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Urakawa H, Andrews GA, Lopez JV, Martens-Habbena W, Klotz MG, Stahl DA. Nitrosomonas supralitoralis sp. nov., an ammonia-oxidizing bacterium from beach sand in a supralittoral zone. Arch Microbiol 2022; 204:560. [PMID: 35978059 DOI: 10.1007/s00203-022-03173-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/24/2022]
Abstract
A betaproteobacterial chemolithotrophic ammonia-oxidizing bacterium designated APG5T was isolated from supralittoral sand of the Edmonds City Beach, WA, USA. Growth was observed at 10-35 °C (optimum, 30 °C), pH 5-9 (optimum, pH 8) and ammonia concentrations as high as 100 mM (optimum, 1-30 mM NH4Cl). The strain grows optimally in a freshwater medium but tolerates up to 400 mM NaCl. It is most closely related to 'Nitrosomonas ureae' (96.7% 16S rRNA and 92.4% amoA sequence identity). The 3.75-Mbp of AGP5T draft genome contained a single rRNA operon and all necessary tRNA genes and has the lowest G+C content (43.5%) when compared to the previously reported genomes of reference strains in cluster 6 Nitrosomonas. Based on an average nucleotide identity of 82% with its closest relative ('N. ureae' Nm10T) and the suggested species boundary of 95-96%, a new species Nitrosomonas supralitoralis sp. nov. is proposed. The type strain of Nitrosomonas supralitoralis is APG5T (= NCIMB 14870T = ATCC TSD-116T).
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Affiliation(s)
- Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA. .,Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
| | - Gabrianna A Andrews
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Institute for Food and Agricultural Sciences, University of Florida, Davie, FL, USA.,Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Martin G Klotz
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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2
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Werba JA, Stucy AL, Peralta AL, McCoy MW. Effects of diversity and coalescence of species assemblages on ecosystem function at the margins of an environmental shift. PeerJ 2020; 8:e8608. [PMID: 32195044 PMCID: PMC7067187 DOI: 10.7717/peerj.8608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/21/2020] [Indexed: 01/20/2023] Open
Abstract
Sea level rise is mixing formerly isolated freshwater communities with saltwater communities. The structure of these new aquatic communities is jointly controlled by pre- and post-colonization processes. Similarly, since salinity is a strong abiotic determinant of post-colonization survival in coastal systems, changes in salinity will likely impact community composition. In this study, we examine how a strong abiotic gradient affects the diversity and structure of bacterial and zooplankton communities and associated ecosystem functions (decomposition and carbon mineralization). We ran a six week dispersal experiment using mesocosm ponds with four distinct salinity profiles (0, 5, 9, and 13 psu). We find that salinity is the primary driver of both bacterial and zooplankton community composition. We find evidence that as bacterial richness increases so does the amount of decomposition. A phenomenological model suggests carbon mineralization may decrease at mid-salinities; this warrants future work into possible mechanisms for this apparent loss of function. Understanding how salinization changes community structure and ecosystem function may be paramount for managing and conserving coastal plain ecosystems where salinity is increasing due to sea level rise, saltwater intrusion, storm surges, and drought.
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Affiliation(s)
- Jo A Werba
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Alexandra L Stucy
- Department of Biology, East Carolina University, Greenville, NC, United States of America
| | - Ariane L Peralta
- Department of Biology, East Carolina University, Greenville, NC, United States of America
| | - Michael W McCoy
- Department of Biology, East Carolina University, Greenville, NC, United States of America
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3
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Molina V, Dorador C, Fernández C, Bristow L, Eissler Y, Hengst M, Hernandez K, Olsen LM, Harrod C, Marchant F, Anguita C, Cornejo M. The activity of nitrifying microorganisms in a high-altitude Andean wetland. FEMS Microbiol Ecol 2018; 94:4969675. [DOI: 10.1093/femsec/fiy062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Avenida Leopoldo Carvallo 270, Playa Ancha, Valparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
| | - Camila Fernández
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
- Interdisciplinary Center for Aquaculture Research (INCAR), COPAS SUR-AUSTRAL Program, Barrio Universitario s/n, Universidad de Concepción, Concepción, Chile
| | - Laura Bristow
- Nordic Center for Earth Evolution (NordCEE), Department of Biology, University of Southern Denmark, Campusvej 55-5230, Odense, Denmark
| | - Yoanna Eissler
- Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso, Chile
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte. Av Angamos 0610 Antofagasta, Chile
| | - Klaudia Hernandez
- Centro de Investigacion Marina Quintay, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Avenida República 440, Santiago, Chile10
| | | | - Chris Harrod
- Fish and Stable Isotope Ecology Laboratory, Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisca Marchant
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
| | - Cristobal Anguita
- Departamento de Ecologia y Biodiversidad, Facultad de Ecologia y Recursos Naturales, Universidad Andres Bello, Av. Republica 440, Santiago, Chile
| | - Marcela Cornejo
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía , Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile, Altamirano 1480, Valparaíso
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4
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Nacke H, Schöning I, Schindler M, Schrumpf M, Daniel R, Nicol GW, Prosser JI. Links between seawater flooding, soil ammonia oxidiser communities and their response to changes in salinity. FEMS Microbiol Ecol 2017; 93:4563574. [DOI: 10.1093/femsec/fix144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 10/23/2017] [Indexed: 11/13/2022] Open
