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Alves RJE, Kerou M, Zappe A, Bittner R, Abby SS, Schmidt HA, Pfeifer K, Schleper C. Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures. Front Microbiol 2019; 10:1571. [PMID: 31379764 PMCID: PMC6657660 DOI: 10.3389/fmicb.2019.01571] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Climate change is causing arctic regions to warm disproportionally faster than those at lower latitudes, leading to alterations in carbon and nitrogen cycling, and potentially higher greenhouse gas emissions. It is thus increasingly important to better characterize the microorganisms driving arctic biogeochemical processes and their potential responses to changing conditions. Here, we describe a novel thaumarchaeon enriched from an arctic soil, Candidatus Nitrosocosmicus arcticus strain Kfb, which has been maintained for seven years in stable laboratory enrichment cultures as an aerobic ammonia oxidizer, with ammonium or urea as substrates. Genomic analyses show that this organism harbors all genes involved in ammonia oxidation and in carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle, characteristic of all AOA, as well as the capability for urea utilization and potentially also for heterotrophic metabolism, similar to other AOA. Ca. N. arcticus oxidizes ammonia optimally between 20 and 28°C, well above average temperatures in its native high arctic environment (-13-4°C). Ammonia oxidation rates were nevertheless much lower than those of most cultivated mesophilic AOA (20-45°C). Intriguingly, we repeatedly observed apparent faster growth rates (based on marker gene counts) at lower temperatures (4-8°C) but without detectable nitrite production. Together with potential metabolisms predicted from its genome content, these observations indicate that Ca. N. arcticus is not a strict chemolithotrophic ammonia oxidizer and add to cumulating evidence for a greater metabolic and physiological versatility of AOA. The physiology of Ca. N. arcticus suggests that increasing temperatures might drastically affect nitrification in arctic soils by stimulating archaeal ammonia oxidation.
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Affiliation(s)
- Ricardo J Eloy Alves
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Anna Zappe
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Romana Bittner
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Sophie S Abby
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Heiko A Schmidt
- Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Kevin Pfeifer
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Institute for Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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Liu H, Li J, Zhao Y, Xie K, Tang X, Wang S, Li Z, Liao Y, Xu J, Di H, Li Y. Ammonia oxidizers and nitrite-oxidizing bacteria respond differently to long-term manure application in four paddy soils of south of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:641-648. [PMID: 29597161 DOI: 10.1016/j.scitotenv.2018.03.108] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Nitrification plays an important role in the soil nitrogen (N) cycle, and fertilizer application may influence soil nitrifiers' abundance and composition. However, the effect of long-term manure application in paddy soils on nitrifying populations is poorly understood. We chose four long-term manure experimental fields in the south of China to study how the abundance and community structure of nitrifiers would change in response to long-term manure application using quantitative PCR and Miseq sequencing analyses. Our results showed that manure application significantly increased ammonia oxidizing archaea (AOA) abundance at the ChangSha (CS) and NanChang (NC) sites, while the abundance of ammonia oxidizing bacteria (AOB) represented 4.8- and 12.8- fold increases at the JiaXing (JX) and YingTan (YT) sites, respectively. Miseq sequencing of 16S rRNA genes indicated that manure application altered the community structure of nitrifying populations, especially at the NC and YT sites. The application of manure significantly changed AOA and nitrite oxidizing bacteria (NOB) community structures but not those of AOB, suggesting that AOA and NOB may be more sensitive to manures. Variation partitioning analysis (VPA) and redundancy analysis (RDA) indicated that soil pH, TN, NO3--N and water content were the main factors in shaping nitrifying communities. These findings suggest that nitrifiers respond diversely to manure application, and soil physiochemical properties play an important role in determining nitrifiers' abundance and communities with long-term manure addition.
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Affiliation(s)
- Haiyang Liu
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Jia Li
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Yan Zhao
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Kexin Xie
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Xianjin Tang
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Shaoxian Wang
- Institute of Soil & Fertilizer and Resource & Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, PR China
| | - Zhongpei Li
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
| | - Yulin Liao
- Soil and Fertilizer Institute of Hunan Province, Changsha, Hunan, PR China
| | - Jianming Xu
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Hongjie Di
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Yong Li
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China.
