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Lin TY, Liu WT. Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor. Water Res 2023; 243:120358. [PMID: 37481999 DOI: 10.1016/j.watres.2023.120358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.
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Affiliation(s)
- Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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2
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Zhao L, Shao H, Zhang L, Panno SV, Kelly WR, Lin TY, Liu WT, Flynn TM, Berger P. Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA. Environ Microbiol 2022; 24:6112-6127. [PMID: 36222141 PMCID: PMC10099389 DOI: 10.1111/1462-2920.16241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 10/10/2022] [Indexed: 01/12/2023]
Abstract
Saline springs within the Illinois Basin result from the discharge of deep-seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%-94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.
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Affiliation(s)
- Linduo Zhao
- Illinois Sustainable Technology Center, Illinois, USA.,Illinois State Water Survey, Illinois, USA
| | - Hongbo Shao
- Illinois State Geology Survey, Illinois, USA
| | - Li Zhang
- Illinois Sustainable Technology Center, Illinois, USA
| | | | | | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Theodore M Flynn
- California Department of Water Resources, West Sacramento, California, USA
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3
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Mei R, Liu WT. Meta-Omics-Supervised Characterization of Respiration Activities Associated with Microbial Immigrants in Anaerobic Sludge Digesters. Environ Sci Technol 2022; 56:6689-6698. [PMID: 35510767 DOI: 10.1021/acs.est.2c01029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Immigration has been recently recognized as an important ecological process that affects the microbial community structure in diverse ecosystems. However, the fate of microbial immigrants in the new environment and their involvement in the local biochemical network remain unclear. In this study, we performed meta-omics-supervised characterization of immigrants' activities in anaerobic sludge digesters. Metagenomic analyses revealed that immigrants from the feed sludge accounted for the majority of populations capable of anaerobic respiration in a digester. Electron acceptors that were predicted to be respired, including nitrate, nitrite, sulfate, and elemental sulfur, were added to digester sludge in batch tests. Consumption of up to 91% of the added electron acceptors was observed within the experiment period. 16S rRNA sequencing detected populations that were stimulated by the electron acceptors, largely overlapping with respiration-capable immigrants identified by metagenomic analysis. Metatranscriptomic analysis of the batch tests provided additional evidence for upregulated expression of respiration genes and concomitant suppressed expression of methanogenesis. Anaerobic respiration activity was further evaluated in full-scale digesters in nine wastewater treatment plants. Although nitrate and sulfate respiration were ubiquitous, the expression level of respiration genes was generally 2-3 orders of magnitude lower than the expression of methanogenesis in most digesters, suggesting marginal ecological roles by immigrants in full-scale digester ecosystems.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Yu YX, Liu WT, Li HY, Wang W, Sun HB, Zhang LL, Wu SL. Decoding molecular mechanism underlying binding of drugs to HIV-1 protease with molecular dynamics simulations and MM-GBSA calculations. SAR QSAR Environ Res 2021; 32:889-915. [PMID: 34551634 DOI: 10.1080/1062936x.2021.1979647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
HIV-1 protease (PR) is thought to be efficient targets of anti-AIDS drug design. Molecular dynamics (MD) simulations and multiple post-processing analysis technologies were applied to decipher molecular mechanism underlying binding of three drugs Lopinavir (LPV), Nelfinavir (NFV) and Atazanavir (ATV) to the PR. Binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA) suggest that compensation between binding enthalpy and entropy plays a vital role in binding of drugs to PR. Dynamics analyses show that binding of LPV, NFV and ATV highly affects structural flexibility, motion modes and dynamics behaviour of the PR, especially for two flaps. Computational alanine scanning and interaction network analysis verify that although three drugs have structural difference, they share similar binding modes to the PR and common interaction clusters with the PR. The current findings also confirm that residues located interaction clusters, such as Asp25/Asp25', Gly27/Gly27', Ala28/Ala28', Asp29, Ile47/Ile47', Gly49/Gly49', Ile50/Ile50', Val82/Val82' and Ile84/Ile84, can be used as efficient targets of clinically available inhibitors towards the PR.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W T Liu
- Shuifa Qilu Cultural Tourism Development Co., Ltd, Shuifa Ecological Industry Group, Jinan, China
| | - H Y Li
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - S L Wu
- School of Science, Shandong Jiaotong University, Jinan, China
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5
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Matar GK, Ali M, Bagchi S, Nunes S, Liu WT, Saikaly PE. Relative Importance of Stochastic Assembly Process of Membrane Biofilm Increased as Biofilm Aged. Front Microbiol 2021; 12:708531. [PMID: 34566913 PMCID: PMC8461090 DOI: 10.3389/fmicb.2021.708531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
The relative importance of different ecological processes controlling biofilm community assembly over time on membranes with different surface characteristics has never been investigated in membrane bioreactors (MBRs). In this study, five ultrafiltration hollow-fiber membranes - having identical nominal pore size (0.1μm) but different hydrophobic or hydrophilic surface characteristics - were operated simultaneously in the same MBR tank with a constant flux of 10 liters per square meter per hour (LMH). In parallel, membrane modules operated without permeate flux (0 LMH) were submerged in the same MBR tank, to investigate the passive microbial adsorption onto different hydrophobic or hydrophilic membranes. Samples from the membrane biofilm were collected after 1, 10, 20, and 30days of continuous filtration. The membrane biofilm microbiome were investigated using 16S rRNA gene amplicon sequencing from DNA and cDNA samples. Similar beta diversity trends were observed for both DNA- and cDNA-based analyses. Beta diversity analyses revealed that the nature of the membrane surface (i.e., hydrophobic vs. hydrophilic) did not seem to have an effect in shaping the bacterial community, and a similar biofilm microbiome evolved for all types of membranes. Similarly, membrane modules operated with and without permeate flux did not significantly influence alpha and beta diversity of the membrane biofilm. Nevertheless, different-aged membrane biofilm samples exhibited significant differences. Proteobacteria was the most dominant phylum in early-stage membrane biofilm after 1 and 10days of filtration. Subsequently, the relative reads abundance of the phyla Bacteroidetes and Firmicutes increased within the membrane biofilm communities after 20 and 30days of filtration, possibly due to successional steps that lead to the formation of a relatively aged biofilm. Our findings indicate distinct membrane biofilm assembly patterns with different-aged biofilm. Ecological null model analyses revealed that the assembly of early-stage biofilm community developed after 1 and 10days of filtration was mainly governed by homogenous selection. As the biofilm aged (days 20 and 30), stochastic processes (e.g., ecological drift) started to become important in shaping the assembly of biofilm community.
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Affiliation(s)
- Gerald K Matar
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Muhammad Ali
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Samik Bagchi
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Suzana Nunes
- Biological and Environmental Science and Engineering Division, Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Wen-Tso Liu
- 3207 Newmark Civil Engineering Laboratory, Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Pascal E Saikaly
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Yu YX, Wang W, Sun HB, Zhang LL, Wu SL, Liu WT. Insights into effect of the Asp25/Asp25' protonation states on binding of inhibitors Amprenavir and MKP97 to HIV-1 protease using molecular dynamics simulations and MM-GBSA calculations. SAR QSAR Environ Res 2021; 32:615-641. [PMID: 34157882 DOI: 10.1080/1062936x.2021.1939149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
The protonation states of two aspartic acids in the catalytic strands of HIV-1 protease (PR) remarkably affect bindings of inhibitors to PR. It is requisite for the design of potent inhibitors towards PR to investigate the influences of Asp25/Asp25' protonated states on dynamics behaviour of PR and binding mechanism of inhibitors to PR. In this work, molecular dynamics (MD) simulations, MM-GBSA method and principal component (PC) analysis were coupled to explore the effect of Asp25/Asp25' protonation states on conformational changes of PR and bindings of Amprenavir and MKP97 to PR. The results show that the Asp25/Asp25' protonation states exert different impacts on structural fluctuations, flexibility and motion modes of PR. Dynamics analysis verifies that Asp25/Asp25' protonated states highly affect conformational dynamics of two flaps in PR. The binding free energy calculations results suggest that the Asp25/Asp25' protonated states obviously strengthen bindings of inhibitors to PR compared to the non-protonation state. Calculations of residue-based free energy decomposition indicate that the Asp25/Asp25' protonation not only disturbs the interaction network of inhibitors with PR but also stabilizes bindings of inhibitors to PR by cancelling the electrostatic repulsive interaction. Therefore, special attentions should be paid to the Asp25/Asp25' protonation in the design of potent inhibitors towards PR.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - S L Wu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W T Liu
- School of Science, Shandong Jiaotong University, Jinan, China
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Yuan H, Wang X, Lin TY, Kim J, Liu WT. Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning. Sci Rep 2021; 11:15140. [PMID: 34302023 PMCID: PMC8302695 DOI: 10.1038/s41598-021-94628-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023] Open
Abstract
Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation, indicating Ca. G. eutrophica's EET ability. The high-quality draft genome further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. A Bayesian network was trained with the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis from dominant fermentative bacteria, Geobacter, and Methanobacterium. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.
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Affiliation(s)
- Heyang Yuan
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA.
| | - Xuehao Wang
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jinha Kim
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
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Roux S, Paul BG, Bagby SC, Nayfach S, Allen MA, Attwood G, Cavicchioli R, Chistoserdova L, Gruninger RJ, Hallam SJ, Hernandez ME, Hess M, Liu WT, McAllister TA, O'Malley MA, Peng X, Rich VI, Saleska SR, Eloe-Fadrosh EA. Ecology and molecular targets of hypermutation in the global microbiome. Nat Commun 2021; 12:3076. [PMID: 34031405 PMCID: PMC8144416 DOI: 10.1038/s41467-021-23402-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/27/2021] [Indexed: 02/04/2023] Open
Abstract
Changes in the sequence of an organism's genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.
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Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Blair G Paul
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Sarah C Bagby
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Stephen Nayfach
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Graeme Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | | | | | - Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, Canada
| | - Maria E Hernandez
- Instituto de Ecología A.C. Red de Manejo Biotechnológico de Recursos. Xalapa, Veracruz, México
| | | | - Wen-Tso Liu
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Xuefeng Peng
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | | | | | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Kim J, Mei R, Wilson FP, Yuan H, Bocher BTW, Liu WT. Ecogenomics-Based Mass Balance Model Reveals the Effects of Fermentation Conditions on Microbial Activity. Front Microbiol 2020; 11:595036. [PMID: 33343535 PMCID: PMC7738435 DOI: 10.3389/fmicb.2020.595036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023] Open
Abstract
Fermentation of waste activated sludge (WAS) is an alternative approach to reduce solid wastes while providing valuable soluble products, such as volatile fatty acids and alcohols. This study systematically identified optimal fermentation conditions and key microbial populations by conducting two sets of experiments under different combinations of biochemical and physical parameters. Based on fermentation product concentrations, methane production, and solid removal, fermentation performance was enhanced under the combined treatments of inoculum heat shock (>60°C), pH 5, 55°C, and short solid retention time (<10 days). An ecogenomics-based mass balance (EGMB) approach was used to determine the net growth rates of individual microbial populations, and classified them into four microbial groups: known syntrophs, known methanogens, fermenters, and WAS-associated populations. Their growth rates were observed to be affected by the treatment conditions. The growth rates of syntrophs and fermenters, such as Syntrophomonas and Parabacteroides increased with a decrease in SRT. In contrast, treatment conditions, such as inoculum heat shock and high incubation temperature inhibited the growth of WAS-associated populations, such as Terrimonas and Bryobacter. There were also populations insensitive to the treatment conditions, such as those related to Microbacter and Rikenellaceae. Overall, the EGMB approach clearly revealed the ecological roles of important microbial guilds in the WAS fermentation system, and guided the selection of optimal conditions for WAS fermentation in future pilot-scale operation.
