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Hao L, Okano K, Zhang C, Zhang Z, Lei Z, Feng C, Utsumi M, Ihara I, Maseda H, Shimizu K. Effects of levofloxacin exposure on sequencing batch reactor (SBR) behavior and microbial community changes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:227-238. [PMID: 30959290 DOI: 10.1016/j.scitotenv.2019.03.272] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/13/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
The adaptation mechanisms of bacterial community for nitrogen removal performance exposed to fluctuated levels of levofloxacin (LVX) during wastewater treatment in SBRs were investigated. Although LVX is completely synthetic, the results of minimum inhibitory concentration (MIC, 32 mg-LVX/L) and minimum bactericidal concentration (MBC, 512 mg-LVX/L) of the sampled sludge showed that the LVX resistance/tolerance for bacterial growth has already existed in the actual wastewater treatment plants (WWTPs). The key bacteria, i.e. Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrospira sp. (nitrite-oxidizing bacteria) and Thauera sp. (the predominant denitrifiers), decreased with LVX exposure, and the recovery of biological process in the reactor was disturbed due to LVX exposure. However, after stopping exposure their population was quickly increased and thus the performance was recovered. The results of the non-metric multidimensional scaling and microbial community by sequencing showed the LVX concentration was a crucial factor to the change of bacterial communities and controlled the quantitative evolution of the communities in our systems. This effect was more pronounced as the LVX concentration was higher. The results suggested the removal of residual antibiotics to accomplish under no effect concentration before biological treatment is important to suppress emerging and increasing of the antibiotic resistant bacteria in WWTPs.
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Affiliation(s)
- Liting Hao
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Kunihiro Okano
- Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano Shimoshinjo, Akita City, Akita 010-0195, Japan
| | - Chi Zhang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhenya Zhang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhongfang Lei
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Chuanping Feng
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China
| | - Motoo Utsumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Ikko Ihara
- Faculty of Agriculture, Kobe University, 1-1 Rokkodai-cho, Nadaku, Kobe 657-8501, Japan
| | - Hideaki Maseda
- National Institute of Advanced Industrial Science and Technology, 1-8-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Kazuya Shimizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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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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Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns. Appl Microbiol Biotechnol 2015; 100:1843-1852. [DOI: 10.1007/s00253-015-7095-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/04/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
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Wang YF, Li XY, Gu JD. Differential responses of ammonia/ammonium-oxidizing microorganisms in mangrove sediment to amendment of acetate and leaf litter. Appl Microbiol Biotechnol 2013; 98:3165-80. [PMID: 24169949 DOI: 10.1007/s00253-013-5318-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/03/2013] [Indexed: 02/07/2023]
Abstract
The effects of acetate and leaf litter powder on ammonia/ammonium-oxidizing microorganisms (AOMs) in mangrove sediment were investigated in a laboratory incubation study for a period of 60 days. The results showed that different AOMs responded differently to the addition of acetate and leaf litter. A higher diversity of anaerobic ammonium-oxidizing (anammox) bacteria was observed when acetate or leaf litter was added than the control. However, acetate and leaf litter generally inhibited the growth of anammox bacteria despite that leaf litter promoted their growth in the first 5 days. The inhibitory effects on anammox bacteria were more pronounced by acetate than by leaf litter. Neither acetate nor leaf litter affected ammonia-oxidizing archaea (AOA) community structures, but promoted their growth. For ammonia-oxidizing bacteria (AOB), the addition of acetate or leaf litter resulted in changes of community structures and promoted their growth in the early phase of the incubation. In addition, the promoting effects by leaf litter on AOB growth were more obvious than acetate. These results indicated that organic substances affect AOM community structures and abundances. The study suggests that leaf litter has an important influence on the community structures and abundances of AOMs in mangrove sediment and affects the nitrogen cycle in such ecosystem.
