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Khan MH, Liu H, Zhu A, Khan MH, Hussain S, Cao H. Conservation tillage practices affect soil microbial diversity and composition in experimental fields. Front Microbiol 2023; 14:1227297. [PMID: 37601340 PMCID: PMC10433396 DOI: 10.3389/fmicb.2023.1227297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/06/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Conservation tillage is a widely used technique worldwide, but the effects of conservation tillage on bacterial community structure are poorly understood. We explored proportional alterations in the bacterial community under different tillage treatments. Methodology Hence, this study utilized high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in different tillage treatments. Results and discussion Tillage treatments included tillage no-straw retention (CntWt), no-tillage with straw retention (CntWntS), tillage with straw retention (CntWtS), no-tillage and no-straw retention (CntWnt). The influence of tillage practices on soil bacterial communities was investigated using Illumina MiSeq sequencing. Different tillage methods and straw retention systems significantly influenced soil parameters such as total potassium and pH were not affected by tillage practices, while straw retention significantly affected soil parameters including nitrogen content, available phosphorus and available potassium. Straw retention decreased bacterial diversity while increased bacterial richness. The effect of straw retention and tillage on bacterial communities was greater than with no tillage. Phylogenetic β-diversity analysis showed that deterministic homogeneous selection processes were dominated, while stochastic processes were more pronounced in tillage without straw retention. Ecological network analysis showed that microbial community correlation was increased in CntWntS and CntWnt. Straw retention treatment significantly increased the relative abundance of bacterial taxa Proteobacteria, Bacteroidetes, and OD1, while Nitrospirae, Actinobacteria, and Verrucomicrobia significantly decreased. Conclusion The conservation tillage practices significantly affect soil properties, bacterial composition, and assembly processes; however, further studies are required to investigate the impact of different crops, tillage practices and physiological characteristics on bacterial community structure and functions.
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Affiliation(s)
- Muzammil Hassan Khan
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Hao Liu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Anning Zhu
- Fengqiu Agro-Ecological Experimental Station, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Mudassir Hassan Khan
- Department of Biological Sciences, Karakoram International University, Gilgit, Pakistan
| | - Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
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2
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Shahin M, Ji B, Dixit PD. EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies. NPJ Syst Biol Appl 2023; 9:26. [PMID: 37339950 PMCID: PMC10282069 DOI: 10.1038/s41540-023-00285-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Dimensionality reduction offers unique insights into high-dimensional microbiome dynamics by leveraging collective abundance fluctuations of multiple bacteria driven by similar ecological perturbations. However, methods providing lower-dimensional representations of microbiome dynamics both at the community and individual taxa levels are not currently available. To that end, we present EMBED: Essential MicroBiomE Dynamics, a probabilistic nonlinear tensor factorization approach. Like normal mode analysis in structural biophysics, EMBED infers ecological normal modes (ECNs), which represent the unique orthogonal modes capturing the collective behavior of microbial communities. Using multiple real and synthetic datasets, we show that a very small number of ECNs can accurately approximate microbiome dynamics. Inferred ECNs reflect specific ecological behaviors, providing natural templates along which the dynamics of individual bacteria may be partitioned. Moreover, the multi-subject treatment in EMBED systematically identifies subject-specific and universal abundance dynamics that are not detected by traditional approaches. Collectively, these results highlight the utility of EMBED as a versatile dimensionality reduction tool for studies of microbiome dynamics.
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Affiliation(s)
- Mayar Shahin
- Department of Physics, University of Florida, Gainesville, FL, 32611, USA.
| | - Brian Ji
- Physician-Scientist Training Pathway, Department of Medicine, UCSD, San Diego, CA, 92103, USA
| | - Purushottam D Dixit
- Department of Physics, University of Florida, Gainesville, FL, 32611, USA.
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
- Department of Chemical Engineering, University of Florida, Gainesville, FL, 32611, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA.
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3
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Li YS, Li BB, Tian T, Yu HQ. Quorum sensing unveils the sludge floccule-assisted stabilization of aerobic granules in granule-dominated sequencing batch reactors. Biotechnol Bioeng 2023; 120:444-455. [PMID: 36303067 DOI: 10.1002/bit.28275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 01/13/2023]
Abstract
Floccules are another major form of microbial aggregates in aerobic granular sludge systems. Previous studies mainly attributed the persistence of floccules to their relatively faster nutrient uptake and higher growth rate over aerobic granules; however, they failed to unravel the underlying mechanism of the long-term coexistence of these two aggregates. In this work, the existence and function of the floccules in an aerobic granule-dominated sequencing batch reactor were investigated from the view of quorum sensing (QS) and quorum quenching (QQ). The results showed that though the floccules were closely associated with the granules in terms of similar community structures (including the QS- and QQ-related ones), they exhibited a relatively higher QQ-related activity but a lower QS-related activity. A compatible proportion of floccules might be helpful to maintain the QS-related activity and keep the granules stable. In addition, the structure difference was demonstrated to diversify the QS- and QQ-related activities of the floccules and the aerobic granules. These findings could broaden our understanding of the interactions between the coexistent floccules and granules in aerobic granule-dominated systems and would be instructive for the development of the aerobic granular sludge process.
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Affiliation(s)
- Yu-Sheng Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Bing-Bing Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Tian Tian
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China.,Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
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Inaba T, Yamaguchi M, Taniguchi A, Sato Y, Aoyagi T, Hori T, Inoue H, Fujita M, Iwata M, Iwata Y, Habe H. Evaluation of dye decolorization using anaerobic granular sludge from an expanded granular sludge bed based on spectrometric and microbiome analyses. J GEN APPL MICROBIOL 2023; 68:242-247. [PMID: 35691891 DOI: 10.2323/jgam.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The decolorization of 11 dyes by granular sludge from an anaerobic expanded granular sludge bed (EGSB) reactor was evaluated. Biological decolorization of Reactive Red 21, 23, and 180, and Reactive Yellow 15, 17, and 23 in model textile wastewater was observed for the first time after a 7-day incubation (over 94% decolorization). According to the sequencing analysis of 16S rRNA gene amplicons from EGSB granular sludge, the operational taxonomic unit related to Paludibacter propionicigenes showed the highest increase in relative abundance ratios in the presence of dyes (7.12 times on average over 11 dyes) compared to those without dyes.
