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Chen C, Ai J, Chen L, Li Y, Tang X, Li J. Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22494-22506. [PMID: 38407711 DOI: 10.1007/s11356-024-32587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
Aha Lake artificial reservoir wetland, Niangniang Mountain karst mountain wetland, and Caohai plateau lake wetland are typical karst wetlands in Guizhou Province with unique topography and geomorphic features. They were selected as research objects in this study to explore microorganisms and functional genes in nitrogen metabolism adopting macro-genome sequencing technology. It was found that Proteobacteria, Actinobacteria, and Acidobacteria were the dominant phyla in nitrogen metabolism in these three wetlands, similar to previous studies. However, at the genus level, there was a significant difference, with the dominant bacteria being Bradyrhizobium, Methylocystis, and Anaeromyxobacter. Six nitrogen metabolism pathways, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction, assimilatory nitrate reduction, and complete nitrification, comammox, were revealed, but anaerobic ammonia oxidation genes were not detected. Nitrogen metabolism microorganisms and pathways were more affected by SOM, pH, NO3-, and EC in karst wetlands. This study further discussed microorganisms and functions of nitrogen metabolism in karst wetlands, which was of great significance to nitrogen cycles of karst wetland ecosystems.
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Affiliation(s)
- Chen Chen
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Jia Ai
- Ecological and Environmental Monitoring Center, Guizhou, 558013, Qiannan, China
| | - Li Chen
- College of Civil Engineering, Chongqing Vocational Institute of Engineering, Chongqing, 402260, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China.
| | - Xin Tang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
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Zhou Z, Liu Y, Wang S, Xiao J, Cao X, Zhou Y, Song C. Interactions between Phosphorus Enrichment and Nitrification Accelerate Relative Nitrogen Deficiency during Cyanobacterial Blooms in a Large Shallow Eutrophic Lake. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2992-3001. [PMID: 36753734 DOI: 10.1021/acs.est.2c07599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Regime shifts between nitrogen (N) and phosphorus (P) limitation, which trigger cyanobacterial succession, occur in shallow eutrophic lakes seasonally. However, the underlying mechanism is not yet fully illustrated. We provide a novel insight to address this from interactions between sediment P and nitrification through monthly field investigations including 204 samples and microcosm experiments in Lake Chaohu. Total N to P mass ratios (TN/TP) varied significantly across seasons especially during algal bloom in summer, with the average value being 26.1 in June and descending to 7.8 in September gradually, triggering dominant cyanobacterial succession from Microcystis to Dolichospermum. The regulation effect of sediment N/P on water column TN/TP was stronger in summer than in other seasons. Iron-bound P and alkaline phosphatase activity in sediment, rather than ammonium, contributed to the higher part of nitrification. Furthermore, our microcosm experiments confirmed that soluble active P and enzymatic hydrolysis of organic P, accumulating during algal bloom, fueled nitrifiers and nitrification in sediments. These processes promoted lake N removal and led to relative N deficiency in turn. Our results highlight that N and P cycles do not exist independently but rather interact with each other during lake eutrophication, supporting the dual N and P reduction program to mitigate eutrophication in shallow eutrophic lakes.
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Affiliation(s)
- Zijun Zhou
- Institute of Yellow River Water Resources Protection, Zhengzhou 450004, PR China
| | - Yuqian Liu
- Institute of Yellow River Water Resources Protection, Zhengzhou 450004, PR China
| | - Siyang Wang
- School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan 430070, PR China
| | - Jian Xiao
- School of Environmental and Chemical Engineering, Jiangsu Ocean University, Lianyungang 222005, PR China
| | - Xiuyun Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Yiyong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Chunlei Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, PR China
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Ohbayashi T, Wang Y, Aoyagi LN, Hara S, Tago K, Hayatsu M. Diversity of the Hydroxylamine Oxidoreductase (HAO) Gene and Its Enzyme Active Site in Agricultural Field Soils. Microbes Environ 2023; 38:ME23068. [PMID: 38092410 PMCID: PMC10728637 DOI: 10.1264/jsme2.me23068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
Nitrification is a key process in the biogeochemical nitrogen cycle and a major emission source of the greenhouse gas nitrous oxide (N2O). The periplasmic enzyme hydroxylamine oxidoreductase (HAO) is involved in the oxidation of hydroxylamine to nitric oxide in the second step of nitrification, producing N2O as a byproduct. Its three-dimensional structure demonstrates that slight differences in HAO active site residues have inhibitor effects. Therefore, a more detailed understanding of the diversity of HAO active site residues in soil microorganisms is important for the development of novel nitrification inhibitors using structure-guided drug design. However, this has not yet been examined. In the present study, we investigated hao gene diversity in beta-proteobacterial ammonia-oxidizing bacteria (β-AOB) and complete ammonia-oxidizing (comammox; Nitrospira spp.) bacteria in agricultural fields using a clone library ana-lysis. A total of 1,949 hao gene sequences revealed that hao gene diversity in β-AOB and comammox bacteria was affected by the fertilizer treatment and field type, respectively. Moreover, hao sequences showed the almost complete conservation of the six HAO active site residues in both β-AOB and comammox bacteria. The diversity of nitrifying bacteria showed similarity between hao and amoA genes. The nxrB amplicon sequence revealed the dominance of Nitrospira cluster II in tea field soils. The present study is the first to reveal hao gene diversity in agricultural soils, which will accelerate the efficient screening of HAO inhibitors and evaluations of their suppressive effects on nitrification in agricultural soils.
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Affiliation(s)
- Tsubasa Ohbayashi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Luciano Nobuhiro Aoyagi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Shintaro Hara
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
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Shay PE, Winder RS, Constabel CP, Trofymow JA(T. Fungal Community Composition as Affected by Litter Chemistry and Weather during Four Years of Litter Decomposition in Rainshadow Coastal Douglas-Fir Forests. J Fungi (Basel) 2022; 8:jof8070735. [PMID: 35887490 PMCID: PMC9323820 DOI: 10.3390/jof8070735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/07/2022] [Accepted: 07/13/2022] [Indexed: 12/04/2022] Open
Abstract
Climate and litter chemistry are major factors influencing litter decay, a process mediated by microbes, such as fungi, nitrogen-fixing bacteria and ammonia-oxidizing bacteria. Increasing atmospheric CO2 concentrations can decrease nitrogen (N) and increase condensed tannin (CT) content in foliar litter, reducing litter quality and slowing decomposition. We hypothesized that reduced litter quality inhibits microbes and is the mechanism causing decomposition to slow. Litterbags of Douglas-fir needles and poplar leaves with a range of N (0.61–1.57%) and CT (2.1–29.1%) treatment and natural acid unhydrolyzable residue (35.3–41.5%) concentrations were placed along climatic gradients in mature Douglas-fir stands of coastal British Columbia rainshadow forests. The structure (diversity, richness and evenness) and composition of microbial communities were analyzed using DGGE profiles of 18S, NifH-universal and AmoA PCR amplicons in foliar litter after 7, 12, 24 and 43 months of decay. High CT and low N concentrations in leaf litter were associated with changes in microbial community composition, especially fungi. Contrary to our hypothesis, high CT and low N treatments did not inhibit microbial colonization or diversity. The joint effects of air temperature and soil moisture on microbial community composition at our sites were more important than the effects of initial litter chemistry.
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Affiliation(s)
- Philip-Edouard Shay
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada; (P.-E.S.); (C.P.C.)
- Pacific Forestry Centre, Canadian Forest Service, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada;
| | - Richard S. Winder
- Pacific Forestry Centre, Canadian Forest Service, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada;
| | - C. Peter Constabel
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada; (P.-E.S.); (C.P.C.)
| | - J. A. (Tony) Trofymow
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada; (P.-E.S.); (C.P.C.)
- Pacific Forestry Centre, Canadian Forest Service, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada;
- Correspondence:
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Zhao M, Tang X, Sun D, Hou L, Liu M, Zhao Q, Klümper U, Quan Z, Gu JD, Han P. Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148768. [PMID: 34247082 DOI: 10.1016/j.scitotenv.2021.148768] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.