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Wang J, Ni L, Song Y, Rhodes G, Li J, Huang Q, Shen Q. Dynamic Response of Ammonia-Oxidizers to Four Fertilization Regimes across a Wheat-Rice Rotation System. Front Microbiol 2017; 8:630. [PMID: 28446904 PMCID: PMC5388685 DOI: 10.3389/fmicb.2017.00630] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/28/2017] [Indexed: 11/23/2022] Open
Abstract
Ammonia oxidation by microorganisms is a rate-limiting step of the nitrification process and determines the efficiency of fertilizer utilized by crops. Little is known about the dynamic response of ammonia-oxidizers to different fertilization regimes in a wheat-rice rotation system. Here, we examined ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities across eight representative stages of wheat and rice growth and under four fertilization regimes: no nitrogen fertilization (NNF), chemical fertilization (CF), organic-inorganic mixed fertilizer (OIMF) and organic fertilization (OF). The abundance and composition of ammonia oxidizers were analyzed using quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) of their amoA genes. Results showed that fertilization but not plant growth stages was the best predictor of soil AOB community abundance and composition. Soils fertilized with more urea-N had higher AOB abundance, while organic-N input showed little effect on AOB abundance. 109 bp T-RF (Nitrosospira Cluster 3b) and 280 bp T-RF (Nitrosospira Cluster 3c) dominated the AOB communities with opposing responses to fertilization regimes. Although the abundance and composition of the AOA community was significantly impacted by fertilization and plant growth stage, it differed from the AOB community in that there was no particular trend. In addition, across the whole wheat-rice rotation stages, results of multiple stepwise linear regression revealed that AOB played a more important role in ammonia oxidizing process than AOA. This study provided insight into the dynamic effects of fertilization strategies on the abundance and composition of ammonia-oxidizers communities, and also offered insights into the potential of managing nitrogen for sustainable agricultural productivity with respect to soil ammonia-oxidizers.
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Affiliation(s)
- Jichen Wang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Lei Ni
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Yang Song
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Geoff Rhodes
- Department of Plant, Soil and Microbial Sciences, Michigan State UniversityEast Lansing, MI, USA
| | - Jing Li
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab and Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural UniversityNanjing, China
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Jung MY, Kim JG, Sinninghe Damsté JS, Rijpstra WIC, Madsen EL, Kim SJ, Hong H, Si OJ, Kerou M, Schleper C, Rhee SK. A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:983-992. [PMID: 27700018 DOI: 10.1111/1758-2229.12477] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
A wide diversity of ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an ammonia-oxidizing archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically, strain MY3 falls in clade 'Nitrosocosmicus' of the thaumarchaeotal group I.1b. The cells of strain MY3 are large 'walnut-like' cocci, divide by binary fission along a central cingulum, and form aggregates. Strain MY3 is mesophilic and neutrophilic. An assay of 13 C-bicarbonate incorporation into archaeal membrane lipids indicated that strain MY3 is capable of autotrophy. In contrast to some other AOA, TCA cycle intermediates, i.e. pruvate, oxaloacetate and α-ketoglutarate, did not affect the growth rates and yields of strain MY3. The attachment of cells of strain MY3 to XAD-7 hydrophobic beads and to the adsorbent vermiculite demonstrated the potential of strain MY3 to form biofilms. The cell surface was confirmed to be hydrophobic by the extraction of strain MY3 from an aqueous medium with p-xylene. Our finding of a strong potential for surface attachment by strain MY3 may reflect an adaptation to the selective pressures in hydrophobic terrestrial environments.
