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Liu H, Jing H, Wang F. Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches. Front Microbiol 2023; 14:1268790. [PMID: 37840747 PMCID: PMC10568479 DOI: 10.3389/fmicb.2023.1268790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH 4 + concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.
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Affiliation(s)
- Hao Liu
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongmei Jing
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Fangzhou Wang
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
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Zou Y, Yang Y, Wu S, Chen F, Zhu R. Effect of steel slag on ammonia removal and ammonia-oxidizing microorganisms in zeolite-based tidal flow constructed wetlands. Chemosphere 2022; 309:136727. [PMID: 36209854 DOI: 10.1016/j.chemosphere.2022.136727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/07/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
The ammonia removal performance of tidal flow constructed wetlands (TFCWs) requires to be improved under high hydraulic loading rates (HLRs). The pH decrease caused by nitrification may adversely affect the NH4+-N removal and ammonia-oxidizing microorganisms (AOMs) of TFCWs. Herein, TFCWs with zeolite (TFCW_Z) and a mixture of zeolite and steel slag (TFCW_S) were built to investigate the influence of steel slag on NH4+-N removal and AOMs. Both TFCWs were operated under short flooding/drying (F/D) cycles and high HLRs (3.13 and 4.69 m3/(m2 d)). The results revealed that a neutral effluent pH (6.98-7.82) was achieved in TFCW_S owing to the CaO dissolution of steel slag. The NH4+-N removal efficiencies in TFCW_S (91.2 ± 5.1%) were much higher than those in TFCW_Z (73.2 ± 7.1%). Total nitrogen (TN) removal was poor in both TFCWs mainly due to the low influent COD/TN. Phosphorus removal in TFCW_S was unsatisfactory because of the short hydraulic retention time. The addition of steel slag stimulated the flourishing AOMs, including Nitrosomonas (ammonia-oxidizing bacteria, AOB), Candidatus_Nitrocosmicus (ammonia-oxidizing archaea, AOA), and comammox Nitrospira, which may be responsible for the better ammonia removal performance in TFCW_S. PICRUSt2 showed that steel slag also enriched the relative abundance of functional genes involved in nitrification (amoCAB, hao, and nxrAB) but inhibited genes related to denitrification (nirK, norB, and nosZ). Quantitative polymerase chain reaction (qPCR) revealed that complete AOB (CAOB) and AOB contributed more to the amoA genes in TFCW_S and TFCW_Z, respectively. Therefore, this study revealed that the dominant AOMs could be significantly changed in zeolite-based TFCW by adding steel slag to regulate the pH in situ, resulting in a more efficient NH4+-N removal performance.
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Affiliation(s)
- Yuhuan Zou
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Yongqiang Yang
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China.
| | - Shijun Wu
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China
| | - Fanrong Chen
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China
| | - Runliang Zhu
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China
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Kim N, Riggins CW, Zabaloy MC, Rodriguez-Zas SL, Villamil MB. Limited Impacts of Cover Cropping on Soil N-Cycling Microbial Communities of Long-Term Corn Monocultures. Front Microbiol 2022; 13:926592. [PMID: 35755999 PMCID: PMC9226624 DOI: 10.3389/fmicb.2022.926592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Cover cropping (CC) is a promising in-field practice to mitigate soil health degradation and nitrogen (N) losses from excessive N fertilization. Soil N-cycling microbial communities are the fundamental drivers of these processes, but how they respond to CC under field conditions is poorly documented for typical agricultural systems. Our objective was to investigate this relationship for a long-term (36 years) corn [Zea mays L.] monocultures under three N fertilizer rates (N0, N202, and N269; kg N/ha), where a mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth.] was introduced for two consecutive years, using winter fallows as controls (BF). A 3 × 2 split-plot arrangement of N rates and CC treatments in a randomized complete block design with three replications was deployed. Soil chemical and physical properties and potential nitrification (PNR) and denitrification (PDR) rates were measured along with functional genes, including nifH, archaeal and bacterial amoA, nirK, nirS, and nosZ-I, sequenced in Illumina MiSeq system and quantified in high-throughput quantitative polymerase chain reaction (qPCR). The abundances of nifH, archaeal amoA, and nirS decreased with N fertilization (by 7.9, 4.8, and 38.9 times, respectively), and correlated positively with soil pH. Bacterial amoA increased by 2.4 times with CC within N269 and correlated positively with soil nitrate. CC increased the abundance of nirK by 1.5 times when fertilized. For both bacterial amoA and nirK, N202 and N269 did not differ from N0 within BF. Treatments had no significant effects on nosZ-I. The reported changes did not translate into differences in functionality as PNR and PDR did not respond to treatments. These results suggested that N fertilization disrupts the soil N-cycling communities of this system primarily through soil acidification and high nutrient availability. Two years of CC may not be enough to change the N-cycling communities that adapted to decades of disruption from N fertilization in corn monoculture. This is valuable primary information to understand the potentials and limitations of CC when introduced into long-term agricultural systems.
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Affiliation(s)
- Nakian Kim
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Chance W. Riggins
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - María C. Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida, UNS-CONICET, Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | | | - María B. Villamil
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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Al-Ajeel S, Spasov E, Sauder LA, McKnight MM, Neufeld JD. Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems. Water Res X 2022; 15:100131. [PMID: 35402889 PMCID: PMC8990171 DOI: 10.1016/j.wroa.2022.100131] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 05/27/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.
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Hu J, Richwine JD, Keyser PD, Li L, Yao F, Jagadamma S, DeBruyn JM. Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C 4 grassland soils. PeerJ 2022; 9:e12592. [PMID: 35003922 PMCID: PMC8684740 DOI: 10.7717/peerj.12592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background Fertilizer addition can contribute to nitrogen (N) losses from soil by affecting microbial populations responsible for nitrification. However, the effects of N fertilization on ammonia oxidizing bacteria under C4 perennial grasses in nutrient-poor grasslands are not well studied. Methods In this study, a field experiment was used to assess the effects of N fertilization rate (0, 67, and 202 kg N ha−1) and grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) on ammonia-oxidizing bacterial (AOB) communities in C4 grassland soils using quantitative PCR, quantitative reverse transcription-PCR, and high-throughput amplicon sequencing of amoA genes. Results Nitrosospira were dominant AOB in the C4 grassland soil throughout the growing season. N fertilization rate had a stronger influence on AOB community composition than C4 grass species. Elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N2O) emission and soil acidity. The abundance and species richness of AOB were higher under switchgrass compared to big bluestem. Soil pH, nitrate, nitrification potential, and N2O emission were significantly related to the variability in AOB community structures (p < 0.05).
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Affiliation(s)
- Jialin Hu
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jonathan D Richwine
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Patrick D Keyser
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Lidong Li
- Agroecosystem Management Research Unit, USDA-Agricultural Research Service, Lincoln, NE, United States of America
| | - Fei Yao
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Sindhu Jagadamma
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
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Allegrini M, Morales ME, Villamil MB, Zabaloy MC. Ammonia Oxidizing Prokaryotes Respond Differently to Fertilization and Termination Methods in Common Oat's Rhizosphere. Front Microbiol 2021; 12:746524. [PMID: 34690996 PMCID: PMC8527175 DOI: 10.3389/fmicb.2021.746524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cover crops (CC) have demonstrated beneficial effects on several soil properties yet questions remain regarding their effects on soil microbial communities. Among them, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) have a key role for N cycling in soil and their responses in the rhizosphere of terminated CC deserve further investigation. A greenhouse experiment was established to assess N fertilization (with or without N) and termination methods (glyphosate, mowing, and untreated control) of common oat (Avena sativa L.) as potential drivers of AOA and AOB responses in the rhizosphere. The abundance of amoA genes was determined by quantitative real-time PCR (qPCR), the community structure was assessed with Illumina amplicon sequencing of these genes, while the function was assessed from potential nitrification activity (PNA). While N fertilization had no influence on AOA, the termination method significantly increased amoA gene copies of AOA in mowed plants relative to glyphosate termination or the untreated control (1.76 and 1.49-fold change, respectively), and shifted AOA community structure (PERMANOVA, p<0.05). Ordination methods indicated a separation between AOA communities from control and glyphosate-terminated plants relative to mowed plants for both UniFrac and Aitchison distance. Converserly, N fertilization significantly increased AOB abundance in the rhizosphere of mowed and control plants, yet not in glyphosate-treated plants. Analyses of community structure showed that AOB changed only in response to N fertilization and not to the termination method. In line with these results, significantly higher PNA values were measured in all fertilized samples, regardless of the termination methods. Overall, the results of this study indicated that bacterial and archaeal nitrifiers have contrasting responses to fertlization and plant termination methods. While AOA were responsive to the termination method, AOB were more sensitive to N additions, although, the stimulative effect of N fertilization on amoAAOB abundance was dependent on the termination method.
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Affiliation(s)
- Marco Allegrini
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Marianela E Morales
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Maria B Villamil
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - María Celina Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina.,Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
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Wei W, Isobe K, Shiratori Y, Yano M, Toyoda S, Koba K, Yoshida N, Shen H, Senoo K. Revisiting the involvement of ammonia oxidizers and denitrifiers in nitrous oxide emission from cropland soils. Environ Pollut 2021; 287:117494. [PMID: 34182387 DOI: 10.1016/j.envpol.2021.117494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/05/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Nitrous oxide (N2O), an ozone-depleting greenhouse gas, is generally produced by soil microbes, particularly NH3 oxidizers and denitrifiers, and emitted in large quantities after N fertilizer application in croplands. N2O can be produced via multiple processes, and reduced, with the involvement of more diverse microbes with different physiological constraints than previously thought; therefore, there is a lack of consensus on the production processes and microbes involved under different agricultural practices. In this study, multiple approaches were applied, including N2O isotopocule analyses, microbial gene transcript measurements, and selective inhibition assays, to revisit the involvement of NH3 oxidizers and denitrifiers, including the previously-overlooked taxa, in N2O emission from a cropland, and address the biological and environmental factors controlling the N2O production processes. Then, we synthesized the results from those approaches and revealed that the overlooked denitrifying bacteria and fungi were more involved in N2O production than the long-studied ones. We also demonstrated that the N2O production processes and soil microbes involved were different based on fertilization practices (plowing or surface application) and fertilization types (manure or urea). In particular, we identified the following intensified activities: (1) N2O production by overlooked denitrifying fungi after manure fertilization onto soil surface; (2) N2O production by overlooked denitrifying bacteria and N2O reduction by long-studied N2O-reducing bacteria after manure fertilization into the plowed layer; and (3) N2O production by NH3-oxidizing bacteria and overlooked denitrifying bacteria and fungi when urea fertilization was applied into the plowed layer. We finally propose the conceptual scheme of N flow after fertilization based on distinct physiological constraints among the diverse NH3 oxidizers and denitrifiers, which will help us understand the environmental context-dependent N2O emission processes.