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5
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Zhu S, Shen J, Ruan Y, Guo X, Ye Z, Deng Y, Shi M. The effects of different seeding ratios on nitrification performance and biofilm formation in marine recirculating aquaculture system biofilter. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:14540-14548. [PMID: 27068911 DOI: 10.1007/s11356-016-6609-1] [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: 12/21/2015] [Accepted: 03/31/2016] [Indexed: 06/05/2023]
Abstract
Rapid start-up of biofilter is essential for intensive marine recirculating aquaculture system (RAS) production. This study evaluated the nitrifying biofilm formation using mature biofilm as an inoculum to accelerate the process in RAS practice. The effects of inoculation ratios (0-15 %) on the reactor performance and biofilm structure were investigated. Complete nitrification was achieved rapidly in reactors with inoculated mature biofilm (even in 32 days when 15 % seeding ratio was applied). However, the growth of target biofilm on blank carrier was affected by the mature biofilm inoculated through substrate competition. The analysis of extracellular polymeric substance (EPS) and nitrification rates confirmed the divergence of biofilm cultivation among reactors. Besides, three N-acyl-homoserine lactones (AHLs) were found in the process, which might regulate the activities of biofilm. Multivariate analysis based on non-metric multidimensional scaling (nMDS) also indicated the great roles of AHLs and substrate supply which might fundamentally determine varied cultivation performance on target biofilm.
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Affiliation(s)
- Songming Zhu
- Institute of Agricultural Bio-Environmental Engineering, College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jiazheng Shen
- Institute of Agricultural Bio-Environmental Engineering, College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yunjie Ruan
- Institute of Agricultural Bio-Environmental Engineering, College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
- Department of Biological and Environmental Engineering, Cornell University, Riley Robb Hall, Ithaca, NY, 14853, USA.
| | - Xishan Guo
- Institute of Agricultural Bio-Environmental Engineering, College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zhangying Ye
- Institute of Agricultural Bio-Environmental Engineering, College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yale Deng
- Institute of Agricultural Bio-Environmental Engineering, College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Mingming Shi
- Institute of Agricultural Bio-Environmental Engineering, College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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6
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Li C, Zhang Z, Cao J, Li Y. Study on poultry manure wastewater treatment by two-stage aerobic coupled process and its microbial community analysis. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Hu W, He Y, Chen D, Mo C, Guo Y, Ma D. Diversity of ammonia-oxidizing bacteria in relation to soil environment in Ebinur Lake Wetland. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2015.1124738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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8
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Fujitani H, Kumagai A, Ushiki N, Momiuchi K, Tsuneda S. Selective isolation of ammonia-oxidizing bacteria from autotrophic nitrifying granules by applying cell-sorting and sub-culturing of microcolonies. Front Microbiol 2015; 6:1159. [PMID: 26528282 PMCID: PMC4607866 DOI: 10.3389/fmicb.2015.01159] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/05/2015] [Indexed: 11/13/2022] Open
Abstract
Nitrification is a key process in the biogeochemical nitrogen cycle and biological wastewater treatment that consists of two stepwise reactions, ammonia oxidation by ammonia-oxidizing bacteria (AOB) or archaea followed by nitrite oxidation by nitrite-oxidizing bacteria. One of the representatives of the AOB group is Nitrosomonas mobilis species. Although a few pure strains of this species have been isolated so far, approaches to their preservation in pure culture have not been established. Here, we report isolation of novel members of the N. mobilis species from autotrophic nitrifying granules used for ammonia-rich wastewater treatment. We developed an isolation method focusing on microcolonies formation of nitrifying bacteria. Two kinds of distinctive light scattering signatures in a cell-sorting system enabled to separate microcolonies from single cells and heterogeneous aggregates within granule samples. Inoculation of a pure microcolony into 96-well microtiter plates led to successful sub-culturing and increased probability of isolation. Obtained strain Ms1 is cultivated in the liquid culture with relatively high ammonia or nitrite concentration, not extremely slow growing. Considering environmental clones that were closely related to N. mobilis and detected in various environments, the availability of this novel strain would facilitate to reveal this member’s ecophysiology in a variety of habitats.
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Affiliation(s)
- Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Asami Kumagai
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Kengo Momiuchi
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
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Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:590434. [PMID: 26379473 PMCID: PMC4561949 DOI: 10.1155/2015/590434] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/17/2015] [Indexed: 01/05/2023]
Abstract
Ammonia-oxidizing Archaea (AOA) play an important role in the oxidation of ammonia in terrestrial, marine, and geothermal habitats, as confirmed by a number of studies specifically focused on those environments. Much less is known about the ecological role of AOA in freshwaters. In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis. We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria. Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.
