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Understanding the Response of Nitrifying Communities to Disturbance in the McMurdo Dry Valleys, Antarctica. Microorganisms 2020; 8:microorganisms8030404. [PMID: 32183078 PMCID: PMC7143839 DOI: 10.3390/microorganisms8030404] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 01/07/2023] Open
Abstract
Polar ecosystems are generally limited in nitrogen (N) nutrients, and the patchy availability of N is partly determined by biological pathways, such as nitrification, which are carried out by distinctive prokaryotic functional groups. The activity and diversity of microorganisms are generally strongly influenced by environmental conditions. However, we know little of the attributes that control the distribution and activity of specific microbial functional groups, such as nitrifiers, in extreme cold environments and how they may respond to change. To ascertain relationships between soil geochemistry and the ecology of nitrifying microbial communities, we carried out a laboratory-based manipulative experiment to test the selective effect of key geochemical variables on the activity and abundance of ammonia-oxidizing communities in soils from the McMurdo Dry Valleys of Antarctica. We hypothesized that nitrifying communities, adapted to different environmental conditions within the Dry Valleys, will have distinct responses when submitted to similar geochemical disturbances. In order to test this hypothesis, soils from two geographically distant and geochemically divergent locations, Miers and Beacon Valleys, were incubated over 2 months under increased conductivity, ammonia concentration, copper concentration, and organic matter content. Amplicon sequencing of the 16S rRNA gene and transcripts allowed comparison of the response of ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) to each treatment over time. This approach was combined with measurements of 15NH4+ oxidation rates using 15N isotopic additions. Our results showed a higher potential for nitrification in Miers Valley, where environmental conditions are milder relative to Beacon Valley. AOA exhibited better adaptability to geochemical changes compared to AOB, particularly to the increase in copper and conductivity. AOA were also the only nitrifying group found in Beacon Valley soils. This laboratorial manipulative experiment provided new knowledge on how nitrifying groups respond to changes on key geochemical variables of Antarctic desert soils, and we believe these results offer new insights on the dynamics of N cycling in these ecosystems.
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152
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Taylor HB, Kurtz HD. Composition, diversity, and activity of aerobic ammonia-oxidizing Bacteria and Archaea in the intertidal sands of a grand strand South Carolina beach. Microbiologyopen 2020; 9:e1011. [PMID: 32126588 PMCID: PMC7221436 DOI: 10.1002/mbo3.1011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 01/22/2023] Open
Abstract
Aerobic ammonia oxidation to nitrite has been established as an important ecosystem process in regulating the level of nitrogen in marine ecosystems. This process is carried out by ammonia-oxidizing bacteria (AOB) within the classes Betaproteobacteria and Gammaproteobacteria and ammonia-oxidizing Archaea (AOA) from the phylum Thaumarchaeota, and the latter of which has been established as more prevalent in marine systems. This study investigated the presence, abundance, and activity of these groups of microbes at a beach near Springmaid Pier in Myrtle Beach, South Carolina, through the implementation of next generation sequencing, quantitative PCR (qPCR), and microcosm experiments to monitor activity. Sequencing analysis revealed a diverse community of ammonia-oxidizing microbes dominated by AOA classified within the family Nitrosopumilaceae, and qPCR revealed the abundance of AOA amoA genes over AOB by at least an order of magnitude in most samples. Microcosm studies indicate that the rates of potential ammonia oxidation in these communities satisfy Michaelis-Menten substrate kinetics and this process is more active at temperatures corresponding to summer months than winter. Potential rates in AOA medium were higher than that of AOB medium, indicating a potentially greater contribution of AOA to this process in this environment. In conclusion, this study provides further evidence of the dominance of AOA in these environments compared with AOB and highlights the overall efficiency of this process at turning over excess ammonium that may be present in these environments.
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Affiliation(s)
- Harrison B Taylor
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States
| | - Harry D Kurtz
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States
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153
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Yan C, Huang J, Cao C, Li R, Ma Y, Wang Y. Effects of PVP-coated silver nanoparticles on enzyme activity, bacterial and archaeal community structure and function in a yellow-brown loam soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:8058-8070. [PMID: 31897981 DOI: 10.1007/s11356-019-07347-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
The undesirable effects of silver nanoparticles (AgNPs) on soil environment have caused much concern. The previous studies, however, focused on sandy soil, with little known on others. In present study, the effects of polyvinylpyrrolidone-coated AgNPs (0, 1, 10, and 100 mg kg- 1 soil) on enzyme activities (urease and dehydrogenase), ammonia-oxidizing bacteria (AOB) and archaea (AOA), bacterial and archaeal communities, and microbial function profile in a yellow-brown loam soil were investigated. The significant dose-response inhibitions of AgNPs on enzyme activities were observed, with dehydrogenase more susceptible to AgNPs. Both of bacterial and archaeal amoA genes were reduced by AgNPs above 10 mg kg- 1, with AOB more susceptible to AgNPs than AOA. AgNPs at 100 mg kg- 1 caused reductions on the dominant Nitrosospira and Nitrosomonas, and even disappearance on Nitrosovibrio, while increase on Nitrososphaera significantly. AgNPs also changed bacterial and archaeal community structure. Exposure to AgNPs at 100 mg kg- 1 caused significant increases by 186.79% and 44.89% for Bacteroidetes and Proteobacteria, while decreases by 47.82%, 44.09%, 43.67%, and 80.44% for Actinobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia, respectively. Moreover, three dominant archaeal phyla (Thaumarchaeota, Euryarchaeota, and Parvarchaeota) were also reduced in the presence of AgNPs, especially Thaumarchaeota with the significant reduction of 13.71%. PICRUSt prediction revealed that AgNPs indeed had the potential to change soil microbial community's functional contributions. It must be cautious on the interference of AgNPs to soil ecological functions in the future.
