1
|
Li S, Zhen Y, Chen Y, Mi T. Geochemical and microbial controls on methane distribution in coastal sediments: A case study from the Bohai and South Yellow Seas, China. MARINE POLLUTION BULLETIN 2024; 211:117448. [PMID: 39671837 DOI: 10.1016/j.marpolbul.2024.117448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 12/06/2024] [Accepted: 12/08/2024] [Indexed: 12/15/2024]
Abstract
CH4 is among the most potent greenhouse gases. In this study, we investigated one of the important CH4 production hotspots, the continental margins. We examined the spatiotemporal distributions of CH4 in sediment cores from the Bohai and South Yellow Seas, China. Using real-time PCR and metagenomic sequencing, we analyzed the microbial communities related to CH4 production. Our results indicated that concentrations of CH4 generally increased with depth gradually, minimal seasonal variation observed between spring and summer. Notably, spatial heterogeneity, rather than temporal variation, was the predominant factor affecting CH4 distribution and methanogen community differences in sediments. Furthermore, the structure of microbial communities, in conjunction with environmental factors, significantly impacts potential CH4 production. These findings provide valuable insights into the mechanisms underlying methane production and its environmental controls in marine sediments.
Collapse
Affiliation(s)
- Siqi Li
- Department of Military Oceanography and Hydrography & Cartography, Dalian Naval Academy, Dalian 116018, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China.
| | - Ye Chen
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266071, China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| |
Collapse
|
2
|
Tufail MA, Jordan B, Hadjeras L, Gelhausen R, Cassidy L, Habenicht T, Gutt M, Hellwig L, Backofen R, Tholey A, Sharma CM, Schmitz RA. Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions. Nat Commun 2024; 15:8659. [PMID: 39370430 PMCID: PMC11456600 DOI: 10.1038/s41467-024-53008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 09/25/2024] [Indexed: 10/08/2024] Open
Abstract
The mesophilic methanogenic archaeal model organism Methanosarcina mazei strain Gö1 is crucial for climate and environmental research due to its ability to produce methane. Here, we establish a Ribo-seq protocol for M. mazei strain Gö1 under two growth conditions (nitrogen sufficiency and limitation). The translation of 93 previously annotated and 314 unannotated small ORFs, coding for proteins ≤ 70 amino acids, is predicted with high confidence based on Ribo-seq data. LC-MS analysis validates the translation for 62 annotated small ORFs and 26 unannotated small ORFs. Epitope tagging followed by immunoblotting analysis confirms the translation of 13 out of 16 selected unannotated small ORFs. A comprehensive differential transcription and translation analysis reveals that 29 of 314 unannotated small ORFs are differentially regulated in response to nitrogen availability at the transcriptional and 49 at the translational level. A high number of reported small RNAs are emerging as dual-function RNAs, including sRNA154, the central regulatory small RNA of nitrogen metabolism. Several unannotated small ORFs are conserved in Methanosarcina species and overproducing several (small ORF encoded) small proteins suggests key physiological functions. Overall, the comprehensive analysis opens an avenue to elucidate the function(s) of multitudinous small proteins and dual-function RNAs in M. mazei.
Collapse
Affiliation(s)
| | - Britta Jordan
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Lydia Hadjeras
- Institute of Molecular Infection Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Tim Habenicht
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Lisa Hellwig
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Cynthia M Sharma
- Institute of Molecular Infection Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany.
| |
Collapse
|
3
|
Larson J, Tokmina-Lukaszewska M, Payne D, Spietz RL, Fausset H, Alam MG, Brekke BK, Pauley J, Hasenoehrl EJ, Shepard EM, Boyd ES, Bothner B. Impact of mineral and non-mineral sources of iron and sulfur on the metalloproteome of Methanosarcina barkeri. Appl Environ Microbiol 2024; 90:e0051624. [PMID: 39023267 PMCID: PMC11337800 DOI: 10.1128/aem.00516-24] [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: 03/21/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
Methanogens often inhabit sulfidic environments that favor the precipitation of transition metals such as iron (Fe) as metal sulfides, including mackinawite (FeS) and pyrite (FeS2). These metal sulfides have historically been considered biologically unavailable. Nonetheless, methanogens are commonly cultivated with sulfide (HS-) as a sulfur source, a condition that would be expected to favor metal precipitation and thus limit metal availability. Recent studies have shown that methanogens can access Fe and sulfur (S) from FeS and FeS2 to sustain growth. As such, medium supplied with FeS2 should lead to higher availability of transition metals when compared to medium supplied with HS-. Here, we examined how transition metal availability under sulfidic (i.e., cells provided with HS- as sole S source) versus non-sulfidic (cells provided with FeS2 as sole S source) conditions impact the metalloproteome of Methanosarcina barkeri Fusaro. To achieve this, we employed size exclusion chromatography coupled with inductively coupled plasma mass spectrometry and shotgun proteomics. Significant changes were observed in the composition and abundance of iron, cobalt, nickel, zinc, and molybdenum proteins. Among the differences were alterations in the stoichiometry and abundance of multisubunit protein complexes involved in methanogenesis and electron transport chains. Our data suggest that M. barkeri utilizes the minimal iron-sulfur cluster complex and canonical cysteine biosynthesis proteins when grown on FeS2 but uses the canonical Suf pathway in conjunction with the tRNA-Sep cysteine pathway for iron-sulfur cluster and cysteine biosynthesis under sulfidic growth conditions.IMPORTANCEProteins that catalyze biochemical reactions often require transition metals that can have a high affinity for sulfur, another required element for life. Thus, the availability of metals and sulfur are intertwined and can have large impacts on an organismismal biochemistry. Methanogens often occupy anoxic, sulfide-rich (euxinic) environments that favor the precipitation of transition metals as metal sulfides, thereby creating presumed metal limitation. Recently, several methanogens have been shown to acquire iron and sulfur from pyrite, an abundant iron-sulfide mineral that was traditionally considered to be unavailable to biology. The work presented here provides new insights into the distribution of metalloproteins, and metal uptake of Methanosarcina barkeri Fusaro grown under euxinic or pyritic growth conditions. Thorough characterizations of this methanogen under different metal and sulfur conditions increase our understanding of the influence of metal availability on methanogens, and presumably other anaerobes, that inhabit euxinic environments.
Collapse
Affiliation(s)
- James Larson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | | | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Rachel L. Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Hunter Fausset
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Md Gahangir Alam
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Brooklyn K. Brekke
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jordan Pauley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Ethan J. Hasenoehrl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric M. Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| |
Collapse
|
4
|
Paul R, Maibam A, Chatterjee R, Wang W, Mukherjee T, Das N, Yellappa M, Banerjee T, Bhaumik A, Venkata Mohan S, Babarao R, Mondal J. Purification of Waste-Generated Biogas Mixtures Using Covalent Organic Framework's High CO 2 Selectivity. ACS APPLIED MATERIALS & INTERFACES 2024; 16:22066-22078. [PMID: 38629710 DOI: 10.1021/acsami.4c03245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Development of crystalline porous materials for selective CO2 adsorption and storage is in high demand to boost the carbon capture and storage (CCS) technology. In this regard, we have developed a β-keto enamine-based covalent organic framework (VM-COF) via the Schiff base polycondensation technique. The as-synthesized VM-COF exhibited excellent thermal and chemical stability along with a very high surface area (1258 m2 g-1) and a high CO2 adsorption capacity (3.58 mmol g-1) at room temperature (298 K). The CO2/CH4 and CO2/H2 selectivities by the IAST method were calculated to be 10.9 and 881.7, respectively, which were further experimentally supported by breakthrough analysis. Moreover, theoretical investigations revealed that the carbonyl-rich sites in a polymeric backbone have higher CO2 binding affinity along with very high binding energy (-39.44 KJ mol-1) compared to other aromatic carbon-rich sites. Intrigued by the best CO2 adsorption capacity and high CO2 selectivity, we have utilized the VM-COF for biogas purification produced by the biofermentation of municipal waste. Compared with the commercially available activated carbon, VM-COF exhibited much better purification ability. This opens up a new opportunity for the creation of functionalized nanoporous materials for the large-scale purification of waste-generated biogases to address the challenges associated with energy and the environment.
Collapse
Affiliation(s)
- Ratul Paul
- Department of Catalysis & Fine Chemicals, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashakiran Maibam
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Physical and Materials Division, CSIR-National Chemical Laboratory, Pune 411 008, India
- School of Science, Centre for Advanced Materials and Industrial Chemistry (CAMIC), RMIT University, Melbourne 3001, Victoria, Australia
| | - Rupak Chatterjee
- School of Materials Science, Indian Association for the Cultivation of Science, 2A & B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Wenjing Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Triya Mukherjee
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| | - Nitumani Das
- Department of Catalysis & Fine Chemicals, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Masapogu Yellappa
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| | - Tanmay Banerjee
- Department of Chemistry, BITS Pilani, Pilani 333031, Gujarat, India
| | - Asim Bhaumik
- School of Materials Science, Indian Association for the Cultivation of Science, 2A & B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - S Venkata Mohan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| | - Ravichandar Babarao
- School of Science, Centre for Advanced Materials and Industrial Chemistry (CAMIC), RMIT University, Melbourne 3001, Victoria, Australia
- CSIRO, Normanby Road, Clayton 3168, Victoria, Australia
- ARC Centre of Excellence for Green Electrochemical Transformation of Carbon Dioxide, School of Science, RMIT University, Melbourne 3000, Australia
| | - John Mondal
- Department of Catalysis & Fine Chemicals, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
5
|
Ungerfeld EM, Pitta D. Review: Biological consequences of the inhibition of rumen methanogenesis. Animal 2024:101170. [PMID: 38772773 DOI: 10.1016/j.animal.2024.101170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/23/2024] Open
Abstract
Decreasing enteric CH4 emissions from ruminants is important for containing global warming to 1.5 °C and avoid the worst consequences of climate change. However, the objective of mitigating enteric CH4 emissions is difficult to reconcile with the forecasted increase in production of ruminant meat and milk, unless CH4 production per animal and per kilogram of animal product are decreased substantially. Chemical compound 3-nitrooxypropanol and bromoform-containing red algae Asparagopsis are currently the most potent inhibitors of rumen methanogenesis, but their average efficacy would have to be increased to mitigate enteric CH4 emissions to contain global warming to 1.5 °C, if the demand for ruminant products increases as predicted. We propose that it may be possible to enhance the efficacy of inhibitors of methanogenesis through understanding the mechanisms that cause variation in their efficacy across studies. We also propose that a more thorough understanding of the effects of inhibiting methanogenesis on rumen and postabsorptive metabolism may help improve feed efficiency and cost-effectiveness as co-benefits of the methanogenesis inhibition intervention. For enhancing efficacy, we examine herein how different inhibitors of methanogenesis affect the composition of the rumen microbial community and discuss some mechanisms that may explain dissimilar sensitivities among methanogens to different types of inhibitors. For improving feed efficiency and cost-effectiveness, we discuss the consequences of inhibiting methanogenesis on rumen fermentation, and how changes in rumen fermentation can in turn affect postabsorptive metabolism and animal performance. The objectives of this review are to identify knowledge gaps of the consequences of inhibiting methanogenesis on rumen microbiology and rumen and postabsorptive metabolism, propose research to address those knowledge gaps and discuss the implications that this research can have for the efficacy and adoption of inhibitors of methanogenesis. Depending on its outcomes, research on the microbiological, biochemical, and metabolic consequences of the inhibition of rumen methanogenesis could help the adoption of feed additives inhibitors of methanogenesis to mitigate enteric CH4 emissions from ruminants to ameliorate climate change.