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10
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Guevara R, Ikenaga M, Dean AL, Pisani C, Boyer JN. Changes in sediment bacterial community in response to long-term nutrient enrichment in a subtropical seagrass-dominated estuary. MICROBIAL ECOLOGY 2014; 68:427-40. [PMID: 24760169 DOI: 10.1007/s00248-014-0418-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 04/04/2014] [Indexed: 05/03/2023]
Abstract
Florida Bay exhibits a natural gradient of strong P limitation in the east which shifts to weak P or even N limitation at the western boundary. This nutrient gradient greatly affects seagrass abundance and productivity across the bay. We assessed the effects of N and P additions on sediment bacterial community structure in relation to the existing nutrient gradient in Florida Bay. Sediment samples from 24 permanent 0.25 m(2) plots in each of six sites across Florida Bay were fertilized with granular N and P in a factorial design for 26 months. Sediment bacterial community structure was analyzed using PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal RNA (rRNA) genes and a cloning strategy from DGGE bands. The phylogenetic positions of 16S rRNA sequences mostly fell into common members found in marine sediments such as sulfate-reducing Deltaproteobacteria, Gammaproteobacteria, Spirochaetes, and Bacteriodetes. Twenty-eight common DGGE bands were found in all sediment samples; however, some DGGE bands were only found or were better represented in eastern sites. Bacterial community diversity (Shannon-Weiner index) showed similar values throughout all sediment samples. The N treatment had no effect on the bacterial community structures across the bay. Conversely, the addition of P significantly influenced the bacterial community structure at all but the most western site, where P is least limiting due to inputs from the Gulf of Mexico. P additions enhanced DGGE band sequences related to Cytophagales, Ectothiorhodospiraceae, and Desulfobulbaceae, suggesting a shift toward bacterial communities with increased capability to degrade polymeric organic matter. In addition, a band related to Deferribacteres was enhanced in eastern sites. Thus, indigenous environmental conditions were the primary determining factors controlling the bacterial communities, while the addition of P was a secondary determining factor. This P-induced change in community composition tended to be proportional to the amount of P limitation obviated by the nutrient additions.
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Affiliation(s)
- Rafael Guevara
- Southeast Environmental Research Center, OE-148, Florida International University, Miami, FL, 33199, USA
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11
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Chen Y, Zhen Y, He H, Lu X, Mi T, Yu Z. Diversity, abundance, and spatial distribution of ammonia-oxidizing β-proteobacteria in sediments from Changjiang Estuary and its adjacent area in East China Sea. MICROBIAL ECOLOGY 2014; 67:788-803. [PMID: 24362769 DOI: 10.1007/s00248-013-0341-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/02/2013] [Indexed: 06/03/2023]
Abstract
Changjiang Estuary, the largest estuary in China, encompasses a wide range of nutrient loading and trophic levels from the rivers to the sea, providing an ideal natural environment to explore relationships between functional diversity, physical/chemical complexity, and ecosystem function. In this study, molecular biological techniques were used to analyze the community structure and diversity of ammonia-oxidizing bacteria (AOB) in the sediments of Changjiang Estuary and its adjacent waters in East China Sea. The amoA gene (encoding ammonia monooxygenase subunit A) libraries analysis revealed extensive diversity within the β-Proteobacteria group of AOB, which were grouped into Nitrosospira-like and Nitrosomonas-like lineages. The majority of amoA gene sequences fell within Nitrosospira-like clade, and only a few sequences were clustered with the Nitrosomonas-like clade, indicating that Nitrosospira-like lineage may be more adaptable than Nitrosomonas-like lineage in this area. Multivariate statistical analysis indicated that the spatial distribution of the sedimentary β-Proteobacterial amoA genotype assemblages correlated significantly with nitrate, nitrite, and salinity. The vertical profile of amoA gene copies in gravity cores showed that intense sediment resuspension led to a deeper mixing layer. The horizontal distribution pattern of amoA gene copies was nearly correlated with the clayey mud belt in Changjiang Estuary and its adjacent area in East China Sea, where higher β-Proteobacteria phylogenetic diversity was observed. Meanwhile, those areas with high amoA copies in the surface sediments nearly matched those with low concentrations of dissolved oxygen and ammonium in the bottom water.
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Affiliation(s)
- Yangyang Chen
- College of Environmental Science and Engineering, Ocean University of China, 238 Songling Road, Qingdao, 266100, People's Republic of China
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12
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Qiu G, Ting YP. Osmotic membrane bioreactor for wastewater treatment and the effect of salt accumulation on system performance and microbial community dynamics. BIORESOURCE TECHNOLOGY 2013; 150:287-297. [PMID: 24177162 DOI: 10.1016/j.biortech.2013.09.090] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/18/2013] [Accepted: 09/21/2013] [Indexed: 06/02/2023]
Abstract
An osmotic membrane bioreactor was developed for wastewater treatment. The effects of salt accumulation on system performance and microbial community dynamics were investigated. Evident deterioration of biological activity, especially nitrification, was observed, which resulted in significant accumulation of organic matter and NH4(+)-N within the bioreactor. Arising from the elevation of salinity, almost all the dominant species was taken over by high salt-tolerant species. Significant succession among different species of Nitromonas was observed for ammonia-oxidizing bacteria. For nitrite-oxidizing bacteria, Nitrospira was not evidently affected, whereas Nitrobacter was eliminated from the system. Salt accumulation also caused significant shifts in denitrifying bacterial community from α- to γ-Proteobacteria members. Overall, the microbial community adapted to the elevated salinity conditions and brought about a rapid recovery of the biological activity. Membrane fouling occurred but was insignificant. Biofouling and inorganic scaling coexisted, with magnesium/calcium phosphate/carbonate compounds identified as the inorganic foulants.