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Affiliation(s)
- Jinha Kim
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Fernanda P Wilson
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Heyang Yuan
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Benjamin T W Bocher
- British Petroleum America, Petrochemicals Technology, Naperville, IL, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, United States
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Mei R, Nobu MK, Narihiro T, Liu WT. Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters. Front Microbiol 2020; 11:593006. [PMID: 33193263 PMCID: PMC7661554 DOI: 10.3389/fmicb.2020.593006] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 10/13/2020] [Indexed: 01/22/2023] Open
Abstract
Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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11
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Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH, Lee PH, McInerney MJ, Liu WT. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome 2020; 8:111. [PMID: 32709258 PMCID: PMC7382037 DOI: 10.1186/s40168-020-00885-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/25/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H2 accumulation and can be inhibited by H2 produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored. RESULTS To uncover how anaerobes combat this H2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H2-sensitive metabolisms through (i) metabolic coupling with concurrent H2-tolerant catabolism, (ii) forgoing H2 generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O2 metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H2 oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate. CONCLUSION Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H2 to formate transfer, respiring low-concentration O2, performing direct interspecies electron transfer, and interacting with high H2-affinity methanogenesis. These findings shed light on how microorganisms overcome a critical obstacle in methanogenic carbon cycles we had hitherto disregarded and provide foundational insight into anaerobic microbial ecology. Video Abstract.
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Affiliation(s)
- Masaru K. Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, HK Hong Kong
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College, London, UK
| | - Michael J. McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
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12
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Lam TYC, Mei R, Wu Z, Lee PKH, Liu WT, Lee PH. Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing. Water Res 2020; 178:115815. [PMID: 32380296 DOI: 10.1016/j.watres.2020.115815] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/18/2020] [Accepted: 04/08/2020] [Indexed: 05/24/2023]
Abstract
In the past decade, the characterisation of the microbial community in anaerobic digestion was primarily done by using high-throughput short-read amplicon sequencing. However, the short-read approach has inherent primer bias and low phylogenetic resolution. Our previous study using Illumina MiSeq suggested that the heterogeneity of AD microbiome was operation-driven. To advance our knowledge towards the complexity of the AD microbiome, we performed full-length 16S rRNA gene amplicon sequencing using PacBio Sequel for a more accurate phylogenetic identification. To this end, purified DNA samples from 19 global anaerobic digesters were sequenced. Sixteen methanogenic archaea were identified at the species level. Among them, Methanosarcina horonobensis and Methanosarcina flavescens had significant presence under specific operating conditions. Methanothrix concilii presented in all digesters sequenced. Unexpectedly, over 90% of the Smithella detected were closely related to alkane-degrading Smithella strains D17 and M82, not Smithella propionica. Using LEfSe and network analysis, the interspecies relationship between the fermentative and syntrophic bacteria was addressed. Comparison of the short- and long-read sequencing results were performed and discussed. From sample preparation to data analysis, this work characterised the digester microbiomes in a superior resolution.
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Affiliation(s)
- Theo Y C Lam
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Zhuoying Wu
- Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Department of Civil and Environmental Engineering, Imperial College London, London, SW7 2AZ, UK.
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13
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Cao JJ, Ji XN, Mao YY, Zhang PP, Liu WT, Zhang HZ, Ding N, Chen Q. [Clinical and genetic characteristics of children with STXBP1 encephalopathy]. Zhonghua Er Ke Za Zhi 2020; 58:493-498. [PMID: 32521962 DOI: 10.3760/cma.j.cn112140-20191028-00683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Objective: To investigate the clinical and genetic characteristics of developmental and epileptic encephalopathy (DEE) caused by syntaxin-binding protein 1 (STXBP1) gene mutation. Methods: The clinical data, gene variation and treatment outcome of 15 children with STXBP1 encephalopathy admitted to Children's Hospital Affiliated to Capital Institute of Pediatrics from January 2014 to June 2019 were analyzed retrospectively. Results: Among 15 patients, 11 were male and 4 were female, age ranged from 2 months to 69 months. The clinical manifestations of 14 children were epilepsy and developmental delay (DD) and the remaining one showed developmental delay without seizure. The onset age of epilepsy ranged from two days to 19 months and 11 of them experienced the first attack before 1 year of age. The common seizure types were epileptic spasms and tonic seizures. Seven patients were diagnosed with Ohtahara syndrome or West syndrome. Epileptic form discharges were observed in the interictal electroencephalograms (EEG) of 11 patients, including multifocal discharges, suppression-burst and hypsarrhythmia. The brain magnetic resonance imaging of 7 children were abnormal, including myelin dysplasia, less white matter, lack of corpus callosum or hypoplasia. The follow-up time ranged from 2 months to 57 months, after the last follow-up, 3 cases were seizure free, 6 children showed partial response and the other 5 patients had no response on multitherapy. Six of 8 patients showed good responses to levetiracetam (LEV) monotherapy or in combination with other antiepileptic drugs (AEDs). Vigabatrin (VGB) was applied to 5 patients with epileptic spasms and 4 of them showed response. All patients showed different degrees of developmental delay while four of them showed autistic features. STXBP1 gene mutations were identified in all cases and there were 15 types of gene variations, including 8 missense mutations, 1 nonsense mutation, 5 frame shift mutations and 1 complex mutation. Five novel mutations were unreported before, including c.1193A>G, c.172delG, c.1769C>T, c.1038_1039delCC, c.348_351dupTGAA. Conclusions: Development delay and epilepsy are the major and independent clinical phenotypes in children with STXBP1 encephalopathy. The variation of STXBP1 gene is mainly de novo. Levetiracetam and vigabatrin may be more effective in epilepsy control than other AEDs.
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Affiliation(s)
- J J Cao
- Department of Neurology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - X N Ji
- Department of Neurology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - Y Y Mao
- Department of Neurology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - P P Zhang
- Department of Neurology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - W T Liu
- Department of Neurology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - H Z Zhang
- Department of Neurology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - N Ding
- Department of Neurology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
| | - Q Chen
- Department of Neurology, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China
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14
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Liu G, Zhang Y, Liu X, Hammes F, Liu WT, Medema G, Wessels P, van der Meer W. 360-Degree Distribution of Biofilm Quantity and Community in an Operational Unchlorinated Drinking Water Distribution Pipe. Environ Sci Technol 2020; 54:5619-5628. [PMID: 32259432 PMCID: PMC7203839 DOI: 10.1021/acs.est.9b06603] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In the present study, triplicate rings of 360° pipe surfaces of an operational drinking water distribution pipe were swabbed. Each ring was equally divided into 16 parts for swabbing. The collected swabs were grouped into 3 sections and compared with the biofilm samples sampled by sonication of specimens from the same pipe. The results showed that the biofilm is unevenly distributed over the 16 parts and the 3 sections of the pipe surface. Both the active biomass and the number of observed OTUs increased as the measurements proceeded from the top to the bottom of the pipe. The bacterial community was dominated in all sections by Proteobacteria. At the genus level, Nitrospira spp., Terrimonas spp., and Hyphomicrobium spp. were dominant in all sections. Gaiella spp. and Vicinamibacter spp. dominated in S-I, Blastopirellula spp. and Pirellula spp. dominated in S-II, while Holophaga spp. and Phaeodactylibacter spp. dominated in S-III. When swabbing and pipe specimen sonication were compared, the results showed that the sampling strategy significantly influences the obtained biofilm bacterial community. A consistent multisectional swabbing strategy is proposed for future biofilm sampling; it involves collecting swabs from all sections and comparing the swabs from the same position/section across locations.
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Affiliation(s)
- Gang Liu
- Key
Laboratory of Drinking Water Science and Technology, Research Centre
for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing, 100085, P. R. China
- Oasen
Drinkwater, P.O. Box
122, 2801SB, Gouda, The Netherlands
- Sanitary
Engineering, Department of Water Management, Faculty of Civil Engineering
and Geosciences, Delft University of Technology, P.O. Box 5048, 2600GA Delft, The Netherlands
- Phone: 0086 17600879707; e-mail: ,
| | - Ya Zhang
- Department
of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, 205 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Xinlei Liu
- Catalysis
Engineering, Chemical Engineering Department, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Frederik Hammes
- Eawag,
Swiss
Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Wen-Tso Liu
- Department
of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, 205 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Gertjan Medema
- Sanitary
Engineering, Department of Water Management, Faculty of Civil Engineering
and Geosciences, Delft University of Technology, P.O. Box 5048, 2600GA Delft, The Netherlands
- KWR
Watercycle Research Institute, P.O. Box 1072, 3430 BB Nieuwegein, The Netherlands
| | - Peter Wessels
- Oasen
Drinkwater, P.O. Box
122, 2801SB, Gouda, The Netherlands
| | - Walter van der Meer
- Oasen
Drinkwater, P.O. Box
122, 2801SB, Gouda, The Netherlands
- Science
and Technology, University of Twente, P.O. Box 217, 7500AE Enschede, The Netherlands
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15
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Mei R, Nobu MK, Liu WT. Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments. Environ Microbiol Rep 2020; 12:173-184. [PMID: 31965729 DOI: 10.1111/1758-2229.12821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/24/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Degradation of amino acids is an important process in methanogenic environments. Early studies in the 1980s focused on isolated clostridia species to study the degradation behaviours. However, it is now well-recognized that isolated species may not represent those with important roles in situ. This study conducted a continuous enrichment experiment with focus on the comparison of the microbial communities after short-term enrichment (SE) and long-term enrichment (LE). Individual amino acids were used as the substrate, and two different anaerobic digester sludge were used as the inoculum. Based on 16S rRNA and 16S rRNA gene, a clear community shift was observed during a time course of 18 months. The SE communities were dominated by microbial populations such as an uncultured Bacteroidales that was different from known fermenters. In the LE communities, known amino acids fermenters were consistently observed with high abundance, including Peptoclostridium acidaminophilum, Acidaminobacter hydrogenoformans and Propionivibrio pelophilus. The community structures could be classified into four types depending on the diversity of fermenters and syntrophs. A culturability index was developed to compare the SE and LE community and revealed that long-term enrichment tended to select microbial populations closely related to species that has been cultivated whereas larger fractions of the inoculum and SE communities remained uncultured.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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16
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Sun H, Mei R, Zhang XX, Ren H, Liu WT, Ye L. Bacterial enrichment in highly-selective acetate-fed bioreactors and its application in rapid biofilm formation. Water Res 2020; 170:115359. [PMID: 31821931 DOI: 10.1016/j.watres.2019.115359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/19/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
In this study, we systematically investigated the bacterial community dynamics in highly-selective (strong hydraulic selection pressure and high organic loading rate) bioreactors with acetate as the sole carbon source. 16S rRNA gene high-throughput sequencing and metagenomic sequencing results showed that phenolics-degrading bacteria (PDB), which were mainly Acinetobacter species, in the newly-formed aerobic granules could account for >70% of the total bacteria. Near full-length 16S rRNA gene sequences obtained by cloning suggest that the PDB are potentially novel species because they are distantly related to known Acinetobacter species. However, these PDB only temporarily appeared in the early stage of the granule formation and their abundance quickly decreased along the reactor operation. To retain these PDB, we demonstrated that the newly-formed aerobic granules could accelerate biofilm formation in moving bed biofilm reactors (MBBRs), and the biofilm carriers showed gradually-increased phenol degradation performance in the MBBRs. While, the bacterial community in biofilm significantly changed during the operation process of the MBBRs and the community structure became more complicated than that in the aerobic granules. Collectively, this study provides new insights into the microbial ecology of sludge granulation and biofilm formation process in the wastewater treatment systems for remediating phenolic matters.
