline E Newcombe
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.,Hewlett Packard Enterprises, Minneapolis, MN, USA
| | - Rachel A Brennan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.
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21
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Zheng T, Li W, Ma Y, Liu J. Sewers induce changes in the chemical characteristics, bacterial communities, and pathogen distribution of sewage and greywater. ENVIRONMENTAL RESEARCH 2020; 187:109628. [PMID: 32438098 DOI: 10.1016/j.envres.2020.109628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/27/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
Sewers may affect the characteristics and bacterial communities of wastewater, and need be studied as they may impact treatment facilities and recycling operations. In this study, the wastewater characteristics and bacterial communities from the inflow and outflow of two sewers (sewage and greywater) were analyzed. The chemical oxygen demand was significantly reduced in the sewage and greywater sewer and the greywater sewer generated less sulfide and methane. Proteobacteria, Bacteroidetes, and Firmicutes as the major phyla in sewage and greywater and sewer biofilms. Sewer conveyance caused changes in the distribution and community interaction of suspended bacteria. Greywater contained abundant water-related pathogenic bacteria (WPB) and some WPB (e.g. Aeromonas, Klebsiella and Shigella) number in greywater were not lower than sewage. Sewers could increase the number of Shigella in sewage and decrease the number of Acinetobacter in greywater. Further treatment or disinfection of greywater collected by sewers was necessary and directly reuse of greywater without treatment should be avoided.
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Affiliation(s)
- Tianlong Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; University of Chinese Academy of Sciences, 19 (A) Yuquan Road, Shijingshan District, Beijing, 100049, China.
| | - Wenkai Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; University of Chinese Academy of Sciences, 19 (A) Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yingqun Ma
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore, 637141, Singapore
| | - Junxin Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; University of Chinese Academy of Sciences, 19 (A) Yuquan Road, Shijingshan District, Beijing, 100049, China.
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22
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Liu Y, Luo M, Ye R, Huang J, Xiao L, Hu Q, Zhu A, Tong C. Impacts of the rhizosphere effect and plant species on organic carbon mineralization rates and pathways, and bacterial community composition in a tidal marsh. FEMS Microbiol Ecol 2020; 95:5538758. [PMID: 31344237 DOI: 10.1093/femsec/fiz120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/18/2019] [Indexed: 11/13/2022] Open
Abstract
Despite the growing recognition regarding the carbon cycle in the rhizosphere of upland ecosystems, little is known regarding the rhizosphere effect on soil organic carbon (SOC) mineralization in tidal marsh soils. In the current study, in situ rhizobox experiments (including rhizosphere and inner and outer bulk soil) were conducted in an estuarine tidal marsh. Our results showed that a higher abundance of total bacteria, Geobacter, dsrA and mcrA and lower α-diversity were observed in the rhizosphere relative to the bulk soil. Rhizosphere effects shifted the partition of terminal metabolic pathways from sulfate reduction in the bulk soil to the co-dominance of microbial Fe(III) and sulfate reduction in the rhizosphere. Although the rhizosphere effect promoted the rates of three terminal metabolic pathways, it showed greater preference towards microbial Fe(III) reduction in the tidal marsh soils. Plant species had little impact on the partitioning of terminal metabolic pathways, but did affect the potential of total SOC mineralization together with the abundance and diversity of total bacteria. Both the rhizosphere effect and plant species influenced the bacterial community composition in the tidal marsh soils; however, plant species had a less pronounced impact on the bacterial community compared with that of the rhizosphere effect.
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Affiliation(s)
- Yuxiu Liu
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Min Luo
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China.,School of Environment and Resource, Fuzhou University, Fuzhou 350116, China
| | - Rongzhong Ye
- Pee Dee Research & Education Centers, Clemson University, Florence, SC 29506, USA
| | - Jiafang Huang
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Leilei Xiao
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Qikai Hu
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China.,School of Environment and Resource, Fuzhou University, Fuzhou 350116, China
| | - Aijv Zhu
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Chuan Tong
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
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23
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Lackner N, Wagner AO, Illmer P. Effect of sulfate addition on carbon flow and microbial community composition during thermophilic digestion of cellulose. Appl Microbiol Biotechnol 2020; 104:4605-4615. [PMID: 32219464 PMCID: PMC7190589 DOI: 10.1007/s00253-020-10546-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 01/20/2020] [Accepted: 03/15/2020] [Indexed: 01/04/2023]
Abstract
Substrates with high sulfate levels pose problems for biogas production as they allow sulfate reducing bacteria to compete with syntrophic and methanogenic members of the community. In addition, the end product of sulfate reduction, hydrogen sulfide, is toxic and corrosive. Here we show how sulfate addition affects physiological processes in a thermophilic methanogenic system by analyzing the carbon flow and the microbial community with quantitative PCR and amplicon sequencing of the 16s rRNA gene. A sulfate addition of 0.5 to 3 g/L caused a decline in methane production by 73-92%, while higher sulfate concentrations had no additional inhibitory effect. Generally, sulfate addition induced a shift in the composition of the microbial community towards a higher dominance of Firmicutes and decreasing abundances of Bacteroidetes and Euryarchaeota. The abundance of methanogens (e.g., Methanoculleus and Methanosarcina) was reduced, while sulfate reducing bacteria (especially Candidatus Desulforudis and Desulfotomaculum) increased significantly in presence of sulfate. The sulfate addition had a significant impact on the carbon flow within the system, shifting the end product from methane and carbon dioxide to acetate and carbon dioxide. Interestingly, methane production quickly resumed, when sulfate was no longer present in the system. Despite the strong impact of sulfate addition on the carbon flow and the microbial community structure during thermophilic biogas production, short-term process disturbances caused by unexpected introduction of sulfate may be overcome due to the high resilience of the engaged microorganisms.