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Affiliation(s)
- Guanglei Qiu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore
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13
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Laanbroek HJ, Keijzer RM, Verhoeven JTA, Whigham DF. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans) in response to ammonia enrichment and more oxic conditions. Front Microbiol 2013; 4:343. [PMID: 24312088 PMCID: PMC3834342 DOI: 10.3389/fmicb.2013.00343] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/30/2013] [Indexed: 11/13/2022] Open
Abstract
In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e., Cluster 1) and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA). Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests.
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Affiliation(s)
- Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University Utrecht, Netherlands ; Smithsonian Environmental Research Center Edgewater, MD, USA
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Wu YJ, Whang LM, Fukushima T, Chang SH. Responses of ammonia-oxidizing archaeal and betaproteobacterial populations to wastewater salinity in a full-scale municipal wastewater treatment plant. J Biosci Bioeng 2013; 115:424-32. [DOI: 10.1016/j.jbiosc.2012.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 11/06/2012] [Accepted: 11/06/2012] [Indexed: 11/17/2022]
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Sims A, Zhang Y, Gajaraj S, Brown PB, Hu Z. Toward the development of microbial indicators for wetland assessment. WATER RESEARCH 2013; 47:1711-1725. [PMID: 23384515 DOI: 10.1016/j.watres.2013.01.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 06/01/2023]
Abstract
Wetland assessment tools are being developed and employed in wetland monitoring and conservation based on physical, chemical and biological characterization. In wetland biological assessment, various ecological functions have been described by biological traits of an entire species pool that adapts to different types of wetland environments. Since microorganisms play a key role in wetland biogeochemical processes and respond quickly to environmental disturbances, this review paper describes the different macro indicators used in wetland biological monitoring and expands the potential use of microbial indicators in wetland assessment and management. Application of molecular microbial technologies paves the path to an integrated measure of wetland health conditions. For example, the ratio of ammonia-oxidizing archaeal and bacterial populations has been proposed to serve as a microbial indicator of wetland nutrient conditions. The microbial indicators coupled with physical, chemical and other biological parameters are vital to the development of multi-metric index for measuring wetland health conditions. Inclusion of microbial indicators will lead to a more comprehensive wetland assessment for wetland restoration and management practices.
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Affiliation(s)
- Atreyee Sims
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO 65211, USA
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Sims A, Horton J, Gajaraj S, McIntosh S, Miles RJ, Mueller R, Reed R, Hu Z. Temporal and spatial distributions of ammonia-oxidizing archaea and bacteria and their ratio as an indicator of oligotrophic conditions in natural wetlands. WATER RESEARCH 2012; 46:4121-4129. [PMID: 22673339 DOI: 10.1016/j.watres.2012.05.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 03/18/2012] [Accepted: 05/04/2012] [Indexed: 06/01/2023]
Abstract
Ammonia-oxidizing organisms play an important role in wetland water purification and nitrogen cycling. We determined soil nitrification rates and investigated the seasonal and spatial distributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in three freshwater wetlands by using specific primers targeting the amoA genes of AOA and AOB and real-time quantitative polymerase chain reaction (qPCR). The nitrifying potentials of wetland soils ranged from 1.4 to 4.0 μg g(-1) day(-1). The specific rates of ammonia oxidation activity by AOA and AOB at the Bee Hollow wetlands were 1.9 fmol NH(3) cell(-1) day(-1) and 36.8 fmol NH(3) cell(-1) day(-1), respectively. Soil nitrification potential was positively correlated with both archaeal and bacterial amoA abundance. However, the gene copies of AOA amoA were higher than those of AOB amoA by at least an order of magnitude in wetland soils and water in both summer and winter over a three year study period. AOB were more sensitive to low temperature than AOA. The amoA gene copy ratios of AOA to AOB in top soils (0-10 cm) ranged from 19 ± 4 to 100 ± 11 among the wetland sites. In contrast, the ratio of the wetland boundary soil was 10 ± 2, which was significantly lower than that of the wetland soils (P < 0.001). The NH(4)(+)-N concentrations in wetland water were lower than 2 mg/L throughout the study. The results suggest that ammonium concentration is a major factor influencing AOA and AOB population in wetlands, although other factors such as temperature, dissolved oxygen, and soil organic matter are involved. AOA are more persistent and more abundant than AOB in the nutrient-depleted oligotrophic wetlands. Therefore, ratio of AOA amoA gene copies to AOB amoA gene copies may serve as a new biological indicator for wetland condition assessment and wetland restoration applications.