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Affiliation(s)
- Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China.
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17
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Ye L, Mei R, Liu WT, Ren H, Zhang XX. Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes. Microbiome 2020; 8:16. [PMID: 32046778 PMCID: PMC7014675 DOI: 10.1186/s40168-020-0794-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/20/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Microorganisms in activated sludge (AS) play key roles in the wastewater treatment processes. However, their ecological behaviors and differences from microorganisms in other environments have mainly been studied using the 16S rRNA gene that may not truly represent in situ functions. RESULTS Here, we present 2045 archaeal and bacterial metagenome-assembled genomes (MAGs) recovered from 1.35 Tb of metagenomic data generated from 114 AS samples of 23 full-scale wastewater treatment plants (WWTPs). We found that the AS MAGs have obvious plant-specific features and that few proteins are shared by different WWTPs, especially for WWTPs located in geographically distant areas. Further, we developed a novel machine learning approach that can distinguish between AS MAGs and MAGs from other environments based on the clusters of orthologous groups of proteins with an accuracy of 96%. With the aid of machine learning, we also identified some functional features (e.g., functions related to aerobic metabolism, nutrient sensing/acquisition, and biofilm formation) that are likely vital for AS bacteria to adapt themselves in wastewater treatment bioreactors. CONCLUSIONS Our work reveals that, although the bacterial species in different municipal WWTPs could be different, they may have similar deterministic functional features that allow them to adapt to the AS systems. Also, we provide valuable genome resources and a novel approach for future investigation and better understanding of the microbiome of AS and other ecosystems. Video Abtract.
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Affiliation(s)
- Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China.
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, China.
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18
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Chen L, Ling F, Bakker G, Liu WT, Medema G, van der Meer W, Liu G. Assessing the transition effects in a drinking water distribution system caused by changing supply water quality: an indirect approach by characterizing suspended solids. Water Res 2020; 168:115159. [PMID: 31614234 DOI: 10.1016/j.watres.2019.115159] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 05/16/2023]
Abstract
Worldwide, it is common that the drinking water distribution systems (DWDSs) may be subjected to changes of supply water quality due to the needs of upgrading the treatment processes or switching the source water. However, the potential impacts of quality changed supply water on the stabilized ecological niches within DWDSs and the associated water quality deterioration risks were poorly documented. In the present study, such transition effects caused by changing the supply water quality that resulted from destabilization of biofilm and loose deposits in DWDS were investigated by analyzing the physiochemical and microbiological characteristics of suspended particles before (T0), during (T3-weeks) and after upgrading the treatments (T6-months) in an unchlorinated DWDS in the Netherlands. Our results demonstrated that after 6 months' time the upgraded treatments significantly improved the water quality. Remarkably, water quality deterioration was observed at the initial stage when the quality-improved treated water distributed into the network at T3-weeks, observed as a spike of total suspended solids (TSS, 50-260%), active biomass (ATP, 95-230%) and inorganic elements (e.g. Mn, 130-250%). Furthermore, pyrosequencing results revealed sharp differences in microbial community composition and structure for the bacteria associated with suspended particles between T0 and T3-weeks, which re-stabilized after 6 months at T6-months. The successful capture of transition effects was especially confirmed by the domination of Nitrospira spp. and Polaromonas spp. in the distribution system at T3-weeks, which were detected at rather low relative abundance at treatment plant. Though the transitional effects were captured, this study shows that the introduction of softening and additional filtration did not have an effect on the water quality for the consumer which improved considerably after 6-months' period. The methodology of monitoring suspended particles with MuPFiSs and additional analysis is capable of detecting transitional effects by monitoring the dynamics of suspended particles and its physiochemical and microbiological composition.
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Affiliation(s)
- Lihua Chen
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600, GA, Delft, the Netherlands
| | - Fangqiong Ling
- Department of Energy, Environmental and Chemical Engineering, School of Engineering and Applied Science, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Geo Bakker
- Vitens N.V., P.O. Box 1205, 8001, BE, Zwolle, the Netherlands
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, 205 N. Mathews Ave., Urbana, IL, 61801, USA
| | - Gertjan Medema
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; KWR Watercycle Research Institute, P.O. Box 1072, 3430, BB, Nieuwegein, the Netherlands
| | - Walter van der Meer
- Oasen Water Company, PO BOX 122, 2800, AC, Gouda, the Netherlands; Science and Technology, University of Twente, P.O. Box 217, 7500, AE, Enschede, the Netherlands
| | - Gang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600, GA, Delft, the Netherlands.
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19
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Abstract
Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counting shared microbial species, microbial source tracking, and neutral community model, rely on abundance profile to reveal the extent of overlapping between the upstream and downstream communities. Thus, they cannot suggest the quantitative contribution of immigrants to the downstream community function because activities of individual immigrants are not considered after entering the receiving environment. This limitation can be overcome by using an approach that couples a mass balance model with high-throughput DNA sequencing, i.e., ecogenomics-based mass balance. It calculates the net growth rate of individual microbial immigrants and partitions the entire community into active populations that contribute to the community function and inactive ones that carry minimal function. Linking activities of immigrants to their abundance further provides quantification of the contribution from an upstream environment to the downstream community. Considering only active populations can improve the accuracy of identifying key environmental parameters dictating process performance using methods such as machine learning.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
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20
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Shi HP, Wang ZQ, Fan ZY, Zang MD, Pan JM, Dai QQ, Zheng YN, Zhu ZL, Sah RD, Liu WT, Yang ZY, Feng RH, Yao XX, Chen MM, Yan C, Yan M, Zhu ZG, Li C. [Analysis and comparison of the clinical features and prognosis between extra - gastrointestinal stromal tumors and duodenal gastrointestinal stromal tumors]. Zhonghua Wei Chang Wai Ke Za Zhi 2019; 22:856-860. [PMID: 31550825 DOI: 10.3760/cma.j.issn.1671-0274.2019.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the differences of clinicopathological features, diagnosis, treatment and prognosis between patients with extra-gastrointestinal stromal tumors (EGIST) and duodenal gastrointestinal stromal tumors (DGIST). Methods: A retrospective case - control study was performed. Case inclusion criteria: (1) tumor confirmed by histology and pathology; (2) primary tumor locating in the extra - gastrointestinal tract or duodenum; (3) without other synchronous tumors; (4) complete clinical and pathological data. Clinical data of 20 EGIST patients and 32 DGIST patients from March 2011 to September 2016 at Department of Gastrointestinal Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine were retrospectively collected and analyzed. The observational parameters included clinicopathological characteristics, treatment and prognosis conditions. Continuous data of abnormal distribution were expressed as median (range) and compared using the Mann-Whitney U-test. Survival curves were drawn by the Kaplan-Meier method and compared with the Log-rank test. Results: Of the 20 EGIST patients, 8 were males and 12 were females with age of 61.0 (30.0 to 86.0) years and of the 32 DGIST patients, 12 were males and 20 were females with age of 55.5 (27.0 to 70.0) years. Compared with DGIST patients, EGIST patients were older (U=188.000, P=0.012], had larger tumor size [10.0 (3.0 to 29.0) cm vs. 4.0 (1.5 to 10.0) cm, U=98.500, P<0.001] and higher ratio of high risk classification [85.0% (17/20) vs. 12.5% (4/32), χ(2)=26.870, P<0.001]. Among the 20 EGIST patients, 5 were diagnosed with distal metastasis and received imatinib (400 mg/d), and the other 15 patients underwent radical resection who were included in survival analysis. All the 32 DGIST patients underwent radical resection. The median follow-up of whole group was 43 (14 to 76) months. The 3-year recurrence/metastasis-free survival rate of 15 cases undergoing radical resection in the EGIST group was 85.6%, which was lower than that of the DGIST group (88.6%), and the difference was not statistically significant (P=0.745). There was no significant difference in the 3-year overall survival rate between the EGIST group (92.9%) and the DGIST group (100%) (P=0.271). Conclusions: As compared to DGIST, EGIST mostly occurs in those with older age, larger tumor size and higher risk grade. The prognosis of EGIST patients after radical resection is similar to that of DGIST patients.
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Affiliation(s)
- H P Shi
- Department of Gastrointestinal Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
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21
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Yamamoto K, Hackley KC, Kelly WR, Panno SV, Sekiguchi Y, Sanford RA, Liu WT, Kamagata Y, Tamaki H. Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States. Sci Rep 2019; 9:13484. [PMID: 31530884 PMCID: PMC6748922 DOI: 10.1038/s41598-019-49996-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/04/2019] [Indexed: 01/24/2023] Open
Abstract
Natural microbial communities consist of a limited number of abundant species and an extraordinarily diverse population of rare species referred to as the rare biosphere. Recent studies have revealed that the rare biosphere is not merely an inactive dormant population but may play substantial functional roles in the ecosystem. However, structure, activity and community assembly processes of the rare biosphere are poorly understood. In this study, we evaluated the present and living microbial community structures including rare populations in an aquifer ecosystem, the Mahomet Aquifer, USA, by both 16S rDNA and rRNA amplicon deep sequencing. The 13 groundwater samples formed three distinct groups based on the “entire” community structure, and the same grouping was obtained when focusing on the “rare” subcommunities (<0.1% of total abundance), while the “abundant” subcommunities (>1.0%) gave a different grouping. In the correlation analyses, the observed grouping pattern is associated with several geochemical factors, and structures of not only the entire community but also the rare subcommunity are correlated with geochemical profiles in the aquifer ecosystem. Our findings first indicate that the living rare biosphere in the aquifer system has the metabolic potential to adapt to local geochemical factors which dictate the community assembly processes.