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Affiliation(s)
- Man-Young Jung
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, P.O. Box 59, AB Den Burg, 1790, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, Utrecht, 3508, TA, The Netherlands
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, P.O. Box 59, AB Den Burg, 1790, The Netherlands
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA
| | - So-Jeong Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Heeji Hong
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Ok-Ja Si
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Melina Kerou
- Department of Genetics in Ecology, University of Vienna, Vienna, A-1090, Austria
| | - Christa Schleper
- Department of Genetics in Ecology, University of Vienna, Vienna, A-1090, Austria
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
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5
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Awolusi OO, Nasr M, Kumari S, Bux F. Artificial Intelligence for the Evaluation of Operational Parameters Influencing Nitrification and Nitrifiers in an Activated Sludge Process. MICROBIAL ECOLOGY 2016; 72:49-63. [PMID: 26906468 DOI: 10.1007/s00248-016-0739-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
Nitrification at a full-scale activated sludge plant treating municipal wastewater was monitored over a period of 237 days. A combination of fluorescent in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qPCR) were used for identifying and quantifying the dominant nitrifiers in the plant. Adaptive neuro-fuzzy inference system (ANFIS), Pearson's correlation coefficient, and quadratic models were employed in evaluating the plant operational conditions that influence the nitrification performance. The ammonia-oxidizing bacteria (AOB) abundance was within the range of 1.55 × 10(8)-1.65 × 10(10) copies L(-1), while Nitrobacter spp. and Nitrospira spp. were 9.32 × 10(9)-1.40 × 10(11) copies L(-1) and 2.39 × 10(9)-3.76 × 10(10) copies L(-1), respectively. Specific nitrification rate (qN) was significantly affected by temperature (r 0.726, p 0.002), hydraulic retention time (HRT) (r -0.651, p 0.009), and ammonia loading rate (ALR) (r 0.571, p 0.026). Additionally, AOB was considerably influenced by HRT (r -0.741, p 0.002) and temperature (r 0.517, p 0.048), while HRT negatively impacted Nitrospira spp. (r -0.627, p 0.012). A quadratic combination of HRT and food-to-microorganism (F/M) ratio also impacted qN (r (2) 0.50), AOB (r (2) 0.61), and Nitrospira spp. (r (2) 0.72), while Nitrobacter spp. was considerably influenced by a polynomial function of F/M ratio and temperature (r (2) 0.49). The study demonstrated that ANFIS could be used as a tool to describe the factors influencing nitrification process at full-scale wastewater treatment plants.
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Affiliation(s)
- Oluyemi Olatunji Awolusi
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Mahmoud Nasr
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4000, South Africa.
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6
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Smith MW, Davis RE, Youngblut ND, Kärnä T, Herfort L, Whitaker RJ, Metcalf WW, Tebo BM, Baptista AM, Simon HM. Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River. Front Microbiol 2015; 6:1074. [PMID: 26483785 PMCID: PMC4589670 DOI: 10.3389/fmicb.2015.01074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/18/2015] [Indexed: 11/27/2022] Open
Abstract
Lateral bays of the lower Columbia River estuary are areas of enhanced water retention that influence net ecosystem metabolism through activities of their diverse microbial communities. Metagenomic characterization of sediment microbiota from three disparate sites in two brackish lateral bays (Baker and Youngs) produced ∼100 Gbp of DNA sequence data analyzed subsequently for predicted SSU rRNA and peptide-coding genes. The metagenomes were dominated by Bacteria. A large component of Eukaryota was present in Youngs Bay samples, i.e., the inner bay sediment was enriched with the invasive New Zealand mudsnail, Potamopyrgus antipodarum, known for high ammonia production. The metagenome was also highly enriched with an archaeal ammonia oxidizer closely related to Nitrosoarchaeum limnia. Combined analysis of sequences and continuous, high-resolution time series of biogeochemical data from fixed and mobile platforms revealed the importance of large-scale reciprocal particle exchanges between the mainstem estuarine water column and lateral bay sediments. Deposition of marine diatom particles in sediments near Youngs Bay mouth was associated with a dramatic enrichment of Bacteroidetes (58% of total Bacteria) and corresponding genes involved in phytoplankton polysaccharide degradation. The Baker Bay sediment metagenome contained abundant Archaea, including diverse methanogens, as well as functional genes for methylotrophy and taxonomic markers for syntrophic bacteria, suggesting that active methane cycling occurs at this location. Our previous work showed enrichments of similar anaerobic taxa in particulate matter of the mainstem estuarine water column. In total, our results identify the lateral bays as both sources and sinks of biogenic particles significantly impacting microbial community composition and biogeochemical activities in the estuary.