Collapse
Affiliation(s)
- E M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias INIA, Camino Cajón a Vilcún km 10, 4880000 Vilcún, La Araucanía, Chile.
| | - D Pitta
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center, 19348 Kenneth Square, PA, United States
| |
Collapse
|
6
|
Bährle R, Böhnke S, Englhard J, Bachmann J, Perner M. Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications. BIORESOUR BIOPROCESS 2023; 10:84. [PMID: 38647803 PMCID: PMC10992861 DOI: 10.1186/s40643-023-00705-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/16/2023] [Indexed: 04/25/2024] Open
Abstract
Anthropogenic carbon dioxide (CO2) levels are rising to alarming concentrations in earth's atmosphere, causing adverse effects and global climate changes. In the last century, innovative research on CO2 reduction using chemical, photochemical, electrochemical and enzymatic approaches has been addressed. In particular, natural CO2 conversion serves as a model for many processes and extensive studies on microbes and enzymes regarding redox reactions involving CO2 have already been conducted. In this review we focus on the enzymatic conversion of CO2 to carbon monoxide (CO) as the chemical conversion downstream of CO production render CO particularly attractive as a key intermediate. We briefly discuss the different currently known natural autotrophic CO2 fixation pathways, focusing on the reversible reaction of CO2, two electrons and protons to CO and water, catalyzed by carbon monoxide dehydrogenases (CODHs). We then move on to classify the different type of CODHs, involved catalyzed chemical reactions and coupled metabolisms. Finally, we discuss applications of CODH enzymes in photochemical and electrochemical cells to harness CO2 from the environment transforming it into commodity chemicals.
Collapse
Affiliation(s)
- Rebecca Bährle
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Stefanie Böhnke
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Jonas Englhard
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Julien Bachmann
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Mirjam Perner
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany.
| |
Collapse
|
7
|
Wang Y, Xu W, Cong Q, Wang Y, Wang W, Zhang W, Zhu Z, Dong H. Responses of CH 4, N 2O, and NH 3 emissions to different slurry pH values of 5.5-10.0: Characteristics and mechanisms. ENVIRONMENTAL RESEARCH 2023; 234:116613. [PMID: 37437873 DOI: 10.1016/j.envres.2023.116613] [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: 05/10/2023] [Revised: 06/29/2023] [Accepted: 07/09/2023] [Indexed: 07/14/2023]
Abstract
Animal slurry storage is a significant source of greenhouse gas (GHG) and ammonia (NH3) emissions. pH is a basic but key factor that could pose great influence on gas emissions, but the simultaneous evaluation of its influence on GHG and NH3 emissions and the understanding of its underlying mechanism are not enough. In this work, pH was adjusted between 5.5 and 10.0 by a step of 0.5 unit by adding lactic acid and sodium hydroxide (NaOH) properly and frequently to the stored slurry during a 43-day storage period. The cumulative NH3 emissions were linearly correlated with the slurry pH, with R2 being 0.982. Maintaining the slurry pH at 5.5-6.0 could reduce NH3 emissions by 69.4%-85.1% compared with the non-treated group (CK). The pH ranges for maximum methane (CH4) and nitrous oxide (N2O) emissions were 7.5-8.5 and 6.5-8.5, respectively, and the slurry under pH 7.5-8.5 showed the highest GHG emissions. Acidification to pH 5.5 helped reduce the CH4, N2O, and total GHG emissions by 98.0%, 29.3%, and 81.7%, respectively; while alkalinization to pH 10.0 helped achieve the mitigation effects of 74.1%, 24.9%, and 30.6%, respectively. The Pearson's correlation factor between CH4 and the gene copy of mcrA under different pH values was 0.744 (p < 0.05). Meanwhile, the correlation factors between N2O and the gene copies of amoA, narG, and nirS were 0.644 (p < 0.05), 0.719 (p < 0.05), and 0.576 (p = 0.081), respectively. The gene copies of mcrA, amoA, narG, and nirS were maintained at the lowest level under pH 5.5. These results recommended keeping slurry pH lower than 5.5 with lactic acid can help control GHG and NH3 emissions simultaneously and effectively.
Collapse
Affiliation(s)
- Yue Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Wenqian Xu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Qunxin Cong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Youxu Wang
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing 102208, China.
| | - Wenzan Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Wanqin Zhang
- China Huadian Engineering Co.Ltd., Beijing 100160, China.
| | - Zhiping Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Hongmin Dong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
8
|
Chanderban M, Hill CA, Dhamad AE, Lessner DJ. Expression of V-nitrogenase and Fe-nitrogenase in Methanosarcina acetivorans is controlled by molybdenum, fixed nitrogen, and the expression of Mo-nitrogenase. Appl Environ Microbiol 2023; 89:e0103323. [PMID: 37695043 PMCID: PMC10537573 DOI: 10.1128/aem.01033-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/07/2023] [Indexed: 09/12/2023] Open
Abstract
All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N2) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif, vnf, and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif, vnf, and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N2 but not with NH4Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.
Collapse
Affiliation(s)
- Melissa Chanderban
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Christopher A. Hill
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| | - Ahmed E. Dhamad
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
- Department of Biological Sciences, Wasit University, Wasit, Iraq
| | - Daniel J. Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, Arkansas, USA
| |
Collapse
|
9
|
Xu C, Sun S, Li Y, Gao Y, Zhang W, Tian L, Li T, Du Q, Cai J, Zhou L. Methane emission reduction oriented extracellular electron transfer and bioremediation of sediment microbial fuel cell: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162508. [PMID: 36863582 DOI: 10.1016/j.scitotenv.2023.162508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/08/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Sediment is the internal and external source of water environment pollution, so sediment remediation is the premise of water body purification. Sediment microbial fuel cell (SMFC) can remove the organic pollutants in sediment by electroactive microorganisms, compete with methanogens for electrons, and realize resource recycling, methane emission inhibiting and energy recovering. Due to these characteristics, SMFC have attracted wide attention for sediment remediation. In this paper, we comprehensively summarized the recent advances of SMFC in the following areas: (1) The advantages and disadvantages of current applied sediment remediation technologies; (2) The basic principles and influencing factors of SMFC; (3) The application of SMFC for pollutant removal, phosphorus transformation and remote monitoring and power supply; (4) Enhancement strategies for SMFC in sediments remediation such as SMFC coupled with constructed wetland, aquatic plant and iron-based reaction. Finally, we have summarized the drawback of SMFC and discuss the future development directions of applying SMFC for sediment bioremediation.
Collapse
Affiliation(s)
- Chong Xu
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province/School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Shiquan Sun
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province/School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Yifu Li
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province/School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Yang Gao
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province/School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Wei Zhang
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province/School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Liu Tian
- School of Municipal and Geomatics Engineering, Hunan City University, Yiyang 413000, China
| | - Tian Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, Tianjin 300350, China
| | - Qing Du
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China
| | - Jingju Cai
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Lean Zhou
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province/School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, China.
| |
Collapse
|
10
|
Li B, Wang H, Lai A, Xue J, Wu Q, Yu C, Xie K, Mao Z, Li H, Xing P, Wu QL. Hydrogenotrophic pathway dominates methanogenesis along the river-estuary continuum of the Yangtze River. WATER RESEARCH 2023; 240:120096. [PMID: 37229838 DOI: 10.1016/j.watres.2023.120096] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/07/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
Rivers are considered as an important source of methane (CH4) to the atmosphere, but our understanding for the methanogenic pathway in rivers and its linkage with CH4 emission is very limited. Here, we investigated the diffusive flux of CH4 and its stable carbon isotope signature (δ13C-CH4) along the river-estuary continuum of the Yangtze River. The diffusive CH4 flux was estimated to 27.9 ± 11.4 μmol/m2/d and 36.5 ± 24.4 μmol/m2/d in wet season and dry season, respectively. The δ13C-CH4 values were generally lower than -60‰, with the fractionation factor (αc) higher than 1.055 and the isotope separation factor (εc) ranged from 55 to 100. In situ microbial composition showed that hydrogenotrophic methanogens accounts for over 70% of the total reads. Moreover, the incubation test showed that the headspace CH4 concentration by adding CO2/H2 to the sediment was orders of magnitude higher than that by adding trimethylamine and sodium acetate. These results jointly verified the river-estuary continuum is a minor CH4 source and dominated by hydrogenotrophic pathway. Based on the methanogenic pathway here and previous reported data in the same region, the historical variation of diffusive CH4 flux was calculated and results showed that CH4 emission has reduced 82.5% since the construction of Three Gorges Dam (TGD). Our study verified the dominant methanogenic pathway in river ecosystems and clarified the effect and mechanism of dam construction on riverine CH4 emission.
Collapse
Affiliation(s)
- Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hongwei Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Anxing Lai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jingya Xue
- School of Geographical Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Qiong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Yu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Life Sciences, Hebei University, Baoding 071002, China
| | - Ke Xie
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhendu Mao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China.
| |
Collapse
|
11
|
Nakano H, Nakayasu Y, Umetsu M, Tada C. Semi-wet methanogen cathode composed of oak white charcoal for developing sustainable microbial fuel cells. J Biosci Bioeng 2023; 135:480-486. [PMID: 37088674 DOI: 10.1016/j.jbiosc.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 04/25/2023]
Abstract
The present study aimed to evaluate a semi-wet biocathode composed of oak white charcoal and agarose gel as an alternative to the standard carbon felt biocathodes used in microbial fuel cells (MFCs). The MFC containing the oak white charcoal cathode (Oak-MFC) recorded a higher current value than that of the MFC containing a carbon felt cathode (CF-MFC). The Oak-MFC produced approximately 4.0-fold more electrons in the external circuit and 1.7-fold more methane (CH4) than the CF-MFC. A real-time PCR targeting mcrA showed that the number of methanogens adhering to the oak white charcoal cathode was approximately 15-fold that adhering to the carbon felt cathode. These results suggest that the methanogens attached to the cathode of both MFCs received electrons and CH4 was produced from carbon dioxide (CO2). Furthermore, Oak-MFC performed better than CF-MFC, thereby suggesting that oak white charcoal bound by agarose gel can be used as an alternative methanogen cathode. The propionic acid degradation rate of Oak-MFC was faster than that of CF-MFC suggesting that the cathodic reaction may affect the anodic reaction. The use of oak-derived electrode as a methanogen cathode also could contribute to sustainable forest management and promote regular thinning of oak trees. Further, its use will enable carbon fixation and efficient energy conversion from CO2 to CH4, thus contributing to sustainable energy use.