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Affiliation(s)
- Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | - Walton R Kelly
- Groundwater Science Section, Illinois State Water Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign (UIUC), Champaign, IL, USA
| | - Samuel V Panno
- Illinois State Geological Survey, Prairie Research Institute, UIUC, Champaign, IL, USA
| | - Yuji Sekiguchi
- Biomedical Research Institute, AIST, Tsukuba, Ibaraki, Japan
| | | | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, UIUC, Urbana, IL, USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan. .,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan. .,Department of Civil and Environmental Engineering, UIUC, Urbana, IL, USA. .,Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.
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22
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Zealand AM, Mei R, Roskilly AP, Liu W, Graham DW. Molecular microbial ecology of stable versus failing rice straw anaerobic digesters. Microb Biotechnol 2019; 12:879-891. [PMID: 31233284 PMCID: PMC6681398 DOI: 10.1111/1751-7915.13438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/01/2022] Open
Abstract
Waste rice straw (RS) is generated in massive quantities around the world and is often burned, creating greenhouse gas and air quality problems. Anaerobic digestion (AD) may be a better option for RS management, but RS is presumed to be comparatively refractory under anaerobic conditions without pre-treatment or co-substrates. However, this presumption assumes frequent reactor feeding regimes but less frequent feeding may be better for RS due to slow hydrolysis rates. Here, we assess how feeding frequency (FF) and organic loading rate (OLR) impacts microbial communities and biogas production in RS AD reactors. Using 16S rDNA amplicon sequencing and bioinformatics, microbial communities from five bench-scale bioreactors were characterized. At low OLR (1.0 g VS l-1 day-1 ), infrequently fed units (once every 21 days) had higher specific biogas yields than more frequent feeding (five in 7 days), although microbial community diversities were statistically similar (P > 0.05; ANOVA with Tukey comparison). In contrast, an increase in OLR to 2.0 g VS l-1 day-1 significantly changed Archaeal and fermenting Eubacterial sub-communities and the least frequency fed reactors failed. 'Stable' reactors were dominated by Methanobacterium, Methanosarcina and diverse Bacteroidetes, whereas 'failed' reactors saw shifts towards Clostridia and Christensenellaceae among fermenters and reduced methanogen abundances. Overall, OLR impacted RS AD microbial communities more than FF. However, combining infrequent feeding and lower OLRs may be better for RS AD because of higher specific yields.
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Affiliation(s)
- Andrew M. Zealand
- School of EngineeringNewcastle UniversityNewcastle upon TyneNE1 7RUUK
| | - Ran Mei
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐Champaign205 North Mathews AveUrbanaIL61801USA
| | - Anthony P. Roskilly
- Sir Joseph Swan Centre for Energy ResearchNewcastle UniversityNewcastle upon TyneNE1 7RUUK
| | - WenTso Liu
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐Champaign205 North Mathews AveUrbanaIL61801USA
| | - David W. Graham
- School of EngineeringNewcastle UniversityNewcastle upon TyneNE1 7RUUK
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23
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Hull NM, Ling F, Pinto AJ, Albertsen M, Jang HG, Hong PY, Konstantinidis KT, LeChevallier M, Colwell RR, Liu WT. Drinking Water Microbiome Project: Is it Time? Trends Microbiol 2019; 27:670-677. [DOI: 10.1016/j.tim.2019.03.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/15/2019] [Accepted: 03/26/2019] [Indexed: 02/06/2023]
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24
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Pang BR, Zhu ZL, Li C, Liu WT, KumarSah RD, Yan M, Zhu ZG. [Predictive factors for lymph node metastasis in patients with poorly differentiated early gastric cancer]. Zhonghua Wei Chang Wai Ke Za Zhi 2019; 22:446-450. [PMID: 31104430 DOI: 10.3760/cma.j.issn.1671-0274.2019.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objective: This study aimed to identify clinicopathological factors predictive of lymph node metastasis in patients with the poorly differentiated early gastric cancer (EGC) to assess the feasibility of using endoscopic submucosal dissection (ESD). Methods: The records of patients with poorly differentiated early gastric cancer undergoing gastric radical resection between January 2012 and December 2016 were reviewed in Ruijin hospital. Those with distant metastasis, two or more malignant tumors, remnant gastric cancer, neo adjuvant therapy, previous history of gastric surgery or clear history of perigastric lymphadenectomy, and mixed tumors were excluded. Age, sex, presence of ulcerous lesion, tumor size, tumor location, depth of invasion, type of differentiation, lymphatic vessel invasion, vascular invasion, nerve invasion and HER2 expression were collected. Univariate and multivariate stepwise logistic regression analyses were used to identify the independent risk factors of perigastric lymph node metastasis.According to the Guidelines for the Treatment of Gastric Cancer (2018 edition) of the Chinese Society of Clinical Oncology (CSCO), the expanded indications of ESD for EGC are as follows: (1)no ulcerative lesions, the maximum diameter of lesions >2 cm of differentiated intramucosal cancer; (2)ulcerative lesions, the maximum diameter of lesions ≤3 cm of differentiated intramucosal cancer; (3)no ulcerative lesions, undifferentiated intramucosal carcinoma with diameter ≤2 cm. The relationship between clinicopathological factors and lymph node metastasis was analyzed. Results: A total of 517 patients, aged 21-83 (57.1±11.7), including 307 males and 210 females, were enrolled in the study. Among them, 114 (22.0%) patients had lymph node metastasis. Univariate analysis showed that ulcerative lesion (P=0.042), tumor diameter (P=0.048), depth of invasion (P<0.001), location of tumors (P<0.001), lymphatic vessel invasion (P=0.009), vascular invasion (P<0.001) and nerve invasion (P=0.028) were related to lymph node metastasis after radical resection of poorly differentiated early adenocarcinoma. Age, sex, type of differentiation and HER2 expression were not significantly correlated to lymph node metastasis (P>0.05). Multivariate analysis showed that tumor size (OR=1.61, 95% CI: 1.03-2.52, P=0.037), depth of invasion (OR=2.77, 95% CI:1.66-4.63, P<0.001), lymphatic duct invasion (OR=14.74, 95% CI:1.58-137.36, P=0.018) were independent risk factors for lymph node metastasis in poorly differentiated EGC, and ulcerative lesion was not a risk factor for lymph node metastasis (OR=0.82, 95% CI:0.56-1.18,P=0.285). A total of 119 patients with poorly differentiated EGC fully complied with the relative indications of ESD recommended by the Japanese Statute and the criteria for radical resection after ESD. Among them, 14 (11.8%) still had perigastric lymph node metastasis, while the gender, tumor diameter, location, differentiation and HER2 expression were not associated with lymph node metastasis (P>0.05). Conclusion: For patients with poorly differentiated EGC, the application of ESD should be carefully weighed with precise assessment of tumor diameter, depth of invasion, and lymphatic duct invasion.
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Affiliation(s)
- B R Pang
- Department of Surgery, Shanghai institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
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25
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Yuan H, Mei R, Liao J, Liu WT. Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems. Front Microbiol 2019; 10:1536. [PMID: 31333629 PMCID: PMC6621641 DOI: 10.3389/fmicb.2019.01536] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/20/2019] [Indexed: 12/03/2022] Open
Abstract
Microbial community assembly in engineered biological systems is often simultaneously influenced by stochastic and deterministic processes, and the nexus of these two mechanisms remains to be further investigated. Here, three lab-scale activated sludge reactors were seeded with identical inoculum and operated in parallel under eight different sludge retention time (SRT) by sequentially reducing the SRT from 15 days to 1 day. Using 16S rRNA gene amplicon sequencing data, the microbial populations at the start-up (15-day SRT) and SRT-driven (≤10-day SRT) phases were observed to be noticeably different. Clustering results demonstrated ecological succession at the start-up phase with no consistent successional steps among the three reactors, suggesting that stochastic processes played an important role in the community assembly during primary succession. At the SRT-driven phase, the three reactors shared 31 core operational taxonomic units (OTUs). Putative primary acetate utilizers and secondary metabolizers were proposed based on K-means clustering, network and synchrony analysis. The shared core populations accounted for 65% of the total abundance, indicating that the microbial communities at the SRT-driven phase were shaped predominantly by deterministic processes. Sloan’s Neutral model and a null model analysis were performed to disentangle and quantify the relative influence of stochastic and deterministic processes on community assembly. The increased estimated migration rate in the neutral community model and the higher percentage of stochasticity in the null model implied that stochastic community assembly was intensified by strong deterministic factors. This was confirmed by the significantly different α- and β-diversity indices at SRTs shorter than 2 days and the observation that over half of the core OTUs were unshared or unsynchronized. Overall, this study provided quantitative insights into the nexus of stochastic and deterministic processes on microbial community assembly in a biological process.
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Affiliation(s)
- Heyang Yuan
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Junhui Liao
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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26
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Gao H, Mao Y, Zhao X, Liu WT, Zhang T, Wells G. Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess. Water Res 2019; 155:275-287. [PMID: 30852315 DOI: 10.1016/j.watres.2019.02.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Denitrification is the stepwise microbial reduction of nitrate or nitrite (NO2-) to nitrogen gas via the obligate intermediates nitric oxide (NO) and nitrous oxide (N2O). Substantial N2O accumulation has been reported in denitrifying enhanced biological phosphorus removal (EBPR) bioreactors enriched in denitrifying polyphosphate accumulating organisms (DPAOs), but little is known about underlying mechanisms for N2O generation, prevalence of complete versus truncated denitrification pathways, or the impact of NO2- feed on DPAO-enriched consortia. To address this knowledge gap, we employed genome-resolved metagenomics to investigate nitrogen transformation potential in a NO2- fed denitrifying EBPR bioreactor enriched in Candidatus Accumulibacter and prone to N2O accumulation. Our analysis yielded 41 near-complete metagenome-assembled genomes (MAGs), including two co-occurring Accumulibacter strains affiliated with clades IA and IC (the first published genome from this clade) and 39 non-PAO flanking bacterial genomes. The dominant Accumulibacter clade IA encoded genes for complete denitrification, while the lower abundance Accumulibacter clade IC harbored all denitrification genes except for a canonical respiratory NO reductase. Analysis of the 39 non-PAO MAGs revealed a high prevalence of taxa harboring an incomplete denitrification pathway. Of the 27 MAGs harboring capacity for at least one step in the denitrification pathway, 10 were putative N2O producers lacking N2O reductase, 16 were putative N2O reducers that lacked at least one upstream denitrification gene, and only one harbored a complete denitrification pathway. We also documented increasing abundance over the course of reactor operation of putative N2O producers. Our results suggest that the unusually high levels of N2O production observed in this Accumulibacter-enriched consortium are linked in part to the selection for non-PAO flanking microorganisms with truncated denitrification pathways.
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Affiliation(s)
- Han Gao
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, United States
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, Shenzhen University, Shenzhen, 518060, PR China; Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong.
| | - Xiaotian Zhao
- Master of Science in Biotechnology Program, McCormick School of Engineering, Northwestern University, Evanston, IL, 60208, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, United States
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - George Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, United States.