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Affiliation(s)
- Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Mami Yamaguchi
- Textile Technology Center, Ehime Institute of Industrial Technology
| | | | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hiroyuki Inoue
- Textile Technology Center, Ehime Institute of Industrial Technology
| | - Masahiko Fujita
- Textile Technology Center, Ehime Institute of Industrial Technology
| | | | | | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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Linsong H, Lianhua L, Ying L, Changrui W, Yongming S. Bioaugmentation with methanogenic culture to improve methane production from chicken manure in batch anaerobic digestion. CHEMOSPHERE 2022; 303:135127. [PMID: 35654231 DOI: 10.1016/j.chemosphere.2022.135127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
This study sought to investigate the effect of bioaugmentation on batch anaerobic digestion of chicken manure. The digestion performance with and without bioaugmentation and bioaugmented efficiency under different dosages were compared. The results demonstrated that bioaugmentation increased the methane yield and shortened the methane production time in batch reactors. Compared to the un-bioaugmented control, the methane yield of bioaugmented digesters was increased by 1.2-, 1.7-, 2.2-, 3.4-, and 3.6-fold at addition ratios of 0.07, 0.14, 0.21, 0.27, and 0.34 g VS bioaugmentation seed (BS)/g VSCM, respectively. However, higher bioaugmentation doses (0.34 g VSBS/g VSCM) did not exhibit significantly improved bioaugmentation efficiency, thus, the recommended dose is 0.27 g VSBS/g VSCM for biomethane conversion of CM. Moreover, whole genome pyrosequencing revealed that Methanoculleus and Methanobrevibacter predominated the non-bioaugmentation digesters, whereas Methanothrix, Methanobacterium, and Methanomassiliicoccus were the dominant methanogens in bioaugmentation digesters. The increased methane may be explained by an increase in the Methanothrix population, which accelerated acetic acid degradation. With bioaugmentation the mainly methanogenic pathways have become more diverse. From gene function perspective, bioaugmentation enhanced metabolic activities in digestor which function better in metabolism.
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Affiliation(s)
- He Linsong
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510006, China; Laboratory of Biomass Bio-chemical Conversion, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, PR China; Guangdong Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Li Lianhua
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510006, China; Laboratory of Biomass Bio-chemical Conversion, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, PR China; Guangdong Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, PR China
| | - Li Ying
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510006, China; Laboratory of Biomass Bio-chemical Conversion, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, PR China; Guangdong Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, PR China.
| | - Wang Changrui
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510006, China; Laboratory of Biomass Bio-chemical Conversion, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, PR China; Guangdong Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, PR China; Key Laboratory of Complementary Energy System of Biomass and Solar Energy, Gansu Province, Lanzhou, 730050, China
| | - Sun Yongming
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510006, China; Laboratory of Biomass Bio-chemical Conversion, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, PR China; Guangdong Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, PR China
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6
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Zhou Q, Feng F, Li FL, Liu J, Wang M, Huang S, Sun Y. Acylated homoserine lactones regulate the response of methane metabolism and nitrogen metabolism to florfenicol in anaerobic fermentation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155035. [PMID: 35395307 DOI: 10.1016/j.scitotenv.2022.155035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
Antimicrobial agents enter the ecological environment through animal excreta and disrupt metabolism in environmental microorganisms. Quorum sensing (QS) can help bacteria adapt to their surroundings. To explore how acyl-homoserine lactone (AHL) can adjust the influence of florfenicol on nitrogen cycling and methane metabolism in anaerobic fermentation, a small indoor thermostatic anaerobic fermentation model was established by adding exogenous acylated homoserine lactone (AHL) signal molecules with florfenicol as the stress factor. Through bacterial function prediction by PICRUST, we found that the addition of AHL further increased the promotion of methanogenesis_by_CO2_reduction_with_H2 and hydrogenotrophic methanogenesis by florfenicol. Before the third sampling, florfenicol significantly inhibited the enrichment of the denitrification pathway microbiota, whereas the addition of AHL significantly promoted the enrichment of the denitrification pathway microbiota. Functional annotation showed that florfenicol exposure stress significantly affected nitrogen and methane metabolism, and the addition of AHLs reduced the response of functional genes to florfenicol. All nitrogen cycling enzymes with significantly different abundances in treatment groups were substantially associated with methane-metabolizing enzymes. Glutamate metabolism is significant in the process of anaerobic fermentation, and is a correlation point between nitrogen and methane metabolism. In our experiment, AHL was the influencing factor at the highest latitude that directly regulates the metabolism of NO3--N and the degradation process of florfenicol. The addition of AHL curbed the inhibitory effect of florfenicol on some functional microbiota, improved the stability of fermentation microbiota, and weakened the impact of antibiotic residues by improving its degradation efficiency.
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Affiliation(s)
- Qin Zhou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; College of Life Sciences and Engineering, Foshan University, 18 Jiangwan Road, Foshan 528011, Guangdong Province, China
| | - Fengling Feng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Fu Lin Li
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Junlin Liu
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Mianzhi Wang
- Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Shujian Huang
- College of Life Sciences and Engineering, Foshan University, 18 Jiangwan Road, Foshan 528011, Guangdong Province, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
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7
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Zhang B, Deng J, Xie J, Wu H, Wei C, Li Z, Qiu G, Wei C, Zhu S. Microbial community composition and function prediction involved in the hydrolytic bioreactor of coking wastewater treatment process. Arch Microbiol 2022; 204:426. [PMID: 35751757 DOI: 10.1007/s00203-022-03052-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 04/08/2022] [Accepted: 06/03/2022] [Indexed: 11/25/2022]
Abstract
The hydrolytic acidification process has a strong ability to conduct denitrogenation and increase the biological oxygen demand/chemical oxygen demand ratio in O/H/O coking wastewater treatment system. More than 80% of the total nitrogen (TN) was removed in the hydrolytic bioreactor, and the hydrolytic acidification process contributed to the provision of carbon sources for the subsequent nitrification process. The structure and diversity of microbial communities were elaborated using high-throughput MiSeq of the 16S rRNA genes. The results revealed that the operational taxonomic units (OTUs) belonged to phyla Bacteroidetes, Betaproteobacteria, and Alphaproteobacteria were the dominant taxa involved in the denitrogenation and degradation of refractory contaminants in the hydrolytic bioreactor, with relative abundances of 22.94 ± 3.72, 29.77 ± 2.47, and 18.23 ± 0.26%, respectively. The results of a redundancy analysis showed that the OTUs belonged to the genera Thiobacillus, Rhodoplanes, and Hylemonella in the hydrolytic bioreactor strongly positively correlated with the chemical oxygen demand, TN, and the removal of phenolics, respectively. The results of a microbial co-occurrence network analysis showed that the OTUs belonged to the phylum Bacteroidetes and the genus Rhodoplanes had a significant impact on the efficiency of removal of contaminants that contained nitrogen in the hydrolytic bioreactor. The potential function profiling results indicate the complementarity of nitrogen metabolism, methane metabolism, and sulfur metabolism sub-pathways that were considered to play a significant role in the process of denitrification. These results provide new insights into the further optimization of the performance of the hydrolytic bioreactor in coking wastewater treatment.
