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Zhou H, Guo S, Hui C, Zhu M, Shen D, Fang C, Long Y, Hu L. Sulfate reduction behavior in response to landfill dynamic pressure changes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119784. [PMID: 38081091 DOI: 10.1016/j.jenvman.2023.119784] [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: 07/18/2023] [Revised: 11/24/2023] [Accepted: 12/03/2023] [Indexed: 01/14/2024]
Abstract
During the long-term stabilization process of landfills, the pressure field undergoes constant changes. This study constructed dynamic pressure changes scenarios of high-pressure differentials (0.6 MPa) and low-pressure differentials (0.2 MPa) in the landfill pressure field at 25 °C and 50 °C, and investigated the sulfate reduction behavior in response to landfill dynamic pressure changes. The results showed that the pressurization or depressurization of high-pressure differentials caused more significant differences in sulfate reduction behavior than that of low-pressure differentials. The lowest hydrogen sulfide (H2S) release peak concentration under pressurization was only 29.67% of that under initial pressure condition; under depressurization, the highest peak concentration of H2S was up to 21,828 mg m-3, posing a serious risk of H2S pollution. Microbial community and correlation analysis showed that pressure had a negative impact on the sulfate-reducing bacteria (SRB) community, and the SRB community adjusted its structure to adapt to pressure changes. Specific SRBs were further enriched with pressure changes. Differential H2S release behavior under pressure changes in the 25 °C pressure environments were mediated by Desulfofarcimen (ASV343) and Desulfosporosinus (ASV1336), while Candidatus Desulforudis (ASV24) and Desulfohalotomaculum (ASV94) played a key role at 50 °C. This study is helpful in the formulation of control strategies for the source of odor pollution in landfills.
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Affiliation(s)
- Haomin Zhou
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Shuli Guo
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Cai Hui
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Min Zhu
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Dongsheng Shen
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Chengran Fang
- College of Civil Engineering, Zhejiang University of Technology, Hangzhou, 310023, China
| | - Yuyang Long
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Engineering Research Center of Non-ferrous Metal Waste Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.
| | - Lifang Hu
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China.
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Sun Z, He J, Yu N, Chen Y, Chen Y, Tang Y, Kida K. Biomethane production and microbial strategies corresponding to high organic loading treatment for molasses wastewater in an upflow anaerobic filter reactor. Bioprocess Biosyst Eng 2023:10.1007/s00449-023-02882-5. [PMID: 37209175 DOI: 10.1007/s00449-023-02882-5] [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: 01/14/2023] [Accepted: 05/10/2023] [Indexed: 05/22/2023]
Abstract
Molasses wastewater contains high levels of organic compounds, cations, and anions, causing operational problems for anaerobic biological treatment. In this study, an upflow anaerobic filter (UAF) reactor was employed to establish a high organic loading treatment system for molasses wastewater and further investigated the microbial community dynamics in response to this stressful operation. The biogas production increased with an increase in total organic carbon (TOC) loading rate from 1.0 to 14 g/L/day, and then it decreased with further TOC loading rate addition until 16 g/L/day. The UAF reactor achieved a maximum biogas production of 6800 mL/L/day with a TOC removal efficiency of 66.5% at a TOC loading rate of 14 g/L/day. Further microbial analyses revealed that both the bacterial and archaeal communities developed multiple strategies to maintain stable operation of the reactor at high organic loading (e.g., Proteiniphilum and Defluviitoga maintained high abundances throughout the operation; Tissierella temporarily dominated the bacterial community at TOC loading rates of 8.0 to 14 g/L/day; and multi-trophic Methanosarcina shifted as the dominant methanogen at the TOC loading rates of 8.0 to 16 g/L/day). This study presents insights into a high organic loading molasses wastewater treatment system and the microbial flexibility in methane fermentation in response to process disturbances.
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Affiliation(s)
- Zhaoyong Sun
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Jinting He
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Na Yu
- School of Environmental and Planning, Liaocheng University, Liaocheng, 252000, China
| | - Yuwei Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China
| | - Yating Chen
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China.