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27
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Mei R, Kim J, Wilson FP, Bocher BTW, Liu WT. Coupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process. Microbiome 2019; 7:65. [PMID: 30995941 PMCID: PMC6471889 DOI: 10.1186/s40168-019-0682-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/08/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Ubiquitous in natural and engineered ecosystems, microbial immigration is one of the mechanisms shaping community assemblage. However, quantifying immigration impact remains challenging especially at individual population level. The activities of immigrants in the receiving community are often inadequately considered, leading to potential bias in identifying the relationship between community composition and environmental parameters. RESULTS This study quantified microbial immigration from an upstream full-scale anaerobic reactor to downstream activated sludge reactors. A mass balance was applied to 16S rRNA gene amplicon sequencing data to calculate the net growth rates of individual populations in the activated sludge reactors. Among the 1178 observed operational taxonomic units (OTUs), 582 had a positive growth rate, including all the populations with abundance > 0.1%. These active populations collectively accounted for 99% of the total sequences in activated sludge. The remaining 596 OTUs with a growth rate ≤ 0 were classified as inactive populations. All the abundant populations in the upstream anaerobic reactor were inactive in the activated sludge process, indicating a negligible immigration impact. We used a supervised learning regressor to predict environmental parameters based on community composition and compared the prediction accuracy based on either the entire community or the active populations. Temperature was the most predictable parameter, and the prediction accuracy was improved when only active populations were used to train the regressor. CONCLUSIONS Calculating growth rate of individual microbial populations in the downstream system provides an effective approach to determine microbial activity and quantify immigration impact. For the studied biological process, a marginal immigration impact was observed, likely due to the significant differences in the growth environments between the upstream and downstream processes. Excluding inactive populations as a result of immigration further enhanced the prediction of key environmental parameters affecting process performance.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3207 Newmark Civil Engineering Laboratory, 205 North Mathews Ave, Urbana, IL 61801 USA
| | - Jinha Kim
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3207 Newmark Civil Engineering Laboratory, 205 North Mathews Ave, Urbana, IL 61801 USA
| | - Fernanda P. Wilson
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3207 Newmark Civil Engineering Laboratory, 205 North Mathews Ave, Urbana, IL 61801 USA
| | | | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3207 Newmark Civil Engineering Laboratory, 205 North Mathews Ave, Urbana, IL 61801 USA
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28
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Mei R, Nobu MK, Narihiro T, Yu J, Sathyagal A, Willman E, Liu WT. Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors. Water Res 2018; 147:403-412. [PMID: 30336343 DOI: 10.1016/j.watres.2018.10.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 05/20/2023]
Abstract
To determine whether the addition of conductive materials could enhance methane production by direct interspecies electron transfer (DIET), we operated three anaerobic reactors amended with non-conductive (ceramic) or conductive materials (anthracite and granular activated carbon (GAC)). Throughout eight months of operation, ethanol was consistently detected as the major fermentation product. The specific yield in the anthracite and GAC-added reactors increased by 31.5% and 43.3%, respectively, compared to the ceramic-added reactor. 16S rRNA gene sequencing results indicated Geobacter was dominant (up to 55% of total sequences), whereas acids-degrading syntrophic bacteria were low in abundance (<2%). Using metagenomic analysis, the draft genome of the dominant Geobacter population (bin GAC1) was reconstructed and observed to possess genetic abilities of ethanol oxidation, hydrogen production, and extracellular electron transfer, and represented a phylogenetically novel Geobacter species. While Methanosaeta was the dominant methanogen, reactors containing conductive materials harbored more diverse and abundant archaeal populations, as revealed by FISH, qPCR, and metagenomics. Our findings suggested that a novel Geobacter population could oxidize ethanol and employed both hydrogen transfer and DIET depending on the accessibility of conductive materials. Thermodynamic advantages of DIET over hydrogen production could lead to enhanced methane production in reactors with conductive materials.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Jimmy Yu
- PepsiCo Research and Development, Hawthorne, NY, USA
| | | | - Eric Willman
- PepsiCo Research and Development, Hawthorne, NY, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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29
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Narihiro T, Nobu MK, Bocher BTW, Mei R, Liu WT. Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors. Environ Microbiol Rep 2018; 10:673-685. [PMID: 30136425 DOI: 10.1111/1758-2229.12689] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 06/08/2023]
Abstract
Methanogenic bioreactors have been applied to treat purified terephthalic acid (PTA) wastewater containing complex aromatic compounds, such as terephthalic acid, para-toluic acid and benzoic acid. This study characterized the interaction of microbial populations in 42 samples obtained from 10 PTA-degrading methanogenic bioreactors. Approximately, 54 dominant populations (11 methanogens, 8 syntrophs and 35 functionally unknown clades) that represented 73.9% of total 16S rRNA gene iTag sequence reads were identified. Co-occurrence analysis based on the abundance of dominant OTUs showed two non-overlapping networks centred around aromatic compound- (group AR: Syntrophorhabdaceae, Syntrophus and Pelotomaculum) and fatty acid- (group FA: Smithella and Syntrophobacter) degrading syntrophs. Group AR syntrophs have no direct correlation with hydrogenotrophic methanogens, while those from group FA do. As degradation of aromatic compounds has a wider thermodynamic window than fatty acids, Group AR syntrophs may be less influenced by fluctuations in hydrogenotrophic methanogen abundance or may non-specifically interact with diverse methanogens. In both groups, network analysis reveals full-scale- and lab-scale-specific uncultivated taxa that may mediate interactions between syntrophs and methanogens, suggesting that those uncultivated taxa may support the degradation of aromatic compounds through uncharted ecophysiological traits. These observations suggest that organisms from multiple niches orchestrate their metabolic capacity in multiple interaction networks to effectively degrade PTA wastewater.
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Affiliation(s)
- Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, 305-8566, Japan
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ben T W Bocher
- Petrochemicals Technology, BP America, Naperville, IL, 60563, USA
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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30
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Hidalgo-Ahumada CAP, Nobu MK, Narihiro T, Tamaki H, Liu WT, Kamagata Y, Stams AJM, Imachi H, Sousa DZ. Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism. Environ Microbiol 2018; 20:4503-4511. [PMID: 30126076 DOI: 10.1111/1462-2920.14388] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/02/2018] [Accepted: 08/15/2018] [Indexed: 11/29/2022]
Abstract
Under methanogenic conditions, short-chain fatty acids are common byproducts from degradation of organic compounds and conversion of these acids is an important component of the global carbon cycle. Due to the thermodynamic difficulty of propionate degradation, this process requires syntrophic interaction between a bacterium and partner methanogen; however, the metabolic strategies and behaviour involved are not fully understood. In this study, the first genome analysis of obligately syntrophic propionate degraders (Pelotomaculum schinkii HH and P. propionicicum MGP) and comparison with other syntrophic propionate degrader genomes elucidated novel components of energy metabolism behind Pelotomaculum propionate oxidation. Combined with transcriptomic examination of P. schinkii behaviour in co-culture with Methanospirillum hungatei, we found that formate may be the preferred electron carrier for P. schinkii syntrophy. Propionate-derived menaquinol may be primarily re-oxidized to formate, and energy was conserved during formate generation through newly proposed proton-pumping formate extrusion. P. schinkii did not overexpress conventional energy metabolism associated with a model syntrophic propionate degrader Syntrophobacter fumaroxidans MPOB (i.e., CoA transferase, Fix and Rnf). We also found that P. schinkii and the partner methanogen may also interact through flagellar contact and amino acid and fructose exchange. These findings provide new understanding of syntrophic energy acquisition and interactions.
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Affiliation(s)
- Catalina A P Hidalgo-Ahumada
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Wageningen, The Netherlands
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL, 61801, USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Wageningen, The Netherlands.,Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Wageningen, The Netherlands
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Zealand AM, Mei R, Papachristodoulou P, Roskilly AP, Liu WT, Graham DW. Microbial community composition and diversity in rice straw digestion bioreactors with and without dairy manure. Appl Microbiol Biotechnol 2018; 102:8599-8612. [PMID: 30051138 PMCID: PMC6153884 DOI: 10.1007/s00253-018-9243-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/11/2018] [Accepted: 07/13/2018] [Indexed: 12/23/2022]
Abstract
Anaerobic digestion (AD) uses a range of substrates to generate biogas, including energy crops such as globally abundant rice straw (RS). Unfortunately, RS is high in lignocellulosic material and has high to C:N ratios (~80:1), which makes it (alone) a comparatively poor substrate for AD. Co-digestion with dairy manure (DM) has been promoted as a method for balancing C:N ratios to improve RS AD whilst also treating another farm waste and co-producing a potentially useful fertiliser. However, past co-digestion studies have not directly compared RS AD microbial communities with and without DM additions, which has made it hard to assess all impacts of DM addition to RS AD processes. Here, four RS:DM ratios were contrasted in identical semi-continuous-fed AD bioreactors, and 100% RS was found to produce the highest specific methane yields (112 mL CH4/g VS/day; VS, volatile solids), which is over double yields achieved in the reactor with the highest DM content (30:70 RS:DM by mass; 48 mL CH4/g VS/day). To underpin these data, microbial communities were sequenced and characterised across the four reactors. Dominant operational taxonomic units (OTUs) in the 100% RS unit were Bacteroidetes/Firmicutes, whereas the 30:70 RS:DM unit was dominated by Proteobacteria/Spirochaetes, suggesting major microbial community shifts occur with DM additions. However, community richness was lowest with 100% RS (despite higher specific yields), suggesting particular OTUs may be more important to yields than microbial diversity. Further, ambient VFA and VS levels were significantly higher when no DM was added, suggesting DM-amended reactors may cope better with higher organic loading rates (OLR). Results show that RS AD without DM addition is feasible, although co-digestion with DM will probably allow higher OLRs, resulting in great RS throughput in farm AD units.
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Affiliation(s)
- A M Zealand
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne, NE1 7RU, UK
| | - R Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL, 61801, USA
| | - P Papachristodoulou
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne, NE1 7RU, UK
| | - A P Roskilly
- Sir Joseph Swan Centre for Energy Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - W T Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL, 61801, USA
| | - David W Graham
- School of Engineering, Newcastle University, Cassie Building, Newcastle upon Tyne, NE1 7RU, UK.