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Affiliation(s)
- Nina Lackner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria.
| | - Andreas O Wagner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
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24
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Gupta A, Sar P. Characterization and application of an anaerobic, iron and sulfate reducing bacterial culture in enhanced bioremediation of acid mine drainage impacted soil. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 55:464-482. [PMID: 31971065 DOI: 10.1080/10934529.2019.1709362] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Development of an appropriate bioremediation strategy for acid mine drainage (AMD) impacted environment is imperative for sustainable mining but remained critically challenged due to the paucity of knowledge on desired microbiological factors and their nutrient requirements. The present study was conducted to utilize the potential of an anaerobic, acid-tolerant, Fe3+ and SO42- reducing microbial consortium for in situ remediation of highly acidic (pH 3.21), SO42- rich (6285 mg/L) mine drainage impacted soil (AIS). A microbial consortium enriched from AMD system and composed of Clostridiales and Bacillales members was characterized and tested for in situ application through microcosms. A combination of bioaugmentation (enriched consortium) and biostimulation (cellulose) allowed 97% reduction in dissolved sulfate and rise in pH up to 7.5. 16S rRNA gene-based amplicon sequencing confirmed that although the bioaugmented community could survive in AIS, availability of carbon source was necessary for superior iron- and sulfate- reduction. Quantitative PCR of dsrB gene confirmed the role of carbon source in boosting the SO42- reduction activities of sulfate reducers. This study demonstrated that native AIS harbored limited catabolic activities required for the remediation but addition of catabolically active microbial populations along with necessary carbon and energy source facilitate the bioremediation of AIS.
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Affiliation(s)
- Abhishek Gupta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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25
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Zeng Z, Zhang M, Kang D, Li Y, Yu T, Li W, Xu D, Zhang W, Shan S, Zheng P. Enhanced anaerobic treatment of swine wastewater with exogenous granular sludge: Performance and mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134180. [PMID: 32380626 DOI: 10.1016/j.scitotenv.2019.134180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 06/11/2023]
Abstract
Anaerobic biotechnology has been widely used to the treatment of swine wastewater, but its organic loading rate is far lower than the expected. In this study, the fatigue effect was observed for indigenous anaerobic sludge (IAS) of anaerobic digestion system treating swine wastewater. On the contrary, the enhancement effect was demonstrated for exogenous granular sludge (EGS) originated from the internal circulation reactor treating pulping wastewater. The results showed the anaerobic digestion of swine wastewater with acclimatized EGS was much better than with IAS, 10th-day COD removal efficiency of 85% and 37% respectively. The better performance of acclimatized EGS was attributed to the more efficient degradation of volatile fatty acids (VFAs) as well as a stronger tolerance to the ammonia inhibition of swine wastewater. Revealed by molecular techniques, the acclimatized EGS contained more abundant syntrophic bacteria and methanogens than IAS. These functional microbes colonized in the acclimatized EGS could overcome the fatigue effect of IAS which contained a similar microbial community to pig gastrointestinal tract microbes. This study provides a feasible and promising way to enhance the efficiency of anaerobic digestion of swine wastewater.
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Affiliation(s)
- Zhuo Zeng
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Meng Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China; Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Da Kang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Yiyu Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Tao Yu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Wenji Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Dongdong Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Wudi Zhang
- School of Energy & Environmental Science, Yunnan Normal University, Kunming 650500, Yunnan, PR China
| | - Shengdao Shan
- School of Environmental and Natural Resources, Zhejiang University of Science & Technology, 318 Liuhe Rd, Hangzhou 310023, Zhejiang, PR China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, PR China.
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26
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Khan I, Huang G, Li XA, Liao W, Leong WK, Xia W, Bian X, Wu J, Hsiao WW. Mushroom polysaccharides and jiaogulan saponins exert cancer preventive effects by shaping the gut microbiota and microenvironment in Apc mice. Pharmacol Res 2019; 148:104448. [DOI: 10.1016/j.phrs.2019.104448] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/19/2019] [Accepted: 09/05/2019] [Indexed: 02/08/2023]
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27
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Gutleben J, Koehorst JJ, McPherson K, Pomponi S, Wijffels RH, Smidt H, Sipkema D. Diversity of tryptophan halogenases in sponges of the genus Aplysina. FEMS Microbiol Ecol 2019; 95:fiz108. [PMID: 31276591 PMCID: PMC6644159 DOI: 10.1093/femsec/fiz108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/04/2019] [Indexed: 12/21/2022] Open
Abstract
Marine sponges are a prolific source of novel enzymes with promising biotechnological potential. Especially halogenases, which are key enzymes in the biosynthesis of brominated and chlorinated secondary metabolites, possess interesting properties towards the production of pharmaceuticals that are often halogenated. In this study we used a polymerase chain reaction (PCR)-based screening to simultaneously examine and compare the richness and diversity of putative tryptophan halogenase protein sequences and bacterial community structures of six Aplysina species from the Mediterranean and Caribbean seas. At the phylum level, bacterial community composition was similar amongst all investigated species and predominated by Actinobacteria, Chloroflexi, Cyanobacteria, Gemmatimonadetes, and Proteobacteria. We detected four phylogenetically diverse clades of putative tryptophan halogenase protein sequences, which were only distantly related to previously reported halogenases. The Mediterranean species Aplysina aerophoba harbored unique halogenase sequences, of which the most predominant was related to a sponge-associated Psychrobacter-derived sequence. In contrast, the Caribbean species shared numerous novel halogenase sequence variants and exhibited a highly similar bacterial community composition at the operational taxonomic unit (OTU) level. Correlations of relative abundances of halogenases with those of bacterial taxa suggest that prominent sponge symbiotic bacteria, including Chloroflexi and Actinobacteria, are putative producers of the detected enzymes and may thus contribute to the chemical defense of their host.
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Affiliation(s)
- Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Kyle McPherson
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Shirley Pomponi
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
- Florida Atlantic University – Harbor Branch, 5600 U.S. 1, Fort Pierce, FL 34946, the United States
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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28
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Yarwood SA. The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review. FEMS Microbiol Ecol 2019; 94:5087730. [PMID: 30169564 DOI: 10.1093/femsec/fiy175] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 08/29/2018] [Indexed: 02/06/2023] Open
Abstract
New soil organic matter (SOM) models highlight the role of microorganisms in plant litter decomposition and storage of microbial-derived carbon (C) molecules. Wetlands store more C per unit area than any other ecosystem, but SOM storage mechanisms such as aggregation and metal complexes are mostly untested in wetlands. This review discusses what is currently known about the role of microorganisms in SOM formation and C sequestrations, as well as, measures of microbial communities as they relate to wetland C cycling. Studies within the last decade have yielded new insights about microbial communities. For example, microbial communities appear to be adapted to short-term fluctuations in saturation and redox and researchers have observed synergistic pairings that in some cases run counter to thermodynamic theory. Significant knowledge gaps yet to be filled include: (i) What controls microbial access to and decomposition of plant litter and SOM? (ii) How does microbial community structure shape C fate, across different wetland types? (iii) What types of plant and microbial molecules contribute to SOM accumulation? Studies examining the active microbial community directly or that utilize multi-pronged approaches are shedding new light on microbial functional potential, however, and promise to improve wetland C models in the near future.