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Affiliation(s)
- Wei Wei
- School of Agricultural Engineering, Jiangsu University, Jiangsu, 212013, China; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, Niigata, 940-0826, Japan
| | - Midori Yano
- Center for Ecological Research, Kyoto University, Shiga, 5202113, Japan
| | - Sakae Toyoda
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Keisuke Koba
- Center for Ecological Research, Kyoto University, Shiga, 5202113, Japan
| | - Naohiro Yoshida
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan; Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan; National Institute of Information and Communications Technology, Tokyo, 184-8795, Japan
| | - Haoyang Shen
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Keishi Senoo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan
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Nakagawa T, Koji M, Hosoyama A, Yamazoe A, Tsuchiya Y, Ueda S, Takahashi R, Stahl DA. Nitrosopumilus zosterae sp. nov., an autotrophic ammonia-oxidizing archaeon of phylum Thaumarchaeota isolated from coastal eelgrass sediments of Japan. Int J Syst Evol Microbiol 2021; 71. [PMID: 34406920 DOI: 10.1099/ijsem.0.004961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic and aerobic ammonia-oxidizing archaeon of the phylum Thaumarchaeota, strain NM25T, was isolated from coastal eelgrass zone sediment sampled in Shimoda (Japan). The cells were rod-shaped with an S-layer cell wall. The temperature range for growth was 20-37 °C, with an optimum at 30 °C. The pH range for growth was pH 6.1-7.7, with an optimum at pH 7.1. The salinity range for growth was 5-40 %, with an optimum range of 15-32 %. Cells obtained energy from ammonia oxidation and used bicarbonate as a carbon source. Utilization of urea was not observed for energy generation and growth. Strain NM25T required a hydrogen peroxide scavenger, such as α-ketoglutarate, pyruvate or catalase, for sustained growth on ammonia. Growth of strain NM25T was inhibited by addition of low concentrations of some organic compounds and organic mixtures, including complete inhibition by glycerol, peptone and yeast extract. Phylogenetic analysis of four concatenated housekeeping genes (16S rRNA, rpoB, rpsI and atpD) and concatenated AmoA, AmoB, AmoC amino acid sequences indicated that the isolate is similar to members of the genus Nitrosopumilus. The closest relative is Nitrosopumilus ureiphilus PS0T with sequence similarities of 99.5 % for the 16S rRNA gene and 97.2 % for the amoA gene. Genome relatedness between strain NM25T and N. ureiphilus PS0T was assessed by average nucleotide identity and digital DNA-DNA hybridization, giving results of 85.4 and 40.2 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NM25T represents a novel species of the genus Nitrosopumilus, for which the name sp. nov, is proposed. The type strain is NM25T (=NBRC 111181T=ATCC TSD-147T).
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Affiliation(s)
- Tatsunori Nakagawa
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan.,Department of Civil and Environmental Engineering, University of Washington, WA 98195, USA
| | - Mori Koji
- Department of Civil and Environmental Engineering, University of Washington, WA 98195, USA
| | - Akira Hosoyama
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu 292-0818, Japan
| | - Atsushi Yamazoe
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu 292-0818, Japan
| | - Yuki Tsuchiya
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu 292-0818, Japan
| | - Shingo Ueda
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Reiji Takahashi
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, WA 98195, USA
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Ho A, Mendes LW, Lee HJ, Kaupper T, Mo Y, Poehlein A, Bodelier PLE, Jia Z, Horn MA. Response of a methane-driven interaction network to stressor intensification. FEMS Microbiol Ecol 2021; 96:5898668. [PMID: 32857837 DOI: 10.1093/femsec/fiaa180] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/25/2020] [Indexed: 01/04/2023] Open
Abstract
Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.
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Affiliation(s)
- Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Lucas W Mendes
- Center of Nuclear Energy in Agriculture, University of São Paulo (CENA-USP), Avenida Centenario 303, 13416-000, Piracicaba-SP, Brazil
| | - Hyo Jung Lee
- Department of Biology, Kunsan National University, 558 Daehak-ro, Gunsan-si 54150, Republic of Korea
| | - Thomas Kaupper
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Yongliang Mo
- Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Xuan-Wu District, Nanjing 210008, China
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Zhongjun Jia
- Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Xuan-Wu District, Nanjing 210008, China
| | - Marcus A Horn
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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Jiang J, Yu D, Wang Y, Zhang X, Dong W, Zhang X, Guo F, Li Y, Zhang C, Yan G. Use of additives in composting informed by experience from agriculture: Effects of nitrogen fertilizer synergists on gaseous nitrogen emissions and corresponding genes ( amoA and nirS). Bioresour Technol 2021; 319:124127. [PMID: 32971331 DOI: 10.1016/j.biortech.2020.124127] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/05/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
The effects of two nitrogen fertilizer synergists (urease inhibitor, UI; nitrification inhibitor, NI) on NH3 and N2O emissions and the successions of the amoA and nirS genes during composting were assessed. Results showed that the UI and UI + NI treatments reduced NH3 emissions by 26.3% and 24.3%, respectively, and N2O emissions were reduced by 63.9% for UI + NI treatment but were not reduced by UI. The addition of UI and NI significantly reduced the abundance of the nirS gene during thermophilic stage, while significantly increased that of the amoA gene during maturation stage. Crenarchaeota was the principal nitrifying archaeal phylum and was significantly affected by pH. Proteobacteria was the main denitrifying bacterial phylum, whose relative abundance was higher for UI + NI treatment than the other treatments. PICRUSt analysis showed that the addition of UI and NI inhibited enzymatic activity related to N transformation during thermophilic stage while enriching enzymatic activity during maturation phase.
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Affiliation(s)
- Jishao Jiang
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China.
| | - Dou Yu
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Yang Wang
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Xindan Zhang
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Wei Dong
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Xiaofang Zhang
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Fengqi Guo
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Yunbei Li
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Chunyan Zhang
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Guangxuan Yan
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environmental Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, PR China
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11
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Abstract
Quantitative-PCR (qPCR) enables the quantification of specific DNA targets, such as functional or phylogenetic marker genes associated with environmental samples. During each qPCR cycle, the number of copies of a gene (or region) of interest in DNA samples is determined in real time using a fluorescence-based label and compared to a standard serial dilution. Here, we describe a qPCR method to quantify the ammonia oxidizing bacteria involved in the first step of nitrification, using the amoA gene as a proxy of their abundance. The preparation of the standards from environmental samples and qPCR is presented in detail for specifically quantifying microbial abundance in environmental samples such as soil.
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Affiliation(s)
- Aimeric Blaud
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK.
| | - Abadie Maïder
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Herts, UK
| | - Ian M Clark
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Herts, UK
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12
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Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States. Microb Ecol 2020; 80:778-792. [PMID: 32535638 DOI: 10.1007/s00248-020-01534-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.
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Affiliation(s)
- Emily L Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA
| | - John R Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA.
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13
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Cydzik-Kwiatkowska A, Zielińska M, Bernat K, Bułkowska K, Wojnowska-Baryła I. Insights into mechanisms of bisphenol A biodegradation in aerobic granular sludge. Bioresour Technol 2020; 315:123806. [PMID: 32688251 DOI: 10.1016/j.biortech.2020.123806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Wastewater is the major source of bisphenol A (BPA) in the environment, however, the results regarding main mechanisms of BPA biodegradation in wastewater treatment systems are divergent. The effect of BPA concentration in wastewater (0, 2, 6, 12 mg BPA/L) on respirometric activity and expression of selected genes in aerobic granules was examined. A real-time protocol for analysis of direct BPA-degrader activity targeting gene coding for ferredoxin was developed. At 2 mg BPA/L, respirometric activity of granules was the highest, which favored the fastest pollutant removal, and BPA-degraders were active at the beginning of the reactor cycle and no by-products of BPA degradation were detected. At 6 and 12 mg BPA/L, the activity of BPA-degraders was much higher, peaking after feeding and again when a BPA metabolite (3-(benzyloxy)benzoic acid) appeared in the reactor. The upregulation of gene coding for ammonia monooxygenase indicated that co-metabolism occurred mostly at 12 mg BPA/L.
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Affiliation(s)
- Agnieszka Cydzik-Kwiatkowska
- University of Warmia and Mazury in Olsztyn, Faculty of Geoengineering, Department of Environmental Biotechnology, Sloneczna 45G, 10-709 Olsztyn, Poland.