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Affiliation(s)
- Baoshan Zhang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jinsi Deng
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Junting Xie
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Haizhen Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Cong Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Zemin Li
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, China.
| | - Shuang Zhu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China.
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8
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Xu ZM, Zhang YX, Wang L, Liu CG, Sun WM, Wang YF, Long SX, He XT, Lin Z, Liang JL, Zhang JX. Rhizobacteria communities reshaped by red mud based passivators is vital for reducing soil Cd accumulation in edible amaranth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154002. [PMID: 35231517 DOI: 10.1016/j.scitotenv.2022.154002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Red mud (RM) was constantly reported to immobilize soil cadmium (Cd) and reduce Cd uptake by crops, but few studies investigated whether and how RM influenced rhizobacteria communities, which was a vital factor determining Cd bioavailability and plant growth. To address this concern, high-throughput sequencing and bioinformatics were used to analyze microbiological mechanisms underlying RM application reducing Cd accumulation in edible amaranth. Based on multiple statistical models (Detrended correspondence analysis, Bray-Curtis, weighted UniFrac, and Phylogenetic tree), this study found that RM reduced Cd content in plants not only through increasing rhizosphere soil pH, but by reshaping rhizobacteria communities. Special taxa (Alphaproteobacteria, Gammaproteobacteria, Actinobacteriota, and Gemmatimonadota) associated with growth promotion, anti-disease ability, and Cd resistance of plants preferentially colonized in the rhizosphere. Moreover, RM distinctly facilitated soil microbes' proliferation and microbial biofilm formation by up-regulating intracellular organic metabolism pathways and down-regulating cell motility metabolic pathways, and these microbial metabolites/microbial biofilm (e.g., organic acid, carbohydrates, proteins, S2-, and PO43-) and microbial cells immobilized rhizosphere soil Cd via the biosorption and chemical chelation. This study revealed an important role of reshaped rhizobacteria communities acting in reducing Cd content in plants after RM application.
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Affiliation(s)
- Zhi-Min Xu
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300350, China; Guangdong-Hongkong-Macau Joint Laboratory of Collaborative Innovation for Environmental Quality, Guangzhou 510632, China
| | - Yu-Xue Zhang
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Lei Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300350, China
| | - Chun-Guang Liu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300350, China
| | - Wei-Min Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; School of Environment, Henan Normal University, Xinxiang 453007, China
| | - Yi-Fan Wang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Sheng-Xing Long
- College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Xiao-Tong He
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zheng Lin
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jia-Lin Liang
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jie-Xiang Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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9
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Wei Y, Lan Y, Li X, Gao M, Yuan S, Yuan H. Effect of wheat straw pretreated with liquid fraction of digestate from different substrates on anaerobic digestion performance and microbial community characteristics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151764. [PMID: 34800463 DOI: 10.1016/j.scitotenv.2021.151764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
The effects of liquid fraction of digestate (LFD) pretreatment on anaerobic digestion (AD) performance and microbial community characteristics were estimated. Prior to AD, LFD (LFDSM, LFDFW, and LFDWS) collected separately from three continuously stirred tank reactors (CSTRs) using swine manure (SM), food waste (FW), and wheat straw (WS) as the mono-substrate was applied to pretreat WS. The results showed that AD with LFD pretreatment resulted in biomethane yields of 240.2-277.9 mL·gVS-1, a 33.57%-54.54% improvement over the yield of the control, and also produced a time saving of 32.26%-46.77%. The pretreatment parameters were optimized for LFD pretreatment. The enhancement effect was in the order of LFDFW > LFDSM > LFDWS. Simultaneously, the cellulose, hemicellulose and lignin contents in the WS and their characteristics (surface properties, crystallinity index, etc.) varied accordingly. The function of the microbial community was strengthened during the pretreatment stage, but the structure of the microbial community had a clear response to the LFD source substrates. Bacteroidetes was the most dominant phyla and was positively correlated with the hydrolysis rate. Consequently, the LFD from the different substrates used as pretreat agents could improve the AD performance of WS.
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Affiliation(s)
- Yufang Wei
- State Key Laboratory of Chemical Resource Engineering, Department of Environmental Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China; State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Yanyan Lan
- Chang'an Communication Technology Co. Ltd., Building 16, TBD Yunji Center, Qibei Road, Changping District, Beijing 110114, PR China
| | - Xiujin Li
- State Key Laboratory of Chemical Resource Engineering, Department of Environmental Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Minghan Gao
- Qingdao No.58 middle school, Licang District, Qingdao, Shandong 266199, PR China
| | - Shuai Yuan
- Business School, University of Nottingham Ningbo China, Ningbo 315199, PR China
| | - Hairong Yuan
- State Key Laboratory of Chemical Resource Engineering, Department of Environmental Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China.