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China.
| | - Yueqin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Kenji Kida
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
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Fu J, Yan B, Gui S, Fu Y, Xia S. Anaerobic co-digestion of thermo-alkaline pretreated microalgae and sewage sludge: Methane potential and microbial community. J Environ Sci (China) 2023; 127:133-142. [PMID: 36522047 DOI: 10.1016/j.jes.2022.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 06/17/2023]
Abstract
To improve methane production from sewage sludge (SS), co-digestion of SS and microalgae (MA) was studied and the application of thermo-alkaline pretreatment to MA was evaluated. The results showed that thermo-alkaline pretreatment at 90°C for 120 min on MA was the optimum pretreatment condition. Furthermore, when the volatile solids (VS) ratio of SS and MA was 1:2, the methane yield reached maximum (368.94 mL/g VS). Fourier transform infrared (FT-IR) and thermogravimetric analysis confirmed the synergetic effects of thermo-alkaline pretreated MA on its co-digestion with SS. The analyses of microbial community indicated that Methanobacterium and Methanosarcina were the dominant methanogens during the co-digestion process. However, the relative abundance of Methanosarcina in thermo-alkaline pretreated groups was higher compared to unpretreated groups. The microbial community structure might be affected by thermo-alkaline pretreatment rather than by the MA dosage in the co-digestion.
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Affiliation(s)
- Jiaqi Fu
- Institute of Energy Research, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Bing Yan
- Institute of Energy Research, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Shuanglin Gui
- Institute of Energy Research, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Yinxuan Fu
- Institute of Energy Research, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Song Xia
- Institute of Energy Research, Jiangxi Academy of Sciences, Nanchang 330096, China.
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McKay LJ, Smith HJ, Barnhart EP, Schweitzer HD, Malmstrom RR, Goudeau D, Fields MW. Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane. THE ISME JOURNAL 2022; 16:915-926. [PMID: 34689183 PMCID: PMC8941128 DOI: 10.1038/s41396-021-01139-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022]
Abstract
Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.
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Affiliation(s)
- Luke J McKay
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Land Resources & Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA.
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
| | - Elliott P Barnhart
- U.S. Geological Survey, Wyoming-Montana Water Science Center, Helena, MT, 59601, USA
| | - Hannah D Schweitzer
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA
- Arctic University of Norway, Tromsø, Norway
| | | | | | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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Abu Hanifa Jannat M, Hyeok Park S, Chairattanawat C, Yulisa A, Hwang S. Effect of different microbial seeds on batch anaerobic digestion of fish waste. BIORESOURCE TECHNOLOGY 2022; 349:126834. [PMID: 35149182 DOI: 10.1016/j.biortech.2022.126834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Initial microbial compositions would be the precursor for the efficient anaerobic digestion (AD) of fish waste (FW). A mesophilic batch test was conducted using four seeds collected from different digesters treating various combinations of substrates to investigate their effects on FW degradation. Key microbial groups were identified by 16s rRNA gene-based metagenomics analysis. Among four, the seed from the digester co-digesting livestock manure, food waste, and food wastewater showed the best performance and obtained the highest methane yield (350.5 ± 5.2 mL/gVSadded) and lowest lag phase (0.6 ± 0.1 d). Proteiniphilum, Aminobacterium, dgA-11 gut group, and Syntrophomonas were dominant bacterial genera identified in FW degradation. Methanosaeta was the dominant methanogen in the best performing seed and microbial network analysis revealed its contribution to achieving the highest CH4 yield. Obtained results could be useful in selecting microbial seed sources to avoid system imbalance in full-scale digesters that treat FW.
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Affiliation(s)
- Md Abu Hanifa Jannat
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Sang Hyeok Park
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Chayanee Chairattanawat
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Arma Yulisa
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Seokhwan Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea; Yonsei University Institute for Convergence Research and Education in Advanced Technology (I-CREATE), 85, Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea.