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Affiliation(s)
- Atreyee Sims
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO 65211, USA
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Wang J, Krause S, Muyzer G, Meima-Franke M, Laanbroek HJ, Bodelier PLE. Spatial patterns of iron- and methane-oxidizing bacterial communities in an irregularly flooded, riparian wetland. Front Microbiol 2012; 3:64. [PMID: 22375139 PMCID: PMC3284728 DOI: 10.3389/fmicb.2012.00064] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 02/06/2012] [Indexed: 11/13/2022] Open
Abstract
Iron- and methane-cycling are important processes in wetlands with one connected to plant growth and the other to greenhouse gas emission, respectively. In contrast to acidic habitats, there is scarce information on the ecology of microbes oxidizing ferrous iron at circumneutral pH. The latter is mainly due to the lack of isolated representatives and molecular detection techniques. Recently, we developed PCR-DGGE and qPCR assays to detect and enumerate Gallionella-related neutrophilic iron-oxidizers (Ga-FeOB) enabling the assessment of controlling physical as well as biological factors in various ecosystems. In this study, we investigated the spatial distribution of Ga-FeOB in co-occurrence with methane-oxidizing bacteria (MOB) in a riparian wetland. Soil samples were collected at different spatial scales (ranging from meters to centimeters) representing a hydrological gradient. The diversity of Ga-FeOB was assessed using PCR-DGGE and the abundance of both Ga-FeOB and MOB by qPCR. Geostatistical methods were applied to visualize the spatial distribution of both groups. Spatial distribution as well as abundance of Ga-FeOB and MOB was clearly correlated to the hydrological gradient as expressed in moisture content of the soil. Ga-FeOB outnumbered the MOB subgroups suggesting their competitiveness or the prevalence of Fe(2+) over CH(4) oxidation in this floodplain.
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Affiliation(s)
- Juanjuan Wang
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Gerard Muyzer
- Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, AmsterdamNetherlands
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Hendrikus J. Laanbroek
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
- Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
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Community shift of ammonia-oxidizing bacteria along an anthropogenic pollution gradient from the Pearl River Delta to the South China Sea. Appl Microbiol Biotechnol 2011; 94:247-59. [PMID: 22005744 PMCID: PMC3304064 DOI: 10.1007/s00253-011-3636-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/22/2011] [Accepted: 10/06/2011] [Indexed: 11/20/2022]
Abstract
The phylogenetic diversity and abundance of ammonia-oxidizing beta-proteobacteria (beta-AOB) was analyzed along an anthropogenic pollution gradient from the coastal Pearl River Delta to the South China Sea using the ammonia monooxygenase subunit A (amoA) gene. Along the gradient from coastal to the open ocean, the phylogenetic diversity of the dominant genus changed from Nitrosomonas to Nitrosospira, indicating the niche specificity by these two genera as both salinity and anthropogenic influence were major factors involved. The diversity of bacterial amoA gene was also variable along the gradient, with the highest in the deep-sea sediments, followed by the marshes sediments and the lowest in the coastal areas. Within the Nitrosomonas-related clade, four distinct lineages were identified including a putative new one (A5-16) from the different sites over the large geographical area. In the Nitrosospira-related clade, the habitat-specific lineages to the deep-sea and coastal sediments were identified. This study also provides strong support that Nitrosomonas genus, especially Nitrosomonas oligotropha lineage (6a) could be a potential bio-indicator species for pollution or freshwater/wastewater input into coastal environments. A suite of statistical analyses used showed that water depth and temperature were major factors shaping the community structure of beta-AOB in this study area.
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Jaroch D, McLamore E, Zhang W, Shi J, Garland J, Banks MK, Porterfield DM, Rickus JL. Cell-mediated deposition of porous silica on bacterial biofilms. Biotechnol Bioeng 2011; 108:2249-60. [DOI: 10.1002/bit.23195] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/11/2011] [Accepted: 04/22/2011] [Indexed: 11/07/2022]
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Sudarno U, Winter J, Gallert C. Effect of varying salinity, temperature, ammonia and nitrous acid concentrations on nitrification of saline wastewater in fixed-bed reactors. BIORESOURCE TECHNOLOGY 2011; 102:5665-5673. [PMID: 21414774 DOI: 10.1016/j.biortech.2011.02.078] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 02/17/2011] [Accepted: 02/18/2011] [Indexed: 05/30/2023]
Abstract
Nitrification under changing salinities (0-9%), temperatures (6-50°C), ammonia (0-5 g NL(-1)) and nitrite concentrations (0-0.4 g NL(-1)) was investigated in fixed-bed reactors. For all conditions ammonia oxidation rates (AOR) were lower than nitrite oxidation rates (NOR). AORs and NORs increased from 12.5 to 40°C and were very low at 6°C and almost zero at 50°C. No recovery of nitrification was obtained after incubation at 50°C, whereas nitrification was restorable after incubation at 6°C. Ammonia concentrations of 5 g NL(-1) or nitrite concentrations up to 0.125 g NL(-1) decreased AOR to almost zero. AORs and NORs recovered if ammonia or nitrite was removed. At concentrations of 1 and 5 g NL(-1) ammonia AOR and NOR were inhibited by 50%, whereas 27 mg N/L nitrite inhibited AOR by 50%.