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10
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Li K, Zeng Z, Liu J, Pei L, Wang Y, Li A, Kulyar MFEA, Shahzad M, Mehmood K, Li J, Qi D. Effects of Short-Chain Fatty Acid Modulation on Potentially Diarrhea-Causing Pathogens in Yaks Through Metagenomic Sequencing. Front Cell Infect Microbiol 2022; 12:805481. [PMID: 35402298 PMCID: PMC8983862 DOI: 10.3389/fcimb.2022.805481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/25/2022] [Indexed: 12/30/2022] Open
Abstract
Short-chain fatty acids (SCFA) are principal nutrient substrates of intestinal epithelial cells that regulate the epithelial barrier in yaks. Until now, metagenomics sequencing has not been reported in diarrheal yaks. Scarce information is available regarding the levels of fecal SCFA and diarrhea in yaks. So, our study aims to identify the potential pathogens that cause the emerging diarrhea and explore the potential relationship of short-chain fatty acids in this issue. We estimated diarrhea rate in yaks after collecting an equal number of fecal samples from affected animals. Metagenomics sequencing and quantitative analysis of SCFA were performed, which revealed 15%–25% and 5%–10% prevalence of diarrhea in yak’s calves and adults, respectively. Violin box plot also showed a higher degree of dispersion in gene abundance distribution of diarrheal yaks, as compared to normal yaks. We found 366,163 significant differential abundance genes in diarrheal yaks, with 141,305 upregulated and 224,858 downregulated genes compared with normal yaks via DESeq analysis. Metagenomics binning analysis indicated the higher significance of bin 33 (Bacteroidales) (p < 0.05) in diarrheal animals, while bin 10 (p < 0.0001), bin 30 (Clostridiales) (p < 0.05), bin 51 (Lactobacillales) (p < 0.05), bin 8 (Lachnospiraceae) (p < 0.05), and bin 47 (Bacteria) (p < 0.05) were significantly higher in normal yaks. At different levels, a significant difference in phylum (n = 4), class (n = 8), oder (n = 8), family (n = 16), genus (n = 17), and species (n = 30) was noticed, respectively. Compared with healthy yaks, acetic acid (p < 0.01), propionic acid (p < 0.01), butyric acid (p < 0.01), isobutyric acid (p < 0.01), isovaleric acid (p < 0.05), and caproic acid (p < 0.01) were all observed significantly at a lower rate in diarrheal yaks. In conclusion, besides the increased Staphylococcus aureus, Babesia ovata, Anaplasma phagocytophilum, Bacteroides fluxus, viruses, Klebsiella pneumonia, and inflammation-related bacteria, the decrease of SCFA caused by the imbalance of intestinal microbiota was potentially observed in diarrheal yaks.
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Affiliation(s)
- Kun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Kun Li, ; Jiakui Li, ; Desheng Qi,
| | - Zhibo Zeng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Juanjuan Liu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lulu Pei
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yaping Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Aoyun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | | | - Muhammad Shahzad
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Kun Li, ; Jiakui Li, ; Desheng Qi,
| | - Desheng Qi
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Kun Li, ; Jiakui Li, ; Desheng Qi,
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11
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Hassanein A, Naresh Kumar A, Lansing S. Impact of electro-conductive nanoparticles additives on anaerobic digestion performance - A review. BIORESOURCE TECHNOLOGY 2021; 342:126023. [PMID: 34852449 DOI: 10.1016/j.biortech.2021.126023] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic digestion (AD) is a biochemical process that converts waste organic matter into energy-rich biogas with methane as the main component. Addition of electric electro-conductive, such as that nanoparticles (NP), has been shown to improve biogas generation. Interspecies electron transfer and direct interspecies electron transfer (DIET) using conductive materials is one of the mechanisms responsible for observed increases in CH4. This article discusses the effect of the type and size of electro-conductive NPs on improving microbial degradation within AD systems, as well as the effect of electro-conductive NPs on microbial community shifts and syntrophic metabolism. Limitations and future perspectives of using NPs in an AD system is also discussed.
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Affiliation(s)
- Amro Hassanein
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - A Naresh Kumar
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Stephanie Lansing
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742, USA
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12
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Wei Y, Li Z, Ran W, Yuan H, Li X. Performance and microbial community dynamics in anaerobic co-digestion of chicken manure and corn stover with different modification methods and trace element supplementation strategy. BIORESOURCE TECHNOLOGY 2021; 325:124713. [PMID: 33485082 DOI: 10.1016/j.biortech.2021.124713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
The performance and microbial community dynamics in anaerobic co-digestion (ACoD) of chicken manure and corn stover with different modification methods and trace element supplementation strategy were investigated in this study. KOH and liquid fraction of digestate (LFD) were applied for modification; Fe, Co, Mn, Mo, and Ni were used for supplement. Results showed that the selected trace element was insufficient in the partial or whole digestion process. When trace element supplement was combined with KOH or LFD modifications, the ACoD obtained biomethane yields of 245.3-258.0 and 254.0-261.8 mLN·gVS-1, 26.0%-32.5% and 30.5%-34.5% more than that of the control, respectively. Microbial community analyses indicated that the composition and diversity of archaea and bacteria varied at genus level. Main pathways involved in ACoD were affected accordingly, which in turn affected co-digestion performance. This study demonstrated that the combining modification and trace element supplement could improve the digestion performance and achieve higher biomethane yield.
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Affiliation(s)
- Yufang Wei
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China; State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Zipei Li
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Wenjuan Ran
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Hairong Yuan
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Xiujin Li
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China.
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13
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Abstract
Over the past decades, anaerobic biotechnology is commonly used for treating high-strength wastewaters from different industries. This biotechnology depends on interactions and co-operation between microorganisms in the anaerobic environment where many pollutants’ transformation to energy-rich biogas occurs. Properties of wastewater vary across industries and significantly affect microbiome composition in the anaerobic reactor. Methanogenic archaea play a crucial role during anaerobic wastewater treatment. The most abundant acetoclastic methanogens in the anaerobic reactors for industrial wastewater treatment are Methanosarcina sp. and Methanotrix sp. Hydrogenotrophic representatives of methanogens presented in the anaerobic reactors are characterized by a wide species diversity. Methanoculleus sp., Methanobacterium sp. and Methanospirillum sp. prevailed in this group. This work summarizes the relation of industrial wastewater composition and methanogen microbial communities present in different reactors treating these wastewaters.
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14
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Microbial Communities and Sulfate-Reducing Microorganisms Abundance and Diversity in Municipal Anaerobic Sewage Sludge Digesters from a Wastewater Treatment Plant (Marrakech, Morocco). Processes (Basel) 2020. [DOI: 10.3390/pr8101284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Both molecular analyses and culture-dependent isolation were combined to investigate the diversity of sulfate-reducing prokaryotes and explore their role in sulfides production in full-scale anaerobic digesters (Marrakech, Morocco). At global scale, using 16S rRNA gene sequencing, Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Synergistetes, and Euryarchaeota were the most dominant phyla. The abundance of Archaea (3.1–5.7%) was linked with temperature. The mcrA gene ranged from 2.18 × 105 to 1.47 × 107 gene copies.g−1 of sludge. The sulfate-reducing prokaryotes, representing 5% of total sequences, involved in sulfides production were Peptococcaceae, Syntrophaceae, Desulfobulbaceae, Desulfovibrionaceae, Syntrophobacteraceae, Desulfurellaceae, and Desulfobacteraceae. Furthermore, dsrB gene ranged from 2.18 × 105 to 1.92 × 107 gene copies.g−1 of sludge. The results revealed that exploration of diversity and function of sulfate-reducing bacteria may play a key role in decreasing sulfide production, an undesirable by-product, during anaerobic digestion.