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Affiliation(s)
- Stephanie A Yarwood
- Environmental Science and Technology Department, University of Maryland, 1204 HJ Patterson Hall, College Park, MD 20742, USA
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29
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Jin P, Gu Y, Shi X, Yang W. Non-negligible greenhouse gases from urban sewer system. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:100. [PMID: 31057666 PMCID: PMC6486696 DOI: 10.1186/s13068-019-1441-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The urban sewer system is an important component of urban water infrastructure for sewage collection and transportation, and in-sewer transportation of sewage can cause multitudinous contaminant degradations which lead to formation of gaseous products. Although the greenhouse gases of methane and carbon dioxide have been confirmed to consist in the gaseous products, the mechanisms of greenhouse gas generation were unclear and the significances of greenhouse gases emission from sewers were generally underestimated. RESULTS In this study, 3 years of monitoring was conducted to evaluate the greenhouse gases emission in 37-km-long urban sewer systems covering 13 km2. The results showed that the emission of carbon dioxide and methane was extensively existing in sewers, and especially, exhibited a characteristic of regional difference. In order to reveal the formation mechanism of carbon dioxide and methane in sewers, the metagenomic approach was utilized to analyze the annotated pathways and homologous bio-enzymes, and it indicated that fourteen pivotal annotated pathways were involved in the carbon dioxide and methane generation. According to the metagenomics and 3-year monitoring results, the total amounts of carbon dioxide and methane emission in sewers were calculated by the transformation venation of contaminants (such as methyl alcohol, methylamine and acetic acid along branch sewer, sub-main sewer and main sewer, respectively). The calculation results showed that the total greenhouse gas emissions in sewer were calculated to be 199 t/day in Xi'an, and if scaling up as population proportion, the greenhouse gas emission from sewer systems in China could be 30,685 t/day. Comparing with the greenhouse gas emissions from different metropolises (New York City, London and Tokyo) and industries (dairy farms, automobile production and steel enterprises), the amount of greenhouse gases produced by the urban sewer system is much higher. CONCLUSIONS This study revealed the transformation pathways of contaminants which promoted the generation of greenhouse gases in sewers. Based on this analysis, the greenhouse gas emissions along sewer systems were calculated. The results indicate that the greenhouse gas emission from sewer systems is non-negligible, and should be attracted sufficient attention.
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Affiliation(s)
- Pengkang Jin
- School of Environmental and Municipal Engineering, Xi’an University of Architecture and Technology, Xi’an, 710055 Shaanxi China
| | - Yonggang Gu
- School of Environmental and Municipal Engineering, Xi’an University of Architecture and Technology, Xi’an, 710055 Shaanxi China
| | - Xuan Shi
- School of Environmental and Municipal Engineering, Xi’an University of Architecture and Technology, Xi’an, 710055 Shaanxi China
| | - Wenna Yang
- School of Environmental and Municipal Engineering, Xi’an University of Architecture and Technology, Xi’an, 710055 Shaanxi China
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30
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Rossmassler K, Snow CD, Taggart D, Brown C, De Long SK. Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium. Appl Microbiol Biotechnol 2019; 103:4177-4192. [PMID: 30968165 DOI: 10.1007/s00253-019-09762-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/07/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
Abstract
Quantifying functional biomarker genes and their transcripts provides critical lines of evidence for contaminant biodegradation; however, accurate quantification depends on qPCR primers that contain no, or minimal, mismatches with the target gene. Developing accurate assays has been particularly challenging for genes encoding fumarate-adding enzymes (FAE) due to the high level of genetic diversity in this gene family. In this study, metagenomics applied to a field-derived, o-xylene-degrading methanogenic consortium revealed genes encoding FAE that would not be accurately quantifiable by any previously available PCR assays. Sequencing indicated that a gene similar to the napthylmethylsuccinate synthase gene (nmsA) was most abundant, although benzylsuccinate synthase genes (bssA) also were present along with genes encoding alkylsuccinate synthase (assA). Upregulation of the nmsA-like gene was observed during o-xylene degradation. Protein homology modeling indicated that mutations in the active site, relative to a BssA that acts on toluene, increase binding site volume and accessibility, potentially to accommodate the relatively larger o-xylene. The new nmsA-like gene was also detected at substantial concentrations at field sites with a history of xylene contamination.
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Affiliation(s)
- Karen Rossmassler
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA.,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher D Snow
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | | | - Casey Brown
- Microbial Insights, Inc., Knoxville, TN, USA
| | - Susan K De Long
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA.
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31
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Lefevre E, Redfern L, Cooper EM, Stapleton HM, Gunsch CK. Acetate promotes microbial reductive debromination of tetrabromobisphenol A during the startup phase of anaerobic wastewater sludge bioreactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:959-968. [PMID: 30625682 PMCID: PMC6481660 DOI: 10.1016/j.scitotenv.2018.11.403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 05/15/2023]
Abstract
The detection of increasing concentrations of tetrabromobisphenol A (TBBPA) in wastewater treatment plants is raising concerns as TBBPA has been identified as a potentially toxic flame retardant. The objectives of this study were to evaluate the effect of acetate biostimulation on TBBPA microbial reductive debromination, and the response of anaerobic sludge associated microbial communities repeatedly exposed to TBBPA. Results indicate that the bulk of the microbial community did not experience significant shifts as a result of TBBPA exposure, and that only a small fraction of the community responded to the presence of TBBPA. Taxa most likely responsible for TBBPA transformation affiliated to Clostridiales and the wastewater sludge group Blvii28. The biostimulating effect of acetate was only observed during reactor startup, when acetogenesis was likely not yet occurring. However, when acetate likely started to be microbially generated in the reactor, acetate addition resulted in a slight but significant inhibiting effect on TBBPA transformation. A significant increase of hydrogenotrophic methanogens in the TBBPA-spiked reactor overtime implies that TBBPA degraders were not in direct competition with methanogens for H2. These results strongly suggest that TBBPA degrading taxa might have been primarily using acetate as an electron donor for the reductive debromination of TBBPA.