| | - Magdalena Zielińska
- University of Warmia and Mazury in Olsztyn, Faculty of Geoengineering, Department of Environmental Biotechnology, Sloneczna 45G, 10-709 Olsztyn, Poland
| | - Katarzyna Bernat
- University of Warmia and Mazury in Olsztyn, Faculty of Geoengineering, Department of Environmental Biotechnology, Sloneczna 45G, 10-709 Olsztyn, Poland
| | - Katarzyna Bułkowska
- University of Warmia and Mazury in Olsztyn, Faculty of Geoengineering, Department of Environmental Biotechnology, Sloneczna 45G, 10-709 Olsztyn, Poland
| | - Irena Wojnowska-Baryła
- University of Warmia and Mazury in Olsztyn, Faculty of Geoengineering, Department of Environmental Biotechnology, Sloneczna 45G, 10-709 Olsztyn, Poland
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14
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Lin C, Xu H, Qin W, Xu S, Tang X, Kuang L, Wang X, Jiang B, Chen J, Shan J, Adams J, Qin H, Wang B. Evaluation of Two Primer Sets for Amplification of Comammox Nitrospira amoA Genes in Wetland Soils. Front Microbiol 2020; 11:560942. [PMID: 33101233 PMCID: PMC7555835 DOI: 10.3389/fmicb.2020.560942] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/10/2020] [Indexed: 01/23/2023] Open
Abstract
After the discovery of complete ammonia-oxidizing (comammox) Nitrospira, detection and assessments of the contribution of comammox Nitrospira communities to nitrogen cycling are in great demand. PCR-based approach, a common method for the detection of comammox, depends strongly on accurate amplification of the amoA genes from the original DNA samples using appropriate primers. In this study, we reported an evaluation of the performance of two commonly used primer sets, Ntsp-amoA 162F/359R and comaA/B-244f/659r, for amplifying the comammox amoA genes from three representative wetland soils in China [Sangsang (SS), Sanjiang (SJ), and Xianghai (XH)]. Our results demonstrated the two primer sets could both successfully amplify the clades with high relative abundances (RA), and further revealed a broadly similar diversity and community composition of dominant comammox operational taxonomic units (OTUs) (RA ≥ 1%) in each of the three wetland soils. However, the clades with low RA, such as the clade A (1.26%) in SJ and the clade B (11.54%) in XH that were recovered by metagenomics analysis, failed to be amplified using comaA/B-244f/659r, but were successfully amplified and sequenced using Ntsp-amoA 162F/359R. It indicated that, compared to comaA/B-244f/659r, Ntsp-amoA 162F/359R was more sensitive to the clades with low RA. However, it is worth noting that Ntsp-amoA 162F/359R would overestimate the RA of some rare clades. For example, the RAs of clade B in XH were overestimated by 32-fold. Furthermore, high levels of non-target amplification were detected via gel electrophoresis using both primer sets, especially for comammox Clade B amoA genes, implying that we should treat qPCR results based on these primers with caution. Taken together, our study comprehensively compared the performance of the two primer sets on the sensitivity and specificity of amplifying comammox amoA genes in three wetland soils, pointing out the necessity of further development of new primers for the efficient and accurate detection of comammox in various environments.
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Affiliation(s)
- Chenshuo Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China.,Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Hang Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Wei Qin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Shaoyi Xu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiufeng Tang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Kuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xinxin Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Bin Jiang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junhui Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jonathan Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Hua Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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15
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Kong X, Ying S, Yang L, Xin Y, Cai Z, Zhu S, Liu D. Microbial and isotopomer analysis of N 2O generation pathways in ammonia removal biofilters. Chemosphere 2020; 251:126357. [PMID: 32146187 DOI: 10.1016/j.chemosphere.2020.126357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/18/2020] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Ammonia removal biofilters can be a potential source of nitrous oxide (N2O) production as a result of microbial nitrification and denitrification. In this study, these two N2O generation pathways was quantified using isotopic site preference values (SP, 33‰ for nitrification and 0‰ for denitrification) in a 204-d operation. Tests with two moisture conditions (45% and 55%) and three inlet NH3 concentrations (35, 18 and 0 ppmv) were performed. A 55+% NH3 removal efficiency was achieved in biofilters with 35 and 18 ppmv ammonia supply, but no significant difference (p > 0.05) was found between the moisture treatments. Results showed that biofilters were clearly net sources of N2O, and biofilters with higher moisture content generated significantly (p < 0.05) higher N2O concentration. The N2O generation did not stop even after the biofilters were terminated. The percentage of inlet NH3-N converted into N2O-N were 5.2%, 8.5% for biofilters with 45% moisture content, and 14.8%, 10.8% for those with 55% moisture content. Gene abundance of amoA and nosZ in packing materials (taken on days 64, 107, 140, 180 and 204) increased due to NH3 input reaching the highest on day 140 and then decreased in response to reduced NH3 supply on day 180 and 204. The changes of SP values suggested a shift between nitrification and denitrification with regard to N2O generation. Overall, the nitrification was the dominant pathway for N2O generation, but uncertainty exits as well. This study confirmed that NH3-loaded biofilters were net sources of N2O, and use of SP-N2O may be helpful in better understanding the processes responsible for such emissions.
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Affiliation(s)
- Xianwang Kong
- College of Biosystems Engineering and Food Science, Zhejiang University, China
| | - Shihao Ying
- College of Biosystems Engineering and Food Science, Zhejiang University, China
| | - Liangcheng Yang
- Department of Health Sciences Environmental Health Program, Illinois State University, USA.
| | - Yicong Xin
- College of Biosystems Engineering and Food Science, Zhejiang University, China
| | - Zhen Cai
- College of Biosystems Engineering and Food Science, Zhejiang University, China
| | - Songming Zhu
- College of Biosystems Engineering and Food Science, Zhejiang University, China
| | - Dezhao Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, China.
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16
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Keeley RF, Rodriguez-Gonzalez L, Class USFG, Briggs GE, Frazier VE, Mancera PA, Manzer HS, Ergas SJ, Scott KM. Degenerate PCR primers for assays to track steps of nitrogen metabolism by taxonomically diverse microorganisms in a variety of environments. J Microbiol Methods 2020; 175:105990. [PMID: 32603756 DOI: 10.1016/j.mimet.2020.105990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 11/29/2022]
Abstract
Steps in the global nitrogen cycle are mainly catalyzed by microorganisms. Accordingly, the activities of these microorganisms affect the health and productivity of ecosystems. Their activities are also used in wastewater treatment systems to remove reactive nitrogen compounds and prevent eutrophication events triggered by nutrient discharges. Therefore, tracking the activities of these microorganisms can provide insights into the functioning of these systems. The presence and abundance of genes encoding nitrogen-metabolizing enzymes can be traced via polymerase chain reaction (PCR); however, this requires primers that are sensitive to a heterogenous gene pool yet specific enough to the target biomarker. The ever-expanding diversity of sequences available from databases includes many sequences relevant to nitrogen metabolism that match poorly with primers previously designed to track their presence and/or abundance. This includes genes encoding ammonia monooxygenase (AMO) of ammonia oxidizing microorganisms, nitrite oxidoreductase (NXR) of nitrite oxidizing bacteria, and nitrous oxide reductase (NOS) of denitrifying bacteria. Some primers are also not designed to generate the short (~200 nucleotides) amplicons required for real-time quantitative PCR (qPCR) and reverse-transcriptase qPCR (qRT-PCR). In this study, genes collected from the Integrated Microbial Genomes database (IMG) were aligned to design PCR primers that could capture more sequence diversity than is possible using existing primers. Primers were designed to target three clades of AMO (Betaproteobacteria, Chrenarchaeota, and complete ammonia oxidizing Nitrospira), periplasmic NXR and two clades of NOS (Proteobacteria and Bacteroidetes/Firmicutes). These primers successfully amplified target sequences from two wastewater treatment plants with biological nitrogen removal (one with simultaneous nitrification/denitrification and one with distinct anoxic/oxic zones) and estuary sediment. Nucleotide sequences of the amplicons retrieved homologs when used to query GenBank by BLAST. While convincingly identified as target sequences for these primer pairs, these amplicons were divergent from each other, and quite divergent (as low as 73%) from those present in GenBank, suggesting these primers are capable of capturing a diverse range of sequences. A direct comparison showed that primers designed here are better suited to environmental samples, such as wastewater treatment facilities, by producing a greater number of amplicons from the same sample than primers currently established in literature.
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Affiliation(s)
- Ryan F Keeley
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA.
| | | | | | - Gemma E Briggs
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Victoria E Frazier
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Paola A Mancera
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Haider S Manzer
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Sarina J Ergas
- Department of Civil & Environmental Engineering, University of South Florida, Tampa, FL, USA
| | - Kathleen M Scott
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA.
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17
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Cheng C, Ma J, Wang J, Du Z, Li B, Wang J, Gao C, Zhu L. Toxicity comparison of three imidazolium bromide ionic liquids to soil microorganisms. Environ Pollut 2019; 255:113321. [PMID: 31610515 DOI: 10.1016/j.envpol.2019.113321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
Ionic liquids (ILs) are extensively used in several chemistry fields. And research about the effects of ILs on soil microbes is needed. In this study, brown soil was exposed to 1-butyl-3-methylimidazolium bromide ([C4mim]Br), 1-hexyl-3-methylimidazolium bromide ([C6mim]Br) and 1-decyl-3-methylimidazolium bromide ([C10mim]Br). The toxicities of the three ILs are evaluated by measuring the soil culturable microbial number, enzyme activity, microbial diversity and, abundance of the ammonia monooxygenase (amoA) genes of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Results showed that all tested ILs caused a decrease in culturable microbial abundance. Tested ILs exposure inhibit urease activity and promote acid phosphatase and β-glucosidase activities. Tested ILs reduced soil microbial diversity and the abundances of AOB-amoA and AOA-amoA genes significantly. After a comparison of the integrated biomarker response (IBR) index, the toxicities of tested ILs to soil microorganisms were as follows: [C10mim]Br > [C6mim]Br > [C4mim]Br. Among all collected biomarkers, the abundance of the AOA-amoA gene was the most sensitive one and was easily affected after ILs exposure.
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Affiliation(s)
- Chao Cheng
- College of Resources and Environment, Key Laboratory of Agriculture Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, 271018, Shandong Province, China.
| | - Junchao Ma
- College of Resources and Environment, Key Laboratory of Agriculture Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, 271018, Shandong Province, China.
| | - Jinhua Wang
- College of Resources and Environment, Key Laboratory of Agriculture Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, 271018, Shandong Province, China.
| | - Zhongkun Du
- College of Resources and Environment, Key Laboratory of Agriculture Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, 271018, Shandong Province, China.
| | - Bing Li
- College of Resources and Environment, Key Laboratory of Agriculture Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, 271018, Shandong Province, China.
| | - Jun Wang
- College of Resources and Environment, Key Laboratory of Agriculture Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, 271018, Shandong Province, China.
| | - Chong Gao
- College of Resources and Environment, Key Laboratory of Agriculture Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, 271018, Shandong Province, China.
| | - Lusheng Zhu
- College of Resources and Environment, Key Laboratory of Agriculture Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Taian, 271018, Shandong Province, China.