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15
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Xu Z, Wang D, Tang W, Wang L, Li Q, Lu Z, Liu H, Zhong Y, He T, Guo S. Phytoremediation of cadmium-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization in the Solanum nigrum L. rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 732:139265. [PMID: 32416401 DOI: 10.1016/j.scitotenv.2020.139265] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/23/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Microbe-assisted phytoremediation for Cd-polluted soil is being regarded increasingly. However, the availability of microbes that can collaborate with Cd-hyperaccumulators effectively has become one of bottlenecks restricting the remediation efficiency. A siderophore-producing bacterium (Y16; Enterobacter cloacae) isolated from the rhizospheric soil of Cd-hyperaccumulator Solanum nigrum L. was identified by 16S rRNA gene sequencing and biochemical analysis, and then used for analyzing microbial chemotaxis, carbon source utilization, and insoluble P/Cd mobilization capacities. Besides, a soil-pot trial was performed to underlie the phytoremediation mechanism of Cd-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization (DEYC) in the Solanum nigrum L. rhizosphere. Results displayed that D-gluconate was an effective chemoattractant and carbon source strengthening Y16 colonization, and Y16 exhibited strong abilities to mobilize insoluble P/Cd in shake flask by extracellular acidification (p < 0.05). In the soil-pot trial, DEYC observably enhanced soil Cd phytoextraction by Solanum nigrum L., and increased microbial diversity according to alpha- and beta-diversity analysis (p < 0.05). Taxonomic distribution and co-occurrence network analysis suggested that DEYC increased relative abundances of dominant microbial taxa associated with soil acidification (Acidobacteria-6), indoleacetic acid secretion (Ensifer adhaerens), soil fertility improvement (Flavisolibacter, Bdellovibrio bacteriovorus, and Candidatus nitrososphaera), and insoluble Cd mobilization (Massilia timonae) at different classification levels. Importantly, COGs analysis further shown that DEYC aroused the up-regulation of key genes related to chemotactic motility, carbon fixation, TCA cycle, and propanoate metabolism. These results indicated that DEYC drove the rhizospheric enrichment of pivotal microbial taxa directly or indirectly involved in soil Cd mobilization, meanwhile distinctly promoted plant growth for accumulating more mobilizable Cd. Therefore, Y16 could be used as bio-inoculants for assisting phytoremediation of Cd-polluted soil.
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Affiliation(s)
- Zhimin Xu
- School of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China; Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Guangzhou 510225, China
| | - Dongsheng Wang
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Wanpeng Tang
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Lili Wang
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Qusheng Li
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ziyan Lu
- School of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Guangzhou 510225, China
| | - Hui Liu
- School of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Guangzhou 510225, China
| | - Yuming Zhong
- School of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Guangzhou 510225, China
| | - Tao He
- Key Laboratory of Environmental Pollution and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Shihong Guo
- Fujian Provincial Academy of Environmental Science, Fuzhou 350013, China
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16
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Zhang J, Qi Q, Mao L, He Y, Loh KC, Wah Tong Y. Mixing strategies - Activated carbon nexus: Rapid start-up of thermophilic anaerobic digestion with the mesophilic anaerobic sludge as inoculum. BIORESOURCE TECHNOLOGY 2020; 310:123401. [PMID: 32334361 DOI: 10.1016/j.biortech.2020.123401] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
This study evaluated the mixing - activate carbon nexus in anaerobic digestion with the aim of accelerating start-up of thermophilic anaerobic co-digestion of food waste and chicken manure using mesophilic anaerobic sludge as inoculum. Results showed that the methane yield in the continuous stirred reactor is 71.3% higher than that of intermittent agitated reactor, and the addition of activated carbon can further improve the yield of methane by 18.2%. Continuous mixing mode followed by intermittent mixing was proved to be an alternative strategy to accelerate start-up of thermophilic anaerobic digestion. The optimum mixing time of 120 s/hour were obtained using computational fluid dynamics modeling. Analysis of genomic annotation metabolism indicated that the addition of activated carbon enhanced the dominant metabolism pathways of amino acid, methane and energy. Results of enzymes gene expression suggested that carbohydrates esterases, glycoside hydrolases and glycosyl transferases were dominant, respectively.
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Affiliation(s)
- Jingxin Zhang
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 201306, China.
| | - Qiuxian Qi
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 201306, China
| | - Liwei Mao
- Environmental Research Institute, National University of Singapore, Singapore
| | - Yiliang He
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 201306, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, China
| | - Kai-Chee Loh
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, Singapore; Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore
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17
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Kang XH, Leng Y, O MM, Zeng XY, Li SW. The seasonal changes of core bacterial community decide sewage purification in sub-plateau municipal sewage treatment plants. Bioprocess Biosyst Eng 2020; 43:1609-1617. [PMID: 32333195 DOI: 10.1007/s00449-020-02352-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/11/2020] [Indexed: 12/19/2022]
Abstract
The decline of sewage purification efficiency in winter is a frequent problem in sub-plateau municipal sewage treatment plants (MSTPs). Understanding the links between activated sludge (AS) bacterial community and sewage purification is crucial for exploring the cause of this problem. In this study, Illumina high-throughput sequencing technology was applied to investigate the seasonal changes of AS bacterial community in sub-plateau MSTPs. The sequencing result indicates that the bacterial community OTU number, diversity, and relative abundance in winter are significantly lower than that in summer samples. The discriminant linear effect size analysis (LEfSe) reveals that Proteobacteria and Chloroflexi members were enriched in summer AS, while Actinobacteria and Firmicutes were enriched in winter AS. The results indicate that different core bacterial community assembly was developed in summer and winter, respectively. The changes in bacterial community may be the reasons for the lower sewage purification efficiency in winter. Furthermore, redundancy analysis (RDA) shows that temperature and dissolved oxygen (DO) are the principal factors that drive the seasonal changes in the core bacterial community diversity, richness and structure in sub-plateau MSTPs. Thus, the sub-plateau AS selects for a unique community assembly pattern and shapes the particular AS ecosystem. These results expand previous understanding and provide insight into the relationship between bacterial community and performance of sub-plateau MSTPs.