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Affiliation(s)
- Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Qiang Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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Li S, Gao Y, Shang Q, Guo W, Liu H, Wei J, Chen T. Evidence for the existence of microbiota in the placenta and blood of pregnant mice exposed to various bacteria. MEDICINE IN MICROECOLOGY 2021. [DOI: 10.1016/j.medmic.2021.100040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Rangaswamy B, Ramankutty Nair R, Achuthan C, Isaac Sarojini BS. Computational analysis of successional changes in the microbial population and community diversity of the immobilized marine nitrifying bacterial consortium in a nitrifying packed bed bioreactor. 3 Biotech 2020; 10:524. [PMID: 33194528 DOI: 10.1007/s13205-020-02510-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/24/2020] [Indexed: 02/02/2023] Open
Abstract
Nitrifying bioreactor (NBR) connected to the recirculating aquaculture system (RAS), has a greater emphasis on the biological treatment of wastewater. Nitrifying bacterial consortium (NBC) formed bio-film on the substratum activating the NBR, and it was observed with high nitrification potential in shrimp maturation systems. Scanning Electron Microscopy (SEM) revealed the integrity of the biofilm substantiated with biomineralization. The fate of the matured bio-film population on subsequent operation under RAS, and the aggregated population at different points of RAS, including the rearing water were determined using fingerprints of Denaturing Gradient Gel Electrophoresis (DGGE). Altogether, 38 OTUs of biofilm sample and 35 OTUs of water samples represented the bacterial communities; the shared and unique OTUs indicated the diversity of the population at different time intervals in the operation of the NBR. The mathematical (range-weighted richness) and statistical (diversity indices) interpretation unveiled the OTUs based high bacterial diversity in the biofilm supporting the compositional changes and determined the distance between the community cluster. Ordination analyses indicated the population shift and stability of the activated bio-film till the matured biofilm community got established in the RAS. The DGGE with mathematical and statistical analysis revealed microbial diversity (high Shannon index, species richness and evenness), abundance (relative intensity), consecutive change in the population composition (OTUs, Rr index), and the dynamics (Δt) in the system during the operation.
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Deep amoA amplicon sequencing reveals community partitioning within ammonia-oxidizing bacteria in the environmentally dynamic estuary of the River Elbe. Sci Rep 2020; 10:17165. [PMID: 33051504 PMCID: PMC7555866 DOI: 10.1038/s41598-020-74163-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/24/2020] [Indexed: 11/25/2022] Open
Abstract
The community composition of betaproteobacterial ammonia-oxidizing bacteria (ß-AOB) in the River Elbe Estuary was investigated by high throughput sequencing of ammonia monooxygenase subunit A gene (amoA) amplicons. In the course of the seasons surface sediment samples from seven sites along the longitudinal profile of the upper Estuary of the Elbe were investigated. We observed striking shifts of the ß-AOB community composition according to space and time. Members of the Nitrosomonas oligotropha-lineage and the genus Nitrosospira were found to be the dominant ß-AOB within the river transect, investigated. However, continuous shifts of balance between members of both lineages along the longitudinal profile were determined. A noticeable feature was a substantial increase of proportion of Nitrosospira-like sequences in autumn and of sequences affiliated with the Nitrosomonas marina-lineage at downstream sites in spring and summer. Slightly raised relative abundances of sequences affiliated with the Nitrosomonas europaea/Nitrosomonas mobilis-lineage and the Nitrosomonas communis-lineage were found at sampling sites located in the port of Hamburg. Comparisons between environmental parameters and AOB-lineage (ecotype) composition revealed promising clues that processes happening in the fluvial to marine transition zone of the Elbe estuary are reflected by shifts in the relative proportion of ammonia monooxygenase sequence abundance, and hence, we propose ß-AOB as appropriate indicators for environmental dynamics and the ecological condition of the Elbe Estuary.
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Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities. Microorganisms 2019; 8:microorganisms8010009. [PMID: 31861554 PMCID: PMC7022406 DOI: 10.3390/microorganisms8010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 11/17/2022] Open
Abstract
We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three vegetation zones in 2014 (pre-drought), 2016 (drought), and 2017 (post-drought), and analyzed bacterial 16S rRNA genes by QPCR, TRFLP, and MiSeq analyses. AOA and AOB abundance in the Spartina patens zone increased significantly in 2016, while abundance decreased in the tall S. alterniflora zone, and showed little change in the short S. alterniflora zone. Total bacterial abundance declined annually in all vegetation zones. Significant shifts in community composition were detected in 2016 in two of the three vegetation zones for AOA and AOB, and in all three vegetation zones for total bacteria. Abundance and community composition of AOA and AOB returned to pre-drought conditions by 2017, while bacterial abundance continued to decline, suggesting that nitrifiers may be more resilient to drought than other bacterial communities. Finding vegetation-specific drought responses among N-cycling microbes may have broad implications for changes in N availability and marsh productivity, particularly if vegetation patterns continue to shift as predicted due to sea level rise.
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Coupling between Nitrification and Denitrification as well as Its Effect on Phosphorus Release in Sediments of Chinese Shallow Lakes. WATER 2019. [DOI: 10.3390/w11091809] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The coupling of nitrification and denitrification has attracted wide attention since it plays an important role in mitigating eutrophication in aquatic ecosystems. However, the underlying mechanism is largely unknown. In order to study the coupling relationship between nitrification and denitrification, as well as its effect on phosphorus release, nutrient levels, functional gene abundance and potential rates involved in nitrification and denitrification were analyzed in three shallow urban lakes with different nutrient status. Trophic level was found positively related to not only copy numbers of functional genes of nitrosomonas and denitrifiers, but also the potential nitrification and denitrification rates. In addition, the concentrations of different forms of phosphorus showed a positive correlation with the number of nitrosomonas and denitrifiers, as well as potential nitrification and denitrification rates. Furthermore, the number of functional genes of nitrosomonas exhibited positive linear correlations with functional genes and rate of denitrification. These facts suggested that an increase in phosphorus concentration might have promoted the coupling of nitrification and denitrification by increasing their functional genes. Strong nitrification–denitrification fueled the nitrogen removal from the system, and accelerated the phosphorus release due to the anaerobic state caused by organic matter decomposition and nitrification. Moreover, dissolved organic nitrogen was also released into the water column during this process, which was favorable for balancing the nitrogen and phosphorus ratio. In conclusion, the close coupling between nitrification and denitrification mediated by nitrifier denitrification had an important effect on the cycling mode of nitrogen and phosphorus.
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Ziembińska-Buczyńska A, Ciesielski S, Żabczyński S, Cema G. Bacterial community structure in rotating biological contactor treating coke wastewater in relation to medium composition. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:19171-19179. [PMID: 31111385 PMCID: PMC6594990 DOI: 10.1007/s11356-019-05087-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 04/04/2019] [Indexed: 06/09/2023]
Abstract
Biological wastewater treatment using biofilm systems is an effective way to treat difficult wastewater, such as coke wastewater. The information about the structure and the dynamics of this microbial community in biofilm, which are responsible for wastewater treatment, is relevant in the context of treatment efficacy and the biochemical potential to remove various pollutants. However, physico-chemical factors can influence the biofilm community significantly, causing performance disturbances. Therefore, we decided to examine the structure of microbial community in rotating biological contactor (RBC) biofilm during coke wastewater treatment and to investigate the possible shift in the community structure caused by the feeding medium change from synthetic to real coke wastewater. The experiment performed with high-throughput next-generation sequencing (NGS) revealed that bacteria commonly present in wastewater treatment plant (WWTP) systems, responsible for nitrite oxidizing, such as Nitrospira or Nitrobacter, were absent or below detection threshold, while Nitrosomonas, responsible for ammonia oxidizing, was detected in a relatively small number especially after shift to real coke wastewater. This research indicates that medium change could cause the change from autotrophic into heterotrophic nitrification led by Acinetobacter. Moreover, biofilm systems can be also a potential source of bacteria possessing high biochemical potential for pollutants removal but less known in WWTP systems, as well as potentially pathogenic microorganisms.
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Affiliation(s)
| | - Sławomir Ciesielski
- Faculty of Environmental Sciences, Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-719, Olsztyn, Poland
| | - Sebastian Żabczyński
- Environmental Biotechnology Department, Silesian University of Technology, Akademicka 2, 44-100, Gliwice, Poland
| | - Grzegorz Cema
- Environmental Biotechnology Department, Silesian University of Technology, Akademicka 2, 44-100, Gliwice, Poland
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Purkamo L, Kietäväinen R, Miettinen H, Sohlberg E, Kukkonen I, Itävaara M, Bomberg M. Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater. FEMS Microbiol Ecol 2019; 94:5035813. [PMID: 29893836 DOI: 10.1093/femsec/fiy116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/08/2018] [Indexed: 01/19/2023] Open
Abstract
The diversity and metabolic functions of deep subsurface ecosystems remain relatively unexplored. Microbial communities in previously studied deep subsurface sites of the Fennoscandian Shield are distinctive to each site. Thus, we hypothesized that the microbial communities of the deep Archaean bedrock fracture aquifer in Romuvaara, northern Finland, differ both in community composition and metabolic functionality from the other sites in the Fennoscandian Shield. We characterized the composition, functionality and substrate preferences of the microbial communities at different depths in a 600 m deep borehole. In contrast to other Fennoscandian deep biosphere communities studied to date, iron-oxidizing Gallionella dominated the bacterial communities, while methanogenic and ammonia-oxidizing archaea were the most prominent archaea, and a diverse fungal community was also detected. Potential for methane cycling and sulfate and nitrate reduction was confirmed by detection of the functional genes of these metabolic pathways. Organotrophs were less abundant, although carbohydrates were the most preferred of the tested substrates. The microbial communities shared features with those detected from other deep groundwaters with similar geochemistry, but the majority of taxa distinctive to Romuvaara are different from the taxa previously detected in saline deep groundwater in the Fennoscandian Shield, most likely because of the differences in water chemistry.