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18
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Lv B, Zhang D, Chen Q, Cui Y. Effects of earthworms on nitrogen transformation and the correspond genes ( amoA and nirS) in vermicomposting of sewage sludge and rice straw. Bioresour Technol 2019; 287:121428. [PMID: 31096104 DOI: 10.1016/j.biortech.2019.121428] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
The effects of earthworms on nitrogen transformation and the responsible functional genes during disposal of sewage sludge and rice straw were investigated in this study. Vermicomposting resulted in the lower pH and total organic carbon (TOC) compared to the control treatment without earthworms. Moreover, the presence of earthworms could promote the nitrogen mineralization and nitrification process in vermicomposting. Earthworms increased the activity of ammonia monooxygenase and abundance of amoA-nitrifier and reduced its diversity, whereas they reduced the density of nirS-denitrifying bacteria but enhanced its diversity. Nitrosospira was the dominant amoA-nitrifier and earthworms stimulated its growth in the vermicomposting. The presence of earthworms could also affect the community composition of nirS-denitrifying bacteria despite most of the nirS-denitrifier was not be classified at the genus level. In conclusion, the presence of earthworms had significant influence on the diversity and abundances of amoA and nirS genes and affect the nitrogen bio-transformation in vermicomposting.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), Shanghai Maritime University, Shanghai 201306, China.
| | - Di Zhang
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Qihao Chen
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Yuxue Cui
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China
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19
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Aigle A, Prosser JI, Gubry-Rangin C. The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers. Environ Microbiome 2019; 14:3. [PMID: 33902715 PMCID: PMC7989807 DOI: 10.1186/s40793-019-0342-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 06/06/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments in phylogenetic methodology, provides the potential for better analysis of microbial niche specialisation. This study aimed to develop an approach for sequencing of bacterial and archaeal amoA genes amplified from soil using bioinformatics pipelines developed for general analysis of functional genes and employed sequence data to reassess phylogeny and niche specialisation in terrestrial bacterial ammonia oxidisers. RESULTS amoA richness and community composition differed with bioinformatics approaches used but analysis of MiSeq sequences was reliable for both archaeal and bacterial amoA genes and was used for subsequent assessment of potential niche specialisation of soil bacteria ammonia oxidisers. Prior to ecological analysis, phylogenetic analysis of Nitrosospira, which dominates soil AOB, was revisited using a phylogenetic analysis of 16S rRNA and amoA genes in available AOB genomes. This analysis supported congruence between phylogenies of the two genes and increased previous phylogenetic resolution, providing support for additional gene clusters of potential ecological significance. Analysis of environmental sequences using these new sequencing, bioinformatics and phylogenetic approaches demonstrated, for the first time, similar niche specialisation in AOB to that in AOA, indicating pH as a key ecological factor controlling the composition of soil ammonia oxidiser communities. CONCLUSIONS This study presents the first bioinformatics pipeline for optimal analysis of Illumina MiSeq sequencing of a functional gene and is adaptable to any amplicon size (even genes larger than 500 bp). The pipeline was used to provide an up-to-date phylogenetic analysis of terrestrial betaproteobacterial amoA genes and to demonstrate the importance of soil pH for their niche specialisation and is broadly applicable to other ecosystems and diverse microbiomes.
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Affiliation(s)
- Axel Aigle
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, St. Machar Drive, Aberdeen, AB24 3UU UK
| | - James I. Prosser
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, St. Machar Drive, Aberdeen, AB24 3UU UK
| | - Cécile Gubry-Rangin
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, St. Machar Drive, Aberdeen, AB24 3UU UK
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Mohanty SR, Nagarjuna M, Parmar R, Ahirwar U, Patra A, Dubey G, Kollah B. Nitrification Rates Are Affected by Biogenic Nitrate and Volatile Organic Compounds in Agricultural Soils. Front Microbiol 2019; 10:772. [PMID: 31139154 PMCID: PMC6527594 DOI: 10.3389/fmicb.2019.00772] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 03/26/2019] [Indexed: 11/18/2022] Open
Abstract
The processes regulating nitrification in soils are not entirely understood. Here we provide evidence that nitrification rates in soil may be affected by complexed nitrate molecules and microbial volatile organic compounds (mVOCs) produced during nitrification. Experiments were carried out to elucidate the overall nature of mVOCs and biogenic nitrates produced by nitrifiers, and their effects on nitrification and redox metabolism. Soils were incubated at three levels of biogenic nitrate. Soils containing biogenic nitrate were compared with soils containing inorganic fertilizer nitrate (KNO3) in terms of redox metabolism potential. Repeated NH4–N addition increased nitrification rates (mM NO31- produced g-1 soil d-1) from 0.49 to 0.65. Soils with higher nitrification rates stimulated (p < 0.01) abundances of 16S rRNA genes by about eight times, amoA genes of nitrifying bacteria by about 25 times, and amoA genes of nitrifying archaea by about 15 times. Soils with biogenic nitrate and KNO3 were incubated under anoxic conditions to undergo anaerobic respiration. The maximum rates of different redox metabolisms (mM electron acceptors reduced g-1 soil d-1) in soil containing biogenic nitrate followed as: NO31- reduction 4.01 ± 0.22, Fe3+ reduction 5.37 ± 0.12, SO42- reduction 9.56 ± 0.16, and CH4 production (μg g-1 soil) 0.46 ± 0.05. Biogenic nitrate inhibited denitrificaton 1.4 times more strongly compared to mineral KNO3. Raman spectra indicated that aliphatic hydrocarbons increased in soil during nitrification, and these compounds probably bind to NO3 to form biogenic nitrate. The mVOCs produced by nitrifiers enhanced (p < 0.05) nitrification rates and abundances of nitrifying bacteria. Experiments suggest that biogenic nitrate and mVOCs affect nitrification and redox metabolism in soil.
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Affiliation(s)
| | | | - Rakesh Parmar
- ICAR Indian Institute of Soil Science, Bhopal, India
| | - Usha Ahirwar
- ICAR Indian Institute of Soil Science, Bhopal, India
| | - Ashok Patra
- ICAR Indian Institute of Soil Science, Bhopal, India
| | - Garima Dubey
- ICAR Indian Institute of Soil Science, Bhopal, India
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Marques ELS, Dias JCT, Gross E, Silva ABCE, de Moura SR, Rezende RP. Purple Sulfur Bacteria Dominate Microbial Community in Brazilian Limestone Cave. Microorganisms 2019; 7:E29. [PMID: 30678083 DOI: 10.3390/microorganisms7020029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 11/16/2022] Open
Abstract
The mineralogical composition of caves makes the environment ideal for inhabitation by microbes. However, the bacterial diversity in the cave ecosystem remains largely unexplored. In this paper, we described the bacterial community in an oxic chamber of the Sopradeira cave, an iron-rich limestone cave, in the semiarid region of Northeast Brazil. The microbial population in the cave samples was studied by 16S rDNA next-generation sequencing. A type of purple sulfur bacteria (PSB), Chromatiales, was found to be the most abundant in the sediment (57%), gravel-like (73%), and rock samples (96%). The predominant PSB detected were Ectothiorhodospiraceae, Chromatiaceae, and Woeseiaceae. We identified the PSB in a permanently aphotic zone, with no sulfur detected by energy-dispersive X-ray (EDX) spectroscopy. The absence of light prompted us to investigate for possible nitrogen fixing (nifH) and ammonia oxidizing (amoA) genes in the microbial samples. The nifH gene was found to be present in higher copy numbers than the bacterial-amoA and archaeal-amoA genes, and archaeal-amoA dominated the ammonia-oxidizing community. Although PSB dominated the bacterial community in the samples and may be related to both nitrogen-fixing and ammonia oxidizing bacteria, nitrogen-fixing associated gene was the most detected in those samples, especially in the rock. The present work demonstrates that this cave is an interesting hotspot for the study of ammonia-oxidizing archaea and aphotic PSB.
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Du P, Wu X, Xu J, Dong F, Liu X, Zhang Y, Zheng Y. Clomazone influence soil microbial community and soil nitrogen cycling. Sci Total Environ 2018; 644:475-485. [PMID: 29990898 DOI: 10.1016/j.scitotenv.2018.06.214] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/17/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
We designed an indoor mesocosm experiment to investigate the long-term effects of exposure to clomazone, a widely used herbicide, on soil microbial communities and their nitrogen (N) cycling functions. Clomazone was applied to two typical soils from China at three concentrations: 0.8 (the recommended dosage), 8 and 80 mg kg-1 soil dry weight, and the mix was incubated for 90 days. Samples were removed periodically for assay with several techniques. The half-lives of clomazone in this experiment were 11-126 d. Results were significant only for the highest clomazone concentration. Next-generation sequencing of the 16S and 18S rDNA genes revealed that bacterial diversity significantly decreased whereas fungal abundance increased after day 60 but with no detectable effect on the microbial community. Hierarchical cluster and principal coordinates analysis revealed that the bacterial community structure was negatively impacted. Linear discriminant analysis of effect size identified Sphingomonas and Arthrobacter as the predominant bacterial species. Finally, we measured soil NH4+ and NO3- concentrations and used real-time PCR to analyze the abundance of the N-cycling genes, nifH and amoA. In the first 30 days, the NO3--N content and the number of ammonia-oxidizing bacteria increased. N2-fixing bacteria were inhibited after 60 days, but the NH4+-N concentration remained unchanged and was likely provided by ammoniation.
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Affiliation(s)
- Pengqiang Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China; College of Chemistry, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China; Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, China.
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China; Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Ying Zhang
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing 100193, China
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Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.
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Affiliation(s)
| | | | - Shingo Ueda
- College of Bioresource Sciences, Nihon University
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University
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Du Z, Zhu Y, Zhu L, Zhang J, Li B, Wang J, Wang J, Zhang C, Cheng C. Effects of the herbicide mesotrione on soil enzyme activity and microbial communities. Ecotoxicol Environ Saf 2018; 164:571-578. [PMID: 30149356 DOI: 10.1016/j.ecoenv.2018.08.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/11/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
Mesotrione (2-[4-(methylsulfonyl)-2-nithobenzoyl]-1, 3-cyclohexanedione) is a selective triketone herbicide that has been widely used in corn production for the past 15 years. However, its potential for risk to soil ecosystems is poorly documented. The present study investigated the soil enzyme activity and soil microbial community responses to a 20 days' mesotrione exposure at doses of 0.1, 1.0 and 5.0 mg/kg. On days 2, 5, 10 and 20, activities of soil β-glucosidase, urease and acid phosphatase, soil microbe abundances, soil microbial community structure and abundance of the AOA-amoA and AOB-amoA genes were measured. Results showed that activities of urease and acid phosphatase were relatively stable, with no difference found between the mesotrione-treated group and control at the end of exposure. But β-glucosidase activity was reduced in the 5.0 mg/kg mesotrione treatment. In the 1.0 and 5.0 mg/kg mesotrione-treated soil, abundance of bacteria, fungi and actinomycetes all were reduced. In the 0.1 mg/kg mesotrione-treated soil, only fungi abundance was reduced by the end of the exposure. The analysis of terminal restriction fragment length polymorphism (T-RFLP) revealed soil microbial community structure could be affected by mesotrione at all experimental doses, and microbial diversity declined slightly after mesotrione exposure. Abundance of AOA-amoA and AOB-amoA genes were reduced markedly in 1.0 and 5.0 mg/kg mesotrione-treated soil. The present study suggests that mesotrione at higher doses might induce negative impacts on soil microbes, a finding which merits additional research and which should be accounted for when application of this herbicide is considered.