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Affiliation(s)
- Emilie Lefevre
- Department of Civil and Environmental Engineering, Duke University, Hudson Hall, Durham, NC 27708, USA
| | - Lauren Redfern
- Department of Civil and Environmental Engineering, Duke University, Hudson Hall, Durham, NC 27708, USA
| | - Ellen M Cooper
- Nicholas School of the Environment, Duke University, 9 Circuit Drive, Durham, NC 27710, USA
| | - Heather M Stapleton
- Nicholas School of the Environment, Duke University, 9 Circuit Drive, Durham, NC 27710, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, Hudson Hall, Durham, NC 27708, USA.
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Beaton D, Pelletier P, Goulet RR. Microbial Degradation of Cellulosic Material and Gas Generation: Implications for the Management of Low- and Intermediate-Level Radioactive Waste. Front Microbiol 2019; 10:204. [PMID: 30814985 PMCID: PMC6381020 DOI: 10.3389/fmicb.2019.00204] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Deep geologic repositories (DGR) in Canada are designed to contain and isolate low- and intermediate-level radioactive waste. Microbial degradation of the waste potentially produces methane, carbon dioxide and hydrogen gas. The generation of these gases increase rock cavity pressure and limit water ingress which delays the mobility of water soluble radionuclides. The objective of this study was to measure gas pressure and composition over 7 years in experiments containing cellulosic material with various starting conditions relevant to a DGR and to identify micro-organisms generating gas. For this purpose, we conducted experiments in glass bottles containing (1) wet cellulosic material, (2) wet cellulosic material with compost Maker, and (3) wet cellulosic material with compost Accelerator. Results demonstrated that compost accelerated the pressure build-up in the containers and that methane gas was produced in one experiment with compost and one experiment without compost because the pH remained neutral for the duration of the 464 days experiment. Methane was not formed in the other experiment because the pH became acidic. Once the pressure became similar in all containers after 464 days, we then monitored gas pressure and composition in glass bottle containing wet cellulosic material in (1) acidic conditions, (2) neutral conditions, and (3) with an enzyme that accelerated degradation of cellulose over 1965 days. In these experiments, acetogenic bacteria degraded cellulose and produced acetic acid, which acidity suppressed methane production. Microbial community analyses suggested a diverse community of archaea, bacteria and fungi actively degrading cellulose. DNA analyses also confirmed the presence of methanogens and acetogens in our experiments. This study suggests that methane gas will be generated in DGRs if pH remains neutral. However, our results showed that microbial degradation of cellulose not only generated gas, but also generated acidity. This finding is important as acids can limit bentonite swelling and potentially degrade cement and rock barriers, thus this requires consideration in the safety case as appropriate.
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Affiliation(s)
- Danielle Beaton
- Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, Canada
- Orillia Soldiers’ Memorial Hospital, Ottawa, ON, Canada
| | | | - Richard R. Goulet
- Orillia Soldiers’ Memorial Hospital, Ottawa, ON, Canada
- Canadian Nuclear Safety Commission, Ottawa, ON, Canada
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Yazdani R, Shim K, Chen Z, Cheung C, Summers MD, Williams DW, Seiser R, De Long SK. Ambient-temperature co-digestion of low-solids municipal and industrial waste mixtures: Insights from molecular analyses. JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (1995) 2018; 68:1148-1158. [PMID: 29781775 DOI: 10.1080/10962247.2018.1479667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/14/2018] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
The performance of ambient temperature anaerobic co-digestion was investigated for mixtures of six substrates: canned tomato and salsa waste, portable toilet waste, septic tank waste, winery waste, beer and cider waste, and fats, oils, and grease (FOG). Laboratory semi-continuous reactor studies and molecular biological analyses revealed that beer/winery, and tomato/FOG/winery/beer mixtures resulted in the best performance in terms of biogas production (515 and 371 mL CH4/g VS, respectively) and methanogenic populations. A portable toilet/septage mixture resulted in the overall poorest performance and inhibition of microbial activity was evident. Average methane content was ~70% for all mixtures tested. The findings of this study reveal that healthy methanogen populations were present, further supporting the feasibility of biogas production via the novel feedstock mixtures in ambient temperature lagoons. Implications: Disposal of septic tank waste and other high chemical oxygen demand (COD) 10 industrial food processing waste at a small wastewater treatment plant is uncommon, because it can upset the treatment process and requires additional power for treatment. Ambient-temperature covered lagoon digesters can be an alternative low-cost technology for co-digestion of these recalcitrant waste streams while generating bioenergy. The results of this study demonstrated that there is potential for implementation of unheated covered lagoon digester systems 15 for conversion of liquid wastes for production of renewable biomethane while eliminating the need to treat these wastes at a wastewater treatment plant.
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Affiliation(s)
- Ramin Yazdani
- a Air Quality Research Center , University of California , Davis , CA
- b Yolo County Division of Integrated Waste Management , Woodland , CA
| | - Kyuhwan Shim
- b Yolo County Division of Integrated Waste Management , Woodland , CA
| | - Zhi Chen
- c E. & J. Gallo Winery , Modesto , CA
| | | | | | | | - Reinhard Seiser
- g Department of Mechanical and Aerospace Engineering , University of California at San Diego , La Jolla , CA
| | - Susan K De Long
- h Department of Civil and Environmental Engineering , Colorado State University , Fort Collins , CO
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Genetic diversity detection and gene discovery of novel glycoside hydrolase family 48 from soil environmental genomic DNA. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1327-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Jin P, Shi X, Sun G, Yang L, Cai Y, Wang XC. Co-Variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1270-1279. [PMID: 29300470 DOI: 10.1021/acs.est.7b05121] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Distribution characteristics and biodiversity of microbial communities were studied in a 1200 m pilot sewer system. Results showed that the dominant microorganisms, fermentation bacteria (FB), hydrogen-producing acetogen (HPA), sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) changed significantly along the sewer systems, from start to the end. The distribution of the functional microorganisms could induce substrate transformation and lead to the accumulation of micromolecular organics (i.e., acetic acid, propionic acid and amino acid). However, substrate transformation induced by these microbes was affected by environmental factors such as oxidation-reduction potential, pH and dissolved oxygen. Changes in environmental conditions along the sewer resulted in the variation of dominant bioreactions. FB were enriched at the beginning of the sewer, while SRB and MA were found toward the end. Furthermore, based on Spearman rank correlation analysis of microbial communities, environmental factors and substrates, covariation between microbial community distribution and organics metabolization along the sewer was identified. This study could provide a theoretical foundation for understanding wastewater quality variation during transportation from sewers to treatment plants, therefore, promoting optimization of design and operation of wastewater treatment.