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Affiliation(s)
- Maria W Smith
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Richard E Davis
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | | | - Tuomas Kärnä
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Lydie Herfort
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana IL, USA
| | - William W Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana IL, USA
| | - Bradley M Tebo
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - António M Baptista
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Holly M Simon
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
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7
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Wu Y, Conrad R. Ammonia oxidation-dependent growth of group I.1b Thaumarchaeota in acidic red soil microcosms. FEMS Microbiol Ecol 2014; 89:127-34. [PMID: 24724989 DOI: 10.1111/1574-6941.12340] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 11/28/2022] Open
Abstract
Accumulating evidence suggests that Thaumarchaeota may control nitrification in acidic soils. However, the composition of the thaumarchaeotal communities and their functioning is not well known. Therefore, we studied nitrification activity in relation to abundance and composition of Thaumarchaeota in an acidic red soil from China, using microcosms incubated with and without cellulose amendment. Cellulose was selected to simulate the input of crop residues used to increase soil fertility by local farming. Accumulation of NO3-(-N) was correlated with the growth of Thaumarchaeota as determined by qPCR of 16S rRNA and ammonia monooxygenase (amoA) genes. Both nitrification activity and thaumarchaeotal growth were inhibited by acetylene. They were also inhibited by cellulose amendment, possibly due to the depletion of ammonium by enhanced heterotrophic assimilation. These results indicated that growth of Thaumarchaeota was dependent on ammonia oxidation. The thaumarchaeotal 16S rRNA gene sequences in the red soil were dominated by a clade related to soil fosmid clone 29i4 within the group I.1b, which is widely distributed but so far uncultured. The archaeal amoA sequences were mainly related to the Nitrososphaera sister cluster. These observations suggest that fosmid clone 29i4 and Nitrososphaera sister cluster represent the same group of Thaumarchaeota and dominate ammonia oxidation in acidic red soil.
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Affiliation(s)
- Yucheng Wu
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Hernández M, Dumont MG, Calabi M, Basualto D, Conrad R. Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:70-79. [PMID: 24596264 DOI: 10.1111/1758-2229.12109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 09/14/2013] [Indexed: 06/03/2023]
Abstract
Ammonia oxidation, performed by specialized microorganisms belonging to the Bacteria and Archaea, is the first and most limiting step of soil nitrification. Nitrification has not yet been examined in young volcanic soils. The aim of the present work was to evaluate the abundance and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in acidic volcanic soils (andisols) of different defined ages to determine their relative contribution to nitrification and soil colonization. Soil was collected from three vegetated sites on Llaima Volcano (Chile) recolonized after lava eruptions in 1640, 1751 and 1957. Quantitative polymerase chain reaction, terminal restriction fragment length polymorphism and clone sequence analyses of the amoA gene were performed for the AOA and AOB communities. All soils showed high nitrification potentials, but they were highest in the younger soils. Archaeal amoA genes outnumbered bacterial amoA genes at all sites, and AOA abundances were found to be proportional to the nitrification potentials. Sequencing indicated the presence of AOA related to Nitrososphaera and Nitrosotalea, and AOB related primarily to Nitrosospira and sporadically to Nitrosomonas. The study showed that both AOA and AOB are early colonizers of andisols, but that AOA outnumber AOB and play an important role in nitrification.