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Affiliation(s)
- Xiao-Hu Kang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Yan Leng
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Mafiana Macdonald O
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Xiao-Ying Zeng
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Shi-Weng Li
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resource, Chinese Academy of Sciences, Lanzhou, 730070, China.
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18
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Yu H, Tian Z, Zuo J, Song Y. Enhanced nitrite accumulation under mainstream conditions by a combination of free ammonia-based sludge treatment and low dissolved oxygen: reactor performance and microbiome analysis. RSC Adv 2020; 10:2049-2059. [PMID: 35494565 PMCID: PMC9048193 DOI: 10.1039/c9ra07628j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/29/2019] [Indexed: 11/21/2022] Open
Abstract
Partial nitritation under mainstream conditions is one of the major bottlenecks for the application of deammonification processes to municipal wastewater treatment plants. This study aimed at evaluating the combination effect of a side-stream free ammonia (FA) treatment and low dissolved oxygen (0.2 ± 0.1 mg L−1) on inhibiting nitrite oxidizing bacteria (NOB) from enhancing nitrite accumulation in long-term lab-scale experiments. Two continuous floccular sludge reactors treating low-strength synthetic wastewater (60 mg N–NH4+ L−1 without COD) with a fixed nitrogen loading rate of 0.22 ± 0.03 g N per L per day were operated in a varied temperature range of 7–31 °C, with one acting as the experimental reactor and the other as the control. Side-stream sludge treatment with a stepwise elevation of FA concentration (65.2–261.1 mg NH3 L−1) was carried out every day in the experimental reactor; the nitrite accumulation ratio (NAR, (NO2–N/(NO2−–N + NO3−–N) × 100%)) in the experimental reactor was always about twice that in the control one. Quantitative PCR (q-PCR) and high-throughput sequencing analyses showed the dominant NOB was mostly Nitrobacter, while there was an alternating trend between Nitrobacter and Nitrospira. Even though the whole microbial communities of each experimental stage between the two reactors were relatively clustered due to an incomplete NOB washout, three abundant metabolisms (amino acid metabolism, pyruvate metabolism and nitrogen metabolism) and key functional genes of nitrification predicted by PICRUSt in the experimental reactor were enriched, providing a better understanding of nitrite accumulation. These results have demonstrated that the positive hybrid effects of FA side-stream sludge treatment and a low DO could enhance nitrite accumulation. It is expected that a complete washout of NOB would be achieved after further process optimization. An introduction of the combination of side-stream sludge treatment using FA and low DO could more effectively enhance nitrite accumulation than single low DO.![]()
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Affiliation(s)
- Heng Yu
- State Key Joint Laboratory of Environment Simulation and Pollution Control
- School of Environment
- Tsinghua University
- Beijing 100084
- China
| | - Zhiyong Tian
- State Key Laboratory of Environmental Criteria and Risk Assessment
- Chinese Research Academy of Environmental Sciences
- Department of Urban Water Environmental Research
- Beijing 100012
- China
| | - Jiane Zuo
- State Key Joint Laboratory of Environment Simulation and Pollution Control
- School of Environment
- Tsinghua University
- Beijing 100084
- China
| | - Yonghui Song
- State Key Laboratory of Environmental Criteria and Risk Assessment
- Chinese Research Academy of Environmental Sciences
- Department of Urban Water Environmental Research
- Beijing 100012
- China
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19
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Xu M, Stedtfeld RD, Wang F, Hashsham SA, Song Y, Chuang Y, Fan J, Li H, Jiang X, Tiedje JM. Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 689:1172-1180. [PMID: 31466157 DOI: 10.1016/j.scitotenv.2019.06.376] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/21/2019] [Accepted: 06/23/2019] [Indexed: 06/10/2023]
Abstract
Different long-term fertilization regimes may change indigenous microorganism diversity in the arable soil and thus might influence the persistence and transmission of manure-born antibiotic resistance genes (ARGs). Different manure origins and composting techniques might affect the fate of introduced ARGs in farmland. A four-month microcosm experiment was performed using two soils, which originated from the same field and applied with the same chemical fertilizer or swine manure for 26 years, to investigate the dynamics of ARGs in soil amended with manure or compost from the farm and an agro-technology company. High throughput qPCR and sequencing were applied to quantify ARGs using 144 primer sets and microorganism in soil. Fertilization history had little effect on dynamics of manure-borne ARGs in soil regardless of manure origin or composting. Very different half-lives of ARGs and mobile genetic elements from farm manure and commercial manure were observed in both soils. Composting decreased abundance of most ARGs in manure, but increased the persistence of manure-introduced ARGs in soil irrespective of fertilization history, especially for those from farm manure. These findings help understanding the fate of ARGs in manured soil and may inform techniques to mitigate ARGs transmission.
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Affiliation(s)
- Min Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| | - Yang Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yahui Chuang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| | - Jianbo Fan
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
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20
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García‐Ruíz MJ, Castellano‐Hinojosa A, Armato C, González‐Martínez A, González‐López J, Osorio F. Biogas production and microbial community structure in a stable‐stage of a two‐stage anaerobic digester. AIChE J 2019. [DOI: 10.1002/aic.16807] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- María J. García‐Ruíz
- Department of Civil Engineering, Campus of Fuentenueva University of Granada Granada Spain
| | | | - Caterina Armato
- Department of Public Health and Pediatrics University of Torino Torino Italy
- Centre for Sustainable Future Technologies (CSFT@PoliTo) Istituto Italiano di Tecnologia Torino Italy
| | | | | | - Francisco Osorio
- Department of Civil Engineering, Campus of Fuentenueva University of Granada Granada Spain
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21
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Spatial Variations of Bacterial Communities of an Anaerobic Lagoon-Type Biodigester Fed with Dairy Manure. Processes (Basel) 2019. [DOI: 10.3390/pr7070408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Anaerobic digestion technology is being widely employed for sustainable management of organic wastes generated in animal farms, industries, etc. Nevertheless, biodigester microbiome is still considered a “black box” because it is regulated by different physico-chemical and operational factors. In this study, the bacterial diversity and composition in different sites of a full-scale lagoon type biodigester (23,000 m3) fed with dairy manure, viz., the influent, beginning, middle, final and effluent were analyzed. The biodigester registered a total of 1445 OTUs, which demonstrated the complex microbial ecosystem in it. Of them, only six OTUs were shared among all the different sampling points. The most abundant phyla belonged to Firmicutes, Proteobacteria, Latescibacteria and Thermotogae. The Simpson and Shannon index showed that the highest microbial diversity was observed in the beginning point of the biodigester, meanwhile, the lowest diversity was recorded in the middle. Based on the UniFrac distances, microbial communities with high similarity were recorded in the middle and final of the biodigester. It can be clearly observed that bacterial communities varied at the different points of the biodigester. However, based on metagenome predictions using PICRUSt, it was found that independent of the differences in taxonomy and location, bacterial communities maintained similar metabolic functions.