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Affiliation(s)
- Lotta Purkamo
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Riikka Kietäväinen
- Geological Survey of Finland (GTK), Betonimiehenkuja 4, 02151 Espoo, Finland
| | - Hanna Miettinen
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Elina Sohlberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Ilmo Kukkonen
- Geological Survey of Finland (GTK), Betonimiehenkuja 4, 02151 Espoo, Finland
| | - Merja Itävaara
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
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Effect of Liming with Various Water Regimes on Both Immobilization of Cadmium and Improvement of Bacterial Communities in Contaminated Paddy: A Field Experiment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16030498. [PMID: 30754673 PMCID: PMC6388227 DOI: 10.3390/ijerph16030498] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/17/2022]
Abstract
Cadmium (Cd) in paddy soil is one of the most harmful potentially toxic elements threatening human health. In order to study the effect of lime combined with intermittent and flooding conditions on the soil pH, Cd availability and its accumulation in tissues at the tillering, filling and maturity stages of rice, as well as enzyme activity and the microbial community in contaminated soil, a field experiment was conducted. The results showed that liming under flooding conditions is a more suitable strategy for in situ remediation of Cd-contaminated paddy soil than intermittent conditions. The availability of Cd in soils was closely related to the duration of flooding. Liming was an effective way at reducing available Cd in flooding soil because it promotes the transformation of Cd in soil from acid-extractable to reducible fraction or residual fraction during the reproductive growth period of rice. Compared with control, after liming, the concentration of Cd in brown rice was reduced by 34.9% under intermittent condition while reduced by 55.8% under flooding condition. Meanwhile, phosphatase, urease, and invertase activities in soil increased by 116.7%, 61.4% and 28.8%, and 41.3%, 46.5% and 20.8%, respectively. The high urease activity in tested soils could be used to assess soil recovery with liming for the remediation of contaminated soil. Soil microbial diversity was determined by the activities of soil acid phosphatase, urease and available Cd by redundancy analysis (RDA). The results indicated that the problem of Cd-contaminated paddy soil could achieve risk control of agricultural planting by chemical treatment such as lime, combined with various water regimes.
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Wang M, Keeley R, Zalivina N, Halfhide T, Scott K, Zhang Q, van der Steen P, Ergas SJ. Advances in algal-prokaryotic wastewater treatment: A review of nitrogen transformations, reactor configurations and molecular tools. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 217:845-857. [PMID: 29660710 DOI: 10.1016/j.jenvman.2018.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/19/2018] [Accepted: 04/04/2018] [Indexed: 05/21/2023]
Abstract
The synergistic activity of algae and prokaryotic microorganisms can be used to improve the efficiency of biological wastewater treatment, particularly with regards to nitrogen removal. For example, algae can provide oxygen through photosynthesis needed for aerobic degradation of organic carbon and nitrification and harvested algal-prokaryotic biomass can be used to produce high value chemicals or biogas. Algal-prokaryotic consortia have been used to treat wastewater in different types of reactors, including waste stabilization ponds, high rate algal ponds and closed photobioreactors. This review addresses the current literature and identifies research gaps related to the following topics: 1) the complex interactions between algae and prokaryotes in wastewater treatment; 2) advances in bioreactor technologies that can achieve high nitrogen removal efficiencies in small reactor volumes, such as algal-prokaryotic biofilm reactors and enhanced algal-prokaryotic treatment systems (EAPS); 3) molecular tools that have expanded our understanding of the activities of algal and prokaryotic communities in wastewater treatment processes.
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Affiliation(s)
- Meng Wang
- Department of Civil & Environmental Engineering, University of South Florida, 4202 E. Fowler Ave, ENB 118, Tampa, FL 33620, USA.
| | - Ryan Keeley
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, BSF 132, Tampa, FL 33620-5200, USA.
| | - Nadezhda Zalivina
- Department of Civil & Environmental Engineering, University of South Florida, 4202 E. Fowler Ave, ENB 118, Tampa, FL 33620, USA.
| | - Trina Halfhide
- Department of Life Sciences, The University of The West Indies, Natural Sciences Building, New Wing, Room 225, St. Augustine, Trinidad and Tobago.
| | - Kathleen Scott
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Avenue, BSF 132, Tampa, FL 33620-5200, USA.
| | - Qiong Zhang
- Department of Civil & Environmental Engineering, University of South Florida, 4202 E. Fowler Ave, ENB 118, Tampa, FL 33620, USA.
| | - Peter van der Steen
- Department of Environmental Engineering and Water Technology, IHE Institute for Water Education, PO Box 3015, 2601 DA, Delft, The Netherlands.
| | - Sarina J Ergas
- Department of Civil & Environmental Engineering, University of South Florida, 4202 E. Fowler Ave, ENB 118, Tampa, FL 33620, USA.
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Zhang LM, Duff AM, Smith CJ. Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems. Environ Microbiol 2018; 20:2834-2853. [DOI: 10.1111/1462-2920.14238] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/01/2018] [Accepted: 04/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Li-Mei Zhang
- Microbiology, School of Natural Sciences; NUI Galway, University Road; Galway Ireland
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Science, Chinese Academy of Sciences, 18 Shuangqing Rd.; Haidan Beijing 100085 P.R. China
| | - Aoife M. Duff
- Microbiology, School of Natural Sciences; NUI Galway, University Road; Galway Ireland
| | - Cindy J. Smith
- Microbiology, School of Natural Sciences; NUI Galway, University Road; Galway Ireland
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16
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Yan L, Xing W. Methods to Study Magnetotactic Bacteria and Magnetosomes. J Microbiol Methods 2018. [DOI: 10.1016/bs.mim.2018.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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17
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Yang W, Wang Y, Tago K, Tokuda S, Hayatsu M. Comparison of the Effects of Phenylhydrazine Hydrochloride and Dicyandiamide on Ammonia-Oxidizing Bacteria and Archaea in Andosols. Front Microbiol 2017; 8:2226. [PMID: 29184545 PMCID: PMC5694480 DOI: 10.3389/fmicb.2017.02226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/30/2017] [Indexed: 11/13/2022] Open
Abstract
Dicyandiamide, a routinely used commercial nitrification inhibitor (NI), inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO). Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO). The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.
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Affiliation(s)
- Wenjie Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, China
| | - Yong Wang
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kanako Tago
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Shinichi Tokuda
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Kyoto, Japan
| | - Masahito Hayatsu
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
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Zheng M, Fu HZ, Ho YS. Research trends and hotspots related to ammonia oxidation based on bibliometric analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:20409-20421. [PMID: 28707243 DOI: 10.1007/s11356-017-9711-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/04/2017] [Indexed: 06/07/2023]
Abstract
Ammonia oxidation is the rate-limiting and central step in global biogeochemistry cycle of nitrogen. A bibliometric analysis based on 4314 articles extracted from Science Citation Index Expanded database was carried out to provide insights into publication performances and research trends of ammonia oxidation in the period 1991-2014. These articles were originated from a wide range of 602 journals and 95 Web of Science Categories, among which Applied and Environmental Microbiology and Environmental Sciences took the leading position, respectively. Furthermore, co-citation analysis conducted with help of CiteSpace software clearly illustrated that ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia oxidation (anammox) were three dominant research themes. A total of 15 landmark works identified with the highest co-citation frequencies at every 8 years were extracted, which demonstrated that the establishments of culture-independent molecular biotechnologies as well as the discoveries of anammox and AOA played the most significant roles in promoting the evolution and development of ammonia oxidation research. Finally, word cluster analysis further suggested that microbial abundance and community of AOA and AOB was the most prominent hotspot, with soil and high-throughput sequencing as the most promising ecosystem and molecular biotechnology. In addition, application of anammox in nitrogen removal from wastewater has become another attractive research hotspot. This study provides a basis for better understanding the situations and prospective directions of the research field of ammonia oxidation.
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Affiliation(s)
- Maosheng Zheng
- MOE Key Laboratory of Regional Energy Systems Optimization, Sino-Canada Resources and Environmental Research Academy, North China Electric Power University, Beijing, 102206, People's Republic of China
| | - Hui-Zhen Fu
- Department of Information Resources Management, School of Public Affairs, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yuh-Shan Ho
- Trend Research Centre, Asia University, Taichung, 41354, Taiwan.
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Hayatsu M, Tago K, Uchiyama I, Toyoda A, Wang Y, Shimomura Y, Okubo T, Kurisu F, Hirono Y, Nonaka K, Akiyama H, Itoh T, Takami H. An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil. ISME JOURNAL 2017; 11:1130-1141. [PMID: 28072419 DOI: 10.1038/ismej.2016.191] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 11/16/2016] [Accepted: 11/19/2016] [Indexed: 12/22/2022]
Abstract
Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates. Whereas all known gammaproteobacterial AOB (γ-AOB) species, which have been isolated from marine and saline aquatic environments, are halophiles, TAO100 is not phenotypically halophilic. Thus, TAO100 represents the first soil-originated and non-halophilic γ-AOB. The TAO100 genome is considerably smaller than those of other γ-AOB and lacks several genes associated with salt tolerance which are unnecessary for survival in soil. The ammonia monooxygenase subunit A gene of TAO100 and its transcript are higher in abundance than those of ammonia-oxidizing archaea and betaproteobacterial AOB in the strongly acidic soil. These results indicate that TAO100 plays an important role in the nitrification of acidic soils. Based on these results, we propose TAO100 as a novel species of a new genus, Candidatus Nitrosoglobus terrae.