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Affiliation(s)
- Yong-Feng Wang
- Laboratory of Microbial Ecology, Guangdong Academy of Forestry, No. 233, Guangshan 1st Road, Guangzhou, People's Republic of China
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Krieger JR, Kourtev PS. Detection of methanogenic archaea in the pitchers of the Northern pitcher plant (Sarracenia purpurea). Can J Microbiol 2012; 58:189-94. [DOI: 10.1139/w11-117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Joseph R. Krieger
- Department of Biology, Central Michigan University, Mt. Pleasant, MI 48858, USA
| | - Peter S. Kourtev
- Department of Biology, Central Michigan University, Mt. Pleasant, MI 48858, USA
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Qiu S, Chen G, Zhou Y. Abundance and diversity of ammonia-oxidizing bacteria in relation to ammonium in a chinese shallow eutrophic urban lake. Braz J Microbiol 2010; 41:218-26. [PMID: 24031484 PMCID: PMC3768599 DOI: 10.1590/s1517-838220100001000031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 05/01/2009] [Accepted: 07/24/2009] [Indexed: 11/21/2022] Open
Abstract
The measures of most-probable-number and restriction fragment length polymorphism analysis were used to analyze the abundance and diversity of ammonia-oxidizing bacteria in sediment of a Chinese shallow eutrophic urban lake (Lake Yuehu). Among the 5 sampling sites, ammonia concentration in interstitial water was positively proportional not only to the content of organic matter, but also to ammonia-oxidizing bacteria numbers (at a magnitude of 105 cells g-1 dry weight) in sediment significantly. Furthermore, the diversity of ammonia-oxidizing bacteria were determined by means of PCR primers targeting the amoA gene with five gene libraries created and restriction pattern analysis. The 13 restriction patterns were recorded with 4 ones being common among all sampling sites. The 8 restriction patterns including 4 unique ones were found at the site with the highest NH4+ concentrations in interstitial water, while, there were only common patterns without unique ones at the site with the lowest NH4+ concentrations in interstitial water. Phylogenetic analysis showed that the amoA fragments retrieved belong to Nitrosomonas oligotropha & ureae lineage, N. europaea lineage, N. communis lineage and Nitrosospira lineage, most of which were affiliated with the genus Nitrosomonas. The N. oligotropha & ureae-like bacteria were the dominant species. Thus, the abundance and diversity of sediment AOB is closely linked to ammonium status in eutrophic lakes.
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Affiliation(s)
- Shanlian Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences , 7 Donghu Nan Road, Wuhan, Hubei 430072 , China ; Graduate School of the Chinese Academy of Sciences , 19 Yuquan Road, Beijing 100049 , China
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Whang LM, Chien IC, Yuan SL, Wu YJ. Nitrifying community structures and nitrification performance of full-scale municipal and swine wastewater treatment plants. CHEMOSPHERE 2009; 75:234-242. [PMID: 19246073 DOI: 10.1016/j.chemosphere.2008.11.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 11/21/2008] [Accepted: 11/24/2008] [Indexed: 05/27/2023]
Abstract
This study evaluated nitrification performance and microbial ecology of nitrifying sludge in two full-scale wastewater treatment plants (WWTPs) including a municipal WWTP treating 20mgNL(-1) of ammonium and a swine WWTP treating 220mgNL(-1) of ammonium. These two plants differed in both wastewater characteristics and operating parameters, such as influent COD, TKN, ammonium, hydraulic retention time, and solids retention time, even though both plants achieve >85% nitrification efficiency. By employing molecular techniques, including terminal restriction fragment length polymorphism, cloning-sequencing and phylogenetic analyses targeting the 16S ribosomal RNA and group specific ammonia-monooxygenase functional gene (amoA), microbial community structures of nitrifying sludge and their significance to nitrification performance were evaluated. The results reveal that for the municipal WWTP Nitrosomonas marina-like AOB (ammonia-oxidizing bacteria) and Nitrospira-like NOB (nitrite-oxidizing bacteria) were the ubiquitously dominant nitrifiers, while Nitrosomonas europaea-, Nitrosomonas oligotropha-, and Nitrosospira-like AOB and Nitrobacter- and Nitrospira-like NOB were the major nitrifying populations found in the swine WWTP. The observed dissimilar nitrifying populations prevailing in these two plants may be related to niche differentiation concerning ammonium concentrations, system operation, and salinity. Moreover, our results suggest that the swine nitrifying sludge, involving relatively diverse AOB and NOB populations that perform the same task but with distinct growth and survival characters, may allow communities to maintain nitrifying capabilities when conditions change such as sudden increases in ammonium concentrations as examined with nitrification kinetic batch tests.
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Affiliation(s)
- Liang-Ming Whang
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan, ROC.
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Miller DN, Smith RL. Microbial characterization of nitrification in a shallow, nitrogen-contaminated aquifer, Cape Cod, Massachusetts and detection of a novel cluster associated with nitrifying Betaproteobacteria. JOURNAL OF CONTAMINANT HYDROLOGY 2009; 103:182-193. [PMID: 19059672 DOI: 10.1016/j.jconhyd.2008.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Revised: 09/26/2008] [Accepted: 10/25/2008] [Indexed: 05/27/2023]
Abstract
Groundwater nitrification is a poorly characterized process affecting the speciation and transport of nitrogen. Cores from two sites in a plume of contamination were examined using culture-based and molecular techniques targeting nitrification processes. The first site, located beneath a sewage effluent infiltration bed, received treated effluent containing O2 (>300 microM) and NH4+ (51-800 microM). The second site was 2.5 km down-gradient near the leading edge of the ammonium zone within the contaminant plume and featured vertical gradients of O2, NH4+, and NO3- (0-300, 0-500, and 100-200 microM with depth, respectively). Ammonia- and nitrite-oxidizers enumerated by the culture-based MPN method were low in abundance at both sites (1.8 to 350 g(-1) and 33 to 35,000 g(-1), respectively). Potential nitrifying activity measured in core material in the laboratory was also very low, requiring several weeks for products to accumulate. Molecular analysis of aquifer DNA (nested PCR followed by cloning and 16S rDNA sequencing) detected primarily sequences associated with the Nitrosospira genus throughout the cores at the down-gradient site and a smaller proportion from the Nitrosomonas genus in the deeper anoxic, NH4+ zone at the down-gradient site. Only a single Nitrosospira sequence was detected beneath the infiltration bed. Furthermore, the majority of Nitrosospira-associated sequences represent an unrecognized cluster. We conclude that an uncharacterized group associated with Nitrosospira dominate at the geochemically stable, down-gradient site, but found little evidence for Betaproteobacteria nitrifiers beneath the infiltration beds where geochemical conditions were more variable.