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Mallawaarachchi V, Wickramarachchi A, Lin Y. GraphBin: refined binning of metagenomic contigs using assembly graphs. Bioinformatics 2020; 36:3307-3313. [PMID: 32167528 DOI: 10.1093/bioinformatics/btaa180] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 02/18/2020] [Accepted: 03/10/2020] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION The field of metagenomics has provided valuable insights into the structure, diversity and ecology within microbial communities. One key step in metagenomics analysis is to assemble reads into longer contigs which are then binned into groups of contigs that belong to different species present in the metagenomic sample. Binning of contigs plays an important role in metagenomics and most available binning algorithms bin contigs using genomic features such as oligonucleotide/k-mer composition and contig coverage. As metagenomic contigs are derived from the assembly process, they are output from the underlying assembly graph which contains valuable connectivity information between contigs that can be used for binning. RESULTS We propose GraphBin, a new binning method that makes use of the assembly graph and applies a label propagation algorithm to refine the binning result of existing tools. We show that GraphBin can make use of the assembly graphs constructed from both the de Bruijn graph and the overlap-layout-consensus approach. Moreover, we demonstrate improved experimental results from GraphBin in terms of identifying mis-binned contigs and binning of contigs discarded by existing binning tools. To the best of our knowledge, this is the first time that the information from the assembly graph has been used in a tool for the binning of metagenomic contigs. AVAILABILITY AND IMPLEMENTATION The source code of GraphBin is available at https://github.com/Vini2/GraphBin. CONTACT vijini.mallawaarachchi@anu.edu.au or yu.lin@anu.edu.au. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vijini Mallawaarachchi
- Research School of Computer Science, College of Engineering and Computer Science, Australian National University, Canberra ACT 0200, Australia
| | - Anuradha Wickramarachchi
- Research School of Computer Science, College of Engineering and Computer Science, Australian National University, Canberra ACT 0200, Australia
| | - Yu Lin
- Research School of Computer Science, College of Engineering and Computer Science, Australian National University, Canberra ACT 0200, Australia
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Maghembe R, Damian D, Makaranga A, Nyandoro SS, Lyantagaye SL, Kusari S, Hatti-Kaul R. Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae. Antibiotics (Basel) 2020; 9:antibiotics9050229. [PMID: 32375367 PMCID: PMC7277505 DOI: 10.3390/antibiotics9050229] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/10/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
"Omics" represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and 'blind'-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism's inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.
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Affiliation(s)
- Reuben Maghembe
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
| | - Donath Damian
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
| | - Abdalah Makaranga
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- International Center for Genetic Engineering and Biotechnology (ICGEB), Omics of Algae Group, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Stephen Samwel Nyandoro
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania;
| | - Sylvester Leonard Lyantagaye
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biochemistry, Mbeya College of Health and Allied Sciences, University of Dar es Salaam, P.O. Box 608, Mbeya, Tanzania
| | - Souvik Kusari
- Institute of Environmental Research (INFU), Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
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Acclimation Improves Methane Production from Molasses Wastewater with High Salinity in an Upflow Anaerobic Filter Reactor: Performance and Microbial Community Dynamics. Appl Biochem Biotechnol 2020; 191:397-411. [DOI: 10.1007/s12010-020-03236-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/08/2020] [Indexed: 11/26/2022]
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Nie H, Liu X, Dang Y, Ji Y, Sun D, Smith JA, Holmes DE. Efficient nitrous oxide recovery from incineration leachate by a nosZ-deficient strain of Pseudomonas aeruginosa. BIORESOURCE TECHNOLOGY 2020; 297:122371. [PMID: 31753601 DOI: 10.1016/j.biortech.2019.122371] [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: 09/18/2019] [Revised: 11/01/2019] [Accepted: 11/02/2019] [Indexed: 06/10/2023]
Abstract
In this study, nitrous oxide was recovered from a lab-scale moving-bed biofilm reactor (MBBR) treating partial nitrification-treated leachate supplemented with a nosZ-deficient strain of Pseudomonas aeruginosa. Batch culture tests with the nosZ-deficient strain determined that the threshold for free nitrous acid (FNA) inhibition was 0.016 mg/L and that FNA concentrations above this threshold severely inhibited denitrification and transcription of genes from the dissimilatory nitrate reduction pathway (narG, nirS, and norB). High nitrite removal and N2O conversion efficiencies (>95%) were achieved with long-term operation of this MBBR. N2O accounted for the majority of biogas (80%) produced when the MBBR was fed partial nitrification-treated leachate with high nitrite concentrations and the drainage ratio was adjusted to 30%. Bacterial community analysis revealed that the nosZ-deficient Pseudomonas strain remained metabolically active and was primarily responsible for denitrification processes in the reactor. This study presents a promising method for N2O recovery from incineration leachate.