Collapse
Affiliation(s)
- Hiroto Nakano
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Narukoonsen, Osaki, Miyagi 989-6711, Japan
| | - Yuta Nakayasu
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Masaki Umetsu
- Graduate School of Environmental Studies, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Chika Tada
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Narukoonsen, Osaki, Miyagi 989-6711, Japan.
| |
Collapse
|
12
|
Zhang L, Yin Y, Sun Y, Liang X, Graham DE, Pierce EM, Löffler FE, Gu B. Inhibition of Methylmercury and Methane Formation by Nitrous Oxide in Arctic Tundra Soil Microcosms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5655-5665. [PMID: 36976621 PMCID: PMC10100821 DOI: 10.1021/acs.est.2c09457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
Climate warming causes permafrost thaw predicted to increase toxic methylmercury (MeHg) and greenhouse gas [i.e., methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O)] formation. A microcosm incubation study with Arctic tundra soil over 145 days demonstrates that N2O at 0.1 and 1 mM markedly inhibited microbial MeHg formation, methanogenesis, and sulfate reduction, while it slightly promoted CO2 production. Microbial community analyses indicate that N2O decreased the relative abundances of methanogenic archaea and microbial clades implicated in sulfate reduction and MeHg formation. Following depletion of N2O, both MeHg formation and sulfate reduction rapidly resumed, whereas CH4 production remained low, suggesting that N2O affected susceptible microbial guilds differently. MeHg formation strongly coincided with sulfate reduction, supporting prior reports linking sulfate-reducing bacteria to MeHg formation in the Arctic soil. This research highlights complex biogeochemical interactions in governing MeHg and CH4 formation and lays the foundation for future mechanistic studies for improved predictive understanding of MeHg and greenhouse gas fluxes from thawing permafrost ecosystems.
Collapse
Affiliation(s)
- Lijie Zhang
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Yongchao Yin
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center
for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Yanchen Sun
- Center
for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Xujun Liang
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - David E. Graham
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eric M. Pierce
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Frank E. Löffler
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center
for Environmental Biotechnology, University
of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department
of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Baohua Gu
- Environmental
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
13
|
Wang Z, Li K, Shen X, Yan F, Zhao X, Xin Y, Ji L, Xiang Q, Xu X, Li D, Ran J, Xu X, Chen Q. Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159439. [PMID: 36252671 DOI: 10.1016/j.scitotenv.2022.159439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/23/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH4). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO3-), sulfate (SO42-), and nitrous oxide (N2O) flux, among them, soil N substances (TN, NO3-, N2O) have essential regulatory roles in the AOM process, while NO3- and N2O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH4 sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH4 biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.
Collapse
Affiliation(s)
- Zihao Wang
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Kun Li
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Xiaoyan Shen
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Feifei Yan
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, PR China
| | - Xinkun Zhao
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Yu Xin
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Linhui Ji
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Qingyue Xiang
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Xinyi Xu
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Daijia Li
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Junhao Ran
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Xiaoya Xu
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China.
| | - Qingfeng Chen
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China.
| |
Collapse
|
14
|
Characterization of Biofilm Microbiome Formation Developed on Novel 3D-Printed Zeolite Biocarriers during Aerobic and Anaerobic Digestion Processes. FERMENTATION 2022. [DOI: 10.3390/fermentation8120746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Aerobic or anaerobic digestion is involved in treating agricultural and municipal waste, and the addition of biocarriers has been proven to improve them further. We synthesized novel biocarriers utilizing zeolites and different inorganic binders and compared their efficiency with commercially available biocarriers in aerobic and anaerobic digestion systems. Methods: We examined BMP and several physicochemical parameters to characterize the efficiency of novel biocarriers on both systems. We also determined the SMP and EPS content of synthesized biofilm and measured the adherence and size of the forming biofilm. Finally, we characterized the samples by 16S rRNA sequencing to determine the crucial microbial communities involved. Results: Evaluating BMP results, ZSM-5 zeolite with bentonite binder emerged, whereas ZSM-5 zeolite with halloysite nanotubes binder stood out in the wastewater treatment experiment. Twice the relative frequencies of archaea were found on novel biocarriers after being placed in AD batch reactors, and >50% frequencies of Proteobacteria after being placed in WWT reactors, compared to commercial ones. Conclusions: The newly synthesized biocarriers were not only equally efficient with the commercially available ones, but some were even superior as they greatly enhanced aerobic or anaerobic digestion and showed strong biofilm formation and unique microbiome signatures.
Collapse
|
15
|
Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures. Int J Mol Sci 2022; 23:ijms232315149. [PMID: 36499474 PMCID: PMC9741079 DOI: 10.3390/ijms232315149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.
Collapse
|
16
|
Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
Collapse
Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
| |
Collapse
|
17
|
Liu B, Chau J, Dai Q, Zhong C, Zhang J. Exploring Gut Microbiome in Predicting the Efficacy of Immunotherapy in Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:5401. [PMID: 36358819 PMCID: PMC9656313 DOI: 10.3390/cancers14215401] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/29/2022] [Accepted: 10/29/2022] [Indexed: 11/02/2023] Open
Abstract
We performed various analyses on the taxonomic and functional features of the gut microbiome from NSCLC patients treated with immunotherapy to establish a model that may predict whether a patient will benefit from immunotherapy. We collected 65 published whole metagenome shotgun sequencing samples along with 14 samples from our previous study. We systematically studied the taxonomical characteristics of the dataset and used both the random forest (RF) and the multilayer perceptron (MLP) neural network models to predict patients with progression-free survival (PFS) above 6 months versus those below 3 months. Our results showed that the RF classifier achieved the highest F-score (85.2%) and the area under the receiver operating characteristic curve (AUC) (95%) using the protein families (Pfam) profile, and the MLP neural network classifier achieved a 99.9% F-score and 100% AUC using the same Pfam profile. When applying the model trained in the Pfam profile directly to predict the treatment response, we found that both trained RF and MLP classifiers significantly outperformed the stochastic predictor in F-score. Our results suggested that such a predictive model based on functional (e.g., Pfam) rather than taxonomic profile might be clinically useful to predict whether an NSCLC patient will benefit from immunotherapy, as both the F-score and AUC of functional profile outperform that of taxonomic profile. In addition, our model suggested that interactive biological processes such as methanogenesis, one-carbon, and amino acid metabolism might be important in regulating the immunotherapy response that warrants further investigation.
Collapse
Affiliation(s)
- Ben Liu
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045, USA
| | - Justin Chau
- Division of Hematology, Oncology, and Blood & Marrow Transplantation, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | - Qun Dai
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, School of Engineering, University of Kansas, Lawrence, KS 66045, USA
- Center for Computational Biology, University of Kansa, Lawrence, KS 66045, USA
| | - Jun Zhang
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| |
Collapse
|
18
|
Wu C, Jiang Q, Luciano P, Sun Y, Du Y, Zhang TC, Du D. Strategy of optimizing anaerobic digestion of cassava distiller wastewater using a novel automatic biological incubation system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114384. [PMID: 34991022 DOI: 10.1016/j.jenvman.2021.114384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 11/28/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Due to the drawbacks of using fossil fuels and the need to mitigate global warming caused by increasing greenhouse gas emissions, agricultural biomass for bioenergy production is gaining great interest around the world. This work presented a study at a biochemical plant in Lianyungang, Jiangsu Province, China to maximize methane production from cassava distiller wastewater. The plant's annual production of cassava distiller wastewater is more than 3 million tons and currently was treated using a series of 5000 m3 Internal Circulation (IC) reactors. Modification was applied at No.19 IC reactor by connecting it to two 1 m3 automatic biological incubators called Information Bio-Booster (IBB). The effluent of the IC reactor was fed into the IBBs and iron, cobalt and nickel were added directly in the IBBs. The function of the IBBs was to regulate the microbial community. Afterwards, the microorganisms in the IBBs were pumped back into the IC reactor to participate in the methane production reaction. Daily net increase of methane content and COD removal reached 8.02% and 33% respectively in No.19 IC reactor comparing to the unadjusted reactors. Preliminary lab experiments found that improvements of biogas production, enhanced COD removal and VS removal was closely related to the enhancement of anaerobic microbial communities' diversity and the promotion of enzyme activity through the addition of the metal salts. Daily economic value could be estimated to be $218 which indicated the application potential of using the proposed system to enhance anaerobic digestion at industrial plants for bioenergy production.
Collapse
Affiliation(s)
- Chenjie Wu
- Key Laboratory of Catalysis Conversion and Energy Materials Chemistry, Ministry of Education, PR China; Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, Engineering Research Center for Heavy Metal Pollution Control for Hubei Province, College of Resources and Environmental Science, South-Central University for Nationalities, Wuhan, 430074, PR China
| | - Qingken Jiang
- Key Laboratory of Catalysis Conversion and Energy Materials Chemistry, Ministry of Education, PR China; Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, Engineering Research Center for Heavy Metal Pollution Control for Hubei Province, College of Resources and Environmental Science, South-Central University for Nationalities, Wuhan, 430074, PR China
| | | | - Yan Sun
- Key Laboratory of Catalysis Conversion and Energy Materials Chemistry, Ministry of Education, PR China; Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, Engineering Research Center for Heavy Metal Pollution Control for Hubei Province, College of Resources and Environmental Science, South-Central University for Nationalities, Wuhan, 430074, PR China
| | - Yaguang Du
- Key Laboratory of Catalysis Conversion and Energy Materials Chemistry, Ministry of Education, PR China; Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, Engineering Research Center for Heavy Metal Pollution Control for Hubei Province, College of Resources and Environmental Science, South-Central University for Nationalities, Wuhan, 430074, PR China
| | - Tian C Zhang
- Civil & Environmental Engineering Department, College of Engineering, University of Nebraska-Lincoln, Omaha, NE, 68182, USA
| | - Dongyun Du
- Key Laboratory of Catalysis Conversion and Energy Materials Chemistry, Ministry of Education, PR China; Key Laboratory of Resources Conversion and Pollution Control of the State Ethnic Affairs Commission, Engineering Research Center for Heavy Metal Pollution Control for Hubei Province, College of Resources and Environmental Science, South-Central University for Nationalities, Wuhan, 430074, PR China.
| |
Collapse
|
19
|
Ma G, He Y, Chen B, Deng H, Liu Y, Wang X, Zhao Z, Kan R. Quasi-Simultaneous Sensitive Detection of Two Gas Species by Cavity-Ringdown Spectroscopy with Two Lasers. SENSORS (BASEL, SWITZERLAND) 2021; 21:7622. [PMID: 34833699 PMCID: PMC8624139 DOI: 10.3390/s21227622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 11/26/2022]
Abstract
We developed a cavity ringdown spectrometer by utilizing a step-scanning and dithering method for matching laser wavelengths to optical resonances of an optical cavity. Our approach is capable of working with two and more lasers for quasi-simultaneous measurements of multiple gas species. The developed system was tested with two lasers operating around 1654 nm and 1658 nm for spectral detections of 12CH4 and its isotope 13CH4 in air, respectively. The ringdown time of the empty cavity was about 340 µs. The achieved high detection sensitivity of a noise-equivalent absorption coefficient was 2.8 × 10-11 cm-1 Hz-1/2 or 1 × 10-11 cm-1 by averaging for 30 s. The uncertainty of the high precision determination of δ13CH4 in air is about 1.3‰. Such a system will be useful for future applications such as environmental monitoring.