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Affiliation(s)
- U Sudarno
- Institute of Biology for Engineers and Biotechnology of Wastewater Treatment KIT, Karlsruhe Institute of Technology Germany, 76131 Karlsruhe Am Fasanengarten, Germany
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21
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Distribution and diversity of Gallionella-like neutrophilic iron oxidizers in a tidal freshwater marsh. Appl Environ Microbiol 2011; 77:2337-44. [PMID: 21317256 DOI: 10.1128/aem.02448-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting Gallionella-related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay. Gallionella-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of Gallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.
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Diversity, abundance, and spatial distribution of sediment ammonia-oxidizing Betaproteobacteria in response to environmental gradients and coastal eutrophication in Jiaozhou Bay, China. Appl Environ Microbiol 2010; 76:4691-702. [PMID: 20511433 DOI: 10.1128/aem.02563-09] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ongoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, the amoA gene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizing Betaproteobacteria (Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced from amoA gene sequences grouped within four distinct clusters in the Nitrosomonas lineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in the Nitrosospira lineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. Both amoA clone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in the Nitrosomonas oligotropha lineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments.
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Quantitative assessment of ammonia-oxidizing bacterial communities in the epiphyton of submerged macrophytes in shallow lakes. Appl Environ Microbiol 2010; 76:1813-21. [PMID: 20097811 DOI: 10.1128/aem.01917-09] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In addition to the benthic and pelagic habitats, the epiphytic compartment of submerged macrophytes in shallow freshwater lakes offers a niche to bacterial ammonia-oxidizing communities. However, the diversity, numbers, and activity of epiphytic ammonia-oxidizing bacteria have long been overlooked. In the present study, we analyzed quantitatively the epiphytic communities of three shallow lakes by a potential nitrification assay and by quantitative PCR of 16S rRNA genes. On the basis of the m(2) of the lake surface, the gene copy numbers of epiphytic ammonia oxidizers were not significantly different from those in the benthic and pelagic compartments. The potential ammonia-oxidizing activities measured in the epiphytic compartment were also not significantly different from the activities determined in the benthic compartment. No potential ammonia-oxidizing activities were observed in the pelagic compartment. No activity was detected in the epiphyton of Chara aspera, the dominant submerged macrophyte in Lake Nuldernauw in The Netherlands. The presence of ammonia-oxidizing bacterial cells in the epiphyton of Potamogeton pectinatus was also demonstrated by fluorescent in situ hybridization microscopy images. By comparing the community composition as assessed by the 16S rRNA gene PCR-denaturing gradient gel electrophoresis approach, it was concluded that the epiphytic ammonia-oxidizing communities consisted of cells that were also present in the benthic and pelagic compartments. Of the environmental parameters examined, only the water retention time, the Kjeldahl nitrogen content, and the total phosphorus content correlated with potential ammonia-oxidizing activities. None of these parameters correlated with the numbers of gene copies related to ammonia-oxidizing betaproteobacteria.
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Logares R, Bråte J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K. Infrequent marine–freshwater transitions in the microbial world. Trends Microbiol 2009; 17:414-22. [DOI: 10.1016/j.tim.2009.05.010] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 04/28/2009] [Accepted: 05/13/2009] [Indexed: 12/21/2022]
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Kim OS, Junier P, Imhoff JF, Witzel KP. Comparative analysis of ammonia monooxygenase (amoA) genes in the water column and sediment-water interface of two lakes and the Baltic Sea. FEMS Microbiol Ecol 2008; 66:367-78. [PMID: 18721144 DOI: 10.1111/j.1574-6941.2008.00565.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The functional gene amoA was used to compare the diversity of ammonia-oxidizing bacteria (AOB) in the water column and sediment-water interface of the two freshwater lakes Plusssee and Schöhsee and the Baltic Sea. Nested amplifications were used to increase the sensitivity of amoA detection, and to amplify a 789-bp fragment from which clone libraries were prepared. The larger part of the sequences was only distantly related to any of the cultured AOB and is considered to represent new clusters of AOB within the Nitrosomonas/Nitrosospira group. Almost all sequences from the water column of the Baltic Sea and from 1-m depth of Schöhsee were related to different Nitrosospira clusters 0 and 2, respectively. The majority of sequences from Plusssee and Schöhsee were associated with sequences from Chesapeake Bay, from a previous study of Plusssee and from rice roots in Nitrosospira-like cluster A, which lacks sequences from Baltic Sea. Two groups of sequences from Baltic Sea sediment were related to clonal sequences from other brackish/marine habitats in the purely environmental Nitrosospira-like cluster B and the Nitrosomonas-like cluster. This confirms previous results from 16S rRNA gene libraries that indicated the existence of hitherto uncultivated AOB in lake and Baltic Sea samples, and showed a differential distribution of AOB along the water column and sediment of these environments.
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Affiliation(s)
- Ok-Sun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Shillim-dong, Kwanak-gu, Seoul, Korea.