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22
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Performance and dynamic characteristics of microbial communities in multi-stage anaerobic reactors treating gibberellin wastewater. J Biosci Bioeng 2019; 127:318-325. [DOI: 10.1016/j.jbiosc.2018.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/28/2017] [Accepted: 05/24/2018] [Indexed: 01/19/2023]
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23
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Buhlmann CH, Mickan BS, Jenkins SN, Tait S, Kahandawala TKA, Bahri PA. Ammonia stress on a resilient mesophilic anaerobic inoculum: Methane production, microbial community, and putative metabolic pathways. BIORESOURCE TECHNOLOGY 2019; 275:70-77. [PMID: 30579103 DOI: 10.1016/j.biortech.2018.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023]
Abstract
Short term inhibition tests, 16S rRNA tag sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), were employed to visualise the effects of increasing total ammoniacal nitrogen (TAN) concentration (3400-10166 ppm TAN) on microbial community structure and metabolic pathways for acetate degradation. The rate of methane production on acetate was significantly reduced by TAN concentrations above 6133 ppm; however, methane continued to be produced, even at 10166 ppm TAN (0.026 ± 0.0003 gCOD.gVS-1inoculum.day-1). Hydrogenotrophic methanogenesis with syntrophic acetate oxidation (SAO) was identified as the dominant pathway for methane production. A shift towards SAO pathways at higher TAN concentrations and a decrease in the number of 'gene hits' for key genes in specific methanogenesis pathways was observed. Overall, the results highlighted potential for inhibition activity testing to be used together with PICRUSt, to estimate changes in microbial metabolism and to better understand microbial resilience in industrial AD facilities.
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Affiliation(s)
- Christopher H Buhlmann
- Murdoch University School of Engineering and Information Technology, Murdoch University, 90 South St, Murdoch, WA 6150, Australia.
| | - Bede S Mickan
- UWA School of Agriculture and Environment (M079), The University of Western Australia, Perth, WA 6009, Australia; The UWA Institute of Agriculture (M082), The University of Western Australia, Perth, WA 6009, Australia; Richgro Garden Products, 203 Acourt Rd, Jandakot, WA 6164, Australia
| | - Sasha N Jenkins
- UWA School of Agriculture and Environment (M079), The University of Western Australia, Perth, WA 6009, Australia; The UWA Institute of Agriculture (M082), The University of Western Australia, Perth, WA 6009, Australia
| | - Stephan Tait
- Centre for Agricultural Engineering, The University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Tharanga K A Kahandawala
- UWA School of Agriculture and Environment (M079), The University of Western Australia, Perth, WA 6009, Australia
| | - Parisa A Bahri
- Murdoch University School of Engineering and Information Technology, Murdoch University, 90 South St, Murdoch, WA 6150, Australia
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24
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Fernandes CC, Kishi LT, Lopes EM, Omori WP, Souza JAMD, Alves LMC, Lemos EGDM. Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine. Braz J Microbiol 2018; 49:489-502. [PMID: 29452849 PMCID: PMC6066727 DOI: 10.1016/j.bjm.2017.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/06/2017] [Accepted: 12/04/2017] [Indexed: 01/19/2023] Open
Abstract
Human activities on the Earth's surface change the landscape of natural ecosystems. Mining practices are one of the most severe human activities, drastically altering the chemical, physical and biological properties of the soil environment. Bacterial communities in soil play an important role in the maintenance of ecological relationships. This work shows bacterial diversity, metabolic repertoire and physiological behavior in five ecosystems samples with different levels of impact. These ecosystems belong to a historical area in Iron Quadrangle, Minas Gerais, Brazil, which suffered mining activities until its total depletion without recovery since today. The results revealed Proteobacteria as the most predominant phylum followed by Acidobacteria, Verrucomicrobia, Planctomycetes, and Bacteroidetes. Soils that have not undergone anthropological actions exhibit an increase ability to degrade carbon sources. The richest soil with the high diversity was found in ecosystems that have suffered anthropogenic action. Our study shows profile of diversity inferring metabolic profile, which may elucidate the mechanisms underlying changes in community structure in situ mining sites in Brazil. Our data comes from contributing to know the bacterial diversity, relationship between these bacteria and can explore strategies for natural bioremediation in mining areas or adjacent areas under regeneration process in iron mining areas.
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Affiliation(s)
- Camila Cesário Fernandes
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Luciano Takeshi Kishi
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Erica Mendes Lopes
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Wellington Pine Omori
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Jaboticabal, SP, Brazil
| | - Jackson Antonio Marcondes de Souza
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Jaboticabal, SP, Brazil
| | - Lucia Maria Carareto Alves
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil.