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Affiliation(s)
- Masahito Hayatsu
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Kanako Tago
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Ikuo Uchiyama
- National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yong Wang
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yumi Shimomura
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takashi Okubo
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yuhei Hirono
- Institute of Fruit Tree and Tea Science, NARO, Shimada, Shizuoka, Japan
| | - Kunihiko Nonaka
- Institute of Fruit Tree and Tea Science, NARO, Shimada, Shizuoka, Japan
| | - Hiroko Akiyama
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology,Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Hideto Takami
- Yokohama Institute, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
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20
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Yang L, Yang HL, Tu ZC, Wang XL. High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation. PLoS One 2016; 11:e0168166. [PMID: 27992473 PMCID: PMC5167551 DOI: 10.1371/journal.pone.0168166] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/24/2016] [Indexed: 12/02/2022] Open
Abstract
Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p <0.05), and redundancy analysis identified two key genera that are largely responsible for the differences in bacterial composition between the two steps. Staphylococcus was enriched in koji making, while Corynebacterium was enriched in fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food.
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Affiliation(s)
- Lin Yang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Hui-lin Yang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Zong-cai Tu
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Xiao-lan Wang
- Key Lab of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
- * E-mail:
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21
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Chen T, Wu Q, Zhou H, Deng K, Wang X, Meng F, Yang S, Wang X, Shah NP, Wei H. Assessment of commercial probiotic products in China for labelling accuracy and probiotic characterisation of selected isolates. INT J DAIRY TECHNOL 2016. [DOI: 10.1111/1471-0307.12331] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tingtao Chen
- State Key Laboratory of Food Science and Technology; Nanchang University; 235 Nanjing East Road Nanchang Jiangxi 330047 China
- Institute of Translational Medicine; Nanchang University; 999 Xuefu Road Honggutan New District Nanchang Jiangxi 330031 China
| | - Qinglong Wu
- State Key Laboratory of Food Science and Technology; Nanchang University; 235 Nanjing East Road Nanchang Jiangxi 330047 China
- Food and Nutritional Science; School of Biological Sciences; The University of Hong Kong; Pokfulam Road Hong Kong Hong Kong
| | - Haiting Zhou
- Institute of Translational Medicine; Nanchang University; 999 Xuefu Road Honggutan New District Nanchang Jiangxi 330031 China
| | - Kan Deng
- Institute of Translational Medicine; Nanchang University; 999 Xuefu Road Honggutan New District Nanchang Jiangxi 330031 China
| | - Xin Wang
- Institute of Translational Medicine; Nanchang University; 999 Xuefu Road Honggutan New District Nanchang Jiangxi 330031 China
| | - Fanjing Meng
- Institute of Translational Medicine; Nanchang University; 999 Xuefu Road Honggutan New District Nanchang Jiangxi 330031 China
| | - Shaoguo Yang
- Institute of Translational Medicine; Nanchang University; 999 Xuefu Road Honggutan New District Nanchang Jiangxi 330031 China
| | - Xiaolei Wang
- Institute of Translational Medicine; Nanchang University; 999 Xuefu Road Honggutan New District Nanchang Jiangxi 330031 China
| | - Nagendra P Shah
- Food and Nutritional Science; School of Biological Sciences; The University of Hong Kong; Pokfulam Road Hong Kong Hong Kong
| | - Hua Wei
- State Key Laboratory of Food Science and Technology; Nanchang University; 235 Nanjing East Road Nanchang Jiangxi 330047 China
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22
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Zhou Z, Xu P, Cao X, Zhou Y, Song C. Efficiency promotion and its mechanisms of simultaneous nitrogen and phosphorus removal in stormwater biofilters. BIORESOURCE TECHNOLOGY 2016; 218:842-849. [PMID: 27428301 DOI: 10.1016/j.biortech.2016.07.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/04/2016] [Accepted: 07/09/2016] [Indexed: 06/06/2023]
Abstract
Stromwater biofilter technology was greatly improved through adding iron-rich soil, plant detritus and eutrophic lake sediment. Significant ammonium and phosphate removal efficiencies (over 95%) in treatments with iron-rich soil were attributed to strong adsorption capability resulting in high available phosphorus (P) in media, supporting the abundance and activity of nitrifiers and denitrifiers as well as shaping compositions, which facilitated nitrogen (N) removal. Aquatic and terrestrial plant detritus was more beneficial to nitrification and denitrification by stimulating the abundance and activity of nitrifiers and denitrifiers respectively, which increased total nitrogen (TN) removal efficiencies by 17.6% and 22.5%. In addition, bioaugmentation of nitrifiers and denitrifiers from eutrophic sediment was helpful to nutrient removal. Above all, combined application of these materials could reach simultaneously maximum effects (removal efficiencies of P, ammonium and TN were 97-99%, 95-97% and 60-63% respectively), suggesting reasonable selection of materials has important contribution and application prospect in stormwater biofilters.
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Affiliation(s)
- Zijun Zhou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100039, PR China
| | - Peng Xu
- College of Resources and Environment, Huazhong Agriculture University, Wuhan 430070, PR China
| | - Xiuyun Cao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Yiyong Zhou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Chunlei Song
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
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24
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Bacterial microbiota profile in gills of modified atmosphere-packaged oysters stored at 4 °C. Food Microbiol 2016; 61:58-65. [PMID: 27697170 DOI: 10.1016/j.fm.2016.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 06/30/2016] [Accepted: 08/19/2016] [Indexed: 12/21/2022]
Abstract
As filter-feeding bivalves, oysters can accumulate microorganisms into their gills, causing spoilage and potential safety issues. This study aims to investigate the changes in the gill microbiota of oysters packed under air and modified atmospheres (MAs, 50% CO2: 50% N2, 70% CO2: 30% O2, and 50% CO2: 50% O2) during storage at 4 °C. The diversity of bacterial microbiota in oyster gills was profiled through polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis on the 16S rRNA gene V3 region to describe the variation during the entire storage period. The DGGE profile revealed high bacterial diversity in the air- and MA-packaged oyster gills, and the spoilage bacterial microbiota varied in the MA-packaged oyster gills. Results indicated that CO2:O2 (70%:30%) was suitable for oyster MA packaging and that high bacterial loads in oyster gills need to be considered during storage. In addition, Lactobacillus and Lactococcus species were found to grow dominantly in fresh oyster gills under MA packaging, which supports the potential application of MA packaging for oyster storage.
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Cho K, Shin SG, Lee J, Koo T, Kim W, Hwang S. Nitrification resilience and community dynamics of ammonia-oxidizing bacteria with respect to ammonia loading shock in a nitrification reactor treating steel wastewater. J Biosci Bioeng 2016; 122:196-202. [DOI: 10.1016/j.jbiosc.2016.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 11/29/2022]
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Beddow J, Stolpe B, Cole PA, Lead JR, Sapp M, Lyons BP, Colbeck I, Whitby C. Nanosilver inhibits nitrification and reduces ammonia-oxidising bacterial but not archaealamoAgene abundance in estuarine sediments. Environ Microbiol 2016; 19:500-510. [DOI: 10.1111/1462-2920.13441] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 06/30/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Jessica Beddow
- School of Biological Sciences; University of Essex; Essex CO4 3SQ UK
| | - Björn Stolpe
- School of Geography, Earth and Environmental Sciences; University of Birmingham; Birmingham B15 2TT UK
| | - Paula A. Cole
- School of Geography, Earth and Environmental Sciences; University of Birmingham; Birmingham B15 2TT UK
| | - Jamie R. Lead
- School of Geography, Earth and Environmental Sciences; University of Birmingham; Birmingham B15 2TT UK
- Center for Environmental NanoScience and Risk, University of South Carolina; Columbia SC 29028 USA
| | - Melanie Sapp
- Institute of Population Genetics, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University; Düsseldorf 40225 Germany
| | - Brett P. Lyons
- Centre for Environment, Fisheries and Aquaculture Science; The Nothe, Barrack Road Weymouth Dorset DT4 8UB UK
| | - Ian Colbeck
- School of Biological Sciences; University of Essex; Essex CO4 3SQ UK
| | - Corinne Whitby
- School of Biological Sciences; University of Essex; Essex CO4 3SQ UK
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Schreiber L, Kjeldsen KU, Funch P, Jensen J, Obst M, López-Legentil S, Schramm A. Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts. Front Microbiol 2016; 7:1042. [PMID: 27462299 PMCID: PMC4940369 DOI: 10.3389/fmicb.2016.01042] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/21/2016] [Indexed: 11/13/2022] Open
Abstract
Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and -independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae) clade were detected in the ascidian species Ascidiella aspersa, Ascidiella scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25-100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence in situ hybridization (FISH) as extracellular microcolonies in the pharynx. Two strains of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a mucus glycoprotein). The strains tested negative for cytotoxic or antibacterial activity. Based on these observations, we propose ascidian-associated Endozoicomonas to be commensals, living off the mucus continuously secreted into the pharynx. Members of the ascidian-specific Endozoicomonas subclade were also detected in seawater from the Scandinavian sampling site, which suggests acquisition of the symbionts by horizontal transmission. The combined results indicate a host-specific, yet facultative symbiosis between ascidians and Endozoicomonas.