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Affiliation(s)
- Pengkang Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology , Xi'an, Shaanxi Province 710055, China
| | - Xuan Shi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology , Xi'an, Shaanxi Province 710055, China
| | - Guangxi Sun
- Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences , Beijing, 100190, China
| | - Lei Yang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology , Xi'an, Shaanxi Province 710055, China
| | - Yixiao Cai
- NUS Environmental Research Institute, National University of Singapore , 1 Create Way, Singapore 138602, Singapore
| | - Xiaochang C Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology , Xi'an, Shaanxi Province 710055, China
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Reyes-Alvarado LC, Camarillo-Gamboa Á, Rustrian E, Rene ER, Esposito G, Lens PNL, Houbron E. Lignocellulosic biowastes as carrier material and slow release electron donor for sulphidogenesis of wastewater in an inverse fluidized bed bioreactor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:5115-5128. [PMID: 28702909 DOI: 10.1007/s11356-017-9334-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
Industrial wastewaters containing high concentrations of sulphate, such as those generated by mining, metallurgical and mineral processing industries, require electron donor for biological sulfidogenesis. In this study, five types of lignocellulosic biowastes were characterized as potential low-cost slow release electron donors for application in a continuously operated sulphidogenic inverse fluidized bed bioreactor (IFBB). Among them, natural scourer and cork were selected due to their high composition of volatile solids (VS), viz. 89.1 and 96.3%, respectively. Experiments were performed in batch (47 days) and in an IFBB (49 days) using synthetic sulphate-rich wastewater. In batch, the scourer gave higher sulphate reduction rates (67.7 mg SO42- L-1 day-1) in comparison to cork (12.1 mg SO42- L-1 day-1), achieving >82% sulphate reduction efficiencies. In the IFBB packed with the natural scourer, the average sulphate reduction efficiency was 24 (±17)%, while the volumetric sulphate reduction rate was 167 (±117) mg SO42- L-1 day-1. The long incubation time in the batch experiments (47 days) allowed higher sulphate reduction efficiencies in comparison to the short hydraulic retention time (24 h) in the IFBB. This suggests the hydrolysis-fermentation was the rate-limiting step and the electron donor supply (through hydrolysis of the lignocellulosic biowaste) was limiting the sulphate reduction. Lignocellulose as carrier material and slow release electron donor for sulphidogenesis.
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Affiliation(s)
- Luis C Reyes-Alvarado
- UNESCO-IHE Institute for Water Education, P.O. Box 3015, 2601 DA, Delft, The Netherlands.
| | | | - Elena Rustrian
- Facultad de Ciencias Químicas, Universidad Veracruzana, 94340, Orizaba, VER, Mexico
| | - Eldon R Rene
- UNESCO-IHE Institute for Water Education, P.O. Box 3015, 2601 DA, Delft, The Netherlands
| | - Giovanni Esposito
- Department of Mechanics, Structures and Environmental Engineering, University of Cassino, via Di Biasio 43, 03043, Cassino, FR, Italy
| | - Piet N L Lens
- UNESCO-IHE Institute for Water Education, P.O. Box 3015, 2601 DA, Delft, The Netherlands
| | - Eric Houbron
- Facultad de Ciencias Químicas, Universidad Veracruzana, 94340, Orizaba, VER, Mexico
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Vasquez Y, Escobar MC, Saenz JS, Quiceno-Vallejo MF, Neculita CM, Arbeli Z, Roldan F. Effect of hydraulic retention time on microbial community in biochemical passive reactors during treatment of acid mine drainage. BIORESOURCE TECHNOLOGY 2018; 247:624-632. [PMID: 28988048 DOI: 10.1016/j.biortech.2017.09.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
The effect of hydraulic retention time (HRT) on the microbial community during acid mine drainage (AMD) treatment was investigated. Physicochemical and molecular (illumina and qPCR) analyses were performed on reactive mixtures collected from seven bioreactors in three-operation period (8, 17 and 36weeks). Long HRT (4day) favored the relative abundance of SRB, causing the increase of residual sulfides and short HRT (1day) affected the anaerobic conditions of the bioreactors and favored the presence the acidophilic chemolithotrophic microorganisms. Besides qPCR indicated that genes related to cellulose degradation were present in low copy numbers and were affected by the HRT. Finally, environmental factors (pH, organic source, metal sulfides, and sulfate concentrations) had significant impact on relative abundance of the phylogenetic lineages, rather than the types of lineages present in the reactive mixture. The findings of this study indicate that HRT affects the stability of passive bioreactors and their microbial communities.
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Affiliation(s)
- Yaneth Vasquez
- Departamento de Ciencias Naturales, Facultad de Ingeniería y Ciencias Básicas, Universidad Central, Calle 21 No. 4-40, Bogota, Colombia; Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia.
| | - Maria C Escobar
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia
| | - Johan S Saenz
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia
| | - Maria F Quiceno-Vallejo
- Departamento de Ciencias Naturales, Facultad de Ingeniería y Ciencias Básicas, Universidad Central, Calle 21 No. 4-40, Bogota, Colombia
| | - Carmen M Neculita
- Canada Research Chair in Treatment of Contaminated Mine Water, Research Institute on Mines and Environment (RIME), University of Quebec in Abitibi-Temiscamingue (UQAT), 445 Boulevard de l'Universite, Rouyn-Noranda, QC J9X 5E4, Canada
| | - Ziv Arbeli
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia
| | - Fabio Roldan
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia
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Chen L, Brar MS, Leung FCC, Hsiao WLW. Triterpenoid herbal saponins enhance beneficial bacteria, decrease sulfate-reducing bacteria, modulate inflammatory intestinal microenvironment and exert cancer preventive effects in ApcMin/+ mice. Oncotarget 2017; 7:31226-42. [PMID: 27121311 PMCID: PMC5058752 DOI: 10.18632/oncotarget.8886] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/02/2016] [Indexed: 12/26/2022] Open
Abstract
Saponins derived from medicinal plants have raised considerable interest for their preventive roles in various diseases. Here, we investigated the impacts of triterpenoid saponins isolated from Gynostemma pentaphyllum (GpS) on gut microbiome, mucosal environment, and the preventive effect on tumor growth. Six-week old ApcMin/+ mice and their wild-type littermates were fed either with vehicle or GpS daily for the duration of 8 weeks. The fecal microbiome was analyzed by enterobacterial repetitive intergenic consensus (ERIC)-PCR and 16S rRNA gene pyrosequencing. Study showed that GpS treatment significantly reduced the number of intestinal polyps in a preventive mode. More importantly, GpS feeding strikingly reduced the sulfate-reducing bacteria lineage, which are known to produce hydrogen sulfide and contribute to damage the intestinal epithelium or even promote cancer progression. Meanwhile, GpS also boosted the beneficial microbes. In the gut barrier of the ApcMin/+ mice, GpS treatment increased Paneth and goblet cells, up-regulated E-cadherin and down-regulated N-cadherin. In addition, GpS decreased the pro-oncogenic β-catenin, p-Src and the p-STAT3. Furthermore, GpS might also improve the inflamed gut epithelium of the ApcMin/+ mice by upregulating the anti-inflammatory cytokine IL-4, while downregulating pro-inflammatory cytokines TNF-α, IL-1β and IL-18. Intriguingly, GpS markedly stimulated M2 and suppressed M1 macrophage markers, indicating that GpS altered mucosal cytokine profile in favor of the M1 to M2 macrophages switching, facilitating intestinal tissue repair. In conclusion, GpS might reverse the host's inflammatory phenotype by increasing beneficial bacteria, decreasing sulfate-reducing bacteria, and alleviating intestinal inflammatory gut environment, which might contribute to its cancer preventive effects.