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Affiliation(s)
- Daniel N Miller
- U.S. Geological Survey, 3215 Marine Street, Boulder, Colorado 80303, United States.
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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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Schmidt CS, Hultman KA, Robinson D, Killham K, Prosser JI. PCR profiling of ammonia-oxidizer communities in acidic soils subjected to nitrogen and sulphur deposition. FEMS Microbiol Ecol 2007; 61:305-16. [PMID: 17573939 DOI: 10.1111/j.1574-6941.2007.00335.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Communities of ammonia-oxidizing bacteria (AOB) were characterized in two acidic soil sites experimentally subjected to varying levels of nitrogen and sulphur deposition. The sites were an acidic spruce forest soil in Deepsyke, Southern Scotland, with low background deposition, and a nitrogen-saturated upland grass heath in Pwllpeiran, North Wales. Betaproteobacterial ammonia-oxidizer 16S rRNA and ammonia monooxygenase (amoA) genes were analysed by cloning, sequencing and denaturing gradient gel electrophoresis (DGGE). DGGE profiles of amoA and 16S rRNA gene fragments from Deepsyke soil in 2002 indicated no effect of nitrogen deposition on AOB communities, which contained both Nitrosomonas europaea and Nitrosospira. In 2003, only Nitrosospira could be detected, and no amoA sequences could be retrieved. These results indicate a decrease in the relative abundance of AOB from the year 2002 to 2003 in Deepsyke soil, which may be the result of the exceptionally low rainfall in spring 2003. Nitrosospira-related sequences from Deepsyke soil grouped in all clusters, including cluster 1, which typically contains only sequences from marine environments. In Pwllpeiran soil, 16S rRNA gene libraries were dominated by nonammonia oxidizers and no amoA sequences were detectable. This indicates that autotrophic AOB play only a minor role in these soils even at high nitrogen deposition.
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Urakawa H, Kurata S, Fujiwara T, Kuroiwa D, Maki H, Kawabata S, Hiwatari T, Ando H, Kawai T, Watanabe M, Kohata K. Characterization and quantification of ammonia-oxidizing bacteria in eutrophic coastal marine sediments using polyphasic molecular approaches and immunofluorescence staining. Environ Microbiol 2006; 8:787-803. [PMID: 16623737 DOI: 10.1111/j.1462-2920.2005.00962.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Tokyo Bay, a eutrophic bay in Japan, receives nutrients from wastewater plants and other urban diffuse sources via river input. A transect was conducted along a line from the Arakawa River into Tokyo Bay to investigate the ecological relationship between the river outflow and the distribution, abundance and population structure of ammonia-oxidizing bacteria (AOB). Five surficial marine sediments were collected and analysed with polyphasic approaches. Heterogeneity and genetic diversity of beta-AOB populations were examined using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA and amoA genes. A shift of the microbial community was detected in samples along the transect. Both 16S rRNA and amoA genes generated polymorphisms in the restriction profiles that were distinguishable at each sampling site. Two 16S rRNA gene libraries were constructed using the reverse transcription polymerase chain reaction (RT-PCR) method to determine the major ammonia oxidizers maintaining high cellular rRNA content. Two major groups were observed in the Nitrosomonas lineage; no Nitrosospira were detected. The effort to isolate novel AOB was successful; the isolate dominated in the gene libraries. For quantitative analysis, a real-time PCR assay targeting the 16S rRNA gene was developed. The population sizes of beta-AOB ranged from 1.6 x 10(7) to 3.0 x 10(8) cells g(-1) in dry sediments, which corresponded to 0.1-1.1% of the total bacterial population. An immunofluorescence staining using anti-hydroxylamine oxidoreductase (HAO) antibody was also tested to obtain complementary data. The population sizes of ammonia oxidizers ranged between 2.4 x 10(8) and 1.2 x 10(9) cells g(-1) of dry sediments, which corresponded to 1.2-4.3% of the total bacterial fraction. Ammonia-oxidizing bacteria cell numbers deduced by the two methods were correlated (R = 0.79, P < 0.01). In both methods, the number of AOB increased with the distance from the river mouth; ammonia-oxidizing bacteria were most numerous at B30, where the ammonium concentration in the porewater was markedly lower and the nitrite concentration was slightly higher than nearby sites. These results reveal spatial distribution and shifts in the population structure of AOB corresponding to nutrients and organic inputs from the river run-off and phytoplankton bloom.