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Affiliation(s)
- Lars Schreiber
- Department of Bioscience, Center for Geomicrobiology and Section for Microbiology, Aarhus University Aarhus, Denmark
| | - Kasper U Kjeldsen
- Department of Bioscience, Center for Geomicrobiology and Section for Microbiology, Aarhus University Aarhus, Denmark
| | - Peter Funch
- Section of Genetics, Ecology and Evolution, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Jeppe Jensen
- Department of Bioscience, Center for Geomicrobiology and Section for Microbiology, Aarhus University Aarhus, Denmark
| | - Matthias Obst
- Department of Marine Sciences, University of Gothenburg Gothenburg, Sweden
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington Wilmington NC, USA
| | - Andreas Schramm
- Department of Bioscience, Center for Geomicrobiology and Section for Microbiology, Aarhus University Aarhus, Denmark
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Jos eacute GDS, Joaquim JEDC, Jos eacute MRDL, Jos eacute ECDS. Fertigation with domestic wastewater: Uses and implications. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajb2015.15115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Zabaloy MC, Carné I, Viassolo R, Gómez MA, Gomez E. Soil ecotoxicity assessment of glyphosate use under field conditions: microbial activity and community structure of Eubacteria and ammonia-oxidising bacteria. PEST MANAGEMENT SCIENCE 2016; 72:684-91. [PMID: 25960311 DOI: 10.1002/ps.4037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/03/2015] [Accepted: 05/04/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND A plot-scale experiment was conducted to assess the impact of field application rates of glyphosate on soil microbial communities by taking measurements of microbial activity (in terms of substrate-induced respiration and enzyme activity) in parallel with culture-independent approaches to assessing both bacterial abundance and diversity. Two rates of glyphosate, alone or in a mixture with 2,4-dichlorophenoxyacetic acid, were applied directly onto the soil surface, simulating normal use in chemical fallow in no-till systems. RESULTS No consistent rate-dependent responses were observed in the microbial activity parameters investigated in the field plots that were exposed to glyphosate. Denaturant gradient gel electrophoresis (DGGE) of the overall bacterial community (Eubacteria) and ammonia-oxidising bacteria (AOB) revealed no effects of the high rate of glyphosate on the structure of the communities in comparison with the control. No treatment effects were observed on the abundance of Eubacteria shortly after treatment in 2010, while a small but significant difference between the high rate and the control was detected in the first sampling in 2011. The abundance of AOB was relatively low during the study, and treatment effects were undetectable. CONCLUSIONS The absence of negative effects on soil microbial communities in this study suggests that glyphosate use at recommended rates poses low risk to the microbiota.
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Affiliation(s)
- María C Zabaloy
- Microbial Ecology Laboratory, Departamento de Agronomía (UNS), Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Bahía Blanca, Argentina
| | - Ignacio Carné
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, 2125, Zavalla, Argentina
| | - Rodrigo Viassolo
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, 2125, Zavalla, Argentina
| | - Marisa A Gómez
- Microbial Ecology Laboratory, Departamento de Agronomía (UNS), Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Bahía Blanca, Argentina
| | - Elena Gomez
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, 2125, Zavalla, Argentina
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30
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Vetterli A, Hietanen S, Leskinen E. Spatial and temporal dynamics of ammonia oxidizers in the sediments of the Gulf of Finland, Baltic Sea. MARINE ENVIRONMENTAL RESEARCH 2016; 113:153-63. [PMID: 26722795 DOI: 10.1016/j.marenvres.2015.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/10/2015] [Accepted: 12/12/2015] [Indexed: 05/03/2023]
Abstract
The diversity and dynamics of ammonia-oxidizing bacteria (AOB) and archaea (AOA) nitrifying communities in the sediments of the eutrophic Gulf of Finland (GoF) were investigated. Using clone libraries of ammonia monooxygenase (amoA) gene fragments and terminal restriction fragment length polymorphism (TRFLP), we found a low richness of both AOB and AOA. The AOB amoA phylogeny matched that of AOB 16S ribosomal genes from the same samples. AOA communities were characterized by strong spatial variation while AOB communities showed notable temporal patterns. At open sea sites, where transient anoxic conditions prevail, richness of both AOA and AOB was lowest and communities were dominated by organisms with gene signatures unique to the GoF. Given the importance of nitrification as a link between the fixation of nitrogen and its removal from aquatic environments, the low diversity of ammonia-oxidizing microbes across the GoF could be of relevance for ecosystem resilience in the face of rapid global environmental changes.
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Affiliation(s)
- Adrien Vetterli
- Department of Environmental Sciences, University of Helsinki, P.O. Box 65, 00014, Finland; Tvärminne Zoological Station, J.A. Palménin Tie 260, 10900, Hanko, Finland.
| | - Susanna Hietanen
- Department of Environmental Sciences, University of Helsinki, P.O. Box 65, 00014, Finland; Tvärminne Zoological Station, J.A. Palménin Tie 260, 10900, Hanko, Finland
| | - Elina Leskinen
- Department of Environmental Sciences, University of Helsinki, P.O. Box 65, 00014, Finland; Tvärminne Zoological Station, J.A. Palménin Tie 260, 10900, Hanko, Finland
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Sun Y, Xu Y, Xu Y, Wang L, Liang X, Li Y. Reliability and stability of immobilization remediation of Cd polluted soils using sepiolite under pot and field trials. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 208:739-746. [PMID: 26586633 DOI: 10.1016/j.envpol.2015.10.054] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 10/25/2015] [Accepted: 10/28/2015] [Indexed: 06/05/2023]
Abstract
Long-term effectiveness and persistence are two important criterias to evaluate alternative remediation technology of heavy metal polluted soils. Pot and field studies showed addition of sepiolite was effective in immobilizing Cd in polluted soils, with significant reduction in TCLP extracts (0.6%-49.6% and 4.0%-32.5% reduction in pot and field experiments, respectively) and plant uptake (14.4%-84.1% and 22.8%-61.4% declines in pot and field studies, correspondingly). However, the applications of sepiolite offered a limited guarantee for the safety of edible vegetables in Cd-polluted soils, depending on the soil type, the Cd pollution type and level, and the dose and application frequency of chemical amendments. Bioassays, such as plant growth, soil enzymatic activities and microbial community diversity, indicated a certain degree of recovery of soil metabolic function. Therefore, sepiolite-assisted in situ remediation is cost-effective, environmentally friendly, and technically applicable, and can be successfully used to reduce Cd enter into the food chain on field scale.
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Affiliation(s)
- Yuebing Sun
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China; Key Laboratory of Original Environmental Quality, Ministry of Agriculture/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Institute of Agro-Environmental Protection, Ministry of Agriculture, Tianjin 300191, China
| | - Yi Xu
- College of Resources & Environment, Hunan Agricultural University, Changsha 410128, China
| | - Yingming Xu
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China; Key Laboratory of Original Environmental Quality, Ministry of Agriculture/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Institute of Agro-Environmental Protection, Ministry of Agriculture, Tianjin 300191, China.
| | - Lin Wang
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China; Key Laboratory of Original Environmental Quality, Ministry of Agriculture/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Institute of Agro-Environmental Protection, Ministry of Agriculture, Tianjin 300191, China
| | - Xuefeng Liang
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China; Key Laboratory of Original Environmental Quality, Ministry of Agriculture/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Institute of Agro-Environmental Protection, Ministry of Agriculture, Tianjin 300191, China
| | - Ye Li
- Innovation Team of Remediation for Heavy Metal Contaminated Farmlands, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, China; Key Laboratory of Original Environmental Quality, Ministry of Agriculture/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Institute of Agro-Environmental Protection, Ministry of Agriculture, Tianjin 300191, China
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Agrawal PK, Agrawal S, Shrivastava R. Modern molecular approaches for analyzing microbial diversity from mushroom compost ecosystem. 3 Biotech 2015; 5:853-866. [PMID: 28324393 PMCID: PMC4624149 DOI: 10.1007/s13205-015-0289-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/22/2015] [Indexed: 12/20/2022] Open
Abstract
Biosphere is a store house of various microorganisms that may be employed to isolate and exploit microbes for environmental, pharmaceutical, agricultural and industrial applications. There is restricted data regarding the structure and dynamics of microbial communities in several ecosystems because only a little fraction of microbial diversity is accessible by culture methods. Owing to limitations of traditional enrichment methods and pure culture techniques, microbiological studies have offered a narrow portal for investigating microbial flora. The bacterial community represented by the morphological and nutritional criteria failed to provide a natural taxonomic order according to the evolutionary relationship. Genetic diversity among the isolates recovered from mushroom compost has not been widely studied. To understand genetic diversity and community composition of the mushroom compost microflora, different approaches are now followed by taxonomists, to characterize and identify isolates up to species level. Molecular microbial ecology is an emerging discipline of biology under molecular approach which can provide complex community profiles along with useful phylogenetic information. The genomic era has resulted in the development of new molecular tools and techniques for study of culturable microbial diversity including the DNA base ratio (mole% G + C), DNA-DNA hybridization, DNA microarray and reverse sample genome probing. In addition, non-culturable diversity of mushroom compost ecosystem can be characterized by employing various molecular tools which would be discussed in the present review.