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Affiliation(s)
- Hanbing Nie
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Xinying Liu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Yan Dang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Yanan Ji
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Dezhi Sun
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
| | - Jessica A Smith
- Department of Biomolecular Sciences, Central Connecticut State University, 1615 Stanley Street, New Britain, CT 06050, United States
| | - Dawn E Holmes
- Department of Physical and Biological Sciences, Western New England University, 1215 Wilbraham Rd, Springfield, MA 01119, United States
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Transition of microbial community structures after development of membrane fouling in membrane bioreactors (MBRs). AMB Express 2020; 10:18. [PMID: 31993796 PMCID: PMC6987300 DOI: 10.1186/s13568-020-0959-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 11/10/2022] Open
Abstract
Although membrane fouling is a major issue when operating membrane bioreactors (MBRs), information regarding MBR performance and the sludge microbiome after the development of fouling remains limited. For the present study, two MBRs were operated for approximately 1 month under conditions of membrane fouling to investigate the effects of highly stressed environments on the sludge microbiome. After the development of fouling, a Collimonas-related operational taxonomic unit (OTU) was highly dominant in both reactors (relative abundances were ⁓ 63%) and this predomination caused a precipitous decline in the diversity indices of the sludge microbiomes. Because the excessive predomination by limited numbers of OTUs can lead to reductions in the adaptability to environmental changes, monitoring microbial diversity may be a valuable indicator for maintaining the robustness of a sludge microbiome. While, the decrease in the abundance of the Collimonas-related OTU resulted in the predomination of distinct microorganisms in each of the reactors despite being operated under the same conditions; this finding indicates existence of strong pressure to perturb the microbiomes. Detailed analyses suggested that the availability of terminal electron acceptors and competitive interactions between microbes via the secretion of extracellular proteins appeared to differentiate the structures of the respective microbial communities. During the extracellular proteins were secreted in the sludge, considerable portion of microbes were dead and large amounts of biomolecules seemed to be released; resultantly facilitated the predomination of fermentative anaerobes in one reactor as they use organic substances but not inorganic terminal electron acceptors to generate ATP under anaerobic conditions.
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Yu G, Jiang Y, Wang J, Zhang H, Luo H. BMC3C: binning metagenomic contigs using codon usage, sequence composition and read coverage. Bioinformatics 2019; 34:4172-4179. [PMID: 29947757 DOI: 10.1093/bioinformatics/bty519] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 06/26/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation Metagenomics investigates the DNA sequences directly recovered from environmental samples. It often starts with reads assembly, which leads to contigs rather than more complete genomes. Therefore, contig binning methods are subsequently used to bin contigs into genome bins. While some clustering-based binning methods have been developed, they generally suffer from problems related to stability and robustness. Results We introduce BMC3C, an ensemble clustering-based method, to accurately and robustly bin contigs by making use of DNA sequence Composition, Coverage across multiple samples and Codon usage. BMC3C begins by searching the proper number of clusters and repeatedly applying the k-means clustering with different initializations to cluster contigs. Next, a weight graph with each node representing a contig is derived from these clusters. If two contigs are frequently grouped into the same cluster, the weight between them is high, and otherwise low. BMC3C finally employs a graph partitioning technique to partition the weight graph into subgraphs, each corresponding to a genome bin. We conduct experiments on both simulated and real-world datasets to evaluate BMC3C, and compare it with the state-of-the-art binning tools. We show that BMC3C has an improved performance compared to these tools. To our knowledge, this is the first time that the codon usage features and ensemble clustering are used in metagenomic contig binning. Availability and implementation The codes of BMC3C are available at http://mlda.swu.edu.cn/codes.php?name=BMC3C. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Guoxian Yu
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Yuan Jiang
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Jun Wang
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Hao Zhang
- School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Haiwei Luo
- School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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12
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Improved Methanogenic Communities for Biogas Production. BIOFUEL AND BIOREFINERY TECHNOLOGIES 2019. [DOI: 10.1007/978-3-030-10516-7_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Greses S, Zamorano-López N, Borrás L, Ferrer J, Seco A, Aguado D. Effect of long residence time and high temperature over anaerobic biodegradation of Scenedesmus microalgae grown in wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 218:425-434. [PMID: 29709811 DOI: 10.1016/j.jenvman.2018.04.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 04/11/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic digestion of indigenous Scenedesmus spp. microalgae was studied in continuous lab-scale anaerobic reactors at different temperatures (35 °C and 55 °C), and sludge retention time - SRT (50 and 70 days). Mesophilic digestion was performed in a continuous stirred-tank reactor (CSTR) and in an anaerobic membrane bioreactor (AnMBR). Mesophilic CSTR operated at 50 days SRT only achieved 11.9% of anaerobic biodegradability whereas in the AnMBR at 70 days SRT and 50 days HRT reached 39.5%, which is even higher than the biodegradability achieved in the thermophilic CSTR at 50 days SRT (30.4%). Microbial analysis revealed a high abundance of cellulose-degraders in both reactors, AnMBR (mainly composed of 9.4% Bacteroidetes, 10.1% Chloroflexi, 8.0% Firmicutes and 13.2% Thermotogae) and thermophilic CSTR (dominated by 23.8% Chloroflexi and 12.9% Firmicutes). However, higher microbial diversity was found in the AnMBR compared to the thermophilic CSTR which is related to the SRT. since high SRT promoted low growth-rate microorganisms, increasing the hydrolytic potential of the system. These results present the membrane technology as a promising approach to revalue microalgal biomass, suggesting that microalgae biodegradability and consequently the methane production could be improved operating at higher SRT.