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Affiliation(s)
- Hidetoshi Urakawa
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan.
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Whitby C, Earl J, Lanyon C, Gray S, Robinson J, Meadows J, Edwards C. The molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLP. J Appl Microbiol 2005; 97:973-84. [PMID: 15479412 DOI: 10.1111/j.1365-2672.2004.02378.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To combine database-held sequence information with a programme of experimental molecular ecology to define the methanogenic community of a hypereutrophic lake by a PCR-restriction fragment length polymorphism (RFLP) analysis. METHODS AND RESULTS Methanogen diversity in a hypereutrophic freshwater lake was analysed using 16S rDNA PCR-RFLP. Database-held 16S rRNA gene sequences for 76 diverse methanogens were analysed for specific restriction sites that permitted unequivocal differentiation of methanogens. Restriction digestion and agarose gel electrophoresis of the 16S rDNA from selected methanogen pure cultures generated observed restriction profiles that corroborated the expected patterns. This method was then tested by analysing methanogen diversity in samples obtained over 1 year from sediment and water samples taken from the same sampling site. CONCLUSIONS Restriction analysis of the 16S rRNA gene sequences from 157 methanogen clones generated from lakewater and sediment samples showed that over 50% were similar to Methanoculleus spp. Furthermore, a total of 16 RFLP types (1-16) were identified, eight of which contained no cultured representative archaeal 16S rRNA gene sequences. SIGNIFICANCE AND IMPACT OF THE STUDY This RFLP strategy provides a robust and reliable means to rapidly identify methanogens in the environment.
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Affiliation(s)
- C Whitby
- School of Biological Sciences, University of Liverpool, UK
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Bent SJ, Gucker CL, Oda Y, Forney LJ. Spatial distribution of Rhodopseudomonas palustris ecotypes on a local scale. Appl Environ Microbiol 2003; 69:5192-7. [PMID: 12957901 PMCID: PMC194914 DOI: 10.1128/aem.69.9.5192-5197.2003] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The number, spatial distribution, and significance of genetically distinguishable ecotypes of prokaryotes in the environment are poorly understood. Oda et al. (Y. Oda, B. Star, L. A. Huisman, J. C. Gottschal, and L. J. Forney, Appl. Environ. Microbiol. 69:xxx-xxx, 2003) have shown that Rhodopseudomonas palustris ecotypes were lognormally distributed along a 10-m transect and that multiple strains of the species could coexist in 0.5-g sediment samples. To extend these observations, we investigated the clonal diversity of R. palustris in 0.5-g samples taken from the corners and center of a 1-m square. A total of 35 or 36 clones were recovered by direct plating from each sample and were characterized by BOX A1R repetitive element-PCR genomic DNA fingerprinting. Isolates with fingerprint images that were >/=80% similar to each other were defined as the same genotype. Among the 178 isolates studied, 32 genotypes were identified, and each genotype contained between 1 and 40 isolates. These clusters were consistent with minor variations found in 16S rRNA gene sequences. The Shannon indices of the genotypic diversity within each location ranged from 1.08 (5 genotypes) to 2.18 (13 genotypes). Comparison of the rank abundance of genotypes found in pairs of locations showed that strains from three locations were similar to each other, with Morisita-Horn similarity coefficients ranging from 0.59 to 0.71. All comparisons involving the remaining two locations resulted in coefficients between 0 and 0.12. From these results we inferred that the patterns of ecotype diversity at the sampling site are patchy at a 1-m scale and postulated that factors such as mixing, competitive interactions, and microhabitat variability are likely to be responsible for the maintenance of the similarities between some locations and the differences between others.
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Affiliation(s)
- S J Bent
- University of Idaho, Moscow, Idaho, USA
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Bollmann A, Bär-Gilissen MJ, Laanbroek HJ. Growth at low ammonium concentrations and starvation response as potential factors involved in niche differentiation among ammonia-oxidizing bacteria. Appl Environ Microbiol 2002; 68:4751-7. [PMID: 12324316 PMCID: PMC126422 DOI: 10.1128/aem.68.10.4751-4757.2002] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with Nitrosomonas europaea suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better insight into possible methods of niche differentiation among ammonia-oxidizing bacteria, we carried out a growth experiment at low ammonium concentrations with N. europaea and the ammonia oxidizer G5-7, a close relative of Nitrosomonas oligotropha belonging to Nitrosomonas cluster 6a, enriched from a freshwater sediment. Additionally, we compared the starvation behavior of the newly enriched ammonia oxidizer G5-7 to that of N. europaea. The growth experiment at low ammonium concentrations showed that strain G5-7 was able to outcompete N. europaea at growth-limiting substrate concentrations of about 10 micro M ammonium, suggesting better growth abilities of the ammonia oxidizer G5-7 at low ammonium concentrations. However, N. europaea displayed a more favorable starvation response. After 1 to 10 weeks of ammonium deprivation, N. europaea became almost immediately active after the addition of fresh ammonium and converted the added ammonium within 48 to 96 h. In contrast, the regeneration time of the ammonia oxidizer G5-7 increased with increasing starvation time. Taken together, these results provide insight into possible mechanisms of niche differentiation for the ammonia-oxidizing bacteria studied. The Nitrosomonas cluster 6a member, G5-7, is able to grow at ammonium concentrations at which the growth of N. europaea, belonging to Nitrosomonas cluster 7, has already ceased, providing an advantage in habitats with continuously low ammonium concentrations. On the other hand, the ability of N. europaea to become active again after longer periods of starvation for ammonium may allow better exploitation of irregular pulses of ammonium in the environment.