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Affiliation(s)
- Zhongkun Du
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China
| | - Yanyan Zhu
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China
| | - Lusheng Zhu
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China.
| | - Ji Zhang
- College of Mechanical and Electronic Engineering, Key Laboratory of Horticultural Machinery and Equipment of Shandong, Shandong Agricultural University, Taian 271018, PR China
| | - Bing Li
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China
| | - Jinhua Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China.
| | - Jun Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China.
| | - Cheng Zhang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China
| | - Chao Cheng
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China
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Liu XR, Zhao GX, Zhang QW, Tian XP. [Effects of Biochar on Nitrous Oxide Fluxes and the Abundance of Related Functional Genes from Agriculture Soil in the North China Plain]. Huan Jing Ke Xue 2018; 39:3816-3825. [PMID: 29998691 DOI: 10.13227/j.hjkx.201711275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To explore the effect and mechanism of biochar application in reducing nitrous oxide (N2O) content in agricultural soil, from March 27 to June 5 2015, pot experiments were conducted to study the effects of biochar application rates (CK, C1:5%, C2:10%, C3:15%, and C4:30%) (mass fraction) on soil N2O fluxes and the functional marker genes ammonia monooxygenase (amoA), nirK, nirS, and nosZ, which are responsible for nitrification and denitrification. The results revealed the following. ①The application of low doses of biochar (5%) promoted N2O emission. The application of middle and high doses of biochar reduced N2O emission. Furthermore, the application of biochar (15%) was found to be the best practice to reduce N2O emission. ② At the beginning of the experiment, biochar had a significant effect on the abundance of soil amoA and denitrification bacteria gene. Furthermore, the abundance of AOA and nirS had a significant positive correlation with the biochar rate, and the abundance of nirK gene and biochar rate were significant. There was a significant negative correlation between AOB and nosZ gene abundance and biochar rate. At the end of the experiment, AOA abundance correlated negatively with biochar rate, while there was a significantly positive relationship between AOB abundance and biochar rate. ③ At the beginning of the experiment, the N2O fluxes exhibited a significant negative correlation with AOA and nirS gene, indicating that N2O production was controlled by the abundance of AOA and nirS gene under high soil moisture content. At the end of the experiment, there was a significant positive correlation between N2O flux and nosZ gene, indicating that the production of N2O was regulated by the abundance of nosZ gene under low soil water content. The results of this study showed that the application of biochar altered the abundance of amoA and denitrification bacteria genes, and reduced N2O emission. These results provide a theoretical basis for a rational application of biochar in farmland.
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Affiliation(s)
- Xing-Ren Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guang-Xin Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy and Resources Environment, Tianjin Agricultural University, Tianjin 300384, China
| | - Qing-Wen Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiu-Ping Tian
- College of Agronomy and Resources Environment, Tianjin Agricultural University, Tianjin 300384, China
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Du P, Wu X, Xu J, Dong F, Liu X, Zheng Y. Effects of trifluralin on the soil microbial community and functional groups involved in nitrogen cycling. J Hazard Mater 2018; 353:204-213. [PMID: 29674095 DOI: 10.1016/j.jhazmat.2018.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 03/13/2018] [Accepted: 04/04/2018] [Indexed: 06/08/2023]
Abstract
Large amounts of trifluralin are applied each year for weed control; however, its effects on soil microbial communities and functions are unknown. Two agricultural soils, one silty loam and one silty clay were spiked with TFL (0, 0.84, 8.4, and 84 mg kg-1) and studied the effects using a laboratory microcosm approach. The half-lives were 44.19-61.83 d in all cases. Bacterial abundance increased 1.12-5.56 times by TFL, but the diversity decreased. From the next-generation sequencing results, TFL altered the bacterial community structure, which initially diverged from the control community structure, then recovered, and then diverged again. Linear discriminant analysis effect size indicated that Sphingomonas and Xanthomonadaceae were the predominant species on day 7 and 15 in TFL treatments. N2-fixing bacteria were initially increased, then decreased, and then recovered, and it was positively correlated with NH4+-N content. Compared with the control, ammonia-oxidizing bacteria were decreased by 25.51-92.63%, ammonia-oxidizing archaea were decreased by 17.12-85.21% (except day 7), and the NO3--N concentration was also inhibited. In contrast to bacteria, fungal abundance was inhibited without any observable effects on fungal diversity or community structure. These results suggest that TFL impacts soil bacterial community and alters functional microorganisms involved in soil N processing.
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Affiliation(s)
- Pengqiang Du
- College of Chemistry, Central China Normal University, No. 152 Luoyu Road, Wuhan, 430079, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Yongquan Zheng
- College of Chemistry, Central China Normal University, No. 152 Luoyu Road, Wuhan, 430079, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
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McGee CF, Storey S, Clipson N, Doyle E. Concentration-dependent responses of soil bacterial, fungal and nitrifying communities to silver nano and micron particles. Environ Sci Pollut Res Int 2018; 25:18693-18704. [PMID: 29705905 DOI: 10.1007/s11356-018-2087-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/20/2018] [Indexed: 05/16/2023]
Abstract
The growing use of silver nanoparticles (AgNPs) is likely to result in increased environmental contamination. Although AgNPs have been reported to affect microbial communities in a range of ecosystems, there is still a lack of information concerning the effect of low concentrations of AgNPs on soil microbial community structures and functional groups involved in biogeochemical cycling. In this study, the concentration-dependent effects of AgNPs and silver micron particles (AgMPs) on bacterial and fungal community structures in an agricultural pastureland soil were examined in a microcosm-based experiment using enzyme analysis, molecular fingerprinting, qPCR and amplicon sequencing. Soil enzyme processes were impacted by Ag contamination, with soil dehydrogenase activity reduced by 1 mg kg-1 of AgNPs and AgMPs. Soil urease activity was less susceptible, but was inhibited by ≥ 10 mg kg-1 AgNPs. The significant (P ≤ 0.001) decrease in copy numbers of the amoA gene by 10 mg kg-1 AgNPs indicated that archaea ammonia oxidisers may be more sensitive to AgNP contamination than bacteria. Amplicon sequencing revealed the bacterial phyla Acidobacteria and Verrucomicrobia to be highly sensitive to AgNP contamination. A broad reduction in the relative abundance of Acidobacterial genera was observed, with the exception of the genus Geothrix which increased in response to AgNP and AgMP amendment. Broad tolerance to Ag was observed among the Bacteriodetes, with higher relative abundance of most genera observed in the presence of AgNPs and AgMPs. The proteobacterial genus Dyella was highly tolerant to AgNPs and AgMPs and relative abundance of this genus increased with Ag concentration. Soil fungal community structure responded to both AgNPs and AgMPs, but the nanoparticle had an impact at a lower concentration. This study demonstrates that pastureland soil microbial communities are highly sensitive to AgNP amendment and key functional processes may be disrupted by relatively low levels of contamination.
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Affiliation(s)
- Conor Francis McGee
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Sean Storey
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nicholas Clipson
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Evelyn Doyle
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Grün AL, Straskraba S, Schulz S, Schloter M, Emmerling C. Long-term effects of environmentally relevant concentrations of silver nanoparticles on microbial biomass, enzyme activity, and functional genes involved in the nitrogen cycle of loamy soil. J Environ Sci (China) 2018; 69:12-22. [PMID: 29941247 DOI: 10.1016/j.jes.2018.04.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 05/14/2023]
Abstract
The increasing production and use of engineered silver nanoparticles (AgNP) in industry and private households are leading to increased concentrations of AgNP in the environment. An ecological risk assessment of AgNP is needed, but it requires understanding the long term effects of environmentally relevant concentrations of AgNP on the soil microbiome. Hence, the aim of this study was to reveal the long-term effects of AgNP on soil microorganisms. The study was conducted as a laboratory incubation experiment over a period of one year using a loamy soil and AgNP concentrations ranging from 0.01 to 1 mg AgNP/kg soil. The short term effects of AgNP were, in general, limited. However, after one year of exposure to 0.01 mg AgNP/kg, there were significant negative effects on soil microbial biomass (quantified by extractable DNA; p = 0.000) and bacterial ammonia oxidizers (quantified by amoA gene copy numbers; p = 0.009). Furthermore, the tested AgNP concentrations significantly decreased the soil microbial biomass, the leucine aminopeptidase activity (quantified by substrate turnover; p = 0.014), and the abundance of nitrogen fixing microorganisms (quantified by nifH gene copy numbers; p = 0.001). The results of the positive control with AgNO3 revealed predominantly stronger effects due to Ag+ ion release. Thus, the increasing toxicity of AgNP during the test period may reflect the long-term release of Ag+ ions. Nevertheless, even very low concentrations of AgNP caused disadvantages for the microbial soil community, especially for nitrogen cycling, and our results confirmed the risks of releasing AgNP into the environment.