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25
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Gil-Pulido B, Tarpey E, Almeida EL, Finnegan W, Zhan X, Dobson ADW, O'Leary N. Evaluation of dairy processing wastewater biotreatment in an IASBR system: Aeration rate impacts on performance and microbial ecology. ACTA ACUST UNITED AC 2018; 19:e00263. [PMID: 29992097 PMCID: PMC6036646 DOI: 10.1016/j.btre.2018.e00263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/24/2018] [Accepted: 06/02/2018] [Indexed: 02/07/2023]
Abstract
Dairy processing generates large volumes of wastewater that require extensive nutrient remediation prior to discharge. Significant commercial opportunities exist therefore for cost-effective biotechnologies capable of achieving this requirement. In this study the authors evaluated the use of intermittently aerated sequencing batch reactors, (IASBRs), as a single-tank biotreatment system for co-removal of COD, nitrogen and phosphorus from synthetic dairy processing wastewater. Variation of the IASBR aeration rates, (0.8, 0.6 and 0.4 L/min), had significant impacts on the respective nutrient removal efficiencies and underlying microbial diversity profiles. Aeration at 0.6 L/min was most effective and resulted in >90% co-removal of orthophosphate and ammonium. 16S rRNA based pyrosequencing of biomass DNA samples revealed the family Comamonadaceae was notably enriched (>80% relative abundance) under these conditions. In silico predictive metabolic modelling also identified Comamonadaceae as the major contributor of several known genes for nitrogen and phosphorus assimilation (nirK, nosZ, norB, ppK, ppX and phbC).
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Affiliation(s)
- Beatriz Gil-Pulido
- School of Microbiology, University College Cork, College Road, Cork T12 YN60, Ireland.,Environmental Research Institute, University College Cork, Lee Road, Cork T23 XE10, Ireland
| | - Emma Tarpey
- College of Engineering and Informatics, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Eduardo L Almeida
- School of Microbiology, University College Cork, College Road, Cork T12 YN60, Ireland.,Environmental Research Institute, University College Cork, Lee Road, Cork T23 XE10, Ireland
| | - William Finnegan
- College of Engineering and Informatics, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Xinmin Zhan
- College of Engineering and Informatics, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, College Road, Cork T12 YN60, Ireland.,Environmental Research Institute, University College Cork, Lee Road, Cork T23 XE10, Ireland
| | - Niall O'Leary
- School of Microbiology, University College Cork, College Road, Cork T12 YN60, Ireland.,Environmental Research Institute, University College Cork, Lee Road, Cork T23 XE10, Ireland
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26
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Zhang J, Mao F, Loh KC, Gin KYH, Dai Y, Tong YW. Evaluating the effects of activated carbon on methane generation and the fate of antibiotic resistant genes and class I integrons during anaerobic digestion of solid organic wastes. BIORESOURCE TECHNOLOGY 2018; 249:729-736. [PMID: 29096147 DOI: 10.1016/j.biortech.2017.10.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/21/2017] [Accepted: 10/23/2017] [Indexed: 06/07/2023]
Abstract
The effects of activated carbon (AC) on methane production and the fate of antibiotic resistance genes (ARGs) were evaluated through comparing the anaerobic digestion performance and transformation of ARGs among anaerobic mono-digestion of food waste, co-digestion of food waste and chicken manure, and co-digestion of food waste and waste activated sludge. Results showed that adding AC in anaerobic digesters improved methane yield by at least double through the enrichment of bacteria and archaea. Conventional digestion process showed ability in removing certain types of ARGs, such as tetA, tetX, sul1, sul2, cmlA, floR, and intl1. Supplementing AC in anaerobic digester enhanced the removal of most of the ARGs in mono-digestion of food waste. The effects tended to be minimal in co-digestion of co-substrates such as chicken manure and waste activated sludge, both of which contain a certain amount of antibiotics.
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Affiliation(s)
- Jingxin Zhang
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore
| | - Feijian Mao
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Kai-Chee Loh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore; Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Yanjun Dai
- Institute of Refrigeration and Cryogenics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yen Wah Tong
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore.
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27
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Free A, McDonald MA, Pagaling E. Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems. ADVANCES IN APPLIED MICROBIOLOGY 2018; 105:131-189. [PMID: 30342721 DOI: 10.1016/bs.aambs.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.
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Affiliation(s)
- Andrew Free
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Michael A McDonald
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Eulyn Pagaling
- The James Hutton Institute, Craigiebuckler, Aberdeen, United Kingdom
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28
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Garcia-Mazcorro JF, Castillo-Carranza SA, Guard B, Gomez-Vazquez JP, Dowd SE, Brigthsmith DJ. Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing. MICROBIAL ECOLOGY 2017; 73:224-235. [PMID: 27568186 DOI: 10.1007/s00248-016-0840-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples from 22 flocks representing over 150 individual birds of three different species (Melopsittacus undulatus or budgerigars, Nymphicus hollandicus or cockatiels, and Serinus canaria or domestic canaries) were used for analysis using the 16S rRNA gene sequencing in the MiSeq platform (Illumina). Firmicutes was the most abundant phylum (median 88.4 %; range 12.9-98.4 %) followed by other low-abundant phyla such as Proteobacteria (median 2.3 %; 0.1-85.3 %) and Actinobacteria (median 1.7 %; 0-18.3 %). Lactobacillaceae (mostly Lactobacillus spp.) was the most abundant family (median 78.1 %; 1.4-97.5 %), especially in budgerigars and canaries, and it deserves attention because of the ascribed beneficial properties of lactic acid bacteria. Importantly, feces from birds contain intestinal, urinary, and reproductive-associated microbiota thus posing a serious problem to study one anatomical region at a time. Other groups of interest include the family Clostridiaceae that showed very low abundance (overall median <0.1 %) with the exception of two samples from cockatiels (14 and 45.9 %) and one sample from budgerigars (19.9 %). Analysis of UniFrac metrics showed that overall, the microbial communities from the 22 flocks tended to cluster together for each bird species, meaning each species shed distinctive bacterial communities in feces. This descriptive analysis provides insight into the fecal microbiota of pet birds.
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Affiliation(s)
- Jose F Garcia-Mazcorro
- Faculty of Veterinary Medicine, Universidad Autónoma de Nuevo León (UANL), General Escobedo, NL, 66050, Mexico.
- Research Group Medical Eco-Biology, Faculty of Veterinary Medicine, UANL, General Escobedo, NL, 66050, Mexico.
| | | | - Blake Guard
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, 77843-4474, USA
| | - Jose P Gomez-Vazquez
- Faculty of Veterinary Medicine, Universidad Autónoma de Nuevo León (UANL), General Escobedo, NL, 66050, Mexico
| | - Scot E Dowd
- Molecular Research LP, Shallowater, TX, 79363, USA
| | - Donald J Brigthsmith
- Schubot Exotic Bird Health Center, Texas A&M University, College Station, TX, 77843-4467, USA
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