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Affiliation(s)
- Annette Bollmann
- Department of Microbial Ecology, NIOO-KNAW Centre for Limnology, 3631 AC Nieuwersluis, The Netherlands.
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Zehr JP, Ward BB. Nitrogen cycling in the ocean: new perspectives on processes and paradigms. Appl Environ Microbiol 2002; 68:1015-24. [PMID: 11872445 PMCID: PMC123768 DOI: 10.1128/aem.68.3.1015-1024.2002] [Citation(s) in RCA: 187] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Jonathan P Zehr
- Department of Ocean Sciences, Earth and Marine Sciences Building, Room A438, University of California, Santa Cruz, CA 95064, USA.
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17
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Abstract
The eutrophication of many ecosystems in recent decades has led to an increased interest in the ecology of nitrogen transformation. Chemolitho-autotrophic ammonia-oxidizing bacteria are responsible for the rate-limiting step of nitrification in a wide variety of environments, making them important in the global cycling of nitrogen. These organisms are unique in their ability to use the conversion of ammonia to nitrite as their sole energy source. Because of the importance of this functional group of bacteria, understanding of their ecology and physiology has become a subject of intense research over recent years. The monophyletic nature of these bacteria in terrestrial environments has facilitated molecular biological approaches in studying their ecology, and progress in this field has been rapid. The ammonia-oxidizing bacteria of the beta-subclass Proteobacteria have become somewhat of a model system within molecular microbial ecology, and this chapter reviews recent progress in our knowledge of their distribution, diversity, and ecology.
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Affiliation(s)
- G A Kowalchuk
- Netherlands Institute of Ecology, Centre for Terrestrial Ecology, Boterhoeksestraat 48, P.O. Box 40, Heteren, 6666 ZG, The Netherlands.
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Regan JM, Harrington GW, Noguera DR. Ammonia- and nitrite-oxidizing bacterial communities in a pilot-scale chloraminated drinking water distribution system. Appl Environ Microbiol 2002; 68:73-81. [PMID: 11772611 PMCID: PMC126589 DOI: 10.1128/aem.68.1.73-81.2002] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2001] [Accepted: 10/30/2001] [Indexed: 11/20/2022] Open
Abstract
Nitrification in drinking water distribution systems is a common operational problem for many utilities that use chloramines for secondary disinfection. The diversity of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the distribution systems of a pilot-scale chloraminated drinking water treatment system was characterized using terminal restriction fragment length polymorphism (T-RFLP) analysis and 16S rRNA gene (ribosomal DNA [rDNA]) cloning and sequencing. For ammonia oxidizers, 16S rDNA-targeted T-RFLP indicated the presence of Nitrosomonas in each of the distribution systems, with a considerably smaller peak attributable to Nitrosospira-like AOB. Sequences of AOB amplification products aligned within the Nitrosomonas oligotropha cluster and were closely related to N. oligotropha and Nitrosomonas ureae. The nitrite-oxidizing communities were comprised primarily of Nitrospira, although Nitrobacter was detected in some samples. These results suggest a possible selection of AOB related to N. oligotropha and N. ureae in chloraminated systems and demonstrate the presence of NOB, indicating a biological mechanism for nitrite loss that contributes to a reduction in nitrite-associated chloramine decay.