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26
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Izumi H, Anderson IC, Killham K, Moore ERB. Diversity of predominant endophytic bacteria in European deciduous and coniferous trees. Can J Microbiol 2008; 54:173-9. [PMID: 18388988 DOI: 10.1139/w07-134] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The diversity of endophytic bacteria residing in root, stem, and leaf tissues was examined in coniferous and deciduous tree species, Scots pine (Pinus sylvestris L.), silver birch (Betula pendula Roth), and rowan (Sorbus aucuparia L.). Using cultivation-dependent and -independent analyses, the bacterial communities were observed to be significantly different in the belowground (roots and rhizosphere) and aboveground (leaves and stems) samples of the respective host trees. No significant differences, with respect to the different tree species, were observed in the associated communities. Predominant cultivable endophytes isolated included bacteria closely related to Bacillus subtilis, Bacillus licheniformis, Paenibacillus spp., and Acinetobacter calcoaceticus. Comparisons of the most abundant cultivable bacteria in the rhizosphere and root samples suggested that root endophytic bacteria may be in residence through processes of selection or active colonization rather than by passive diffusion from the rhizosphere.
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Affiliation(s)
- Hironari Izumi
- The Macaulay Institute, Craigiebuckler, Aberdeen AB15 8QH, Scotland, UK.
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27
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Laanbroek HJ, Speksnijder AGCL. Niche separation of ammonia-oxidizing bacteria across a tidal freshwater marsh. Environ Microbiol 2008; 10:3017-25. [PMID: 18479444 DOI: 10.1111/j.1462-2920.2008.01655.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Like many functional groups or guilds of microorganisms, the group of ammonia-oxidizing bacteria (AOB) consists of a number of physiologically different species or lineages. These physiological differences suggest niche differentiation among these bacteria depending on the environmental conditions. Species of AOB might be adapted to different zones in the flooding gradient of a tidal marsh. This issue has been studied by sampling sediments from different sites and depths within a tidal freshwater marsh along the river Scheldt near the village of Appels in Belgium. Samples were taken in February, April, July and October 1998. Communities of AOB in the sediment were analysed on the basis of the 16S rRNA gene by application of polymerase chain reaction in combination with denaturing gradient gel electrophoresis (DGGE). In addition, moisture content and concentrations of ammonium and nitrate were determined as well as the potential ammonia-oxidizing activities. Six different DGGE bands belonging to the beta-subclass of the Proteobacteria were observed across the marsh. The community composition of AOB was determined by the elevation in the flooding gradient as well as by the sampling depth. The presence of plants was less important for the community composition of AOB. DGGE bands affiliated with the Nitrosospira lineage were mostly found in the upper part of the marsh and in the deeper layers of the sediment. Two of the three DGGE bands related to the Nitrosomonas oligotropha lineage were more broadly distributed over the marsh, but were predominantly found in the upper layers of the sediment. Members of the environmental Nitrosomonas lineage 5 were predominantly detected in the deeper layers in the lower parts of the marsh. Potential driving factors for niche differentiation are discussed.
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Affiliation(s)
- Hendrikus J Laanbroek
- Department of Microbial Wetland Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Nieuwersluis, the Netherlands.
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Zhang XW, Qin YY, Ren HQ, Li DT, Yang H. Seasonal variation in communities of ammonia-oxidizing bacteria based on polymerase chain reaction – denaturing gradient gel electrophoresis in a biofilm reactor for drinking water pretreatment. Can J Microbiol 2008; 54:358-65. [DOI: 10.1139/w08-011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The diversity and variation of total and active ammonia-oxidizing bacteria in a full-scale aerated submerged biofilm reactor for drinking water pretreatment were characterized by clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA and its gene during a whole year. Sequences obtained from clone libraries affiliated with the Nitrosomonas oligotropha lineage and the Nitrosomonas communis lineage. An uncultured subgroup of Nitrosomonas communis lineage was also detected. Seasonal variations in both total and active ammonia-oxidizing bacteria communities were observed in the DGGE profiles, but an RNA-based analysis reflected more obvious dynamic changes in ammonia-oxidizer community than a DNA-based approach. Statistical study based on canonical correspondence analysis showed that a community shift of active ammonia oxidizers was significantly influenced by temperature and pH, but no significant correlation was found between environmental variables and total ammonia-oxidizer community shift.
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Affiliation(s)
- Xiao-Wen Zhang
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
| | - Ying-Ying Qin
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
| | - Hong-Qiang Ren
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
| | - Dao-Tang Li
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
| | - Hong Yang
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
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Sahan E, Muyzer G. Diversity and spatio-temporal distribution of ammonia-oxidizing Archaea and Bacteria in sediments of the Westerschelde estuary. FEMS Microbiol Ecol 2008; 64:175-86. [PMID: 18336555 DOI: 10.1111/j.1574-6941.2008.00462.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The diversity and spatio-temporal distribution of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) were investigated along a salinity gradient in sediments of the Westerschelde estuary. Sediment samples were collected from three sites with different salinities, and at six time points over the year. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA and amoA gene fragments was used to identify the AOA and AOB present. Members of the AOA were mainly belonging to the Crenarchaeota Group 1, which were found at all sites, while members of the genus Nitrosomonas, which were abundant at the brackish sites, and of the genus Nitrosospira, which were present in early spring at the marine sites, were found to be the dominant AOB. Statistical analysis indicated that salinity and temperature were the main factors controlling the diversity and distribution of both AOA and AOB. Variability in net primary production rates was also correlated with species composition of both groups, but changes in the nitrite concentration only to the distribution of the AOA.