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Affiliation(s)
- Lei Chen
- Center for Cancer & Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Manreetpal S Brar
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Frederick C C Leung
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - W L Wendy Hsiao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China
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Liu T, Sun L, Müller B, Schnürer A. Importance of inoculum source and initial community structure for biogas production from agricultural substrates. BIORESOURCE TECHNOLOGY 2017; 245:768-777. [PMID: 28926908 DOI: 10.1016/j.biortech.2017.08.213] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
This study evaluated the importance of inoculum source for start-up and operation of biogas processes. Three different inocula with different community structure were used to initiate six laboratory continuous stirred tank reactor (CSTR) processes operated with a grass manure mixture as substrate. The processes were evaluated by chemical and microbiological analysis, by targeting the overall bacterial community and potential cellulose-degrading bacteria. As expected, the results showed a large difference in community structure in the inocula and in process performance during the first hydraulic retention time (HRT). However, the performance and overall microbial community structure became similar in the reactors over time. An inoculum from a high-ammonia process, characterized by low diversity and low degradation efficiency, took the longest time to reach stability and final methane yield. The overall bacterial community was mainly shaped by the operating conditions but, interestingly, potential cellulose-degrading bacteria seemed mainly to originate from the substrate.
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Affiliation(s)
- Tong Liu
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-75007 Uppsala, Sweden
| | - Li Sun
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-75007 Uppsala, Sweden
| | - Bettina Müller
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-75007 Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Science, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, SE-75007 Uppsala, Sweden.
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Wolf PG, Parthasarathy G, Chen J, O’Connor HM, Chia N, Bharucha AE, Gaskins HR. Assessing the colonic microbiome, hydrogenogenic and hydrogenotrophic genes, transit and breath methane in constipation. Neurogastroenterol Motil 2017; 29:1-9. [PMID: 28295896 PMCID: PMC5593760 DOI: 10.1111/nmo.13056] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/06/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Differences in the gut microbiota and breath methane production have been observed in chronic constipation, but the relationship between colonic microbiota, transit, and breath tests remains unclear. METHODS In 25 healthy and 25 constipated females we evaluated the sigmoid colonic mucosal and fecal microbiota using 16S rRNA gene sequencing, abundance of hydrogenogenic FeFe (FeFe-hydA) and hydrogenotrophic (methyl coenzyme M reductase A [mrcA] and dissimilatory sulfite reductase A [dsrA]) genes with real-time qPCR assays, breath hydrogen and methane levels after oral lactulose, and colonic transit with scintigraphy. KEY RESULTS Breath hydrogen and methane were not correlated with constipation, slow colon transit, or with abundance of corresponding genes. After adjusting for colonic transit, the abundance of FeFehydA, dsrA, and mcrA were greater (P<.005) in colonic mucosa, but not stool, of constipated patients. The abundance of the selected functional gene targets also correlated with that of selected taxa. The colonic mucosal abundance of FeFe-hydA, but not mcrA, correlated positively (P<.05) with breath methane production, slow colonic transit, and overall microbiome composition. In the colonic mucosa and feces, the abundance of hydrogenogenic and hydrogenotrophic genes were positively correlated (P<.05). Breath methane production was not associated with constipation or colonic transit. CONCLUSIONS & INFERENCES Corroborating our earlier findings with 16S rRNA genes, colonic mucosal but not fecal hydrogenogenic and hydrogenotrophic genes were more abundant in constipated vs. healthy subjects independent of colonic transit. Breath gases do not directly reflect the abundance of target genes contributing to their production.
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Affiliation(s)
- Patricia G. Wolf
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gopanandan Parthasarathy
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Helen M. O’Connor
- Clinical Research and Trials Unit, Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN, 55905 USA
| | - Nicholas Chia
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA,Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Adil E. Bharucha
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - H. Rex Gaskins
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Li S, Song L, Gao X, Jin Y, Liu S, Shen Q, Zou J. Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System. Front Microbiol 2017; 8:409. [PMID: 28373862 PMCID: PMC5357657 DOI: 10.3389/fmicb.2017.00409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/27/2017] [Indexed: 11/22/2022] Open
Abstract
Manure composting is a significant source of atmospheric methane (CH4) and nitrous oxide (N2O) that are two potent greenhouse gases. The CH4 and N2O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH4 and N2O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH4 and N2O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH4-related functional genes (mcrA and pmoA genes) and N2O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH4 and N2O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH4+ together as the best predictors for CH4 fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N2O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH4 and N2O fluxes to elevated atmospheric CO2 concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models.