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32
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Wang YR, Zhou YH, Wang XD, Wei S, Liu WT. [Evaluation of maxillary three-dimensional changes in maxillary protraction with alternating rapid palatal expansion and constriction based on the cone-beam computed tomography]. Beijing Da Xue Xue Bao Yi Xue Ban 2018; 50:685-692. [PMID: 30122772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To use the cone-beam computed tomography (CBCT) to evaluate the three-dimensional (3D) changes of maxillary landmarks in the maxillary protraction with alternating rapid palatal expansion and constriction and with rapid palatal expansion, and to provide some clinical suggestions for the early treatment of Class III malocclusion. METHODS A total of 36 maxillary retrusive patients were included and randomized in a 1:1 ratio to either the intervention group (alternating rapid palatal expansion and constriction group, RPE/C) or the control group (rapid palatal expansion group, RPE). Randomization was accomplished with permuted block randomization based on participation sequence. The patients in the RPE/C were treated for 10 weeks (0.5 mm/d) with the repetition of two-week palatal expansion and two-week palatal constriction. The patients in the RPE were taught to complete rapid palatal expansion for 2 weeks (0.5 mm/d ). The patients were instructed to come to the office for the follow-up to ensure the correct procedures. Damaged expanders were repaired (or replaced) and rebanded quickly. Sequential CBCT images including pretreatment (T1), post-expansion (T2) and post-protraction (T3) were required for 3D reconstruction, establishment of landmarks, measurement and analysis by Mimics 10.01. RESULTS There was significant forward movement of subspinale (A) in the RPE/C after the treatment with (3.06±1.29) mm, compared with RPE (2.16±1.27) mm, P<0.05. There were more symmetrical changes of the landmarks in the RPE/C and there was no statistic significance of the entire treatment time between the two groups. Moreover, the maxillary skeletal landmarks had the following 3D changes of a forward and downward movement during the expansion stages T2-T1, a forward and upward movement during the protraction stages T3-T2 and a forward and downward movement during the total treatments T3-T1 compared with the control group. And the width between the bilateral landmarks increased during the expansion stages T2-T1, narrowed down during the protraction stages T3-T2 and increased during the total treatments T3-T1. CONCLUSION The maxillary protraction with alternating rapid palatal expansion and constriction provided clinical benefits on maxillary advancement and symmetrical changes in the orthopedic treatment of the patients with maxillary retrognathism and it required further study on the orthodontic analysis and measurements of CBCT.
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Affiliation(s)
- Y R Wang
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China; Department of Pediatrics, Stomatological Hospital of Shandong University, Jinan 250012, China
| | - Y H Zhou
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - X D Wang
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - S Wei
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - W T Liu
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China; Institute for Clinical Research and Application of Sunny Dental, Beijing 100022, China
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Shen Y, Huang PC, Huang C, Sun P, Monroy GL, Wu W, Lin J, Espinosa-Marzal RM, Boppart SA, Liu WT, Nguyen TH. Effect of divalent ions and a polyphosphate on composition, structure, and stiffness of simulated drinking water biofilms. NPJ Biofilms Microbiomes 2018; 4:15. [PMID: 30038792 PMCID: PMC6052100 DOI: 10.1038/s41522-018-0058-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 05/24/2018] [Accepted: 06/01/2018] [Indexed: 02/04/2023] Open
Abstract
The biofilm chemical and physical properties in engineered systems play an important role in governing pathogen transmission, fouling facilities, and corroding metal surfaces. Here, we investigated how simulated drinking water biofilm chemical composition, structure, and stiffness responded to the common scale control practice of adjusting divalent ions and adding polyphosphate. Magnetomotive optical coherence elastography (MM-OCE), a tool developed for diagnosing diseased tissues, was used to determine biofilm stiffness in this study. MM-OCE, together with atomic force microscopy (AFM), revealed that the biofilms developed from a drinking water source with high divalent ions were stiffer compared to biofilms developed either from the drinking water source with low divalent ions or the water containing a scale inhibitor (a polyphosphate). The higher stiffness of biofilms developed from the water containing high divalent ions was attributed to the high content of calcium carbonate, suggested by biofilm composition examination. In addition, by examining the biofilm structure using optical coherence tomography (OCT), the highest biofilm thickness was found for biofilms developed from the water containing the polyphosphate. Compared to the stiff biofilms developed from the water containing high divalent ions, the soft and thick biofilms developed from the water containing polyphosphate will be expected to have higher detachment under drinking water flow. This study suggested that water chemistry could be used to predict the biofilm properties and subsequently design the microbial safety control strategies. A variety of analytical techniques are revealing the complex influences of ions in drinking water supplies on the structure of biofilms. Such biofilms often contaminate water supply pipes and machinery. Yun Shen and colleagues at the University of Illinois at Urbana-Champaign in the USA investigated the effects of ions with a double positive charge – ‘divalent cations’ – and polyphosphate ions. Divalent cations, especially calcium and magnesium ions, are abundant in drinking water in many regions, promoting the formation of limescale deposits. Polyphosphates are commonly added to water supplies to reduce limescale formation, inhibit corrosion and discourage biofilm formation. The research revealed that divalent cations increase biofilm stiffness, while polyphosphates promote softer but thicker biofilms that are more easily removed. The results will help optimize water treatment procedures to control both microbial contamination and limescale problems.
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Affiliation(s)
- Yun Shen
- 1Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA.,4Present Address: University of Michigan, 1351 Beal Ave., 219 EWRE Bldg, Ann Arbor, MI 48109-2125 USA
| | - Pin Chieh Huang
- 2Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Conghui Huang
- 1Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Peng Sun
- 1Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Guillermo L Monroy
- 2Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Wenjing Wu
- 1Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Jie Lin
- 1Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Rosa M Espinosa-Marzal
- 1Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Stephen A Boppart
- 2Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL USA.,3Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Wen-Tso Liu
- 1Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Thanh H Nguyen
- 1Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
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Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2018; 36:660. [PMID: 29979671 PMCID: PMC7608355 DOI: 10.1038/nbt0718-660a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Neu L, Bänziger C, Proctor CR, Zhang Y, Liu WT, Hammes F. Ugly ducklings-the dark side of plastic materials in contact with potable water. NPJ Biofilms Microbiomes 2018; 4:7. [PMID: 29619241 PMCID: PMC5869678 DOI: 10.1038/s41522-018-0050-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 02/16/2018] [Accepted: 03/01/2018] [Indexed: 01/06/2023] Open
Abstract
Bath toys pose an interesting link between flexible plastic materials, potable water, external microbial and nutrient contamination, and potentially vulnerable end-users. Here, we characterized biofilm communities inside 19 bath toys used under real conditions. In addition, some determinants for biofilm formation were assessed, using six identical bath toys under controlled conditions with either clean water prior to bathing or dirty water after bathing. All examined bath toys revealed notable biofilms on their inner surface, with average total bacterial numbers of 5.5 × 106 cells/cm2 (clean water controls), 9.5 × 106 cells/cm2 (real bath toys), and 7.3 × 107 cells/cm2 (dirty water controls). Bacterial community compositions were diverse, showing many rare taxa in real bath toys and rather distinct communities in control bath toys, with a noticeable difference between clean and dirty water control biofilms. Fungi were identified in 58% of all real bath toys and in all dirty water control toys. Based on the comparison of clean water and dirty water control bath toys, we argue that bath toy biofilms are influenced by (1) the organic carbon leaching from the flexible plastic material, (2) the chemical and biological tap water quality, (3) additional nutrients from care products and human body fluids in the bath water, as well as, (4) additional bacteria from dirt and/or the end-users’ microbiome. The present study gives a detailed characterization of bath toy biofilms and a better understanding of determinants for biofilm formation and development in systems comprising plastic materials in contact with potable water. While bathing typically means good hygiene, bath toys can serve as incubators for microbial growth. Microbes colonize nearly every natural and human-made surface, sometimes living within complex communities called biofilms. A team led by Frederik Hammes at the Swiss Federal Institute of Aquatic Science and Technology found that tap water bacteria and fungi readily formed biofilms inside bath toys, suggesting that bathing provides food for microbes. These nutrients may come from bath toys’ polymeric material, from care products like soap and from human secretions like sweat. While 16S rRNA sequence analysis found that some of the microbes were related to disease-causing strains, future work is needed to assess the disease risk from these bath toy-associated biofilms. This work sheds light on how microbes are spread by our routine activities and that we are bathed in microbes, literally.
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Affiliation(s)
- Lisa Neu
- 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,2Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Carola Bänziger
- 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Caitlin R Proctor
- 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,2Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Ya Zhang
- 3Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana-Champaign, USA
| | - Wen-Tso Liu
- 3Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana-Champaign, USA
| | - Frederik Hammes
- 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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36
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Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2018; 36:196. [PMID: 29406516 PMCID: PMC7609277 DOI: 10.1038/nbt0218-196a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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37
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Fang T, Cui Q, Huang Y, Dong P, Wang H, Liu WT, Ye Q. Distribution comparison and risk assessment of free-floating and particle-attached bacterial pathogens in urban recreational water: Implications for water quality management. Sci Total Environ 2018; 613-614:428-438. [PMID: 28918274 DOI: 10.1016/j.scitotenv.2017.09.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/30/2017] [Accepted: 09/02/2017] [Indexed: 06/07/2023]
Abstract
The risk of pathogen exposure in recreational water is a concern worldwide. Moreover, suspended particles, as ideal shelters for pathogens, in these waters also need attention. However, the risk caused by the pathogen-particle attachment is largely unknown. Accordingly, water samples in three recreational lakes in Beijing were collected and separated into free-floating (FL, 0.22-5μm) and particle-attached (PA, >5μm) fractions. Next-generation sequencing (NGS) was employed to determine the diversity of genera containing pathogens, and quantitative PCR (qPCR) was used to assess the presence of genes from Escherichia coli (uidA), Salmonella enterica (invA), Aeromonas spp. (aerA), Mycobacterium avium (16S) and Pseudomonas aeruginosa (oaa). The NGS results showed stable pathogen genera composition distinctions between the PA and FL fractions. Some genera, such as Aeromonas and Mycobacterium, exhibited higher abundances in the PA fractions. qPCR revealed that most of the gene concentrations were higher within particles than were FL fractions. Some gene levels showed correlations with the particle concentrations and lake nutrient levels. Further quantitative microbial risk assessment (QMRA) of selected strains (S. enterica and M. avium) indicated a higher health risk during secondary contact activities in lakes with more nutrients and particles. We concluded that suspended particles (mainly composed of algae) in urban recreational water might influence the pathogen distribution and could serve as reservoirs for pathogen contamination, with important management implications.
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Affiliation(s)
- Tingting Fang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qijia Cui
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yong Huang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Peiyan Dong
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL 61801, United States
| | - Quanhui Ye
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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Oh S, Hammes F, Liu WT. Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant. Water Res 2018; 128:278-285. [PMID: 29107912 DOI: 10.1016/j.watres.2017.10.054] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 05/08/2023]
Abstract
Microorganisms inhabiting filtration media of a drinking water treatment plant can be beneficial, because they metabolize biodegradable organic matter from source waters and those formed during disinfection processes, leading to the production of biologically stable drinking water. However, which microbial consortia colonize filters and what metabolic capacity they possess remain to be investigated. To gain insights into these issues, we performed metagenome sequencing and analysis of microbial communities in three different filters of a full-scale drinking water treatment plant (DWTP). Filter communities were sampled from a rapid sand filter (RSF), granular activated carbon filter (GAC), and slow sand filter (SSF), and from the Schmutzdecke (SCM, a biologically active scum layer accumulated on top of SSF), respectively. Analysis of community phylogenetic structure revealed that the filter bacterial communities significantly differed from those in the source water and final effluent communities, respectively. Network analysis identified a filter-specific colonization pattern of bacterial groups. Bradyrhizobiaceae were abundant in GAC, whereas Nitrospira were enriched in the sand-associated filters (RSF, SCM, and SSF). The GAC community was enriched with functions associated with aromatics degradation, many of which were encoded by Rhizobiales (∼30% of the total GAC community). Predicting minimum generation time (MGT) of prokaryotic communities suggested that the GAC community potentially select fast-growers (<15 h of MGT) among the four filter communities, consistent with the highest dissolved organic matter removal rate by GAC. Our findings provide new insights into the community phylogenetic structure, colonization pattern, and metabolic capacity that potentially contributes to organic matter removal achieved in the biofiltration stages of the full-scale DWTP.