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Affiliation(s)
- Anna-Lena Grün
- Faculty of Regional and Environmental Sciences, Department of Soil Science, University of Trier, Trier, Germany.
| | - Susanne Straskraba
- J.W. Goethe University, Institute of Molecular Biosciences, Frankfurt am Main, Germany
| | - Stefanie Schulz
- Research for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleissheim, Germany
| | - Michael Schloter
- Research for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleissheim, Germany; Chair for Soil Science, Technische Universität München, Freising, Germany
| | - Christoph Emmerling
- Faculty of Regional and Environmental Sciences, Department of Soil Science, University of Trier, Trier, Germany
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Wang M, Veldsink JH, Dini-Andreote F, Salles JF. Compositional and abundance changes of nitrogen-cycling genes in plant-root microbiomes along a salt marsh chronosequence. Antonie Van Leeuwenhoek 2018; 111:2061-78. [PMID: 29846874 DOI: 10.1007/s10482-018-1098-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/14/2018] [Indexed: 10/14/2022]
Abstract
Disentangling the relative influences of soil properties and plant-host on root-associated microbiomes in natural systems is challenging, given that spatially segregated soil types display distinct historical legacies. In addition, distant locations may also lead to biogeographical patterns of microbial communities. Here, we used an undisturbed salt marsh chronosequence spanning over a century of ecosystem development to investigate changes in the community composition and abundance of a set of nitrogen-cycling genes. Specifically, we targeted genes of diazotrophs and ammonia oxidizers associated with the bulk and rhizosphere soil of the plant species Limonium vulgare. Samples were collected across five distinct successional stages of the chronosequence (ranging from 5 to 105 years) at two time-points. Our results indicate that soil variables such as sand:silt:clay % content and pH strongly relates to the abundance of N-cycling genes in the bulk soil. However, in the rhizosphere samples, the abundance of ammonia-oxidizing organisms (both bacteria and archaea, AOB and AOA, respectively) was relatively constant across most of the successional stages, albeit displaying seasonal variation. This result indicates a potentially stronger control of plant host (rather than soil) on the abundance of these organisms. Interestingly, the plant host did not have a significant effect on the composition of AOA and AOB communities, being mostly divergent according to soil successional stages. The abundance of diazotrophic communities in rhizosphere samples was more affected by seasonality than those of bulk soil. Moreover, the abundance pattern of diazotrophs in the rhizosphere related to the systematic increase of plant biomass and soil organic matter along the successional gradient. These results suggest a potential season-dependent regulation of diazotrophs exerted by the plant host. Overall, this study contributes to a better understanding of how the natural formation of a soil and host plants influence the compositional and abundance changes of nitrogen-cycling genes in bulk and rhizosphere soil microhabitats.
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Müller O, Wilson B, Paulsen ML, Rumińska A, Armo HR, Bratbak G, Øvreås L. Spatiotemporal Dynamics of Ammonia-Oxidizing Thaumarchaeota in Distinct Arctic Water Masses. Front Microbiol 2018; 9:24. [PMID: 29410658 PMCID: PMC5787140 DOI: 10.3389/fmicb.2018.00024] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/08/2018] [Indexed: 12/01/2022] Open
Abstract
One of the most abundant archaeal groups on Earth is the Thaumarchaeota. They are recognized as major contributors to marine ammonia oxidation, a crucial step in the biogeochemical cycling of nitrogen. Their universal success is attributed to a high genomic flexibility and niche adaptability. Based on differences in the gene coding for ammonia monooxygenase subunit A (amoA), two different ecotypes with distinct distribution patterns in the water column have been identified. We used high-throughput sequencing of 16S rRNA genes combined with archaeal amoA functional gene clone libraries to investigate which environmental factors are driving the distribution of Thaumarchaeota ecotypes in the Atlantic gateway to the Arctic Ocean through an annual cycle in 2014. We observed the characteristic vertical pattern of Thaumarchaeota abundance with high values in the mesopelagic (>200 m) water throughout the entire year, but also in the epipelagic (<200 m) water during the dark winter months (January, March and November). The Thaumarchaeota community was dominated by three OTUs which on average comprised 76% ± 11 and varied in relative abundance according to water mass characteristics and not to depth or ammonium concentration, as suggested in previous studies. The ratios of the abundance of the different OTU types were similar to that of the functional amoA water cluster types. Together, this suggests a strong selection of ecotypes within different water masses, supporting the general idea of water mass characteristics as an important factor in defining microbial community structure. If indeed, as suggested in this study, Thaumarchaeota population dynamics are controlled by a set of factors, described here as water mass characteristics and not just depth alone, then changes in water mass flow will inevitably affect the distribution of the different ecotypes.
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Affiliation(s)
- Oliver Müller
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Bryan Wilson
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Maria L Paulsen
- Department of Microbiology, University of Bergen, Bergen, Norway
| | | | - Hilde R Armo
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Gunnar Bratbak
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Lise Øvreås
- Department of Microbiology, University of Bergen, Bergen, Norway.,University Center in Svalbard (UNIS), Longyearbyen, Norway
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Li J, Jiang LJ, Wang XL, Xiao L. [Effect of Eichhornia crassipes on Ammoxidation and Denitrification Microorganisms in Eutrophic Freshwaters]. Huan Jing Ke Xue 2017; 38:4253-4261. [PMID: 29965209 DOI: 10.13227/j.hjkx.201701179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The water hyacinth, Eichhornia crassipes, is widely used for the ecological restoration of eutrophic freshwater bodies, but little is known about its microbial interactions and nitrogen removal potential. In this study, we compared the relative importance of E. crassipes and bacteria in nitrogen removal. We also examined the plant's ability to modulate the abundance and diversity of nitrifying and denitrifying bacteria. Nitrogen removal and the genetic potential for nitrification and denitrification, determined using quantitative polymerase chain reactions (qPCRs) of the nitrification gene amoA and the denitrification genes nirS/K, were evaluated in microcosms containing water from a eutrophic lake with or without E. crassipes. The results showed that total nitrogen (TN) losses on day 70 of the experiment were similar in all treatments but the uptake by E. crassipes resulted in the rapid (within 24 h) removal of TN and NH4+-N. In microcosms containing E. crassipes, the abundance of amoA increased whereas the abundances of nirS/K decreased. The T-RFLP (terminal restriction fragment length polymorphism) profiles showed that Nitrosomonas dominated the ammonia-oxidizing prokaryotes, based on the DNA and RNA levels of the targeted genes. The E. crassipes cultivation can be used to achieve fast and efficient reductions in NH4+-N concentrations in eutrophic water bodies. While this aquatic macrophyte may not be essential to N removal, considering the potential toxicity of NH4+-N, both aquaphytes and microbes should be fully exploited in the restoration of freshwater ecosystems.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Li-Juan Jiang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiao-Lin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lin Xiao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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Pjevac P, Schauberger C, Poghosyan L, Herbold CW, van Kessel MAHJ, Daebeler A, Steinberger M, Jetten MSM, Lücker S, Wagner M, Daims H. AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment. Front Microbiol 2017; 8:1508. [PMID: 28824606 PMCID: PMC5543084 DOI: 10.3389/fmicb.2017.01508] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/27/2017] [Indexed: 12/03/2022] Open
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.
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Affiliation(s)
- Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Clemens Schauberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Lianna Poghosyan
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Craig W. Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Anne Daebeler
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Michaela Steinberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of ViennaVienna, Austria
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Jing H, Cheung S, Xia X, Suzuki K, Nishioka J, Liu H. Geographic Distribution of Ammonia-Oxidizing Archaea along the Kuril Islands in the Western Subarctic Pacific. Front Microbiol 2017; 8:1247. [PMID: 28713363 PMCID: PMC5492448 DOI: 10.3389/fmicb.2017.01247] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/20/2017] [Indexed: 11/17/2022] Open
Abstract
Community composition and abundance of ammonia-oxidizing archaea (AOA) in the ocean were affected by different physicochemical conditions, but their responses to physical barriers (such as a chain of islands) were largely unknown. In our study, geographic distribution of the AOA from the surface photic zone to the deep bathypelagic waters in the western subarctic Pacific adjacent to the Kuril Islands was investigated using pyrosequencing based on the ammonia monooxygenase subunit A (amoA) gene. Genotypes of clusters A and B dominated in the upper euphotic zone and the deep waters, respectively. Quantitative PCR assays revealed that the occurrence and ammonia-oxidizing activity of ammonia-oxidizing archaea (AOA) reached their maxima at the depth of 200 m, where a higher diversity and abundance of actively transcribed AOA was observed at the station located in the marginal sea exposed to more terrestrial input. Similar community composition of AOA observed at the two stations adjacent to the Kuril Islands maybe due to water exchange across the Bussol Strait. They distinct from the station located in the western subarctic gyre, where sub-cluster WCAII had a specific distribution in the surface water, and this sub-cluster seemed having a confined distribution in the western Pacific. Habitat-specific groupings of different WCB sub-clusters were observed reflecting the isolated microevolution existed in cluster WCB. The effect of the Kuril Islands on the phylogenetic composition of AOA between the Sea of Okhotsk and the western subarctic Pacific is not obvious, possibly because our sampling stations are near to the Bussol Strait, the main gateway through which water is exchanged between the Sea of Okhotsk and the Pacific. The vertical and horizontal distribution patterns of AOA communities among stations along the Kuril Islands were essentially determined by the in situ prevailing physicochemical gradients along the two dimensions.
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Affiliation(s)
- Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of SciencesSanya, China
| | - Shunyan Cheung
- Division of Life Science, The Hong Kong University of Science and TechnologyKowloon, China
| | - Xiaomin Xia
- Division of Life Science, The Hong Kong University of Science and TechnologyKowloon, China
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido UniversitySapporo, Japan
| | - Jun Nishioka
- Institute of Low Temperature Science, Hokkaido UniversitySapporo, Japan
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and TechnologyKowloon, China
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34
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McGee CF, Storey S, Clipson N, Doyle E. Soil microbial community responses to contamination with silver, aluminium oxide and silicon dioxide nanoparticles. Ecotoxicology 2017; 26:449-458. [PMID: 28197855 DOI: 10.1007/s10646-017-1776-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/04/2017] [Indexed: 05/14/2023]
Abstract
Soil microorganisms are key contributors to nutrient cycling and are essential for the maintenance of healthy soils and sustainable agriculture. Although the antimicrobial effects of a broad range of nanoparticulate substances have been characterised in vitro, little is known about the impact of these compounds on microbial communities in environments such as soil. In this study, the effect of three widely used nanoparticulates (silver, silicon dioxide and aluminium oxide) on bacterial and fungal communities in an agricultural pastureland soil was examined in a microcosm-based experiment using a combination of enzyme analysis, molecular fingerprinting and amplicon sequencing. A relatively low concentration of silver nanoparticles (AgNPs) significantly reduced total soil dehydrogenase and urease activity, while Al2O3 and SiO2 nanoparticles had no effect. Amplicon sequencing revealed substantial shifts in bacterial community composition in soils amended with AgNPs, with significant decreases in the relative abundance of Acidobacteria and Verrucomicrobia and an increase in Proteobacteria. In particular, the relative abundance of the Proteobacterial genus Dyella significantly increased in AgNP amended soil. The effects of Al2O3 and SiO2 NPs on bacterial community composition were less pronounced. AgNPs significantly reduced bacterial and archaeal amoA gene abundance in soil, with the archaea more susceptible than bacteria. AgNPs also significantly impacted soil fungal community structure, while Al2O3 and SiO2 NPs had no effect. Several fungal ribotypes increased in soil amended with AgNPs, compared to control soil. This study highlights the need to consider the effects of individual nanoparticles on soil microbial communities when assessing their environmental impact.