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Affiliation(s)
- Marcela Hernández
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str.10, 35043, Marburg, Germany
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9
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Stauffert M, Duran R, Gassie C, Cravo-Laureau C. Response of archaeal communities to oil spill in bioturbated mudflat sediments. MICROBIAL ECOLOGY 2014; 67:108-119. [PMID: 24057322 DOI: 10.1007/s00248-013-0288-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
The response of archaeal community to oil spill with the combined effect of the bioturbation activity of the polychaetes Hediste diversicolor was determined in mudflat sediments from the Aber-Benoît basin (Brittany, French Atlantic coast), maintained in microcosms. The dynamics of the archaeal community was monitored by combining comparative terminal restriction fragment length polymorphism (T-RFLP) fingerprints and sequence library analyses based on 16S rRNA genes and 16S cDNA. Methanogens were also followed by targeting the mcrA gene. Crenarchaeota were always detected in all communities irrespective of the addition of H. diversicolor and/or oil. In the presence of oil, modifications of archaeal community structures were observed. These modifications were more pronounced when H. diversicolor was added resulting in a more diverse community especially for the Euryarchaeota and Thaumarchaeota. The analysis of mcrA transcripts showed a specific structure for each condition since the beginning of the experiment. Overall, oiled microcosms showed different communities irrespective of H. diversicolor addition, while similar hydrocarbon removal capacities were observed.
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Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie, IPREM - UMR CNRS 5254, Université de Pau et des Pays de l'Adour, BP 1155, 64013, Pau Cedex, France
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10
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Rubin-Blum M, Antler G, Turchyn AV, Tsadok R, Goodman-Tchernov BN, Shemesh E, Austin JA, Coleman DF, Makovsky Y, Sivan O, Tchernov D. Hydrocarbon-related microbial processes in the deep sediments of the Eastern Mediterranean Levantine Basin. FEMS Microbiol Ecol 2013; 87:780-96. [DOI: 10.1111/1574-6941.12264] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 11/08/2013] [Accepted: 11/20/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Maxim Rubin-Blum
- The Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | - Gilad Antler
- Department of Earth Sciences; University of Cambridge; Cambridge UK
| | | | - Rami Tsadok
- The Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | | | - Eli Shemesh
- The Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | - James A. Austin
- Institute for Geophysics; Jackson School of Geosciences; University of Texas at Austin; Austin TX USA
| | - Dwight F. Coleman
- Graduate School of Oceanography; The University of Rhode Island; Narragansett RI USA
| | - Yizhaq Makovsky
- The Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | - Orit Sivan
- Department of Geological and Environmental Sciences; Ben-Gurion University of the Negev; Beer-Sheva Israel
| | - Dan Tchernov
- The Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
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11
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Ke X, Lu Y, Conrad R. Different behaviour of methanogenic archaea and Thaumarchaeota in rice field microcosms. FEMS Microbiol Ecol 2013; 87:18-29. [PMID: 23909555 DOI: 10.1111/1574-6941.12188] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 11/27/2022] Open
Abstract
Archaea in rice fields play an important role in carbon and nitrogen cycling. They comprise methane-producing Euryarchaeota as well as ammonia-oxidizing Thaumarchaeota, but their community structures and population dynamics have not yet been studied in the same system. Different soil compartments (surface, bulk, rhizospheric soil) and ages of roots (young and old roots) at two N fertilization levels and at three time points (the panicle initiation, heading and maturity periods) of the season were assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of archaeal genes (mcrA, amoA, 16S rRNA gene). The community of total Archaea in soil and root samples mainly consisted of the methanogens and the Thaumarchaeota and their abundance increased over the season. Methanogens proliferated everywhere, but Thaumarchaeota proliferated only on the roots and in response to nitrogen fertilization. The community structures of Archaea, methanogens and Thaumarchaeota were different in soil and root samples indicating niche differentiation. While Methanobacteriales were generally present, Methanosarcinaceae and Methanocellales were the dominant methanogens in soil and root samples, respectively. The results emphasize the specific colonization of roots by two ecophysiologically different groups of archaea which may belong to the core root biome.