Collapse
Affiliation(s)
- Guosheng Ma
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; (G.M.); (Y.H.); (B.C.); (H.D.); (Y.L.)
- Graduate School of Science Island Branch, University of Science and Technology of China, Hefei 230026, China
| | - Yabai He
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; (G.M.); (Y.H.); (B.C.); (H.D.); (Y.L.)
| | - Bing Chen
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; (G.M.); (Y.H.); (B.C.); (H.D.); (Y.L.)
| | - Hao Deng
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; (G.M.); (Y.H.); (B.C.); (H.D.); (Y.L.)
| | - Ying Liu
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; (G.M.); (Y.H.); (B.C.); (H.D.); (Y.L.)
- Graduate School of Science Island Branch, University of Science and Technology of China, Hefei 230026, China
| | - Xingping Wang
- School of Engineering Science, University of Science and Technology of China, Hefei 230026, China;
| | - Zhihao Zhao
- College of Information Science and Engineering, Northeastern University, Shenyang 110819, China;
| | - Ruifeng Kan
- Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; (G.M.); (Y.H.); (B.C.); (H.D.); (Y.L.)
| |
Collapse
|
20
|
Past, Present and Near Future: An Overview of Closed, Running and Planned Biomethanation Facilities in Europe. ENERGIES 2021. [DOI: 10.3390/en14185591] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The power-to-methane technology is promising for long-term, high-capacity energy storage. Currently, there are two different industrial-scale methanation methods: the chemical one (based on the Sabatier reaction) and the biological one (using microorganisms for the conversion). The second method can be used not only to methanize the mixture of pure hydrogen and carbon dioxide but also to methanize the hydrogen and carbon dioxide content of low-quality gases, such as biogas or deponia gas, enriching them to natural gas quality; therefore, the applicability of biomethanation is very wide. In this paper, we present an overview of the existing and planned industrial-scale biomethanation facilities in Europe, as well as review the facilities closed in recent years after successful operation in the light of the scientific and socioeconomic context. To outline key directions for further developments, this paper interconnects biomethanation projects with the competitiveness of the energy sector in Europe for the first time in the literature. The results show that future projects should have an integrative view of electrolysis and biomethanation, as well as hydrogen storage and utilization with carbon capture and utilization (HSU&CCU) to increase sectoral competitiveness by enhanced decarbonization.
Collapse
|
21
|
Mizrahi I, Wallace RJ, Moraïs S. The rumen microbiome: balancing food security and environmental impacts. Nat Rev Microbiol 2021; 19:553-566. [PMID: 33981031 DOI: 10.1038/s41579-021-00543-6] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2021] [Indexed: 02/03/2023]
Abstract
Ruminants produce edible products and contribute to food security. They house a complex rumen microbial community that enables the host to digest their plant feed through microbial-mediated fermentation. However, the rumen microbiome is also responsible for the production of one of the most potent greenhouse gases, methane, and contributes about 18% of its total anthropogenic emissions. Conventional methods to lower methane production by ruminants have proved successful, but to a limited and often temporary extent. An increased understanding of the host-microbiome interactions has led to the development of new mitigation strategies. In this Review we describe the composition, ecology and metabolism of the rumen microbiome, and the impact on host physiology and the environment. We also discuss the most pertinent methane mitigation strategies that emerged to balance food security and environmental impacts.
Collapse
Affiliation(s)
- Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel.
| | - R John Wallace
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel
| |
Collapse
|
22
|
Hydrogen Economy Development Opportunities by Inter-Organizational Digital Knowledge Networks. SUSTAINABILITY 2021. [DOI: 10.3390/su13169194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Innovative power-to-X (P2X) technologies, as a set of emerging new solutions, could play a crucial role in creating sustainable, carbon-neutral economies, such as the hydrogen economy. These technologies, however, are generally not yet implemented on a commercial scale. This research focuses on how innovative, digital inter-organizational knowledge networks of industry representatives and universities could contribute to the commercial implementation of P2X technologies and increase the pace of sustainable hydrogen-based development. The findings of an extended case study with a hybrid (qualitative–quantitative) methodology and a five-year time horizon, suggest the need for a digital knowledge platform, where universities and industry representatives add and combine their knowledge. In contrast with expectations, however, the empirical results show that academia would, not only be capable of supporting the exploration of new solutions, but foster the exploitation of more mature technologies as well. Similarly, large energy companies could also drive exploratory activities, not only exploitative ones. The findings highlight the possible central role of the “system builder” actor, who integrates exploitative-explorative learning and facilitates the formation of a (digital) innovation ecosystem. By exceeding the dominant techno-economic and environmental aspects, this research contributes to the literature by highlighting the applicability of network-based innovation management theory for hydrogen economy research.
Collapse
|
23
|
Abstract
The accumulation of solid and liquid organic waste requires their treatment to develop energy biotechnologies and prevent environment pollution. Aim. The goal of the work was to study the efficiency of the purification of the filtrate from dissolved organic compounds by aerobic oxidation and methane fermentation. Methods. The standard methods were used to determine рН and redox potential (Eh), the gas composition, the content of short-chain fatty acids, the concentration of dissolved organic compounds counting to the total сarbon. The efficiency of two types of microbial metabolism for the degradation of soluble organic compounds of filtrate was compared. Results. The aerobic oxidation was established to provide 1.9 times more efficient removal of dissolved organic compounds, compared with the anaerobic methane fermentation. However, it provided CH4 yield 1 L/dm3 of filtrate (сarbon concentration — 1071 mg/L). The necessity to optimize the methods for purifying filtrate to increase the efficiency of the process was determined. Conclusions. The obtained results will be the basis to develop complex biotechnology providing not only the production of environmentally friendly energy H2 via the fermentation of solid food waste, but also the purification of filtrate to solve the ecological and energy (CH4 production) problem of society.
Collapse
|
24
|
Liu Y, Qian Y, Yong X, Jia H, Wei P, Zhou J. Effects of granular activated carbon and temperature on the viscosity and methane yield of anaerobically digested of corn straw with different dry matter concentrations. BIORESOURCE TECHNOLOGY 2021; 332:125109. [PMID: 33839508 DOI: 10.1016/j.biortech.2021.125109] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion (AD) systems with high substrate concentrations are characterized by high viscosity, which affects material and energy transfer efficiencies, thereby influencing methane production efficiency. In this study, adding granular activated carbon (GAC) and increasing the temperature decreased the viscosity by 4.56-10.19% and 27.13-28.85%, respectively, and improved AD efficiency. Adding GAC and increasing the temperature enhanced the methane yields by 34.37-38.15% and 25.60-28.31%, respectively. Distance-based redundancy analysis showed that the viscosity, temperature, and GAC had the greatest effects on the composition of the microbial community. The dominant bacteria in the medium-temperature AD system at the phylum level belonged to Firmicutes, Bacteroidetes, and Euryarchaeota. In addition to the dominant bacteria in the medium-temperature AD system, the thermophilic phylum Thermotogae was abundant in the high-temperature AD system. Moreover, the relative abundance of Euryarchaeota, which contained most of the methanogens, was higher in the high-temperature AD system than in the medium-temperature AD system.
Collapse
Affiliation(s)
- Yongdi Liu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheckBiotechnology Co, Ltd, Suzhou, Jiangsu 215000, China
| | - Yulei Qian
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Xiaoyu Yong
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Honghua Jia
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Ping Wei
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Jun Zhou
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China.
| |
Collapse
|
25
|
Gutt M, Jordan B, Weidenbach K, Gudzuhn M, Kiessling C, Cassidy L, Helbig A, Tholey A, Pyper DJ, Kubatova N, Schwalbe H, Schmitz RA. High complexity of Glutamine synthetase regulation in
Methanosarcina mazei
: Small protein 26 interacts and enhances glutamine synthetase activity. FEBS J 2021; 288:5350-5373. [DOI: 10.1111/febs.15799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/05/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Miriam Gutt
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Britta Jordan
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Katrin Weidenbach
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Mirja Gudzuhn
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Claudia Kiessling
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Andreas Helbig
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Andreas Tholey
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Dennis Joshua Pyper
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Nina Kubatova
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Ruth Anne Schmitz
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| |
Collapse
|
26
|
Fischer PQ, Sánchez‐Andrea I, Stams AJM, Villanueva L, Sousa DZ. Anaerobic microbial methanol conversion in marine sediments. Environ Microbiol 2021; 23:1348-1362. [PMID: 33587796 PMCID: PMC8048578 DOI: 10.1111/1462-2920.15434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/15/2023]
Abstract
Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.
Collapse
Affiliation(s)
- Peter Q. Fischer
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de GualtarBraga4710‐057Portugal
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
- Faculty of GeosciencesUtrecht University, Princetonlaan 8aUtrecht3584 CBThe Netherlands
| | - Diana Z. Sousa
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
| |
Collapse
|
27
|
Shalvarjian KE, Nayak DD. Transcriptional regulation of methanogenic metabolism in archaea. Curr Opin Microbiol 2021; 60:8-15. [PMID: 33561735 DOI: 10.1016/j.mib.2021.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 11/25/2022]
Abstract
Methanogenesis is a widespread metabolism of evolutionary and environmental importance that is likely to have originated on early Earth. Microorganisms that perform methanogenesis, termed methanogens, belong exclusively to the domain Archaea. Despite maintaining eukaryotic transcription machinery and homologs of bacterial regulators, archaeal transcription and gene regulation appear to be distinct from either domain. While genes involved in methanogenic metabolism have been identified and characterized, their regulation in response to both extracellular and intracellular signals is less understood. Here, we review recent reports on transcriptional regulation of methanogenesis using two model methanogens, Methanococcus maripaludis and Methanosarcina acetivorans, and highlight directions for future research in this nascent field.