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Affiliation(s)
- John M Regan
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA
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19
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Burrell PC, Phalen CM, Hovanec TA. Identification of bacteria responsible for ammonia oxidation in freshwater aquaria. Appl Environ Microbiol 2001; 67:5791-800. [PMID: 11722936 PMCID: PMC93373 DOI: 10.1128/aem.67.12.5791-5800.2001] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Culture enrichments and culture-independent molecular methods were employed to identify and confirm the presence of novel ammonia-oxidizing bacteria (AOB) in nitrifying freshwater aquaria. Reactors were seeded with biomass from freshwater nitrifying systems and enriched for AOB under various conditions of ammonia concentration. Surveys of cloned rRNA genes from the enrichments revealed four major strains of AOB which were phylogenetically related to the Nitrosomonas marina cluster, the Nitrosospira cluster, or the Nitrosomonas europaea-Nitrosococcus mobilis cluster of the beta subdivision of the class Proteobacteria. Ammonia concentration in the reactors determined which AOB strain dominated in an enrichment. Oligonucleotide probes and PCR primer sets specific for the four AOB strains were developed and used to confirm the presence of the AOB strains in the enrichments. Enrichments of the AOB strains were added to newly established aquaria to determine their ability to accelerate the establishment of ammonia oxidation. Enrichments containing the Nitrosomonas marina-like AOB strain were most efficient at accelerating ammonia oxidation in newly established aquaria. Furthermore, if the Nitrosomonas marina-like AOB strain was present in the original enrichment, even one with other AOB, only the Nitrosomonas marina-like AOB strain was present in aquaria after nitrification was established. Nitrosomonas marina-like AOB were 2% or less of the cells detected by fluorescence in situ hybridization analysis in aquaria in which nitrification was well established.
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Affiliation(s)
- P C Burrell
- Aquatic Research Laboratory, The Aquaria Group, Moorpark, CA 93021, USA
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20
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Bollmann A, Laanbroek HJ. Continuous culture enrichments of ammonia-oxidizing bacteria at low ammonium concentrations. FEMS Microbiol Ecol 2001. [DOI: 10.1111/j.1574-6941.2001.tb00868.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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21
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Koops HP, Pommerening-Röser A. Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 2001. [DOI: 10.1111/j.1574-6941.2001.tb00847.x] [Citation(s) in RCA: 390] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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22
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Whitby CB, Hall G, Pickup R, Saunders JR, Ineson P, Parekh NR, McCarthy A. (13)C incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations. Lett Appl Microbiol 2001; 32:398-401. [PMID: 11412351 DOI: 10.1046/j.1472-765x.2001.00930.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To identify active CO2-assimilating species of ammonia-oxidizing bacteria in fresh water sediment. METHODS AND RESULTS Enrichment cultures were incubated in the presence of 13C labelled CO2, and 13C-DNA successfully resolved from 12C-DNA by caesium chloride density gradient ultracentrifugation of DNA extracts. Ammonia-oxidizer DNA recovered from these gradients was amplified and characterised by Temporal Temperature Gradient Gel Electrophoresis (TTGE), with confirmatory sequence analysis to identify the metabolically active components of the population. CONCLUSION The 12C-DNA fraction was dominated by nitrosospiras, in contrast to the 13C-DNA fraction which was largely nitrosomonad DNA, in support of the hypothesis that nitrosomonads out-compete nitrosospiras in laboratory culture. SIGNIFICANCE AND IMPACT OF THE STUDY The use of stable isotype incorporation into ammonia-oxidizer DNA could therefore circumvent the problems associated with RNA detection to identify metabolically active species in situ.
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Affiliation(s)
- C B Whitby
- School of Biological Sciences, University of Liverpool, UK Institute of Freshwater Ecology, Far Sawrey, UK
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23
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Bothe H, Jost G, Schloter M, Ward BB, Witzel K. Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol Rev 2000; 24:673-90. [PMID: 11077158 DOI: 10.1111/j.1574-6976.2000.tb00566.x] [Citation(s) in RCA: 211] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
This review summarizes aspects of the current knowledge about the ecology of ammonia-oxidizing and denitrifying bacteria. The development of molecular techniques has contributed enormously to the rapid recent progress in the field. Different techniques for doing so are discussed. The characterization of ammonia-oxidizing and -denitrifying bacteria by sequencing the genes encoding 16S rRNA and functional proteins opened the possibility of constructing specific probes. It is now possible to monitor the occurrence of a particular species of these bacteria in any habitat and to get an estimate of the relative abundance of different types, even if they are not culturable as yet. These data indicate that the composition of nitrifying and denitrifying communities is complex and apparently subject to large fluctuations, both in time and in space. More attempts are needed to enrich and isolate those bacteria which dominate the processes, and to characterize them by a combination of physiological, biochemical and molecular techniques. While PCR and probing with nucleotides or antibodies are primarily used to study the structure of nitrifying and denitrifying communities, studies of their function in natural habitats, which require quantification at the transcriptional level, are currently not possible.