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Affiliation(s)
- Xiubin Ke
- College of Resources and Environment Sciences, China Agricultural University, Beijing, China; Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Biotechnology, Ministry of Agriculture, Beijing, China
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Alves RJE, Wanek W, Zappe A, Richter A, Svenning MM, Schleper C, Urich T. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea. THE ISME JOURNAL 2013; 7:1620-31. [PMID: 23466705 PMCID: PMC3721107 DOI: 10.1038/ismej.2013.35] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 11/09/2022]
Abstract
The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota-AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.
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Affiliation(s)
| | - Wolfgang Wanek
- Department of Terrestrial Ecosystem Research, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Anna Zappe
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Department of Terrestrial Ecosystem Research, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, University of Tromsø, Tromsø, Norway
| | - Christa Schleper
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
| | - Tim Urich
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
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Herrmann M, Hädrich A, Küsel K. Predominance of thaumarchaeal ammonia oxidizer abundance and transcriptional activity in an acidic fen. Environ Microbiol 2012; 14:3013-25. [PMID: 23016896 DOI: 10.1111/j.1462-2920.2012.02882.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 08/23/2012] [Indexed: 11/27/2022]
Abstract
We investigated the abundance, community composition and transcriptional activity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the acidic fen Schlöppnerbrunnen (Germany) that was subjected to water table manipulations. Quantitative PCR targeting amoA gene copies and transcripts showed that AOA dominated the ammonia-oxidizing community in the upper 20 cm of the peat soil. Numbers of archaeal amoA gene copies and transcripts as well as the relative fraction of AOA of the total archaea decreased with depth. AOA-AmoA sequences were 96.2-98.9% identical to that of Candidatus Nitrosotalea devanaterra while bacterial AmoA sequences affiliated with Nitrosospira clusters 2 and 4. Archaeal but not bacterial amoA transcripts were detected in short-term laboratory incubations of peat that showed nitrifying activity. Nitrate accumulated in the peat pore water after 6 weeks of induced drought during a field experiment. Subsequent rewetting resulted in a significant decrease of AOA transcriptional activity, indicating that AOA responded to water table fluctuations on the transcriptional level. Our results suggest that nitrification in this fen is primarily linked to archaeal ammonia oxidation. pH and anoxia appear to be key factors regulating AOA community composition, vertical distribution and activity in acidic fens.
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Affiliation(s)
- Martina Herrmann
- Aquatic Geomicrobiology Group, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany.
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Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microbiol 2012; 78:7501-10. [PMID: 22923400 DOI: 10.1128/aem.01960-12] [Citation(s) in RCA: 253] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research.
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French E, Kozlowski JA, Mukherjee M, Bullerjahn G, Bollmann A. Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater. Appl Environ Microbiol 2012; 78:5773-80. [PMID: 22685142 PMCID: PMC3406153 DOI: 10.1128/aem.00432-12] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/30/2012] [Indexed: 11/20/2022] Open
Abstract
Aerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with "Candidatus Nitrosoarchaeum koreensis" and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.
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Affiliation(s)
| | | | - Maitreyee Mukherjee
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, USA
| | - George Bullerjahn
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, USA
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de Gannes V, Eudoxie G, Dyer DH, Hickey WJ. Diversity and abundance of ammonia oxidizing archaea in tropical compost systems. Front Microbiol 2012; 3:244. [PMID: 22787457 PMCID: PMC3391690 DOI: 10.3389/fmicb.2012.00244] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 06/18/2012] [Indexed: 11/13/2022] Open
Abstract
Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems.
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Affiliation(s)
- Vidya de Gannes
- Faculty of Science and Agriculture, Department of Food Production, The University of the West Indies St. Augustine Campus, Republic of Trinidad and Tobago
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Zhalnina K, de Quadros PD, Camargo FAO, Triplett EW. Drivers of archaeal ammonia-oxidizing communities in soil. Front Microbiol 2012; 3:210. [PMID: 22715335 PMCID: PMC3375578 DOI: 10.3389/fmicb.2012.00210] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/22/2012] [Indexed: 01/24/2023] Open
Abstract
Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.
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Affiliation(s)
- Kateryna Zhalnina
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
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