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Affiliation(s)
- Seungdae Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Frederik Hammes
- Eawag, Swiss Federal Institute for Aquatic Science and Technology, Überlandstr. 133, CH-8600 Dübendorf, Switzerland
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Mei R, Nobu MK, Narihiro T, Kuroda K, Muñoz Sierra J, Wu Z, Ye L, Lee PKH, Lee PH, van Lier JB, McInerney MJ, Kamagata Y, Liu WT. Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Water Res 2017; 124:77-84. [PMID: 28750287 DOI: 10.1016/j.watres.2017.07.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 05/11/2023]
Abstract
Anaerobic digester (AD) microbiomes harbor complex, interacting microbial populations to achieve biomass reduction and biogas production, however how they are influenced by operating conditions and feed sludge microorganisms remain unclear. These were addressed by analyzing the microbial communities of 90 full-scale digesters at 51 municipal wastewater treatment plants from five countries. Heterogeneity detected in community structures suggested that no single AD microbiome could be defined. Instead, the AD microbiomes were classified into eight clusters driven by operating conditions (e.g., pretreatment, temperature range, and salinity), whereas geographic location of the digesters did not have significant impacts. Comparing digesters populations with those present in the corresponding feed sludge led to the identification of a hitherto overlooked feed-associated microbial group (i.e., the residue populations). They accounted for up to 21.4% of total sequences in ADs operated at low temperature, presumably due to ineffective digestion, and as low as 0.8% in ADs with pretreatment. Within each cluster, a core microbiome was defined, including methanogens, syntrophic metabolizers, fermenters, and the newly described residue populations. Our work provides insights into the key factors shaping full-scale AD microbiomes in a global scale, and draws attentions to the overlooked residue populations.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Kyohei Kuroda
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Environmental Systems Engineering, Nagaoka University of Technology, Kami-tomioka, Niigata, Japan
| | - Julian Muñoz Sierra
- Section Sanitary Engineering, Department of Water Management, Delft University of Technology, Delft, The Netherlands
| | - Zhuoying Wu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Lin Ye
- School of the Environment, Nanjing University, Nanjing, Jiangsu, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Jules B van Lier
- Section Sanitary Engineering, Department of Water Management, Delft University of Technology, Delft, The Netherlands
| | - Michael J McInerney
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Zhang HW, Liu HM, Lin R, Zhou L, Zhang J, Liu WT. [Clinical features of autoimmune hepatitis patients with poor response to treatment]. Zhonghua Gan Zang Bing Za Zhi 2017; 25:755-759. [PMID: 29108204 DOI: 10.3760/cma.j.issn.1007-3418.2017.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Objective: To investigate the clinical features of autoimmune hepatitis (AIH) patients with poor response to treatment. Methods: A total of 61 AIH patients were enrolled, among whom 49 (80.33%) achieved complete response (good response group) and 12 (19.67%) had incomplete response (poor response group). The two groups were compared in terms of clinical manifestations, laboratory markers, abdominal ultrasound findings, pathological features by liver biopsy, and response to treatment. Continuous data were expressed as mean ± standard deviation (x±s), and the t-test was used for comparison between groups; categorical data were expressed as rates or percentages, and the chi-square test was used for comparison between groups; a binary logistic regression analysis was used to determine influencing factors. Results: Most patients were female in both groups, and there were no significant differences in sex ratio, mean age of onset, and general status including extrahepatic autoimmune disease between the two groups. Compared with the good response group, the poor response group had significantly higher levels of alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase (ALP), total bilirubin, immunoglobulin G, and immunoglobulin M (P < 0.05). Compared with the good response group, the poor response group had a significantly higher positive rate of autoimmune antibodies except anti-nuclear antibody (ANA), anti-smooth muscle antibody (SMA), antimitochondrial antibody (AMA), and AMA/M2 (75% vs 16.3%, P < 0.001), and there was a significant difference in the positive rate of gp210 antibody between the two groups (25% vs 0%, P < 0.01). There were significant differences between the poor response group and the good response group in the proportion of patients with liver cirrhosis (50.0 % vs 16.3%, P < 0.05) and splenomegaly (58.3% vs 22.4%, P < 0.05). The binary logistic regression analysis showed that a high serum level of ALP (odds ratio [OR] = 1.017, 95% confidence interval [CI] 1.001-1.033, P = 0.034), positive autoimmune antibodies except ANA, SMA, and AMA/M2 (OR = 70.842, 95% CI 2.132-2 354.371, P = 0.017), and liver cirrhosis (OR = 28.777, 95% CI 1.015-815.854, P = 0.049) were independent risk factors for initial treatment outcome. Conclusion: A high serum level of ALP, positive autoimmune antibodies except ANA, SMA, and AMA/M2, and liver cirrhosis are closely associated with poor response in AIH patients.
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Affiliation(s)
- H W Zhang
- Department of gastroenterology, The General Hospital of Tianjin Medical University Tianjin 300052, China
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Oh S, Yap GC, Hong PY, Huang CH, Aw MM, Shek LPC, Liu WT, Lee BW. Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema. PLoS One 2017; 12:e0184955. [PMID: 29049378 PMCID: PMC5648123 DOI: 10.1371/journal.pone.0184955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 08/28/2017] [Indexed: 12/13/2022] Open
Abstract
Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months. Microbial genomic DNA were extracted from stool samples and used for shotgun sequencing. Comparative metagenomic analysis showed that immune-regulatory TCAAGCTTGA motifs were significantly enriched in the six healthy controls (C) communities compared to the six eczema subjects (E), with many encoded by Bifidobacterium (38% of the total motifs in the C communities). Draft genomes of five Bifidobacterium species populations (B. longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum) were recovered from metagenomic datasets. The B. longum BFN-121-2 genome encoded more TCAAGCTTGA motifs (4.2 copies per one million genome sequence) than other Bifidobacterium genomes. Additionally, the communities in the stool of controls (C) were also significantly enriched in functions associated with tetrapyrrole biosynthesis compared to those of eczema (E). Our results show distinct immune-modulatory genomic properties of gut microbiota in infants associated with eczema and provide new insights into potential role of gut microbiota in affecting human immune homeostasis.
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Affiliation(s)
- Seungdae Oh
- Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Gaik Chin Yap
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pei-Ying Hong
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Chiung-Hui Huang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Marion M. Aw
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Lynette Pei-Chi Shek
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
- * E-mail: (BWL); (WTL)
| | - Bee Wah Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
- * E-mail: (BWL); (WTL)
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42
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Zhang Y, Kitajima M, Whittle AJ, Liu WT. Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems. Front Microbiol 2017; 8:2036. [PMID: 29097994 PMCID: PMC5654357 DOI: 10.3389/fmicb.2017.02036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 11/22/2022] Open
Abstract
The occurrence of pathogenic bacteria in drinking water distribution systems (DWDSs) is a major health concern, and our current understanding is mostly related to pathogenic species such as Legionella pneumophila and Mycobacterium avium but not to bacterial species closely related to them. In this study, genomic-based approaches were used to characterize pathogen-related species in relation to their abundance, diversity, potential pathogenicity, genetic exchange, and distribution across an urban drinking water system. Nine draft genomes recovered from 10 metagenomes were identified as Legionella (4 draft genomes), Mycobacterium (3 draft genomes), Parachlamydia (1 draft genome), and Leptospira (1 draft genome). The pathogenicity potential of these genomes was examined by the presence/absence of virulence machinery, including genes belonging to Type III, IV, and VII secretion systems and their effectors. Several virulence factors known to pathogenic species were detected with these retrieved draft genomes except the Leptospira-related genome. Identical clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) genetic signatures were observed in two draft genomes recovered at different stages of the studied system, suggesting that the spacers in CRISPR-Cas could potentially be used as a biomarker in the monitoring of Legionella related strains at an evolutionary scale of several years across different drinking water production and distribution systems. Overall, metagenomics approach was an effective and complementary tool of culturing techniques to gain insights into the pathogenic characteristics and the CRISPR-Cas signatures of pathogen-related species in DWDSs.
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Affiliation(s)
- Ya Zhang
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Andrew J Whittle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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43
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Nobu MK, Narihiro T, Liu M, Kuroda K, Mei R, Liu WT. Thermodynamically diverse syntrophic aromatic compound catabolism. Environ Microbiol 2017; 19:4576-4586. [PMID: 28892300 DOI: 10.1111/1462-2920.13922] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/19/2017] [Indexed: 11/28/2022]
Abstract
Specialized organotrophic Bacteria 'syntrophs' and methanogenic Archaea 'methanogens' form a unique metabolic interaction to accomplish cooperative mineralization of organic compounds to CH4 and CO2 . Due to challenges in cultivation of syntrophs, mechanisms for how their organotrophic catabolism circumvents thermodynamic restrictions remain unclear. In this study, we investigate two communities hosting diverse syntrophic aromatic compound metabolizers (Syntrophus, Syntrophorhabdus, Pelotomaculum and an uncultivated Syntrophorhabdacaeae member) to uncover their catabolic diversity and flexibility. Although syntrophs have been generally presumed to metabolize aromatic compounds to acetate, CO2 , H2 and formate, combined metagenomics and metatranscriptomics show that uncultured syntrophs utilize unconventional alternative metabolic pathways in situ producing butyrate, cyclohexanecarboxylate and benzoate as catabolic byproducts. In addition, we also find parallel utilization of diverse H2 and formate generating pathways to facilitate interactions with partner methanogens. Based on thermodynamic calculations, these pathways may enable syntrophs to combat thermodynamic restrictions. In addition, when fed with specific substrates (i.e., benzoate, terephthalate or trimellitate), each syntroph population expresses different pathways, suggesting ecological diversification among syntrophs. These findings suggest we may be drastically underestimating the biochemical capabilities, strategies and diversity of syntrophic bacteria thriving at the thermodynamic limit.