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Affiliation(s)
- H Bothe
- Botanical Institute, University of Cologne, Germany
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24
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Purkhold U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops HP, Wagner M. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 2000; 66:5368-82. [PMID: 11097916 PMCID: PMC92470 DOI: 10.1128/aem.66.12.5368-5382.2000] [Citation(s) in RCA: 601] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2000] [Accepted: 10/04/2000] [Indexed: 11/20/2022] Open
Abstract
The current perception of evolutionary relationships and the natural diversity of ammonia-oxidizing bacteria (AOB) is mainly based on comparative sequence analyses of their genes encoding the 16S rRNA and the active site polypeptide of the ammonia monooxygenase (AmoA). However, only partial 16S rRNA sequences are available for many AOB species and most AOB have not yet been analyzed on the amoA level. In this study, the 16S rDNA sequence data of 10 Nitrosomonas species and Nitrosococcus mobilis were completed. Furthermore, previously unavailable 16S rRNA sequences were determined for three Nitrosomonas sp. isolates and for the gamma-subclass proteobacterium Nitrosococcus halophilus. These data were used to revaluate the specificities of published oligonucleotide primers and probes for AOB. In addition, partial amoA sequences of 17 AOB, including the above-mentioned 15 AOB, were obtained. Comparative phylogenetic analyses suggested similar but not identical evolutionary relationships of AOB by using 16S rRNA and AmoA as marker molecules, respectively. The presented 16S rRNA and amoA and AmoA sequence data from all recognized AOB species significantly extend the currently used molecular classification schemes for AOB and now provide a more robust phylogenetic framework for molecular diversity inventories of AOB. For 16S rRNA-independent evaluation of AOB species-level diversity in environmental samples, amoA and AmoA sequence similarity threshold values were determined which can be used to tentatively identify novel species based on cloned amoA sequences. Subsequently, 122 amoA sequences were obtained from 11 nitrifying wastewater treatment plants. Phylogenetic analyses of the molecular isolates showed that in all but two plants only nitrosomonads could be detected. Although several of the obtained amoA sequences were only relatively distantly related to known AOB, none of these sequences unequivocally suggested the existence of previously unrecognized species in the wastewater treatment environments examined.
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Affiliation(s)
- U Purkhold
- Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany
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25
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Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 2000. [PMID: 11097916 DOI: 10.1128/aem.66.12.5368‐5382.2000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The current perception of evolutionary relationships and the natural diversity of ammonia-oxidizing bacteria (AOB) is mainly based on comparative sequence analyses of their genes encoding the 16S rRNA and the active site polypeptide of the ammonia monooxygenase (AmoA). However, only partial 16S rRNA sequences are available for many AOB species and most AOB have not yet been analyzed on the amoA level. In this study, the 16S rDNA sequence data of 10 Nitrosomonas species and Nitrosococcus mobilis were completed. Furthermore, previously unavailable 16S rRNA sequences were determined for three Nitrosomonas sp. isolates and for the gamma-subclass proteobacterium Nitrosococcus halophilus. These data were used to revaluate the specificities of published oligonucleotide primers and probes for AOB. In addition, partial amoA sequences of 17 AOB, including the above-mentioned 15 AOB, were obtained. Comparative phylogenetic analyses suggested similar but not identical evolutionary relationships of AOB by using 16S rRNA and AmoA as marker molecules, respectively. The presented 16S rRNA and amoA and AmoA sequence data from all recognized AOB species significantly extend the currently used molecular classification schemes for AOB and now provide a more robust phylogenetic framework for molecular diversity inventories of AOB. For 16S rRNA-independent evaluation of AOB species-level diversity in environmental samples, amoA and AmoA sequence similarity threshold values were determined which can be used to tentatively identify novel species based on cloned amoA sequences. Subsequently, 122 amoA sequences were obtained from 11 nitrifying wastewater treatment plants. Phylogenetic analyses of the molecular isolates showed that in all but two plants only nitrosomonads could be detected. Although several of the obtained amoA sequences were only relatively distantly related to known AOB, none of these sequences unequivocally suggested the existence of previously unrecognized species in the wastewater treatment environments examined.
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Spring S, Schulze R, Overmann J, Schleifer K. Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies. FEMS Microbiol Rev 2000; 24:573-90. [PMID: 11077151 DOI: 10.1111/j.1574-6976.2000.tb00559.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The aim of this review is to interpret recent studies in which molecular methods were used to identify and characterize prokaryotes in lake sediments and related habitats. In the first part studies based on the phylogenetic diversity of prokaryotes found in lacustrine habitats are summarized. The application of various cultivation-independent methods for the characterization of distinct groups of sediment bacteria is exemplified with morphologically conspicuous, colorless sulfur bacteria in the second part of this review. Finally, traditional and recently developed methods are described which could be used for linking the function of microbial populations with their identification. The potential of these approaches for the study of lake sediments is discussed in order to give a perspective for future studies in this habitat.
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Affiliation(s)
- S Spring
- Lehrstuhl für Mikrobiologie, Technische Universität München, Freising,Germany.