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Affiliation(s)
- Shuqing Li
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Lina Song
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Xiang Gao
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Yaguo Jin
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Shuwei Liu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Qirong Shen
- Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University Nanjing, China
| | - Jianwen Zou
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
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Singh G, Chandoha-Lee C, Zhang W, Renneckar S, Vikesland PJ, Pruden A. Biodegradation of nanocrystalline cellulose by two environmentally-relevant consortia. WATER RESEARCH 2016; 104:137-146. [PMID: 27522024 DOI: 10.1016/j.watres.2016.07.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/12/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Nanocellulose is growing in popularity due to its versatile properties and applications. However, there is a void of knowledge regarding the environmental fate of nanocellulose and the response of environmental microbial communities that are historically adapted to non-nano cellulose forms. Given its distinction in terms of size and chemical and physical properties, nanocellulose could potentially resist biodegradation and/or pose a xenobiotic influence on microbial communities during wastewater treatment or in receiving environments. In this study, biodegradation of H2SO4 hydrolyzed nanocrystalline cellulose (HNC) was compared with that of microcrystalline cellulose using two distinct anaerobic cellulose-degrading microbial consortia initially sourced from anaerobic digester (AD) and wetland (W) inocula. Equivalent cellulose masses were dosed and monitored with time by measurement of liberated glucose. HNC biodegraded at slightly faster rate than microcrystalline cellulose (1st order decay constants: 0.62 ± 0.08 wk-1 for HNC versus 0.39 ± 0.05 wk-1 for microcrystalline cellulose for the AD consortium; 0.69 ± 0.04 wk-1for HNCversus 0.58 ± 0.05 wk-1 for microcrystalline cellulose for the W consortium). 16S rRNA (total bacteria) and cel48 (glycoside hydrolase gene family 48, indicative of cellulose-degrading potential) genes were observed to be more enriched in the HNC condition for both consortia. According to Illumina amplicon sequencing of 16S rRNA genes, the composition of the consortia underwent distinct shifts in concert with HNC versus microcrystalline cellulose degradation. This study demonstrates that the biodegradation of cellulose is not inhibited in the nano-size range, particularly in the crystalline form, though the microbes and pathways involved likely differ.
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Affiliation(s)
- Gargi Singh
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | | | - Wei Zhang
- Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, VA 24060, USA; Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, VA 24060, USA
| | - Scott Renneckar
- Department of Wood Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA.
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Incubation of innovative methanogenic communities to seed anaerobic digesters. Appl Microbiol Biotechnol 2016; 100:9795-9806. [PMID: 27717964 DOI: 10.1007/s00253-016-7875-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 09/06/2016] [Accepted: 09/20/2016] [Indexed: 10/20/2022]
Abstract
The methanogenic communities in alternative inocula and their potential to increase CH4 production in mesophilic and psychrophilic dairy manure-based anaerobic digesters were examined. Quantitative-PCR and terminal restriction fragment length polymorphism (T-RFLP) profiles were used to determine archaeal and methanogenic community changes when three inocula (wetland sediment (WS), landfill leachate (LL), and mesophilic digestate (MD)) were incubated at 15, 25, and 35 °C for 91 and 196 days. After each incubation period, the inocula were used in biochemical methane potential (BMP) tests at the incubation temperatures. There was no significant correlation between inoculum mcrA gene copy numbers and CH4 produced in BMP tests, suggesting that population size was not a distinguishing characteristic for predicting CH4 production. Archaeal composition in LL and WS reactors generally converged with MD reactors after incubation at 25 and 35 °C for 196 days. These MD reactors had high relative abundance of TRF 302, likely Methanosaetaceae, and low acetic acid (0.62-1.61 mM). At 15 °C incubation, most reactors were associated with high acetic acid (1.61-133.6 mM) and dominated by TRF 199, likely Methanosarcinaceae. The LL reactor incubated at 25 °C for 91 days had higher relative abundance of TRF 199 and produced significantly higher CH4 than WS and MD reactors in BMP test. In the future, it may be possible to create enrichment cultures that favor particular methanogens and use them as inoculum to benefit digesters at low mesophilic temperatures. Our data provides evidence that tailoring the archaeal community could benefit digesters operating under different conditions.
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Abdelrhman KFA, Bacci G, Marras B, Nistri A, Schintu M, Ugolini A, Mengoni A. Exploring the bacterial gut microbiota of supralittoral talitrid amphipods. Res Microbiol 2016; 168:74-84. [PMID: 27531409 DOI: 10.1016/j.resmic.2016.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/24/2016] [Accepted: 07/25/2016] [Indexed: 12/22/2022]
Abstract
Talitrid amphipods (sandhoppers and beach fleas) are typical of the supralittoral zone. They are known to thrive on stranded materials, including detrital marine angiosperms and macroalgae, as well as occasional dead animals. In this work, the gut microbiota of five species of talitrid amphipods (Talitrus saltator, Talorchestia ugolinii, Sardorchestia pelecaniformis, Orchestia montagui and Orchestia stephenseni) collected in Sardinia (Italy) has been investigated through: i) metabarcoding analysis of the amplified 16S rRNA V4 region; and ii) quantification of family 48 glycosyl hydrolase genes (GHF48), involved in cellulose degradation. Results indicate that, though talitrid gut biodiversity is not directly related to taxon or sampling locality, the animals' digestive tracts may host species-specific bacterial communities. In particular, gut microbiota of O. montagui, an inhabitant of Posidonia banquettes and macro-algae mat, showed the greatest differences in taxonomic composition and the highest proportion of GHF48 genes with respect to 16S rRNA genes. These results suggest that the different talitrid species may host species-specific bacterial communities whose function could partially reflect the different microhabitats and food preferences of their host.
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Affiliation(s)
- Khaled F A Abdelrhman
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Firenze, Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Firenze, Italy
| | - Barbara Marras
- Department of Public Health, Molecular and Clinical Medicine, University of Cagliari, I-09124, Cagliari, Italy
| | - Annamaria Nistri
- Museum of Natural History, Zoological Section "La Specola", University of Florence, via Romana 17, I-50125, Firenze, Italy
| | - Marco Schintu
- Department of Public Health, Molecular and Clinical Medicine, University of Cagliari, I-09124, Cagliari, Italy
| | - Alberto Ugolini
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Firenze, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Firenze, Italy
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Lefevre E, Cooper E, Stapleton HM, Gunsch CK. Characterization and Adaptation of Anaerobic Sludge Microbial Communities Exposed to Tetrabromobisphenol A. PLoS One 2016; 11:e0157622. [PMID: 27463972 PMCID: PMC4963083 DOI: 10.1371/journal.pone.0157622] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/02/2016] [Indexed: 11/22/2022] Open
Abstract
The increasing occurrence of tetrabromobisphenol A (TBBPA) in the environment is raising questions about its potential ecological and human health impacts. TBBPA is microbially transformed under anaerobic conditions to bisphenol A (BPA). However, little is known about which taxa degrade TBBPA and the adaptation of microbial communities exposed to TBBPA. The objectives of this study were to characterize the effect of TBBPA on microbial community structure during the start-up phase of a bench-scale anaerobic sludge reactor, and identify taxa that may be associated with TBBPA degradation. TBBPA degradation was monitored using LC/MS-MS, and the microbial community was characterized using Ion Torrent sequencing and qPCR. TBBPA was nearly completely transformed to BPA via reductive debromination in 55 days. Anaerobic reactor performance was not negatively affected by the presence of TBBPA and the bulk of the microbial community did not experience significant shifts. Several taxa showed a positive response to TBBPA, suggesting they may be associated with TBBPA degradation. Some of these taxa had been previously identified as dehalogenating bacteria including Dehalococcoides, Desulfovibrio, Propionibacterium, and Methylosinus species, but most had not previously been identified as having dehalogenating capacities. This study is the first to provide in-depth information on the microbial dynamics of anaerobic microbial communities exposed to TBBPA.