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Affiliation(s)
- C F McGee
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - S Storey
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - N Clipson
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - E Doyle
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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35
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Pjevac P, Schauberger C, Poghosyan L, Herbold CW, van Kessel MAHJ, Daebeler A, Steinberger M, Jetten MSM, Lücker S, Wagner M, Daims H. AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment. Front Microbiol 2017. [PMID: 28824606 DOI: 10.1101/096891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.
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Affiliation(s)
- Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Clemens Schauberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Lianna Poghosyan
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Maartje A H J van Kessel
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Anne Daebeler
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Michaela Steinberger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud UniversityNijmegen, Netherlands
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry meets Microbiology', University of ViennaVienna, Austria
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36
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Zhang Z, Zhang W, Yang H, Sheng R, Wei W, Qin H. Elevated N 2O emission by the rice roots: based on the abundances of narG and bacterial amoA genes. Environ Sci Pollut Res Int 2017; 24:2116-2125. [PMID: 27812967 DOI: 10.1007/s11356-016-7993-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 10/25/2016] [Indexed: 06/06/2023]
Abstract
Rice fields are an important source of nitrous oxide (N2O), where rice plants could act as a key factor controlling N2O fluxes during the flooding-drying process; however, the microbial driving mechanisms are unclear. In this study, specially designed equipment was used to grow rice plants and collect emitted N2O from the root-growing zone (zone A), root-free zones (zones B, C, and D) independently, at tillering and booting stages under flooding and drying conditions. Soil samples from the four zones were also taken separately. Nitrifying and denitrifying community abundances were detected using quantitative polymerase chain reaction (qPCR). The N2O emission increased significantly along with drying, but the N2O emission capabilities varied among the four zones under drying, while zone B possessed the highest N2O fluxes that were 2.7~4.5 times higher than those from zones C and D. However, zone A showed N2O consumption potential. Notably, zone B also harbored the highest numbers of narG-containing denitrifiers and amoA-containing nitrifiers under drying at both tillering and booting stages. This study demonstrates that drying caused significant increase in N2O emission from rhizosphere soil, in which the higher abundance of AOB would help to produce more nitrate and significantly higher narG-containing microbes would drive more N2O production and emission.
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Affiliation(s)
- Zhenxing Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenzhao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Huicui Yang
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rong Sheng
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Wenxue Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Hongling Qin
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Taoyuan Agro-ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China.
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Xiao PY, Zhang DJ, Lu PL. [Characteristics of Nitrobacteria in SBR with Trace N 2H 4 Addition]. Huan Jing Ke Xue 2016; 37:4734-4740. [PMID: 29965315 DOI: 10.13227/j.hjkx.201601196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A sequencing batch reactor (SBR) was conducted to perform nitrification process. The influence of long-term trace hydrazine (N2H4) addition (about 3 mg·L-1) on ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in nitrifying sludge was investigated. The result indicated that Nitrosococcu, Nitrosomonas and Nitrosospira were related to AOB, and Nitrobacter was related to NOB in nitrifying sludge with N2H4 addition, respectively. The estimates of AOB population (in dry sludge) with N2H4 addition decreased from 1.0×109 to 2.09×104 copies·g-1, and those of NOB decreased from 1.28×107 to 2.56×105 copies·g-1. AOB was more sensitive to environmental factors than NOB, the effect of inhibition and toxicity on nitrobacteria caused more loss of AOB abundances than that of NOB, but quantitative real-time PCR could not determine the inhibition of N2H4 on microbial activity of AOB and NOB. The nitrobacteria activity was destroyed with long-term trace N2H4 addition, and the reactor collapsed. Consequently, it was possibly unable to inhibit NOB activity by controlling the added N2H4 concentration, and further take off NOB in nitrification process for improving nitrogen removal.
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Affiliation(s)
- Peng-Ying Xiao
- School of Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Dai-Jun Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, College of Resources and Environmental Science, Chongqing University, Chongqing 400030, China
| | - Pei-Li Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, College of Resources and Environmental Science, Chongqing University, Chongqing 400030, China
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Rughöft S, Herrmann M, Lazar CS, Cesarz S, Levick SR, Trumbore SE, Küsel K. Corrigendum: Community Composition and Abundance of Bacterial, Archaeal, and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa. Front Microbiol 2016; 7:1954. [PMID: 27904470 PMCID: PMC5126705 DOI: 10.3389/fmicb.2016.01954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 11/21/2016] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article on p. 1638 in vol. 7, PMID: 27807431.].
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Affiliation(s)
- Saskia Rughöft
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Martina Herrmann
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Cassandre S Lazar
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany; Institute of Biology, Leipzig UniversityLeipzig, Germany
| | - Shaun R Levick
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | - Susan E Trumbore
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | - Kirsten Küsel
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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Chen X, Yang J, Zhu X, Liang X, Lei Y, He C. N-fixing trees in wetland restoration plantings: effects on nitrogensupply and soil microbial communities. Environ Sci Pollut Res Int 2016; 23:24749-24757. [PMID: 27658403 DOI: 10.1007/s11356-016-7454-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 08/10/2016] [Indexed: 06/06/2023]
Abstract
To investigate the impact of an exotic Frankia nodulated tree (Alnus trabeculosa) on soil nitrogen content, soil microbial composition, and the abundance of N turnover-related functional microorganism community, we compared the community structure and abundance of key functional genes (nifH, bacterial/archaeal amoA, and nosZ) in the rhizosphere and nonrhizosphere of monoculture of Phragmites australis and A.trabeculosa-P.australis mixed communities by MiSeq Illumina sequencing and real-time PCR, respectively. The introduction of Frankia nodulated tree to recover degraded wetland was effective in the accumulation of soil organic carbon and nitrogen, which was the key factor to impact on the bacterial community composition revealed by canonical correspondence analysis. Acidobacteria and Proteobacteria were the dominant bacterial phylums while seven rare phyla appeared the most phylogenetically different among the investigated soil of two vegetations, including Chlorobi, Cyanobacteria, OD1, OP11, TM6, TM7, and GN02. The gene copy numbers of nifH were ranged from 2.28 × 108 to 2.96 × 109 copies g-1 dry soil in the wetland, and which were significantly higher in soil samples from P. australis than that from A.trabeculosa. While the abundance of nosZ in both rhizosphere and nonrhizosphere soils of A.trabeculosa-P.australis mixed communities was significantly lower compared with P.australis monoculture. The potential nitrification (PNA) (0.15-0.41 mg NOx-N kg-1 dry soil d-1) in the rhizosphere of A. trabeculosa was significantly higher than that of P. australis, and the soil denitrification enzyme activity (DEA) (0.42-0.90 nmol N2O-N g-1 dry soil h-1) was lower in the mixed community compared with monoculture of P. australis. The introduced planting of Frankia nodulated tree effectively accumulated soil organic carbon and nitrogen and reduce the relative abundance and activity of nitrogen-fixing bacteria and denitrification bacteria.
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Affiliation(s)
- XuePing Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - JunNa Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - XiE Zhu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - Xia Liang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - YanRu Lei
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - ChiQuan He
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China.
- , 150#, 99 Shangda Road, Shanghai, 200444, China.
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Cydzik-Kwiatkowska A, Rusanowska P, Zielińska M, Bernat K, Wojnowska-Baryła I. Microbial structure and nitrogen compound conversions in aerobic granular sludge reactors with non-aeration phases and acetate pulse feeding. Environ Sci Pollut Res Int 2016; 23:24857-24870. [PMID: 27662853 PMCID: PMC5124037 DOI: 10.1007/s11356-016-7709-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/13/2016] [Indexed: 05/13/2023]
Abstract
A technological system was developed for efficient nitrogen removal from real digester supernatant in a single reactor with shortened aeration to increase the economical aspects of wastewater treatment. The supernatant (600 mg TKN/L, low COD/N ratio of 2.2) was treated in batch reactors with aerobic granules (GSBRs) to test how one, two, or three non-aeration phases and acetate pulse feeding in the cycle affect the morphological and microbial properties of biomass. Introduction of one non-aeration phase in the cycle increased nitrogen removal efficiency by 11 % in comparison with constantly aerated GSBR. The additional non-aeration phases did not diminish the efficiency of ammonia oxidation but did favor nitrification to nitrate. Acetate pulse feeding in the reactor with three non-aeration phases raised the efficiency of nitrogen removal to 77 %; in parallel, the number of denitrifiers possessing nosZ genes and performing denitrification to N2 increased. Ammonia was oxidized by aerobic and anaerobic ammonia-oxidizing bacteria and heterotrophic nitrifiers (Pseudomonas sp. and Alcaligenes faecalis) that coexisted in granules. Azoarcus sp., Rhizobium sp., and Thauera sp. were core genera of denitrifiers in granules. An increase in the number of non-aeration phases diminished EPS content in the biomass and granule diameters and increased granule density.
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Affiliation(s)
| | - Paulina Rusanowska
- University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-709, Olsztyn, Poland
| | - Magdalena Zielińska
- University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-709, Olsztyn, Poland
| | - Katarzyna Bernat
- University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-709, Olsztyn, Poland
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Rughöft S, Herrmann M, Lazar CS, Cesarz S, Levick SR, Trumbore SE, Küsel K. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa. Front Microbiol 2016; 7:1638. [PMID: 27807431 PMCID: PMC5069293 DOI: 10.3389/fmicb.2016.01638] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/30/2016] [Indexed: 11/13/2022] Open
Abstract
Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20-66%), Chloroflexi (9-29%), and Firmicutes (7-42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43-99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g-1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g-1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our results suggest a strong effect of the savanna soils' nutrient scarcity on all microbial communities, resulting in a distinct community structure that differs markedly from nutrient-rich, temperate grasslands, along with a high relevance of archaeal ammonia oxidation in savanna soils.