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Hayashi K, Shimomura Y, Morimoto S, Uchida M, Nakatsubo T, Hayatsu M. Characteristics of ammonia oxidation potentials and ammonia oxidizers in mineral soil under Salix polaris–moss vegetation in Ny-Ålesund, Svalbard. Polar Biol 2015. [DOI: 10.1007/s00300-015-1829-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kutvonen H, Rajala P, Carpén L, Bomberg M. Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms. Front Microbiol 2015; 6:1079. [PMID: 26528251 PMCID: PMC4606121 DOI: 10.3389/fmicb.2015.01079] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/21/2015] [Indexed: 11/13/2022] Open
Abstract
We investigated the N-utilizing bacterial community in anoxic brackish groundwater of the low and intermediate level nuclear waste repository cave in Olkiluoto, Finland, at 100 m depth using 15N-based stable isotope probing (SIP) and enrichment with 14∕15N-ammonium or 14∕15N-nitrate complemented with methane. Twenty-eight days of incubation at 12°C increased the concentration of bacterial 16S rRNA and nitrate reductase (narG) gene copies in the substrate amended microcosms simultaneously with a radical drop in the overall bacterial diversity and OTU richness. Hydrogenophaga/Malikia were enriched in all substrate amended microcosms and Methylobacter in the ammonium and ammonium+methane supplemented microcosms. Sulfuricurvum was especially abundant in the nitrate+methane treatment and the unamended incubation control. Membrane-bound nitrate reductase genes (narG) from Polarimonas sp. were detected in the original groundwater, while Burkholderia, Methylibium, and Pseudomonas narG genes were enriched due to substrate supplements. Identified amoA genes belonged to Nitrosomonas sp. 15N-SIP revealed that Burkholderiales and Rhizobiales clades belonging to the minority groups in the original groundwater used 15N from ammonium and nitrate as N source indicating an important ecological function of these bacteria, despite their low number, in the groundwater N cycle in Olkiluoto bedrock system.
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Affiliation(s)
- Heini Kutvonen
- Material Recycling and Geotechnology, VTT Technical Research Centre of Finland Espoo, Finland
| | - Pauliina Rajala
- Materials Performance, VTT Technical Research Centre of Finland Espoo, Finland
| | - Leena Carpén
- Materials Performance, VTT Technical Research Centre of Finland Espoo, Finland
| | - Malin Bomberg
- Material Recycling and Geotechnology, VTT Technical Research Centre of Finland Espoo, Finland
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36
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Shay PE, Winder RS, Trofymow JA. Nutrient-cycling microbes in coastal Douglas-fir forests: regional-scale correlation between communities, in situ climate, and other factors. Front Microbiol 2015; 6:1097. [PMID: 26500636 PMCID: PMC4597117 DOI: 10.3389/fmicb.2015.01097] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/22/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes such as fungi and bacteria play fundamental roles in litter-decay and nutrient-cycling; however, their communities may respond differently than plants to climate change. The structure (diversity, richness, and evenness) and composition of microbial communities in climate transects of mature Douglas-fir stands of coastal British Columbia rainshadow forests was analyzed, in order to assess in situ variability due to different temperature and moisture regimes. We compared denaturing gradient gel electrophoresis profiles of fungi (18S-FF390/FR1), nitrogen-fixing bacteria (NifH-universal) and ammonia-oxidizing bacteria (AmoA) polymerase chain reaction amplicons in forest floor and mineral soil samples from three transects located at different latitudes, each transect spanning the Coastal Western Hemlock and Douglas-fir biogeoclimatic zones. Composition of microbial communities in both soil layers was related to degree days above 0°C (2725–3489), while pH (3.8–5.5) best explained shifts in community structure. At this spatial scale, climatic conditions were likely to directly or indirectly select for different microbial species while local site heterogeneity influenced community structure. Significant changes in microbial community composition and structure were related to differences as small as 2.47% and 2.55°C in mean annual moisture and temperature variables, respectively. The climatic variables best describing microbial composition changed from one functional group to the next; in general they did not alter community structure. Spatial distance, especially associated with latitude, was also important in accounting for community variability (4–23%); but to a lesser extent than the combined influence of climate and soil characteristics (14–25%). Results suggest that in situ climate can independently account for some patterns of microbial biogeography in coastal Douglas-fir forests. The distribution of up to 43% of nutrient-cycling microorganisms detected in forest soils responded to smaller abiotic gradients than host trees.
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Affiliation(s)
- Philip-Edouard Shay
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria BC, Canada
| | - Richard S Winder
- Canadian Forest Service, Pacific Forestry Centre, Natural Resources Canada, Victoria BC, Canada
| | - J A Trofymow
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria BC, Canada ; Canadian Forest Service, Pacific Forestry Centre, Natural Resources Canada, Victoria BC, Canada
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37
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Reis MP, Ávila MP, Keijzer RM, Barbosa FAR, Chartone-Souza E, Nascimento AMA, Laanbroek HJ. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments. Front Microbiol 2015; 6:898. [PMID: 26379659 PMCID: PMC4553384 DOI: 10.3389/fmicb.2015.00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.
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Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil ; Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
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38
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Frenk S, Dag A, Yermiyahu U, Zipori I, Hadar Y, Minz D. Seasonal effect and anthropogenic impact on the composition of the active bacterial community in Mediterranean orchard soil. FEMS Microbiol Ecol 2015; 91:fiv096. [PMID: 26253508 DOI: 10.1093/femsec/fiv096] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2015] [Indexed: 01/25/2023] Open
Abstract
Several anthropogenic interventions, common in agriculture, may influence active bacterial communities in soil without affecting their total composition. Therefore, the composition of an active bacterial community in soil may reflect its relation to biogeochemical processes. This issue was addressed during two consecutive years in olive-orchard soil, irrigated with treated wastewater (TWW) in a Mediterranean climate, by following the active (rRNA) and total (rRNA gene) bacterial community in the soil. Although TWW irrigation did not affect the composition of the total soil bacterial community, it had an effect on the active fraction of the community. These results, based on 16S rRNA data, indicate that the organic matter and minerals in TWW were not directly utilized for the rapid proliferation of specific taxonomic groups. Activity levels, manifested by variance in the relative abundance of the active and total communities of selected operational taxonomic units, revealed annual and seasonal fluctuations and fluctuations dependent on the type of irrigation. The potential activity (nitrification rates) and community composition of ammonia-oxidizing bacteria were affected by TWW irrigation, and this group of bacteria was therefore further explored. It was concluded that irrigation with TWW had little effect on "who is there", i.e. which bacteria were present, but influenced "who is active", with a distinct effect on bacteria associated with the biochemical cycling of nitrogen.