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Affiliation(s)
- Emilie Lefevre
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, United States of America
| | - Ellen Cooper
- Nicholas School of the Environment, Duke University, Durham, NC, United States of America
| | - Heather M. Stapleton
- Nicholas School of the Environment, Duke University, Durham, NC, United States of America
| | - Claudia K. Gunsch
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, United States of America
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Goswami R, Mukherjee S, Chakraborty AK, Balachandran S, Sinha Babu SP, Chaudhury S. Optimization of growth determinants of a potent cellulolytic bacterium isolated from lignocellulosic biomass for enhancing biogas production. CLEAN TECHNOLOGIES AND ENVIRONMENTAL POLICY 2016; 18:1565-1583. [DOI: 10.1007/s10098-016-1141-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Archaeal rhizosphere communities differ between the native and invasive lineages of the wetland plant Phragmites australis (common reed) in a Chesapeake Bay subestuary. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1144-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Reitschuler C, Spötl C, Hofmann K, Wagner AO, Illmer P. Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential. MICROBIAL ECOLOGY 2016; 71:686-699. [PMID: 26790864 DOI: 10.1007/s00248-015-0727-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
(Alpine) caves are, in general, windows into the Earth's subsurface. Frequently occurring structures in caves such as moonmilk (secondary calcite deposits) offer the opportunity to study intraterrestrial microbial communities, adapted to oligotrophic and cold conditions. This is an important research field regarding the dimensions of subsurface systems and cold regions on Earth. On a methodological level, moonmilk deposits from 11 caves in the Austrian Alps were collected aseptically and investigated using a molecular (qPCR and DGGE sequencing-based) methodology in order to study the occurrence, abundance, and diversity of the prevailing native Archaea community. Furthermore, these Archaea were enriched in complex media and studied regarding their physiology, with a media selection targeting different physiological requirements, e.g. methanogenesis and ammonia oxidation. The investigation of the environmental samples showed that all moonmilk deposits were characterized by the presence of the same few habitat-specific archaeal species, showing high abundances and constituting about 50 % of the total microbial communities. The largest fraction of these Archaea was ammonia-oxidizing Thaumarchaeota, while another abundant group was very distantly related to extremophilic Euryarchaeota (Moonmilk Archaea). The archaeal community showed a depth- and oxygen-dependent stratification. Archaea were much more abundant (around 80 %), compared to bacteria, in the actively forming surface part of moonmilk deposits, decreasing to about 5 % down to the bedrock. Via extensive cultivation efforts, it was possible to enrich the enigmatic Moonmilk Archaea and also AOA significantly above the level of bacteria. The most expedient prerequisites for cultivating Moonmilk Archaea were a cold temperature, oligotrophic conditions, short incubation times, a moonmilk surface inoculum, the application of erythromycin, and anaerobic (microaerophilic) conditions. On a physiological level, it seems that methanogenesis is of marginal importance, while ammonia oxidation and a still undiscovered metabolic pathway are vital elements in the (archaeal) moonmilk biome.
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Affiliation(s)
- Christoph Reitschuler
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria.
| | - Christoph Spötl
- Institute of Geology, University of Innsbruck, Innrain 52, A-6020, Innsbruck, Austria
| | - Katrin Hofmann
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Andreas O Wagner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Paul Illmer
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
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Decline in Performance of Biochemical Reactors for Sulphate Removal from Mine-Influenced Water is Accompanied by Changes in Organic Matter Characteristics and Microbial Population Composition. WATER 2016. [DOI: 10.3390/w8040124] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters. Antonie van Leeuwenhoek 2016; 109:855-68. [PMID: 27002962 DOI: 10.1007/s10482-016-0685-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 03/18/2016] [Indexed: 01/19/2023]
Abstract
The objectives of this study were to assess abundances and community compositions of Archaea within a heterogeneous set of freshwater systems in the Austrian Alps. Seasonal changes and geographical differences within Archaea, considering abiotic and biotic factors (e.g. temperature, pH, total organic carbon (TOC), NH4 (+), bacteria, fungi), were analysed in this context. Water samples were collected from 8 lakes, 10 creeks and the river Inn in 2014. Qualitative-quantitative data were derived via a comprehensive set of (quantitative) PCR assays and PCR-DGGE (denaturing gradient gel electrophoresis) based methodology, which was evaluated concerning specificity and reliability either previously or in this study. QPCR-derived archaeal abundances reached values of 10(3) copies mL(-1) on average, with a peak in winter-spring ('Cold Peak'), and covered 0-15 % (average: 1 %) of the microbial populations. This peak correlated with significantly raised TOC and low NH4 (+) levels during the cold seasons. Stagnant waters showed significantly higher archaeal abundances and diversities than flowing ones. Among methanogens, Methanosarcinales were the most common order. PCR-DGGE data showed that the archaeal communities were site-specific and could function as an ecological marker, in contrast to the more heterogeneous and unsteady bacterial and fungal community. This is attributable to the highly heterogeneous community of methanogenic Archaea (MA, Euryarchaeota), while only two species, Nitrosopumilus maritimus and Ca. Nitrososphaera gargensis, were found to be the ubiquitous representatives of ammonia-oxidizing Archaea (AOA, Thaumarchaeota) in Alpine freshwaters. This work emphasises the diversity, distribution and seasonality of non-extremophilic Archaea in Alpine freshwaters, with a first insight into their ecophysiological potential.
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