Collapse
Affiliation(s)
- Katie E Shalvarjian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dipti D Nayak
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
| |
Collapse
|
28
|
Su F, Yang YY. Microbially induced carbonate precipitation via methanogenesis pathway by a microbial consortium enriched from activated anaerobic sludge. J Appl Microbiol 2020; 131:236-256. [PMID: 33187022 DOI: 10.1111/jam.14930] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 10/14/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022]
Abstract
AIMS Various applications of microbially induced carbonate precipitation (MICP) has been proposed. However, most studies use cultured pure strains to obtain MICP, ignoring advantages of microbial consortia. The aims of this study were to: (i) test the feasibility of a microbial consortium to produce MICP; (ii) identify functional micro-organisms and their relationship; (iii) explain the MICP mechanism; (iv) propose a way of applying the MICP technique to soil media. METHODS AND RESULTS Anaerobic sludge was used as the source of the microbial consortium. A laboratory anaerobic sequencing batch reactor and beaker were used to perform precipitation experiment. The microbial consortium produced MICP with an efficiency of 96·6%. XRD and SEM analysis showed that the precipitation composed of different-size calcite crystals. According to high-throughput 16S rRNA gene sequencing, the functional micro-organisms included acetogenic bacteria, acetate-oxidizing bacteria and archaea Methanosaeta and Methanobacterium beijingense. The methanogenesis acetate degradation provides dissolved inorganic carbon and increases pH for MICP. A series of reactions catalysed by many enzymes and cofactors of methanogens and acetate-oxidizers are involved in the acetate degradation. CONCLUSION This work demonstrates the feasibility of using the microbial consortium to achieve MICP from an experimental and theoretical perspective. SIGNIFICANCE AND IMPACT OF THE STUDY A method of applying the microbial-consortium MICP to soil media is proposed. It has the advantages of low cost, low environmental impact, treatment uniformity and less limitations from natural soils. This method could be used to improve mechanical properties, plug pores and fix harmful elements of soil media, etc.
Collapse
Affiliation(s)
- F Su
- School of Engineering and Technology, China University of Geosciences (Beijing), Beijing, P. R. China
| | - Y Y Yang
- School of Engineering and Technology, China University of Geosciences (Beijing), Beijing, P. R. China
| |
Collapse
|
29
|
Deere TM, Prakash D, Lessner FH, Duin EC, Lessner DJ. Methanosarcina acetivorans contains a functional ISC system for iron-sulfur cluster biogenesis. BMC Microbiol 2020; 20:323. [PMID: 33096982 PMCID: PMC7585200 DOI: 10.1186/s12866-020-02014-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The production of methane by methanogens is dependent on numerous iron-sulfur (Fe-S) cluster proteins; yet, the machinery involved in Fe-S cluster biogenesis in methanogens remains largely unknown. Methanogen genomes encode uncharacterized homologs of the core components of the ISC (IscS and IscU) and SUF (SufBC) Fe-S cluster biogenesis systems found in bacteria and eukaryotes. Methanosarcina acetivorans contains three iscSU and two sufCB gene clusters. Here, we report genetic and biochemical characterization of M. acetivorans iscSU2. RESULTS Purified IscS2 exhibited pyridoxal 5'- phosphate-dependent release of sulfur from L-cysteine. Incubation of purified IscU2 with IscS2, cysteine, and iron (Fe2+) resulted in the formation of [4Fe-4S] clusters in IscU2. IscU2 transferred a [4Fe-4S] cluster to purified M. acetivorans apo-aconitase. IscU2 also restored the aconitase activity in air-exposed M. acetivorans cell lysate. These biochemical results demonstrate that IscS2 is a cysteine desulfurase and that IscU2 is a Fe-S cluster scaffold. M. acetivorans strain DJL60 deleted of iscSU2 was generated to ascertain the in vivo importance of IscSU2. Strain DJL60 had Fe-S cluster content and growth similar to the parent strain but lower cysteine desulfurase activity. Strain DJL60 also had lower intracellular persulfide content compared to the parent strain when cysteine was an exogenous sulfur source, linking IscSU2 to sulfur metabolism. CONCLUSIONS This study establishes that M. acetivorans contains functional IscS and IscU, the core components of the ISC Fe-S cluster biogenesis system and provides the first evidence that ISC operates in methanogens.
Collapse
Affiliation(s)
- Thomas M Deere
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, 72701, USA
| | - Divya Prakash
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Faith H Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, 72701, USA
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA
| | - Daniel J Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, 72701, USA.
| |
Collapse
|
30
|
Seasonal Energy Storage Potential Assessment of WWTPs with Power-to-Methane Technology. ENERGIES 2020. [DOI: 10.3390/en13184973] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Power-to-methane technology (P2M) deployment at wastewater treatment plants (WWTPs) for seasonal energy storage might land on the agenda of decision-makers across EU countries, since large WWTPs produce a notable volume of biogas that could be injected into the natural gas grid with remarkable storage capacities. Because of the recent rapid increase of local photovoltaics (PV), it is essential to explore the role of WWTPs in energy storage and the conditions under which this potential can be realized. This study integrates a techno-economic assessment of P2M technology with commercial/investment attractiveness of seasonal energy storage at large WWTPs. Findings show that a standardized 1 MWel P2M technology would fit with most potential sites. This is in line with the current technology readiness level of P2M, but increasing electricity prices and limited financial resources of WWTPs would decrease the commercial attractiveness of P2M technology deployment. Based on a Hungarian case study, public funding, biomethane feed-in tariff and minimized or compensated surplus electricity sourcing costs are essential to realize the energy storage potential at WWTPs.
Collapse
|
31
|
Liu Y, Lin C, Jia H, Yong X, Xie X, Wu X, Zhou J, Wei P. Effects of amino-modified biofilm carriers on biogas production in the anaerobic digestion of corn straw. ENVIRONMENTAL TECHNOLOGY 2020; 41:2806-2816. [PMID: 30767709 DOI: 10.1080/09593330.2019.1583290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
This paper studied the property of three different biofilm carriers added into the anaerobic digestion systems, a granular activated carbon, a polyacrylonitrile, and a polyacrylonitrile modified with diethylenetriamine (PAN-NH2). The PAN-NH2 system kept the maximum biogas and methane production, which were 42.69% and 37.29% higher than the control system, respectively. The value of pH and chemical oxygen demand, the content of total solid and volatile solid, volatile fatty acids concentration, coenzyme F420 concentration, and microbial community analysis were investigated during the anaerobic digestion process. The PAN-NH2 system had the highest removal efficiency of the pollutants and regulated the pH of the system better than other systems. The result of high-throughput sequencing analysis showed that the addition of biofilm carriers and mediation with amino-groups adjusted system pH and improved biogas and CH4 production by reducing the relative abundance of bacteria in the hydrolysis/acidogenesis stages. Methanosarcina gradually replaced other methanogens during the experimental runs and was the dominant methanogen at the end of the anaerobic digestion process.
Collapse
Affiliation(s)
- Yongdi Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
- Bioenergy Research Institute, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
| | - Chaoba Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
- Bioenergy Research Institute, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
| | - Honghua Jia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
| | - Xiaoyu Yong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
- Bioenergy Research Institute, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
| | - Xinxin Xie
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
- Bioenergy Research Institute, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
| | - Xiayuan Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
- Bioenergy Research Institute, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
| | - Jun Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
- Bioenergy Research Institute, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
| | - Ping Wei
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, People's Republic of China
| |
Collapse
|
32
|
Zaporski J, Jamison M, Zhang L, Gu B, Yang Z. Mercury methylation potential in a sand dune on Lake Michigan's eastern shoreline. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:138879. [PMID: 32371207 DOI: 10.1016/j.scitotenv.2020.138879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Lake Michigan hosts the largest freshwater sand dune system in the world and is economically important for the fishery industry and tourism. Due to industrial pollution and atmospheric mercury (Hg) deposition, toxic levels of methylmercury (MeHg) have been found in the Lake biota, but little information is known regarding MeHg sources and Hg methylation potential in the shoreline sand dunes. We conducted anaerobic incubation experiments with beach sands collected from Ludington, Michigan, and examined the effects of organic carbon substrate addition, inorganic nitrogen, and mineral magnetite on Hg methylation. Despite nutrient poor and low-organic carbon conditions, appreciable Hg methylation activity coupled with carbon degradation was observed in the sands. Addition of acetate as a carbon source substantially increased MeHg production from 2 to 380 ng/kg sediment while acetate was rapidly degraded in the first 19 days of incubation. Ammonium addition showed little influence on carbon degradation or Hg methylation, whereas iron oxide addition (~1% dry weight) significantly inhibited both carbon degradation and MeHg production (by up to 90%), highlighting strongly coupled interactions between microbes, carbon substrates, and minerals. This research demonstrates the potential of microbial Hg methylation in the sand dunes, which may play a role in MeHg input and bioaccumulation in the Lake Michigan ecosystem.
Collapse
Affiliation(s)
- Jared Zaporski
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Megan Jamison
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Lijie Zhang
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Ziming Yang
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.
| |
Collapse
|
33
|
Muchowska KB, Varma SJ, Moran J. Nonenzymatic Metabolic Reactions and Life's Origins. Chem Rev 2020; 120:7708-7744. [PMID: 32687326 DOI: 10.1021/acs.chemrev.0c00191] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.