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Affiliation(s)
- Emel Sahan
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Epiphyton as a niche for ammonia-oxidizing bacteria: detailed comparison with benthic and pelagic compartments in shallow freshwater lakes. Appl Environ Microbiol 2008; 74:1963-71. [PMID: 18263748 DOI: 10.1128/aem.00694-07] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated.
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Miletto M, Bodelier PLE, Laanbroek HJ. Improved PCR-DGGE for high resolution diversity screening of complex sulfate-reducing prokaryotic communities in soils and sediments. J Microbiol Methods 2007; 70:103-11. [PMID: 17481757 DOI: 10.1016/j.mimet.2007.03.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2006] [Revised: 03/22/2007] [Accepted: 03/28/2007] [Indexed: 11/20/2022]
Abstract
In this study we evaluated a high resolution PCR-DGGE strategy for the characterization of complex sulfate-reducing microbial communities inhabiting natural environments. dsrB fragments were amplified with a two-step nested PCR protocol using combinations of primers targeting the dissimilatory (bi)sulfite reductase genes. The PCR-DGGE conditions were initially optimized using a dsrAB clone library obtained from a vegetated intertidal riparian soil along the river Rhine (Rozenburg, the Netherlands). Partial dsrB were successfully amplified from the same environmental DNA extracts used to construct the library, DGGE-separated and directly sequenced. The two approaches were in good agreement: the phylogenetic distribution of clones and DGGE-separated dsrB was comparable, suggesting the presence of sulfate-reducing prokaryotes (SRP) belonging to the families 'Desulfobacteraceae,' 'Desulfobulbaceae' and 'Syntrophobacteraceae,' and to the Desulfomonile tiedjei- and Desulfobacterium anilini-groups. The nested PCR-DGGE was also used to analyze sediment samples (Appels, Belgium) from a series of microcosms subjected to a tidal flooding regime with water of different salinity, and proved to be a valid tool also to monitor the SRP community variation over time and space as a consequence of environmental changes.
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Affiliation(s)
- Marzia Miletto
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Wetland Ecology, Rijksstraatweg 6, 3631 AC Nieuwersluis, The Netherlands.
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32
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Gorra R, Coci M, Ambrosoli R, Laanbroek H. Effects of substratum on the diversity and stability of ammonia-oxidizing communities in a constructed wetland used for wastewater treatment. J Appl Microbiol 2007; 103:1442-52. [DOI: 10.1111/j.1365-2672.2007.03357.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Satoh H, Nakamura Y, Okabe S. Influences of infaunal burrows on the community structure and activity of ammonia-oxidizing bacteria in intertidal sediments. Appl Environ Microbiol 2006; 73:1341-8. [PMID: 17189445 PMCID: PMC1828680 DOI: 10.1128/aem.02073-06] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influences of infaunal burrows constructed by the polychaete (Tylorrhynchus heterochaetus) on O(2) concentrations and community structures and abundances of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in intertidal sediments were analyzed by the combined use of a 16S rRNA gene-based molecular approach and microelectrodes. The microelectrode measurements performed in an experimental system developed in an aquarium showed direct evidence of O(2) transport down to a depth of 350 mm of the sediment through a burrow. The 16S rRNA gene-cloning analysis revealed that the betaproteobacterial AOB communities in the sediment surface and the burrow walls were dominated by Nitrosomonas sp. strain Nm143-like sequences, and most of the clones in Nitrospira-like NOB clone libraries of the sediment surface and the burrow walls were related to the Nitrospira marina lineage. Furthermore, we investigated vertical distributions of AOB and NOB in the infaunal burrow walls and the bulk sediments by real-time quantitative PCR (Q-PCR) assay. The AOB and Nitrospira-like NOB-specific 16S rRNA gene copy numbers in the burrow walls were comparable with those in the sediment surfaces. These numbers in the burrow wall at a depth of 50 to 55 mm from the surface were, however, higher than those in the bulk sediment at the same depth. The microelectrode measurements showed higher NH(4)(+) consumption activity at the burrow wall than those at the surrounding sediment. This result was consistent with the results of microcosm experiments showing that the consumption rates of NH(4)(+) and total inorganic nitrogen increased with increasing infaunal density in the sediment. These results clearly demonstrated that the infaunal burrows stimulated O(2) transport into the sediment in which otherwise reducing conditions prevailed, resulting in development of high NH(4)(+) consumption capacity. Consequently, the infaunal burrow became an important site for NH(4)(+) consumption in the intertidal sediment.
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Affiliation(s)
- Hisashi Satoh
- Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University, North-13, West-8, Sapporo 060-8628, Japan
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Revsbech NP, Risgaard-Petersen N, Schramm A, Nielsen LP. Nitrogen transformations in stratified aquatic microbial ecosystems. Antonie van Leeuwenhoek 2006; 90:361-75. [PMID: 17033881 DOI: 10.1007/s10482-006-9087-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Accepted: 05/11/2006] [Indexed: 10/24/2022]
Abstract
New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a microm-mm scale. A large and ever-expanding knowledge base about nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.
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Affiliation(s)
- Niels Peter Revsbech
- Institute of Biological Sciences, Microbiology, University of Aarhus, bd. 540, DK-8000, Aarhus C, Denmark.
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