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Affiliation(s)
- S Greses
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Av. de la Universitat s/n, 46100, Burjassot, Valencia, Spain.
| | - N Zamorano-López
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Av. de la Universitat s/n, 46100, Burjassot, Valencia, Spain.
| | - L Borrás
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Av. de la Universitat s/n, 46100, Burjassot, Valencia, Spain.
| | - J Ferrer
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de Valencia, Camí de Vera s/n, 46022, Valencia, Spain.
| | - A Seco
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Av. de la Universitat s/n, 46100, Burjassot, Valencia, Spain.
| | - D Aguado
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de Valencia, Camí de Vera s/n, 46022, Valencia, Spain.
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Greses S, Gaby JC, Aguado D, Ferrer J, Seco A, Horn SJ. Microbial community characterization during anaerobic digestion of Scenedesmus spp. under mesophilic and thermophilic conditions. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.09.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Sanz JL, Rojas P, Morato A, Mendez L, Ballesteros M, González-Fernández C. Microbial communities of biomethanization digesters fed with raw and heat pre-treated microalgae biomasses. CHEMOSPHERE 2017; 168:1013-1021. [PMID: 27836273 DOI: 10.1016/j.chemosphere.2016.10.109] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/11/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
Microalgae biomasses are considered promising feedstocks for biofuel and methane productions. Two Continuously Stirred Tank Reactors (CSTR), fed with fresh (CSTR-C) and heat pre-treated (CSTR-T) Chlorella biomass were run in parallel in order to determine methane productions. The methane yield was 1.5 times higher in CSTR-T with regard to CSTR-C. Aiming to understand the microorganism roles within of the reactors, the sludge used as an inoculum (I), plus raw (CSTR-C) and heat pre-treated (CSTR-T) samples were analyzed by high-throughput pyrosequencing. The bacterial communities were dominated by Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes. Spirochaetae and Actinobacteria were only detected in sample I. Proteobacteria, mainly Alfaproteobacteria, were by far the dominant phylum within of the CSTR-C bioreactor. Many of the sequences retrieved were related to bacteria present in activated sludge treatment plants and they were absent after thermal pre-treatment. Most of the sequences affiliated to the Bacteroidetes were related to uncultured groups. Anaerolineaceae was the sole family found of the Chloroflexi phylum. All of the genera identified of the Firmicutes phylum carried out macromolecule hydrolysis and by-product fermentation. The proteolytic bacteria were prevalent over the saccharolytic microbes. The percentage of the proteolytic genera increased from the inoculum to the CSTR-T sample in a parallel fashion with an available protein increase owing to the high protein content of Chlorella. To relate the taxa identified by high-throughput sequencing to their functional roles remains a future challenge.
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Affiliation(s)
- Jose Luis Sanz
- Department of Molecular Biology, Universidad Autónoma de Madrid, c/ Darwin 2, 28049, Madrid, Spain.
| | - Patricia Rojas
- Department of Molecular Biology, Universidad Autónoma de Madrid, c/ Darwin 2, 28049, Madrid, Spain.
| | - Ana Morato
- Department of Molecular Biology, Universidad Autónoma de Madrid, c/ Darwin 2, 28049, Madrid, Spain.
| | - Lara Mendez
- IMDEA Energy, Avda. Ramón de la Sagra 3, 28935, Móstoles, Madrid, Spain.
| | - Mercedes Ballesteros
- IMDEA Energy, Avda. Ramón de la Sagra 3, 28935, Móstoles, Madrid, Spain; CIEMAT, Avda Complutense, 28040, Madrid, Spain.
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Klassen V, Blifernez-Klassen O, Wobbe L, Schlüter A, Kruse O, Mussgnug JH. Efficiency and biotechnological aspects of biogas production from microalgal substrates. J Biotechnol 2016; 234:7-26. [DOI: 10.1016/j.jbiotec.2016.07.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/13/2016] [Accepted: 07/18/2016] [Indexed: 11/17/2022]
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