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Affiliation(s)
- Sammy Frenk
- Department of Soil, Water, and Environmental Sciences, Agricultural Research Organization, Volcani Center, Bet-Dagan, 5025001, Israel Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Arnon Dag
- Gilat Research Center, Agricultural Research Organization, MP Negev, 8528000, Israel
| | - Uri Yermiyahu
- Gilat Research Center, Agricultural Research Organization, MP Negev, 8528000, Israel
| | - Isaac Zipori
- Gilat Research Center, Agricultural Research Organization, MP Negev, 8528000, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Dror Minz
- Department of Soil, Water, and Environmental Sciences, Agricultural Research Organization, Volcani Center, Bet-Dagan, 5025001, Israel
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Shanqimuge, Liang H, Zhang C, Shao C, Peng X, Liang L, Su J, Li C. A DGGE Marker-Mediated Fast Monitoring of Bacterial Diversity and Comprehensive Identification of High-Temperature Daqu Starter. J Food Sci 2015; 80:M1519-25. [PMID: 26081439 DOI: 10.1111/1750-3841.12903] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/27/2015] [Accepted: 04/15/2015] [Indexed: 11/27/2022]
Abstract
UNLABELLED Bacteria play an essential role in Daqu starter (Daqu) fermentation. The identification of Daqu bacteria was investigated by polymerase chain reaction (PCR) based denaturing gradient gel electrophoresis (DGGE) analysis of the highly variable V3 region of the 16S rRNA gene. Here, we define a novel DGGE marker for the quick identification of Daqu bacteria. A dynamic alteration of the bacterial populations at different stages of fermentation was determined through a 2-y continuous monitoring. The physicochemical parameters of Daqu at different fermentation stages were investigated by weighing, NaOH titration, and HCl hydrolysis together with Fehling reagent methods. Furthermore, infrared spectral analysis using Fourier Transformed Infrared Spectroscopy was performed to determine physicochemical changes of Daqu. Therefore, our studies provide key insight for a comprehensive quality control of Daqu at different fermentation stages using the PCR-DGGE analysis combined with the physicochemical measurement. PRACTICAL APPLICATION Chinese liquor is one of the 6 well-known distilled spirits in the world. High-temperature Daqu acts as an important source of nutrients and of microorganisms in the solid-state fermentation of Chinese Moutai-flavor liquor, which has a critical impact on the final flavor of the liquor. The study identifies a novel DGGE marker and provides an efficient way to identify bacterial diversity in Daqu from different fermentation stages. Importantly, the study defines dynamic changes of the physicochemical parameters and the infrared spectra analysis of Daqu during the fermentation process. These studies will help to (1) establish a standard operation procedure for Daqu production; (2) stabilize manufacturing process for Daqu fermentation and even for liquor brewing.
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Affiliation(s)
- Shanqimuge
- Div. of Nutraceutical Products, Tasly Holding Group, Tianjin, 300040, China
| | - Huizhen Liang
- Div. of Nutraceutical Products, Tasly Holding Group, Tianjin, 300040, China
| | - Changxia Zhang
- Div. of Nutraceutical Products, Tasly Holding Group, Tianjin, 300040, China
| | - Chunfu Shao
- Div. of Nutraceutical Products, Tasly Holding Group, Tianjin, 300040, China
| | - Xiaopei Peng
- Div. of Nutraceutical Products, Tasly Holding Group, Tianjin, 300040, China
| | - Liquan Liang
- Div. of Nutraceutical Products, Tasly Holding Group, Tianjin, 300040, China
| | - Jing Su
- Div. of Nutraceutical Products, Tasly Holding Group, Tianjin, 300040, China
| | - Changwen Li
- Div. of Nutraceutical Products, Tasly Holding Group, Tianjin, 300040, China
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40
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Liu H, Tan S, Sheng Z, Yu T, Liu Y. Impact of oxygen on the coexistence of nitrification, denitrification, and sulfate reduction in oxygen-based membrane aerated biofilm. Can J Microbiol 2015; 61:237-42. [PMID: 25688805 DOI: 10.1139/cjm-2014-0574] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Membrane aerated biofilms (MABs) are subject to "counter diffusion" of oxygen and substrates. In a membrane aerated biofilm reactor, gases (e.g., oxygen) diffuse through the membrane into the MAB, and liquid substrates pass from the bulk liquid into the MAB. This behavior can result in a unique biofilm structure in terms of microbial composition, distribution, and community activity in the MAB. Previous studies have shown simultaneous aerobic oxidation, nitrification, and denitrification within a single MAB. Using molecular techniques, we investigated the growth of sulfate-reducing bacteria (SRB) in the oxygen-based MAB attached to a flat sheet membrane. Denaturing gradient gel electrophoresis of the amplified 16S rRNA gene fragments and functional gene fragments specific for ammonia-oxidizing bacteria (amoA), denitrifying bacteria (nirK), and SRB (dsrB) demonstrated the coexistence of nitrifiers, denitrifiers, and SRB communities within a single MAB. The functional diversities of SRB and denitrifiers decreased with an increase in the oxygen concentration in the bulk water of the reactor.
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Affiliation(s)
- Hong Liu
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 2W2, Canada
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Purkamo L, Bomberg M, Nyyssönen M, Kukkonen I, Ahonen L, Itävaara M. Heterotrophic communities supplied by ancient organic carbon predominate in deep fennoscandian bedrock fluids. MICROBIAL ECOLOGY 2015; 69:319-332. [PMID: 25260922 DOI: 10.1007/s00248-014-0490-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/29/2014] [Indexed: 06/03/2023]
Abstract
The deep subsurface hosts diverse life, but the mechanisms that sustain this diversity remain elusive. Here, we studied microbial communities involved in carbon cycling in deep, dark biosphere and identified anaerobic microbial energy production mechanisms from groundwater of Fennoscandian crystalline bedrock sampled from a deep drill hole in Outokumpu, Finland, by using molecular biological analyses. Carbon cycling pathways, such as carbon assimilation, methane production and methane consumption, were studied with cbbM, rbcL, acsB, accC, mcrA and pmoA marker genes, respectively. Energy sources, i.e. the terminal electron accepting processes of sulphate-reducing and nitrate-reducing communities, were assessed with detection of marker genes dsrB and narG, respectively. While organic carbon is scarce in deep subsurface, the main carbon source for microbes has been hypothesized to be inorganic carbon dioxide. However, our results demonstrate that carbon assimilation is performed throughout the Outokumpu deep scientific drill hole water column by mainly heterotrophic microorganisms such as Clostridia. The source of carbon for the heterotrophic microbial metabolism is likely the Outokumpu bedrock, mainly composed of serpentinites and metasediments with black schist interlayers. In addition to organotrophic metabolism, nitrate and sulphate are other possible energy sources. Methanogenic and methanotrophic microorganisms are scarce, but our analyses suggest that the Outokumpu deep biosphere provides niches for these organisms; however, they are not very abundant.
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Affiliation(s)
- Lotta Purkamo
- VTT Technical Research Centre of Finland, PL1000, 02044, Espoo, Finland,
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Kalle E, Kubista M, Rensing C. Multi-template polymerase chain reaction. BIOMOLECULAR DETECTION AND QUANTIFICATION 2014; 2:11-29. [PMID: 27896140 PMCID: PMC5121205 DOI: 10.1016/j.bdq.2014.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 12/12/2022]
Abstract
PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.
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Affiliation(s)
- Elena Kalle
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Allmas alle 5, 75007 Uppsala, Sweden
| | - Mikael Kubista
- TATAA Biocenter, Odinsgatan 28, 41103 Göteborg, Sweden; Institute of Biotechnology, Czech Academy of Sciences
| | - Christopher Rensing
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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da Luz JMR, Paes SA, Bazzolli DMS, Tótola MR, Demuner AJ, Kasuya MCM. Abiotic and biotic degradation of oxo-biodegradable plastic bags by Pleurotus ostreatus. PLoS One 2014; 9:e107438. [PMID: 25419675 PMCID: PMC4242504 DOI: 10.1371/journal.pone.0107438] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 08/13/2014] [Indexed: 11/24/2022] Open
Abstract
In this study, we evaluated the growth of Pleurotus ostreatus PLO6 using oxo-biodegradable plastics as a carbon and energy source. Oxo-biodegradable polymers contain pro-oxidants that accelerate their physical and biological degradation. These polymers were developed to decrease the accumulation of plastic waste in landfills. To study the degradation of the plastic polymers, oxo-biodegradable plastic bags were exposed to sunlight for up to 120 days, and fragments of these bags were used as substrates for P. ostreatus. We observed that physical treatment alone was not sufficient to initiate degradation. Instead, mechanical modifications and reduced titanium oxide (TiO2) concentrations caused by sunlight exposure triggered microbial degradation. The low specificity of lignocellulolytic enzymes and presence of endomycotic nitrogen-fixing microorganisms were also contributing factors in this process.
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Affiliation(s)
| | - Sirlaine Albino Paes
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Marcos Rogério Tótola
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Zielińska M, Cydzik-Kwiatkowska A, Bernat K, Bułkowska K, Wojnowska-Baryła I. Removal of bisphenol A (BPA) in a nitrifying system with immobilized biomass. BIORESOURCE TECHNOLOGY 2014; 171:305-313. [PMID: 25218202 DOI: 10.1016/j.biortech.2014.08.087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/18/2014] [Accepted: 08/21/2014] [Indexed: 06/03/2023]
Abstract
The potential for bisphenol A (BPA) removal by mixed consortia of immobilized microorganisms with high nitrification activity was investigated with BPA concentrations in the influent from 2.5 to 10.0 mg/L. The presence of BPA limited ammonium oxidation; nitrification efficiency decreased from 91.2±1.3% in the control series to 47.4±9.4% when BPA concentration in wastewater was the highest. The efficiency of BPA removal rose from 87.1±5.5% to 92.9±2.9% with increased BPA concentration in the influent. Measurement of oxygen uptake rates by biomass exposed to BPA showed that BPA was mainly removed by heterotrophic bacteria. A strong negative correlation between the BPA removal efficiency and nitrification efficiency indicated the limited contribution of ammonia-oxidizing bacteria (AOB) to BPA biodegradation. Exposure of biomass to BPA changed the quantity and diversity of AOB in the biomass as shown by real-time PCR and denaturing gradient gel electrophoresis.