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Affiliation(s)
- Masaru Konishi Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Miaomiao Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Kyohei Kuroda
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
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44
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Liu M, Wang S, Nobu MK, Bocher BTW, Kaley SA, Liu WT. Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater. Water Res 2017; 122:308-316. [PMID: 28614743 DOI: 10.1016/j.watres.2017.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/08/2017] [Accepted: 06/03/2017] [Indexed: 06/07/2023]
Abstract
Up-flow anaerobic sludge blanket (UASB) processes treating purified terephthalic acid (PTA) wastewater often face challenges associated with biomass loss. As excessive biomass loss could lead to deterioration of PTA removal, biostimulation and bioaugmentation were often practiced without understanding the microbial impact in UASB. Three laboratory-scale UASB reactors were operated with synthetic PTA wastewater as the feed, with two added with co-substrate (glucose or molasses) on Day 170 for 90 days, and one with external granules on Day 118. Throughout the operation, treatment performance was measured together with the analysis of microbial communities of biomass samples using 16S rRNA-based gene Illumina sequencing. Glucose amendment destabilized both terephthalic acid and para-toluic acid removal, while molasses amendment improved para-toluic acid removal. Both substrate addition generally led to decreases in the abundances of syntrophs and methanogens and increases in carbohydrate-fermenting bacteria in the granular sludge. Regarding bioaugmentation, paper mill granule addition led to a temporary crash of terephthalic acid removal for 42 days, and deterioration of para-toluic acid removal throughout the operation. Syntrophs and methanogens were observed to colonize on the paper mill granules after three months, meanwhile growth of methanogens were stimulated on the PTA granules added initially. Overall, proper level of molasses amendment and external granule inoculation could be promising strategies to make up for biomass loss during the operation of PTA-degrading UASB.
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Affiliation(s)
- Miaomiao Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Shanquan Wang
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Masaru Konishi Nobu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | | | - Scott A Kaley
- BP America, Petrochemicals Technology, Naperville, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, USA.
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45
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Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2017; 35:725-731. [PMID: 28787424 PMCID: PMC6436528 DOI: 10.1038/nbt.3893] [Citation(s) in RCA: 975] [Impact Index Per Article: 139.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/27/2017] [Indexed: 12/20/2022]
Abstract
Standards for sequencing the microbial 'uncultivated majority', namely bacterial and archaeal single-cell genome sequences, and genome sequences from metagenomic datasets, are proposed. We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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Affiliation(s)
- Robert M Bowers
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Devin Doud
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Jessica Jarett
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Adam R Rivers
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,United States Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Gainesville, Florida, USA
| | | | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,School of Natural Sciences, University of California Merced, Merced, California, USA
| | - Natalia N Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Alex Copeland
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oakridge Tennessee, USA
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - George M Garrity
- Department of Microbiology &Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, California, USA
| | - Shibu Yooseph
- J. Craig Venter Institute, San Diego, California, USA
| | | | - Frank O Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - William C Nelson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Steven J Hallam
- Department of Microbiology &Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P Jungbluth
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,Center for Dark Energy Biosphere Investigation, University of Southern California, Los Angeles, California, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Scott Tighe
- Advanced Genomics Lab, University of Vermont Cancer Center, Burlington Vermont, USA
| | | | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas-Austin, Marine Science Institute, Austin, Texas, USA
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Brian Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Rob Knight
- Center for Microbiome Innovation, and Departments of Pediatrics and Computer Science &Engineering, University of California San Diego, La Jolla, California, USA
| | - Rob Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Welcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Alla Lapidus
- Centre for Algorithmic Biotechnology, ITBM, St. Petersburg State University, St. Petersburg, Russia
| | - Folker Meyer
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - A M Eren
- Knapp Center for Biomedical Discovery, Chicago, Illinois, USA
| | - Lynn Schriml
- National Cancer Institute, Frederick, Maryland, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,School of Natural Sciences, University of California Merced, Merced, California, USA
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46
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Chang DT, Zhou YH, Liu WT. [Evaluation of cone-beam computed tomography on upper airway changes after alternating rapid palatal expansion and constriction]. Beijing Da Xue Xue Bao Yi Xue Ban 2017; 49:685-690. [PMID: 28816289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To evaluate the changes of different parts of upper airway after alternating rapid palatal expansion and constriction via three dimensional measurement, compared with the protocol of rapid palatal expansion alone. METHODS In the study, 36 patients with retrognathic maxilla were selected and randomized to either group A or group B. The patients in group A were treated with rapid palatal expansion alone. The patients in group B were treated with alternating rapid palatal expansion and constriction. Three dimensional analyses were performed on all pre- and post-treatment cone-beam computed tomography (CBCT) images with the software Dolphin. RESULTS Two subjects in group B were lost to follow up during the treatment. The gender distributions, ages and all measuring items before treatment had no significant difference between group A and group B (P>0.05). Nasal floor width, nasal lateral width, nasal volume, and nasopharynx volume increased significantly in each group after rapid palatal expansion alone or rapid palatal expansion and constriction (P<0.05). The variations of oropharyngeal volume and hypopharyngeal volume had no significant difference (P>0.05). No significant difference was observed in the nasal floor width and nasal lateral width increment among the anterior, median and posterior parts in each group either (P>0.05). No significant difference in all the measuring items was observed between the two groups (P>0.05). CONCLUSION Alternating rapid palatal expansion and constriction could increase the volume of nasal and naopharynx cavities by the similar way of rapid palatal expansion alone, and had no obvious effect on oropharynx and hypopharynx cavities.
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Affiliation(s)
- D T Chang
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100181, China
| | - Y H Zhou
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100181, China
| | - W T Liu
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100181, China
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47
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Zhang Y, Oh S, Liu WT. Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance's perspective. Environ Microbiol 2017; 19:3163-3174. [PMID: 28654183 DOI: 10.1111/1462-2920.13800] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/30/2017] [Accepted: 05/12/2017] [Indexed: 12/01/2022]
Abstract
While microbes are known to be present at different stages of a drinking water system, their potential functions and ability to grow in such systems are poorly understood. In this study, we demonstrated that treatment and distribution processes could be viewed as ecological disturbances exhibited over space on the microbiome continuum in a groundwater-derived system. Results from 16S rRNA gene amplicon analysis and metagenomics suggested that disturbances in the system were intense as the community diversity was substantially reduced during the treatment steps. Specifically, syntrophs and methanogens dominant in raw water (RW) disappeared after water abstraction, accompanied by a substantial decrease in both the abundance and number of functional genes related to methanogenesis. The softening effluent was dominated by an Exiguobacterium-related population, likely due to its ability to use the phosphotransferase system (PTS) as regulatory machinery to control the energy conditions of the cell. After disinfection and entering the distribution system, community-level functionality remained relatively stable, whereas the community structure differed from those taken in the treatment steps. The diversity and high abundance of some eukaryotic groups in the system suggested that predation could be a disturbance to the bacterial microbiome, which could further drive the diversification of the bacterial community.
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Affiliation(s)
- Ya Zhang
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL, 61810, USA
| | - Seungdae Oh
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL, 61810, USA
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48
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Liao J, Fang C, Yu J, Sathyagal A, Willman E, Liu WT. Direct treatment of high-strength soft drink wastewater using a down-flow hanging sponge reactor: performance and microbial community dynamics. Appl Microbiol Biotechnol 2017; 101:5925-5936. [DOI: 10.1007/s00253-017-8326-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 11/24/2022]
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49
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Gao H, Liu M, Griffin JS, Xu L, Xiang D, Scherson YD, Liu WT, Wells GF. Complete Nutrient Removal Coupled to Nitrous Oxide Production as a Bioenergy Source by Denitrifying Polyphosphate-Accumulating Organisms. Environ Sci Technol 2017; 51:4531-4540. [PMID: 28212019 DOI: 10.1021/acs.est.6b04896] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Coupled aerobic-anoxic nitrous decomposition operation (CANDO) is a promising emerging bioprocess for wastewater treatment that enables direct energy recovery from nitrogen (N) in three steps: (1) ammonium oxidation to nitrite; (2) denitrification of nitrite to nitrous oxide (N2O); and (3) N2O conversion to N2 with energy generation. However, CANDO does not currently target phosphorus (P) removal. Here, we demonstrate that denitrifying polyphosphate-accumulating organism (PAO) enrichment cultures are capable of catalyzing simultaneous biological N and P removal coupled to N2O generation in a second generation CANDO process, CANDO+P. Over 7 months (>300 cycles) of operation of a prototype lab-scale CANDO+P sequencing batch reactor treating synthetic municipal wastewater, we observed stable and near-complete N removal accompanied by sustained high-rate, high-yield N2O production with partial P removal. A substantial increase in abundance of the PAO Candidatus Accumulibacter phosphatis was observed, increasing from 5% of the total bacterial community in the inoculum to over 50% after 4 months. PAO enrichment was accompanied by a strong shift in the dominant Accumulibacter population from clade IIC to clade IA, based on qPCR monitoring of polyphosphate kinase 1 (ppk1) gene variants. Our work demonstrates the feasibility of combining high-rate, high-yield N2O production for bioenergy production with combined N and P removal from wastewater, and it further suggests a putative denitrifying PAO niche for Accumulibacter clade IA.
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Affiliation(s)
| | - Miaomiao Liu
- Department of Civil and Environmental Engineering, University of Illinoisat Urbana-Champaign , Urbana, Illinois 61801, United States
| | | | | | | | | | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinoisat Urbana-Champaign , Urbana, Illinois 61801, United States
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50
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Shen Y, Huang C, Lin J, Wu W, Ashbolt NJ, Liu WT, Nguyen TH. Effect of Disinfectant Exposure on Legionella pneumophila Associated with Simulated Drinking Water Biofilms: Release, Inactivation, and Infectivity. Environ Sci Technol 2017; 51:2087-2095. [PMID: 28085262 DOI: 10.1021/acs.est.6b04754] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Legionella pneumophila, the most commonly identified causative agent in drinking water associated with disease outbreaks, can be harbored by and released from drinking water biofilms. In this study, the release of biofilm-associated L. pneumophila under simulated drinking water flow containing a disinfectant residual was examined. Meanwhile, the inactivation and infectivity (to amoebae) of the released L. pneumophila were studied. To simulate drinking water system conditions, biofilms were prepared under either disinfectant exposure (predisinfected biofilms) or disinfectant-free (untreated biofilms) conditions, respectively. For experiments with water flow containing a disinfectant to release the biofilm-associated L. pneumophila from these two types of biofilms, the L. pneumophila release kinetics values from predisinfected and untreated biofilms under flow condition were not statistically different (one-way ANOVA, p > 0.05). However, inactivation of the L. pneumophila released from predisinfected biofilms was 1-2 times higher and amoeba infectivity was 2-29 times lower than that from untreated biofilms. The higher disinfectant resistance of L. pneumophila released from untreated biofilms was presumably influenced by the detachment of a larger amount of biofilm material (determined by 16S rRNA qPCR) surrounding the released L. pneumophila. This study highlights the interaction among disinfectant residual, biofilms, and L. pneumophila, which provides guidelines to assess and control pathogen risk.
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Affiliation(s)
- Yun Shen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2352, United States
| | - Conghui Huang
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2352, United States
| | - Jie Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2352, United States
| | - Wenjing Wu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2352, United States
| | - Nicholas J Ashbolt
- School of Public Health, University of Alberta , Edminton, Alberta AB T6G 2G7, Canada
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2352, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2352, United States
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