Collapse
Affiliation(s)
| | - Sreejith J Varma
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
| | - Joseph Moran
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
| |
Collapse
|
34
|
He P, Xie L, Zhang X, Li J, Lin X, Pu X, Yuan C, Tian Z, Li J. Microbial Diversity and Metabolic Potential in the Stratified Sansha Yongle Blue Hole in the South China Sea. Sci Rep 2020; 10:5949. [PMID: 32249806 PMCID: PMC7136235 DOI: 10.1038/s41598-020-62411-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/11/2020] [Indexed: 01/08/2023] Open
Abstract
The Sansha Yongle Blue Hole is the world’s deepest (301 m) underwater cave and has a sharp redox gradient, with oligotrophic, anoxic, and sulfidic bottom seawater. In order to discover the microbial communities and their special biogeochemical pathways in the blue hole, we analyzed the 16S ribosomal RNA amplicons and metagenomes of microbials from seawater depths with prominent physical, chemical, and biological features. Redundancy analysis showed that dissolved oxygen was the most important factor affecting the microbial assemblages of the blue hole and surrounding open sea waters, and significantly explained 44.7% of the total variation, followed by silicate, temperature, sulfide, ammonium, methane, nitrous oxide, nitrate, dissolved organic carbon, salinity, particulate organic carbon, and chlorophyll a. We identified a bloom of Alteromonas (34.9%) at the primary nitrite maximum occurring in close proximity to the chlorophyll a peak in the blue hole. Genomic potential for nitrate reduction of Alteromonas might contribute to this maximum under oxygen decrease. Genes that would allow for aerobic ammonium oxidation, complete denitrification, and sulfur-oxidization were enriched at nitrate/nitrite-sulfide transition zone (90 and 100 m) of the blue hole, but not anammox pathways. Moreover, γ-Proteobacterial clade SUP05, ε-Proteobacterial genera Sulfurimonas and Arcobacter, and Chlorobi harbored genes for sulfur-driven denitrification process that mediated nitrogen loss and sulfide removal. In the anoxic bottom seawater (100-300 m), high levels of sulfate reducers and dissimilatory sulfite reductase gene (dsrA) potentially created a sulfidic zone of ~200 m thickness. Our findings suggest that in the oligotrophic Sansha Yongle Blue Hole, O2 deficiency promotes nitrogen- and sulfur-cycling processes mediated by metabolically versatile microbials.
Collapse
Affiliation(s)
- Peiqing He
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China. .,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China. .,Key Laboratory of Natural Products of Qingdao, Qingdao, 266061, China.
| | - Linping Xie
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xuelei Zhang
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Jiang Li
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Key Laboratory of Natural Products of Qingdao, Qingdao, 266061, China
| | - Xuezheng Lin
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Key Laboratory of Natural Products of Qingdao, Qingdao, 266061, China
| | - Xinming Pu
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Chao Yuan
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Ziwen Tian
- Research Center for Islands and Coastal Zone, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China
| | - Jie Li
- Marine Engineering Environment and Geomatic Center, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao, 266061, China
| |
Collapse
|
35
|
Nagoya M, Kouzuma A, Ueno Y, Watanabe K. Isolation of an Obligate Mixotrophic Methanogen That Represents the Major Population in Thermophilic Fixed-Bed Anaerobic Digesters. Microorganisms 2020; 8:microorganisms8020217. [PMID: 32041148 PMCID: PMC7074840 DOI: 10.3390/microorganisms8020217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
Methanothermobacter Met2 is a metagenome-assembled genome (MAG) that encodes a putative mixotrophic methanogen constituting the major populations in thermophilic fixed-bed anaerobic digesters. In order to characterize its physiology, the present work isolated an archaeon (strain Met2-1) that represents Met2-type methanogens by using a combination of enrichments under a nitrogen atmosphere, colony formation on solid media and limiting dilution under high partial pressures of hydrogen. Strain Met2-1 utilizes hydrogen and carbon dioxide for methanogenesis, while the growth is observed only when culture media are additionally supplemented with acetate. It does not grow on acetate in the absence of hydrogen. The results demonstrate that Methanothermobacter sp. strain Met2-1 is a novel methanogen that exhibits obligate mixotrophy.
Collapse
Affiliation(s)
- Misa Nagoya
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; (M.N.); (A.K.)
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; (M.N.); (A.K.)
| | - Yoshiyuki Ueno
- Kajima Technical Research Institute, Chofu, Tokyo 182-0036, Japan;
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; (M.N.); (A.K.)
- Correspondence: ; Tel.: +81-42-676-7079
| |
Collapse
|
36
|
Xiang Y, Yang Z, Zhang Y, Xu R, Zheng Y, Hu J, Li X, Jia M, Xiong W, Cao J. Influence of nanoscale zero-valent iron and magnetite nanoparticles on anaerobic digestion performance and macrolide, aminoglycoside, β-lactam resistance genes reduction. BIORESOURCE TECHNOLOGY 2019; 294:122139. [PMID: 31525586 DOI: 10.1016/j.biortech.2019.122139] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/05/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
The effect of nanoscale zero-valent iron (NZVI) and magnetite nanoparticles (Fe3O4 NPs) on anaerobic digestion (AD) performance was investigated through a series of 100-day semi-continuous mesophilic anaerobic digestions. The results indicated that biogas production had increased by 24.44% and 21.66% with the addition of 0.5 g/L Fe3O4 NPs and 1.0 g/L NZVI, respectively. Besides, the abundance of five widespread antibiotic resistance genes (ARGs) (ermF, ermA, ermT, aac(6')-IB, blaOXA-1) was also studied. The decrease in abundance of aac(6')-IB and blaOXA-1 was observed during the AD process with an average removal rate of 95.69% and 44.82%, respectively. Most of the ARGs, especially ermA and ermT, were less abundant in NZVI group compared with control group. The overall results suggested that the addition of NZVI and Fe3O4 NPs contributed to a better sludge anaerobic digestion performance, and NZVI was beneficial to the removal of some ARGs.
Collapse
Affiliation(s)
- Yinping Xiang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Yanru Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Rui Xu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, PR China
| | - Jiahui Hu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xiaoyang Li
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, PR China
| | - Meiying Jia
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Weiping Xiong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jiao Cao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| |
Collapse
|
37
|
Ma J, Pan J, Qiu L, Wang Q, Zhang Z. Biochar triggering multipath methanogenesis and subdued propionic acid accumulation during semi-continuous anaerobic digestion. BIORESOURCE TECHNOLOGY 2019; 293:122026. [PMID: 31449922 DOI: 10.1016/j.biortech.2019.122026] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
The semi-continuous anaerobic digestion (AD) performances of dry chicken manure (DCM) were investigated at the temperature of 35 ± 1 °C with and without biochar. The average specific methane productions of 0.18 L/g VSadded and 0.17 L/g VSadded were achieved without biochar at the organic loading rate (OLR) of 3.125 and 6.25 g VS/L/d, respectively. An increase of 12% in methane production was obtained in the presence of biochar at the two operational OLRs. Accumulation of propionic acid was observed associating with AD of DCM, which was substantially alleviated by biochar supplement. The buffer capacity of biochar was supposed to develop through strengthening the buffer system established by NH4+ and volatile fatty acids. Methanosarcina that can utilize multiple nutrients for methanogenesis was the dominant archaea in the presence of biochar, while the strictly aceticlastic Methanosaeta was dominant in control digester. These results suggest that biochar enhanced methanogenesis through intensifying its available pathway.
Collapse
Affiliation(s)
- Junyi Ma
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Western Scientific Observation and Experiment Station of Development and Utilization of Rural Renewable Energy of Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junting Pan
- Key Laboratory of Non-point Source Pollution of Ministry of Agricultural and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Qiu
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Western Scientific Observation and Experiment Station of Development and Utilization of Rural Renewable Energy of Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
38
|
Ali N, Gong H, Liu X, Giwa AS, Wang K. Evaluation of bacterial association in methane generation pathways of an anaerobic digesting sludge via metagenomic sequencing. Arch Microbiol 2019; 202:31-41. [PMID: 31456050 DOI: 10.1007/s00203-019-01716-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/09/2019] [Accepted: 08/18/2019] [Indexed: 12/31/2022]
Abstract
Anaerobic digestion, a recently hot technology to produce biogases especially methane generation for biofuel from wastewater, is considered an effective explanation for energy crisis and global pollution threat. A complex microbiome population is present in sludge, which plays an important role in the digestion of complex polymer into simple monomers. 16S rRNA approaches simply are not enough for amplification due to the involvement of extreme complex population. However, Illumina sequencing is a recent powerful technology to reveal the entire microbiome structure and methane generation pathways in anaerobic digestion. Metagenomic sequencing was tested to reveal the microbial structure of a digested sludge from a local wastewater treatment plant in Beijing. The Illumina HiSeq program was used to extract about 5 GB of data for metagenomic analysis. The classification investigation revealed about 97.64% dominancy of bacteria while 1.78% were detected to be archaea using MG-RAST server. The most abundant bacterial communities were reported to be Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. Furthermore, the important microbiome involved in methane generation was revealed. The dominant methanogens were detected (Methanosaeta and Methanosarcina), with affiliation of dominant genes involved in acetoclastic methanogenesis in a digesting sludge. The metagenomic analysis showed that microbial structure and methane generation pathways were successfully dissected in an anaerobic digester.
Collapse
Affiliation(s)
- Nasir Ali
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China.,Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong Province, People's Republic of China
| | - Hui Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Xiang Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Abdulmoseen Segun Giwa
- Green Intelligence Environmental School, Yangtze Normal University, Chongqing, 408003, People's Republic of China
| | - Kaijun Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China.
| |
Collapse
|
39
|
Wu L, Zeng T, Zinellu A, Rubino S, Kelvin DJ, Carru C. A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians. mSystems 2019; 4:4/4/e00325-19. [PMID: 31289141 PMCID: PMC6616150 DOI: 10.1128/msystems.00325-19] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 06/18/2019] [Indexed: 02/05/2023] Open
Abstract
Sardinia, Italy, has a high prevalence of residents who live more than 100 years. The reasons for longevity in this isolated region are currently unknown. Gut microbiota may hold a clue. To explore the role gut microbiota may play in healthy aging and longevity, we used metagenomic sequencing to determine the compositional and functional differences in gut microbiota associated with populations of different ages in Sardinia. Our data revealed that the gut microbiota of both young and elderly Sardinians shared similar taxonomic and functional profiles. A different pattern was found in centenarians. Within the centenarian group, the gut microbiota was correlated with the functional independence measurement of the host. Centenarians had a higher diversity of core microbiota species and microbial genes than those in the young and elderly. We found that the gut microbiota in Sardinian centenarians displayed a rearranged taxonomic pattern compared with those of the young and elderly, featured by depletion of Faecalibacterium prausnitzii and Eubacterium rectale and enriched for Methanobrevibacter smithii and Bifidobacterium adolescentis Moreover, functional analysis revealed that the microbiota in centenarians had high capacity for central metabolism, especially glycolysis and fermentation to short-chain fatty acids (SCFAs), although the gut microbiota in centenarians was low in genes encoding enzymes involved in degradation of carbohydrates, including fibers and galactose.IMPORTANCE The gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment that is regarded as beneficial for host gut epithelium. The low abundance of genes encoding components of pathways involved in carbohydrate degradation was also found in the gut microbiota of Sardinian centenarians and is often associated with poor gut health. Overall, our study here represents an expansion of previous research investigating the age-related changes in gut microbiota. Furthermore, our study provides a new prospective for potential targets for gut microbiota intervention directed at limiting gut inflammation and pathology and enhancing a healthy gut barrier.