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Affiliation(s)
- Magdalena Zielińska
- University of Warmia and Mazury in Olsztyn, Department of Environmental Biotechnology, Słoneczna Str. 45G, 10-709 Olsztyn, Poland.
| | - Agnieszka Cydzik-Kwiatkowska
- University of Warmia and Mazury in Olsztyn, Department of Environmental Biotechnology, Słoneczna Str. 45G, 10-709 Olsztyn, Poland.
| | - Katarzyna Bernat
- University of Warmia and Mazury in Olsztyn, Department of Environmental Biotechnology, Słoneczna Str. 45G, 10-709 Olsztyn, Poland.
| | - Katarzyna Bułkowska
- University of Warmia and Mazury in Olsztyn, Department of Environmental Biotechnology, Słoneczna Str. 45G, 10-709 Olsztyn, Poland.
| | - Irena Wojnowska-Baryła
- University of Warmia and Mazury in Olsztyn, Department of Environmental Biotechnology, Słoneczna Str. 45G, 10-709 Olsztyn, Poland.
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da Silva MDCS, Paula TDA, Moreira BC, Carolino M, Cruz C, Bazzolli DMS, Silva CC, Kasuya MCM. Nitrogen-fixing bacteria in Eucalyptus globulus plantations. PLoS One 2014; 9:e111313. [PMID: 25340502 PMCID: PMC4207822 DOI: 10.1371/journal.pone.0111313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 09/23/2014] [Indexed: 11/23/2022] Open
Abstract
Eucalypt cultivation is an important economic activity worldwide. In Portugal, Eucalyptus globulus plantations account for one-third of the total forested area. The nutritional requirements of this crop have been well studied, and nitrogen (N) is one of the most important elements required for vegetal growth. N dynamics in soils are influenced by microorganisms, such as diazotrophic bacteria (DB) that are responsible for biological nitrogen fixation (BNF), so the aim of this study was to evaluate and identity the main groups of DB in E. globulus plantations. Samples of soil and root systems were collected in winter and summer from three different Portuguese regions (Penafiel, Gavião and Odemira). We observed that DB communities were affected by season, N fertilization and moisture. Furthermore Bradyrhizobium and Burkholderia were the most prevalent genera in these three regions. This is the first study describing the dynamic of these bacteria in E. globulus plantations, and these data will likely contribute to a better understanding of the nutritional requirements of eucalypt cultivation and associated organic matter turnover.
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Affiliation(s)
| | | | - Bruno Coutinho Moreira
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Manuela Carolino
- Faculdade de Ciências da Universidade de Lisboa, Centro de Biologia Ambiental, Lisboa, Campo Grande, Portugal
| | - Cristina Cruz
- Faculdade de Ciências da Universidade de Lisboa, Centro de Biologia Ambiental, Lisboa, Campo Grande, Portugal
| | | | - Cynthia Canedo Silva
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Wan C, Yang X, Lee DJ, Liu X, Sun S. Partial nitrification using aerobic granule continuous-flow reactor: Operations and microbial community. J Taiwan Inst Chem Eng 2014. [DOI: 10.1016/j.jtice.2014.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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47
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Wan C, Yang X, Lee DJ, Sun S, Liu X, Zhang P. Influence of hydraulic retention time on partial nitrification of continuous-flow aerobic granular-sludge reactor. ENVIRONMENTAL TECHNOLOGY 2014; 35:1760-1765. [PMID: 24956768 DOI: 10.1080/09593330.2014.881423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This study investigated the effects of hydraulic retention time (HRT) at 12 h, 7.2 h and 2.4 h on partial nitrification efficiency of continuous-flow aerobic granular reactors (CFAGRs) with mature aerobic granules (500 +/- 20mg l-1). At HRT 12 h and 7.2h, the removal efficiency of both ammonia-nitrogen (NH4+ - N) and nitrite accumulation rate were exceeding 90%. At HRT 2.4 h, NH4+ - N removal efficiency was reduced but most of the conversion efficiency to nitrite was only slightly reduced. At HRT < 2.4 h, washout of aerobic granules occurred. In all tests conducted herein, the chemical oxygen demand removal efficiencies exceeded 90%. The clone library results noted the presence of ammonia-oxidizing bacteria belonged to beta-Proteobacteria subclass, including 94% of Nitrosomonas europaea and 6% of Nitrosomonas sp. The polymerase chain reaction and denaturing gradient gel electrophoresis results suggested that Alpha proteobacterium, Pseudoxanthomonas mexicana strain, Sphaerotilus natans and Uncultured gamma proteobacterium were responsible for the aerobic granular stability and processing performance. The present CFAGR successfully implemented continuous partial nitrification using aerobic granules at low HRT.
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Opitz S, Küsel K, Spott O, Totsche KU, Herrmann M. Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany. FEMS Microbiol Ecol 2014; 90:39-53. [PMID: 24953994 DOI: 10.1111/1574-6941.12370] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 05/30/2014] [Accepted: 06/11/2014] [Indexed: 01/27/2023] Open
Abstract
We followed the abundance and compared the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months. Groundwater obtained from the upper aquifer (12 m depth) was characterized by low oxygen saturation (0-20%) and low nitrate concentrations (0-20 μM), contrasting with 50-80% oxygen saturation and 40-200 μM nitrate in the lower aquifer (48 m and 88 m depth). Quantitative PCR targeting bacterial and archaeal amoA and 16S rRNA genes suggested a much higher ammonia oxidizer fraction in the lower aquifer (0.4-7.8%) compared with the upper aquifer (0.01-0.29%). In both aquifers, AOB communities were dominated by one phylotype related to Nitrosomonas ureae, while AOA communities were more diverse. Multivariate analysis of amoA DGGE profiles revealed a stronger temporal variation of AOA and AOB community composition in the upper aquifer, pointing to a stronger influence of surface environments. Parallel fluctuations of AOA, AOB, and total microbial abundance suggested that hydrological factors (heavy rain falls, snow melt) rather than specific physicochemical parameters were responsible for the observed community dynamics.
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Affiliation(s)
- Sebastian Opitz
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
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Hardoim CCP, Costa R. Temporal dynamics of prokaryotic communities in the marine spongeSarcotragus spinosulus. Mol Ecol 2014; 23:3097-112. [DOI: 10.1111/mec.12789] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/30/2014] [Accepted: 05/05/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Cristiane C. P. Hardoim
- Microbial Ecology and Evolution Research Group; Centre of Marine Sciences (CCMar); University of Algarve (UAlg); Gambelas 8005-139 Faro Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group; Centre of Marine Sciences (CCMar); University of Algarve (UAlg); Gambelas 8005-139 Faro Portugal
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Wang C, Zhao Y, Xie B, Peng Q, Hassan M, Wang X. Nitrogen removal pathway of anaerobic ammonium oxidation in on-site aged refuse bioreactor. BIORESOURCE TECHNOLOGY 2014; 159:266-271. [PMID: 24657757 DOI: 10.1016/j.biortech.2014.02.093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/19/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
The nitrogen removal pathways and nitrogen-related functional genes in on-site three-stage aged refuse bioreactor (ARB) treating landfill leachate were investigated. It was found that on average 90.0% of CODCr, 97.6% of BOD5, 99.3% of NH4(+)-N, and 81.0% of TN were removed with initial CODCr, BOD5, NH4(+)-N, and TN concentrations ranging from 2323 to 2754, 277 to 362, 1237 to 1506, and 1251 to 1580 mg/L, respectively. Meanwhile, the functional genes amoA, nirS and anammox 16S rRNA gene were found to coexist in every bioreactor, and their relative proportions in each bioreactor were closely related to the pollutant removal performance of the corresponding bioreactor, which indicated the coexistence of multiple nitrogen removal pathways in the ARB. Detection of anammox expression proved the presence of the anammox nitrogen removal pathway during the process of recirculating mature leachate to the on-site ARB, which provides important information for nitrogen management in landfills.
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Affiliation(s)
- Chao Wang
- Shanghai Key Lab for Urban Ecological Process and Eco-Restoration, Department of Environmental Science & Technology, East China Normal University, Shanghai 200062, China
| | - Youcai Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Engineering and Science, Tongji University, Shanghai 200092, China
| | - Bing Xie
- Shanghai Key Lab for Urban Ecological Process and Eco-Restoration, Department of Environmental Science & Technology, East China Normal University, Shanghai 200062, China.
| | - Qing Peng
- Shanghai Key Lab for Urban Ecological Process and Eco-Restoration, Department of Environmental Science & Technology, East China Normal University, Shanghai 200062, China
| | - Muhammad Hassan
- Shanghai Key Lab for Urban Ecological Process and Eco-Restoration, Department of Environmental Science & Technology, East China Normal University, Shanghai 200062, China
| | - Xiaoyuan Wang
- Shanghai Key Lab for Urban Ecological Process and Eco-Restoration, Department of Environmental Science & Technology, East China Normal University, Shanghai 200062, China
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