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Ivanova IA, Stephen JR, Chang YJ, Brüggemann J, Long PE, McKinley JP, Kowalchuk GA, White DC, Macnaughton SJ. A survey of 16S rRNA and amoA genes related to autotrophic ammonia-oxidizing bacteria of the beta-subdivision of the class proteobacteria in contaminated groundwater. Can J Microbiol 2000; 46:1012-20. [PMID: 11109489 DOI: 10.1139/w00-099] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we investigated the size and structure of autotrophic ammonia oxidizer (AAO) communities in the groundwater of a contamination plume originating from a mill-tailings disposal site. The site has high levels of dissolved N from anthropogenic sources, and exhibited wide variations in the concentrations of NO3- and NH3 + NH4+. Community structures were examined by PCR-DGGE targeting 16S rDNA with band excision and sequence analysis, and by analysis of amoA fragment clone libraries. AAO population sizes were estimated by competitive PCR targeting the gene amoA, and correlated significantly with nitrate concentration. Most samples revealed novel diversity in AAO 16S rDNA and amoA gene sequences. Both 16S rDNA and amoA analyses suggested that all samples were dominated by Nitrosomonas sp., Nitrosospira sp. being detected in only 3 of 15 samples. This study indicated numerical dominance of Nitrosomonas over Nitrosospira in groundwater, and suggests that groundwater ammonia oxidizers are more similar to those dominating freshwater sediments than bulk soil.
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Affiliation(s)
- I A Ivanova
- University of Tennessee, Center for Environmental Biotechnology, Knoxville 37923, USA
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28
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Ward BB, Martino DP, Diaz MC, Joye SB. Analysis of ammonia-oxidizing bacteria from hypersaline Mono Lake, California, on the basis of 16S rRNA sequences. Appl Environ Microbiol 2000; 66:2873-81. [PMID: 10877781 PMCID: PMC92086 DOI: 10.1128/aem.66.7.2873-2881.2000] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/1999] [Accepted: 05/02/2000] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing bacteria were detected by PCR amplification of DNA extracted from filtered water samples throughout the water column of Mono Lake, California. Ammonia-oxidizing members of the beta subdivision of the division Proteobacteria (beta-subdivision Proteobacteria) were detected using previously characterized PCR primers; target sequences were detected by direct amplification in both surface water and below the chemocline. Denaturing gradient gel electrophoresis analysis indicated the presence of at least four different beta-subdivision ammonia oxidizers in some samples. Subsequent sequencing of amplified 16S rDNA fragments verified the presence of sequences very similar to those of cultured Nitrosomonas strains. Two separate analyses, carried out under different conditions (different reagents, locations, PCR machines, sequencers, etc.), 2 years apart, detected similar ranges of sequence diversity in these samples. It seems likely that the physiological diversity of nitrifiers exceeds the diversity of their ribosomal sequences and that these sequences represent members of the Nitrosomonas europaea group that are acclimated to alkaline, high-salinity environments. Primers specific for Nitrosococcus oceanus, a marine ammonia-oxidizing bacterium in the gamma subdivision of the Proteobacteria, did not amplify target from any samples.
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Affiliation(s)
- B B Ward
- Institute of Marine Sciences, University of California, Santa Cruz, California, USA.
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Bano N, Hollibaugh JT. Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Arctic Ocean. Appl Environ Microbiol 2000; 66:1960-9. [PMID: 10788367 PMCID: PMC101440 DOI: 10.1128/aem.66.5.1960-1969.2000] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/1999] [Accepted: 02/15/2000] [Indexed: 11/20/2022] Open
Abstract
The spatial distribution and diversity of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria (hereinafter referred to as ammonia oxidizers) in the Arctic Ocean were determined. The presence of ammonia oxidizers was detected by PCR amplification of 16S rRNA genes using a primer set specific for this group of organisms (nitA and nitB, which amplifies a 1.1-kb fragment between positions 137 and 1234, corresponding to Escherichia coli 16S rDNA numbering). We analyzed 246 samples collected from the upper water column (5 to 235 m) during March and April 1995, September and October 1996, and September 1997. Ammonia oxidizers were detected in 25% of the samples from 5 m, 80% of the samples from 55 m, 88% of the samples from 133 m, and 50% of the samples from 235 m. Analysis of nitA-nitB PCR product by nested PCR-denaturing gradient gel electrophoresis (DGGE) showed that all positive samples contained the same major band (band A), indicating the presence of a dominant, ubiquitous ammonia oxidizer in the Arctic Ocean basin. Twenty-two percent of the samples contained additional major bands. These samples were restricted to the Chukchi Sea shelf break, the Chukchi cap, and the Canada basin; areas likely influenced by Pacific inflow. The nucleotide sequence of the 1.1-kb nitA-nitB PCR product from a sample that contained only band A grouped with sequences designated group 1 marine Nitrosospira-like sequences. PCR-DGGE analysis of 122 clones from four libraries revealed that 67 to 71% of the inserts contained sequences with the same mobility as band A. Nucleotide sequences (1.1 kb) of another distinct group of clones, found only in 1995 samples (25%), fell into the group 5 marine Nitrosomonas-like sequences. Our results suggest that the Arctic Ocean beta-proteobacterial ammonia oxidizers have low diversity and are dominated by marine Nitrosospira-like organisms. Diversity appears to be higher in Western Arctic Ocean regions influenced by inflow from the Pacific Ocean through the Bering and Chukchi seas.
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Affiliation(s)
- N Bano
- Department of Marine Sciences, University of Georgia, Athens, Georgia 30602-3636, USA
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