Collapse
Affiliation(s)
- Lu Wu
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tiansheng Zeng
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - David J Kelvin
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou, Guangdong, China
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| |
Collapse
|
40
|
Song L, Li D, Fang H, Cao X, Liu R, Niu Q, Li YY. Revealing the correlation of biomethane generation, DOM fluorescence, and microbial community in the mesophilic co-digestion of chicken manure and sheep manure at different mixture ratio. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:19411-19424. [PMID: 31073832 DOI: 10.1007/s11356-019-05175-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Batch co-digestion tests of chicken manure (CM) and sheep manure (SM) at different ratio (Rs/c) were conducted under mesophilic condition (35 °C). Batch kinetic analysis of bioCH4 production, excitation-emission matrix (EEM) fluorescence of dissolved organic matter (DOM), and microbial community were investigated. The well-fitted modified Gompertz model (R2, 0.98-0.99) resulted that the co-digestion markedly improved the methane production rate and shortened the lag phase time. The highest bioCH4 yield of 219.67 mL/gVSadd and maximum production rate of 0.378 mL/gVSadd/h were obtained at an optimum Rs/c of 0.4. Additionally, a significant variation of DOM was detected at the Rs/c of 0.4 with a consistent degradation of soluble microbial byproduct-like and protein-like organics. The positive synergy effects of co-digestion conspicuously enhanced the bioCH4 production efficiency. FI370 and NADH were significantly correlated to Rs/c (p < 0.05). Moreover, the correlations among process indicator, EEM-peaks and different environmental parameters were evaluated by Pearson correlation analysis. The high diversity of acetoclastic methanogens and hydrogenotrophic methanogens in the co-digestion improved the stability of process. Graphical Abstract.
Collapse
Affiliation(s)
- Liuying Song
- School of Environmental Science and Engineering, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Dunjie Li
- School of Environmental Science and Engineering, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Hongli Fang
- School of Environmental Science and Engineering, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Xiangyunong Cao
- School of Environmental Science and Engineering, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Rutao Liu
- School of Environmental Science and Engineering, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China
| | - Qigui Niu
- School of Environmental Science and Engineering, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, People's Republic of China.
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| |
Collapse
|
41
|
The acetotrophic pathway dominates methane production in Zoige alpine wetland coexisting with hydrogenotrophic pathway. Sci Rep 2019; 9:9141. [PMID: 31235734 PMCID: PMC6591398 DOI: 10.1038/s41598-019-45590-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 04/08/2019] [Indexed: 11/16/2022] Open
Abstract
As a typical alpine wetland on the Tibetan Plateau, the Zoige wetland processes a large carbon stock and is a hotspot of methane emission. To date, many studies have investigated the methane flux in this wetland; however, the research on the source of methane in the soils of Zoige wetland is not clear enough. In this study, we determined the dynamic characteristics of the stable carbon isotopes during the methanogenesis of Zoige wetland soil and the corresponding microbial changes. The results showed that the δ13CH4 varied between −19.86‰ and −28.32‰ and the αC ranged from 1.0029 to 1.0104 in the methanogenesis process, which suggests the dominance of acetotrophic methanogenesis. And among the increased methanogens, acetotrophic methanogens multiplied more obviously than hydrogenotrophic menthanogens. In addition, the results of structural equation models showed that the variations in stable carbon isotopes during the process were mainly affected by acetotrophic methanogens. Although the acetotrophic pathway was dominate, the varied isotope characteristics, increased methanogens and ratio of carbon dioxide to methane all showed that hydrogenotrophic and acetotrophic methanogenesis coexisted in the Zoige wetland. Overall, our study provided a detailed and definitive information to the source of methane in the soil of the Zoige wetland and laid a foundation of mechanism to the research of greenhouse gas in this alpine wetland.
Collapse
|
42
|
Song L, Li D, Cao X, Tang Y, Liu R, Niu Q, Li YY. Optimizing biomethane production of mesophilic chicken manure and sheep manure digestion: Mono-digestion and co-digestion kinetic investigation, autofluorescence analysis and microbial community assessment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 237:103-113. [PMID: 30780051 DOI: 10.1016/j.jenvman.2019.02.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/29/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
Optimization of mesophilic methane production from Chicken manure (CM) and Sheep manure (SM) at total solid (TS) of 8% and 1.6% were obtained by sequence tests in mono-digestion. However, the positive synergy of co-digestion with an optimum CM/SM of 2.5 (310 mLCH4/gVSadded) resulted in a high hydrolytic capacity and methane production. The modified Gompertz model (R2 > 0.98) and modified Aiba model (R2 > 0.88) illustrated co-digestion significantly improved the methane generation rate with strong ammonia tolerance. Dissolved Organic Matter (DOM) variation in response to the metabolic rate of microbial community illustrated that the SMP-like and protein-like components half-split by EEM-PARAFAC were significantly negative corresponded to bio-methane production. Moreover, the canonical correlation analysis (CCA) resulted a significant difference between the substrate and DOM composition. Potential functional metabolic illustrated statistically significance difference between mono and co-digestion, however, Methanosaeta and Syntrophobacter predominated the syntrophic methanogenesis. The constructed complex metabolic cooperation caused the co-digestion stable and high efficiency.
Collapse
Affiliation(s)
- Liuying Song
- School of Environmental Science and Engineering, Shandong University, Shandong Province, 72#Jimo Binhai Road, Qingdao, 266237, PR China
| | - Dunjie Li
- School of Environmental Science and Engineering, Shandong University, Shandong Province, 72#Jimo Binhai Road, Qingdao, 266237, PR China
| | - Xiangyunong Cao
- School of Environmental Science and Engineering, Shandong University, Shandong Province, 72#Jimo Binhai Road, Qingdao, 266237, PR China
| | - Yu Tang
- School of Environmental Science and Engineering, Shandong University, Shandong Province, 72#Jimo Binhai Road, Qingdao, 266237, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, Shandong Province, 72#Jimo Binhai Road, Qingdao, 266237, PR China
| | - Qigui Niu
- School of Environmental Science and Engineering, Shandong University, Shandong Province, 72#Jimo Binhai Road, Qingdao, 266237, PR China; Jiangsu Key Laboratory of Anaerobic Biotechnology (Jiangnan University), Wuxi, 214122, PR China.
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| |
Collapse
|
43
|
Wyman V, Serrano A, Fermoso FG, Villa Gomez DK. Trace elements effect on hydrolytic stage towards biogas production of model lignocellulosic substrates. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 234:320-325. [PMID: 30634124 DOI: 10.1016/j.jenvman.2019.01.015] [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: 07/16/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
The effect and the response of several trace elements (TE) addition to the anaerobic degradation of key compounds of lignocellulosic biomass were evaluated. Lignin, cellulose and xylose were selected as principal compounds of lignocellulosic biomass. Lignin degradation was only improved by the addition of 1000 mg Fe/L, which allowed an improvement on the methane yield coefficient of 28% compared to control. SEM images from an abiotic assay showed that this effect is more likely related with a chemical effect induced by the Fe solution, instead of an enzymatic response. Pre-treatments focused on breaking the recalcitrant structure of the lignin could be more promising than TE addition for rich lignin-content substrates. Unlike to the response observed with lignin, cellulose showed a clear effect of the TE addition on methane production rate, indicating a higher preponderance of the enzymatic activity compared to the lignin biomethanization. Experiments with xylose resulted in a strong accumulation of volatile fatty acids. TE addition should be adapted to the substrate composition given the different response of each lignocellulosic compound to the different TE addition.
Collapse
Affiliation(s)
- Valentina Wyman
- School of Civil Engineering, The University of Queensland, Campus St. Lucia - AEB Ed 49, St Lucia, 4067, QLD, Australia; Departamento de Ingeniería Química y Ambiental, Universidad Técnica Federico Santa María, Avenida Vicuña Mackenna, 3939, Santiago, Chile
| | - Antonio Serrano
- School of Civil Engineering, The University of Queensland, Campus St. Lucia - AEB Ed 49, St Lucia, 4067, QLD, Australia; Instituto de Grasa, Spanish National Research Council (CSIC), Ctra. de Utrera, km. 1, Seville, Spain.
| | - Fernando G Fermoso
- Instituto de Grasa, Spanish National Research Council (CSIC), Ctra. de Utrera, km. 1, Seville, Spain
| | - Denys K Villa Gomez
- School of Civil Engineering, The University of Queensland, Campus St. Lucia - AEB Ed 49, St Lucia, 4067, QLD, Australia
| |
Collapse
|
44
|
Wu M, Xu X, Lu K, Li X. Effects of the presence of nanoscale zero-valent iron on the degradation of polychlorinated biphenyls and total organic carbon by sediment microbial fuel cell. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:39-44. [PMID: 30502733 DOI: 10.1016/j.scitotenv.2018.11.326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/06/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
The degradation of polychlorinated biphenyls (PCBs) and total organic carbon (TOC) by sediment microbial fuel cell (SMFC) with/without nanoscale zero-valent iron (NZVI) addition was investigated. It was found that the combined application led to the highest removal efficiencies of PCBs (37.55 ± 1.11%) and TOC (49.72 ± 1.54%) in all circumstances and produced a higher power density (108.89 mW/m2) and a corresponding lower internal resistance (264 Ω) than operation employing SMFC only. The TOC removal efficiency and the total production of electricity were linear. High-throughput sequencing of anodic microbial communities indicated that the electrode participation can increase the abundance of electrogenic bacteria (Geobacter and Pseudomonas) and the NZVI addition can reduce the oxidation reduction potential of the system and therefore enrich some bacteria (Longilinea and Desulfofustis) beneficial to the degradation of organic matter.