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Affiliation(s)
- Saskia Rughöft
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Martina Herrmann
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Cassandre S Lazar
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany; Institute of Biology, Leipzig UniversityLeipzig, Germany
| | - Shaun R Levick
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | - Susan E Trumbore
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | - Kirsten Küsel
- Chair of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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Watanabe K, Kohzu A, Suda W, Yamamura S, Takamatsu T, Takenaka A, Koshikawa MK, Hayashi S, Watanabe M. Microbial nitrification in throughfall of a Japanese cedar associated with archaea from the tree canopy. Springerplus 2016; 5:1596. [PMID: 27652169 PMCID: PMC5026986 DOI: 10.1186/s40064-016-3286-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/11/2016] [Indexed: 12/29/2022]
Abstract
To investigate the nitrification potential of phyllospheric microbes, we incubated throughfall samples collected under the canopies of Japanese cedar (Cryptomeria japonica) and analyzed the transformation of inorganic nitrogen in the samples. Nitrate concentration increased in the unfiltered throughfall after 4 weeks of incubation, but remained nearly constant in the filtered samples (pore size: 0.2 and 0.4 µm). In the unfiltered samples, δ18O and δ15N values of nitrate decreased during incubation. In addition, archaeal ammonia monooxygenase subunit A (amoA) genes, which participate in the oxidation of ammonia, were found in the throughfall samples, although betaproteobacterial amoA genes were not detected. The amoA genes recovered from the leaf surface of C. japonica were also from archaea. Conversely, nitrate production, decreased isotope ratios of nitrate, and the presence of amoA genes was not observed in rainfall samples collected from an open area. Thus, the microbial nitrification that occurred in the incubated throughfall is likely due to ammonia-oxidizing archaea that were washed off the tree canopy by precipitation.
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Affiliation(s)
- Keiji Watanabe
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan ; Center for Environmental Science in Saitama, Kazo, Saitama 347-0115 Japan
| | - Ayato Kohzu
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Wataru Suda
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562 Japan
| | - Shigeki Yamamura
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Takejiro Takamatsu
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Akio Takenaka
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Masami Kanao Koshikawa
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Seiji Hayashi
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
| | - Mirai Watanabe
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506 Japan
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Zhou X, Fornara D, Ikenaga M, Akagi I, Zhang R, Jia Z. The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils. Front Microbiol 2016; 7:1101. [PMID: 27486444 PMCID: PMC4949271 DOI: 10.3389/fmicb.2016.01101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/01/2016] [Indexed: 02/04/2023] Open
Abstract
Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations, such as significant changes in water availability.
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Affiliation(s)
- Xue Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of SciencesNanjing, China; University of Chinese Academy of SciencesBeijing, China
| | - Dario Fornara
- Agri-Food and Biosciences Institute Belfast, Ireland
| | - Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University Kagoshima, Japan
| | - Isao Akagi
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University Kagoshima, Japan
| | - Ruifu Zhang
- National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agriculture University Nanjing, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
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Bernhard AE, Sheffer R, Giblin AE, Marton JM, Roberts BJ. Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill. Front Microbiol 2016; 7:854. [PMID: 27375576 PMCID: PMC4899434 DOI: 10.3389/fmicb.2016.00854] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
Abstract
The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain.
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Affiliation(s)
| | | | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory Woods Hole, MA, USA
| | - John M Marton
- Louisiana Universities Marine Consortium Chauvin, LA, USA
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Herbold CW, Pelikan C, Kuzyk O, Hausmann B, Angel R, Berry D, Loy A. Corrigendum: A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes. Front Microbiol 2016; 7:870. [PMID: 27375591 PMCID: PMC4893487 DOI: 10.3389/fmicb.2016.00870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/23/2016] [Indexed: 11/27/2022] Open
Abstract
[This corrects the article on p. 731 in vol. 6, PMID: 26236305.].
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Affiliation(s)
| | | | | | | | | | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of ViennaVienna, Austria
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Nagymáté Z, Homonnay ZG, Márialigeti K. Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms. Microbiol Res 2016; 188-189:80-89. [PMID: 27296965 DOI: 10.1016/j.micres.2016.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/24/2016] [Accepted: 04/30/2016] [Indexed: 10/21/2022]
Abstract
Total microbial community structure, and particularly nitrifying communities inhabiting five different small drinking water networks characterized with different water physical and chemical parameters was investigated, using cultivation-based methods and sequence aided Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis. Ammonium ion, originated from well water, was only partially oxidized via nitrite to nitrate in the drinking water distribution systems. Nitrification occurred at low ammonium ion concentration (27-46μM), relatively high pH (7.6-8.2) and over a wide range of dissolved oxygen concentrations (0.4-9.0mgL(-1)). The nitrifying communities of the distribution systems were characterized by variable most probable numbers (2×10(2)-7.1×10(4) MPN L(-1)) and probably originated from the non-treated well water. The sequence aided T-RFLP method revealed that ammonia-oxidizing microorganisms and nitrite-oxidizing Bacteria (Nitrosomonas oligotropha, Nitrosopumilus maritimus, and Nitrospira moscoviensis, 'Candidatus Nitrospira defluvii') were present in different ratios in the total microbial communities of the distinct parts of the water network systems. The nitrate generated by nitrification was partly utilized by nitrate-reducing (and denitrifying) Bacteria, present in low MPN and characterized by sequence aided T-RFLP as Comamonas sp. and Pseudomonas spp. Different environmental factors, like pH, chemical oxygen demand, calculated total inorganic nitrogen content (moreover nitrite and nitrate concentration), temperature had important effect on the total bacterial and archaeal community distribution.
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Affiliation(s)
- Zsuzsanna Nagymáté
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, 1117 Budapest, Hungary.
| | - Zalán G Homonnay
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, 1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, 1117 Budapest, Hungary
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Banerjee S, Kennedy N, Richardson AE, Egger KN, Siciliano SD. Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis. Can J Microbiol 2016; 62:485-91. [PMID: 27045904 DOI: 10.1139/cjm-2015-0669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2-5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.
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Affiliation(s)
- Samiran Banerjee
- a Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.,b CSIRO Agriculture, Crace, ACT 2911, Australia
| | - Nabla Kennedy
- c Ecosystem Science & Management Program, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | | | - Keith N Egger
- c Ecosystem Science & Management Program, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Steven D Siciliano
- a Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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Fan X, Yu H, Wu Q, Ma J, Xu H, Yang J, Zhuang Y. Effects of fertilization on microbial abundance and emissions of greenhouse gases (CH4 and N2O) in rice paddy fields. Ecol Evol 2016; 6:1054-63. [PMID: 26811747 PMCID: PMC4722792 DOI: 10.1002/ece3.1879] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/20/2015] [Accepted: 11/25/2015] [Indexed: 11/09/2022] Open
Abstract
This study is to explore effects of nitrogen application and straw incorporation on abundance of relevant microbes and CH4 and N2O fluxes in a midseason aerated rice paddy field. Fluxes of CH4 and N2O were recorded, and abundance of relevant soil microbial functional genes was determined during rice‐growing season in a 6‐year‐long fertilization experiment field in China. Results indicate that application of urea significantly changed the functional microbial composition, while the influence of straw incorporation was not significant. Application of urea significantly decreased the gene abundances of archaeal amoA and mcrA, but it significantly increased the gene abundances of bacterial amoA. CH4 emission was significantly increased by fresh straw incorporation. Incorporation of burnt straw tended to increase CH4 emission, while the urea application had no obvious effect on CH4 emission. N2O emission was significantly increased by urea application, while fresh or burnt straw incorporation tended to decrease N2O emission. The functional microbial composition did not change significantly over time, although the abundances of pmoA, archaeal amoA, nirS, and nosZ genes changed significantly. The change of CH4 emission showed an inverse trend with the one of the N2O emissions over time. To some extent, the abundance of some functional genes in this study can explain CH4 and N2O emissions. However, the correlation between CH4 and N2O emissions and the abundance of related functional genes was not significant. Environmental factors, such as soil Eh, may be more related to CH4 and N2O emissions.
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Affiliation(s)
- Xianfang Fan
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing 210008 China
| | - Haiyang Yu
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing 210008 China; University of the Chinese Academy of Sciences Beijing 100039 China
| | - Qinyan Wu
- Zhenjiang Institute of Agricultural Science Jurong 212400 China
| | - Jing Ma
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing 210008 China
| | - Hua Xu
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing 210008 China
| | - Jinghui Yang
- Zhenjiang Institute of Agricultural Science Jurong 212400 China
| | - Yiqing Zhuang
- Zhenjiang Institute of Agricultural Science Jurong 212400 China
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Abstract
The first step of nitrification, the oxidation of ammonia to nitrite, can be performed by ammonia-oxidizing archaea (AOA) or ammonium-oxidizing bacteria (AOB). We investigated the presence of these two groups in three structurally different types of coastal microbial mats that develop along the tidal gradient on the North Sea beach of the Dutch barrier island Schiermonnikoog. The abundance and transcription of amoA, a gene encoding for the alpha subunit of ammonia monooxygenase that is present in both AOA and AOB, were assessed and the potential nitrification rates in these mats were measured. The potential nitrification rates in the three mat types were highest in autumn and lowest in summer. AOB and AOA amoA genes were present in all three mat types. The composition of the AOA and AOB communities in the mats of the tidal and intertidal stations, based on the diversity of amoA, were similar and clustered separately from the supratidal microbial mat. In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes. The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were positively correlated with the potential nitrification rate. The composition and abundance of amoA genes seemed to be partly driven by salinity, ammonium, temperature, and the nitrate/nitrite concentration. We conclude that AOB are responsible for the bulk of the ammonium oxidation in these coastal microbial mats.
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Affiliation(s)
- Haoxin Fan
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands
| | - Lucas J Stal
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands ; Department of Aquatic Microbiology, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
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50
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Sterngren AE, Hallin S, Bengtson P. Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil. Front Microbiol 2015; 6:1350. [PMID: 26648926 PMCID: PMC4663241 DOI: 10.3389/fmicb.2015.01350] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/16/2015] [Indexed: 12/02/2022] Open
Abstract
Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil.
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Affiliation(s)
- Anna E Sterngren
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
| | - Sara Hallin
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Per Bengtson
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
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