Collapse
Affiliation(s)
- Mingsong Wu
- College of Resources and Civil Engineering, Northeastern University, Shenyang 100819, China; School of Resources and Materials, Northeastern University at Qinhuangdao, Qinhuangdao 066004, China; Qinhuangdao Key Laboratory of Water Conservation and Pollution Control and Ecological Restoration, Qinhuangdao 066004, China.
| | - Xun Xu
- Tongji Zhejiang College, Jiaxing 314051, China
| | - Kexiang Lu
- Tongji Zhejiang College, Jiaxing 314051, China
| | - Xueqi Li
- School of Resources and Materials, Northeastern University at Qinhuangdao, Qinhuangdao 066004, China
| |
Collapse
|
45
|
Wyman V, Serrano A, Borja R, Jiménez A, Carvajal A, Lenz M, Bartacek J, Fermoso FG. Effects of barium on the pathways of anaerobic digestion. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 232:397-403. [PMID: 30500703 DOI: 10.1016/j.jenvman.2018.11.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
The sufficient presence of trace elements (TE) is essential for anaerobic digestion. Barium (Ba) is considered a non-essential trace element that can be collaterally added to digesters as part of low-cost trace element sources or because of its presence in some feedstocks, such as crude glycerol. In the present study, the impact of Ba supplementation (2-2000 mg/L) on each stage of the anaerobic digestion (AD) process was evaluated using pure substrates (i.e., cellulose, glucose, a mixture of volatile fatty acids, sodium acetate and hydrogen) as well as a complex substrate (i.e., dried green fodder). Hydrolytic activity was affected at dosages higher than 200 mg Ba/L, whereas cellulose degradation was completely inhibited at 2000 mg Ba/L. The negative effects of the addition of Ba to methane production were observed only in the hydrolytic activity, and no effects were detected at any barium dosage in the subsequent anaerobic steps. Because Ba does not have a reported role as a cofactor of enzymes, this response could have been due to a direct inhibitory effect, a variation in the bioavailability of other trace elements, or even the availability of CO2/SO4 through precipitation as Ba-carbonates and sulphates. The results showed that the addition of Ba modified the chemical equilibrium of the studied system by varying the soluble concentration of some TEs and therefore their bioavailability. The highest variation was detected in the soluble concentration of zinc, which increased as the amount of Ba increased. Although little research has shown that Ba has some utility in anaerobic processes, its addition must be carefully monitored to avoid an undesirable modification of the chemical equilibrium in the system.
Collapse
Affiliation(s)
- V Wyman
- Universidad Técnica Federico Santa María, Avenida Vicuña Mackenna 3939, San Joaquín, Santiago, Chile; Universidad Pablo de Olavide, Carretera de Utrera, 1, 41013, Seville, Spain
| | - A Serrano
- Instituto de la Grasa (CSIC), Seville, Spain; School of Civil Engineering, The University of Queensland, Ed. 49, Campus St Lucia, 4067, Brisbane, Australia.
| | - R Borja
- Instituto de la Grasa (CSIC), Seville, Spain
| | - A Jiménez
- Universidad Pablo de Olavide, Carretera de Utrera, 1, 41013, Seville, Spain
| | - A Carvajal
- Universidad Técnica Federico Santa María, Avenida Vicuña Mackenna 3939, San Joaquín, Santiago, Chile
| | - M Lenz
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Switzerland; Sub-Department of Environmental Technology, Wageningen University, 6700 AA, Wageningen, the Netherlands
| | - J Bartacek
- University of Chemistry and Technology Prague, Czech Republic
| | - F G Fermoso
- Instituto de la Grasa (CSIC), Seville, Spain
| |
Collapse
|
46
|
Moraïs S, Mizrahi I. The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States. Trends Microbiol 2019; 27:538-549. [PMID: 30679075 DOI: 10.1016/j.tim.2018.12.011] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/28/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023]
Abstract
The rumen ecosystem represents a classic example of host-microbiome symbiosis. In this obligatory relationship, the host feeds on plant fibers that can only be degraded through a set of complex metabolic cascades, exclusively encoded in rumen-associated microbes. These various metabolic pathways are distributed across a multitude of microbial populations. Application of basic ecological principles to this ecosystem can contribute to profound understanding of the rules that shape it. Here, we discuss recent studies by examining the mapping between host attributes, rumen ecosystem composition, and functionality to propose simple, yet powerful concepts to guide the interpretation of microbiome data and enable a better understanding of how the system responds to perturbations.
Collapse
Affiliation(s)
- Sarah Moraïs
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel.
| |
Collapse
|
47
|
Song L, Song Y, Li D, Liu R, Niu Q. The auto fluorescence characteristics, specific activity, and microbial community structure in batch tests of mono-chicken manure digestion. WASTE MANAGEMENT (NEW YORK, N.Y.) 2019; 83:57-67. [PMID: 30514471 DOI: 10.1016/j.wasman.2018.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 10/22/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
Batch tests inoculated with granular and suspended sludge of mono chicken manure (CM) digestion were conducted. Kinetic analysis showed a maximum bio-CH4 generation (6 mL/gVS/d) at an optimal TS of 10-12%. At a TS of 25%, serious inhibition was found for granular sludge and even greater inhibition for the suspended sludge caused by free ammonia. The auto fluorescence of Excitation-mission matrix with parallel factor analysis (PARAFAC) showed that the dissolved organic matter (DOM) varied between the form C1, C2, C3 and C4. The split component of the SMP-like C2 and protein-like C4 significantly related to the bio-methane production in time series. The canonical correlation analysis (CCA) indicated that ammonia, pH, and TS influenced the PARAFAC component significantly. The aceticlastic methanogens of the genus Methanosaeta and acetogens of the genus Syntrophobacter predominated in the CM sludge. The methanogens and acetogens formed a metabolic cooperation, making the process a stable methane produced activity.
Collapse
Affiliation(s)
- Liuying Song
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Yong Song
- College of Agronomy, Liaocheng University, No.1 Hunan Road, Liaocheng, Shandong 252000, PR China
| | - Dunjie Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Qigui Niu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China; Jiangsu Key Laboratory of Anaerobic Biotechnology (Jiangnan University), Wuxi 214122, PR China.
| |
Collapse
|
48
|
Muñoz-Velasco I, García-Ferris C, Hernandez-Morales R, Lazcano A, Peretó J, Becerra A. Methanogenesis on Early Stages of Life: Ancient but Not Primordial. ORIGINS LIFE EVOL B 2018; 48:407-420. [PMID: 30612264 DOI: 10.1007/s11084-018-9570-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
Abstract
Of the six known autotrophic pathways, the Wood-Ljungdahl pathway (WL) is the only one present in both the acetate producing Bacteria (homoacetogens) and the methane producing Archaea (hydrogenotrophic methanogens), and it has been suggested that WL is one of the oldest metabolic pathways. However, only the so-called carbonyl branch is shared by Archaea and Bacteria, while the methyl branch is different, both in the number of reactions and enzymes, which are not homologous among them. In this work we show that some parts of the methyl branch of archaeal Wood-Ljungdahl pathway (MBWL) are present in bacteria as well as in non-methanogen archaea, although the tangled evolutionary history of MBWL cannot be traced back to the Last Common Ancestor. We have also analyzed the different variants of methanogenesis (hydrogenotrophic, acetoclastic and methylotrophic pathways), and concluded that each of these pathways, and every different enzyme or subunit (in the case of multimeric enzymes), has their own intricate evolutionary history. Our study supports the scenario of hydrogenotrophic methanogenesis being older than the other variants, albeit not old enough to be present in the last archaeal common ancestor.
Collapse
Affiliation(s)
- Israel Muñoz-Velasco
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70-407 Cd. Universitaria, 04510, Ciudad de México, Mexico
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, C.P., 04510, Ciudad de México, Mexico
| | - Carlos García-Ferris
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Apartat Postal 22085, 46071, València, Spain
- Institute for Integrative Systems Biology, (I2SysBio, Universitat de València-CSIC), Apartat Postal 22085, 46071, València, Spain
| | - Ricardo Hernandez-Morales
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70-407 Cd. Universitaria, 04510, Ciudad de México, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70-407 Cd. Universitaria, 04510, Ciudad de México, Mexico
- Miembro de El Colegio Nacional, El Colegio Nacional, Donceles 104, Centro Histórico, 06020, Ciudad de México, Mexico
| | - Juli Peretó
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Apartat Postal 22085, 46071, València, Spain
- Institute for Integrative Systems Biology, (I2SysBio, Universitat de València-CSIC), Apartat Postal 22085, 46071, València, Spain
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70-407 Cd. Universitaria, 04510, Ciudad de México, Mexico.
| |
Collapse
|
49
|
Wirth R, Kádár G, Kakuk B, Maróti G, Bagi Z, Szilágyi Á, Rákhely G, Horváth J, Kovács KL. The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing. Front Microbiol 2018; 9:2285. [PMID: 30319585 PMCID: PMC6165872 DOI: 10.3389/fmicb.2018.02285] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/07/2018] [Indexed: 12/31/2022] Open
Abstract
The cow rumen harbors a great variety of diverse microbes, which form a complex, organized community. Understanding the behavior of this multifarious network is crucial in improving ruminant nutrient use efficiency. The aim of this study was to expand our knowledge by examining 10 Holstein dairy cow rumen fluid fraction whole metagenome and transcriptome datasets. DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements. The taxonomic core microbiome consisted of 48 genera belonging to Bacteria (47) and Archaea (1). The genus Prevotella predominated the planktonic core community. Core functional groups were identified using co-occurrence analysis and resulted in 587 genes, from which 62 could be assigned to metabolic functions. Although this was a minimal functional core, it revealed key enzymes participating in various metabolic processes. A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified. Transcripts coding for enzymes active in methanogenesis made up 1% of the core functions. The genera associated with the core enzyme functions were also identified. Linking genera to functions showed that the main metabolic pathways are primarily provided by Bacteria and several genera may serve as a “back-up” team for the central functions. The key actors in most essential metabolic routes belong to the genus Prevotella. Confirming earlier studies, the genus Methanobrevibacter carries out the overwhelming majority of rumen methanogenesis and therefore methane emission mitigation seems conceivable via targeting the hydrogenotrophic methanogenesis.
Collapse
Affiliation(s)
- Roland Wirth
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Balázs Kakuk
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - József Horváth
- Faculty of Agriculture, University of Szeged, Hódmezövásárhely, Hungary
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary.,Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary
| |
Collapse
|
50
|
Ito H, Kondo R, Yoshimori K, Kamachi T. Methane Hydroxylation with Water as an Electron Donor under Light Irradiation in the Presence of Reconstituted Membranes Containing both Photosystem II and a Methane Monooxygenase. Chembiochem 2018; 19:2152-2155. [DOI: 10.1002/cbic.201800324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Hidehiro Ito
- Department of Life Science and Technology; Tokyo Institute of Technology; 2-12-1-M6-7 Ookayama Meguro-ku Tokyo 152-8550 Japan
| | - Ryuichi Kondo
- Department of Life Science and Technology; Tokyo Institute of Technology; 2-12-1-M6-7 Ookayama Meguro-ku Tokyo 152-8550 Japan
| | - Kosei Yoshimori
- Department of Life Science and Technology; Tokyo Institute of Technology; 2-12-1-M6-7 Ookayama Meguro-ku Tokyo 152-8550 Japan
| | - Toshiaki Kamachi
- Department of Life Science and Technology; Tokyo Institute of Technology; 2-12-1-M6-7 Ookayama Meguro-ku Tokyo 152-8550 Japan
| |
Collapse
|