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Affiliation(s)
- Chunni Yan
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Juan Huang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China.
| | - Chong Cao
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Runqing Li
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yixuan Ma
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yaoyao Wang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
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154
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Castellano-Hinojosa A, Strauss SL. Impact of Cover Crops on the Soil Microbiome of Tree Crops. Microorganisms 2020; 8:E328. [PMID: 32110988 PMCID: PMC7143828 DOI: 10.3390/microorganisms8030328] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/19/2020] [Accepted: 02/22/2020] [Indexed: 12/21/2022] Open
Abstract
Increased concerns associated with interactions between herbicides, inorganic fertilizers, soil nutrient availability, and plant phytotoxicity in perennial tree crop production systems have renewed interest in the use of cover crops in the inter-row middles or between trees as an alternative sustainable management strategy for these systems. Although interactions between the soil microbiome and cover crops have been examined for annual cropping systems, there are critical differences in management and growth in perennial cropping systems that can influence the soil microbiome and, therefore, the response to cover crops. Here, we discuss the importance of cover crops in tree cropping systems using multispecies cover crop mixtures and minimum tillage and no-tillage to not only enhance the soil microbiome but also carbon, nitrogen, and phosphorus cycling compared to monocropping, conventional tillage, and inorganic fertilization. We also identify potentially important taxa and research gaps that need to be addressed to facilitate assessments of the relationships between cover crops, soil microbes, and the health of tree crops. Additional evaluations of the interactions between the soil microbiome, cover crops, nutrient cycling, and tree performance will allow for more effective and sustainable management of perennial cropping systems.
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Affiliation(s)
| | - Sarah L. Strauss
- Department of Soil and Water Sciences, Southwest Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Immokalee, FL 34142, USA;
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155
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Presence of Archaea in dental caries biofilms. Arch Oral Biol 2020; 110:104606. [DOI: 10.1016/j.archoralbio.2019.104606] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/31/2019] [Accepted: 11/08/2019] [Indexed: 12/21/2022]
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156
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Reyes C, Hodgskiss LH, Baars O, Kerou M, Bayer B, Schleper C, Kraemer SM. Copper limiting threshold in the terrestrial ammonia oxidizing archaeon Nitrososphaera viennensis. Res Microbiol 2020; 171:134-142. [PMID: 31991171 DOI: 10.1016/j.resmic.2020.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 11/25/2022]
Abstract
Ammonia oxidizing archaea (AOA) inhabiting soils have a central role in the global nitrogen cycle. Copper (Cu) is central to many enzymes in AOA including ammonia monooxygenase (AMO), the enzyme involved in the first step of ammonia oxidation. This study explored the physiological response of the AOA soil isolate, Nitrososphaera viennensis (EN76T) to Cu-limiting conditions in order to approach its limiting threshold under laboratory conditions. The chelator TETA (1,4,8,11-tetraazacyclotetradecane N, N', N″, N‴-tetraacetic acid hydrochloride hydrate) with selective affinity for Cu2+ was used to lower bioavailable Cu2+ in culture experiments as predicted by thermodynamic speciation calculations. Results show that N. viennensis is Cu-limited at concentrations ≤10-15 mol L-1 free Cu2+ compared to standard conditions (10-12 mol L-1). This Cu2+ limiting threshold is similar to pure cultures of denitrifying bacteria and other AOA and AOB inhabiting soils, freshwaters and sewage (<10-16 mol L-1), and lower than pure cultures of the marine AOA Nitrosopumilus maritimus (<10-12.7 mol L-1), which also possesses a high amount of Cu-dependent enzymes.
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Affiliation(s)
- Carolina Reyes
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Oliver Baars
- North Carolina State University, Department of Entomology and Plant Pathology, 840 Main Campus Drive, Raleigh, NC, 27695, USA.
| | - Melina Kerou
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Division of Bio-Oceanography, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Christa Schleper
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Stephan M Kraemer
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
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157
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Pinto OHB, Silva TF, Vizzotto CS, Santana RH, Lopes FAC, Silva BS, Thompson FL, Kruger RH. Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume. BMC Microbiol 2020; 20:13. [PMID: 31941452 PMCID: PMC6964070 DOI: 10.1186/s12866-020-1698-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/09/2020] [Indexed: 11/15/2022] Open
Abstract
Background Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume. Results The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25. Conclusions Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.
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Affiliation(s)
- Otávio H B Pinto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Thais F Silva
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Carla S Vizzotto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.,Department of Civil and Environmental Engineering, University of Brasília, Brasilia, 70910-900, Brazil
| | | | - Fabyano A C Lopes
- Laboratory of Microbiology, Federal University of Tocantins, Palmas, 77500-000, Brazil
| | - Bruno S Silva
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Fabiano L Thompson
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Ricardo H Kruger
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.
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158
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Ginawi A, Wang L, Wang H, Yu B, Yunjun Y. Effects of environmental variables on abundance of ammonia-oxidizing communities in sediments of Luotian River, China. PeerJ 2020; 8:e8256. [PMID: 31934502 PMCID: PMC6951284 DOI: 10.7717/peerj.8256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022] Open
Abstract
Ammonia-oxidizing communities play important functional roles in the nitrification. However, environmental stresses can significantly affect this process by controlling the abundant communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. In this study, we examined the abundance variations of ammonia-oxidizing communities using quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) in a typical subtropical river, Luotian County, South Dabie Mountains, China. Clone libraries were conducted to evaluate the community structure and abundance of AOA and AOB in sediments. Results showed that Nitrososphaera sp and Nitrosopumilus sp were the most dominant AOA. The abundance of the AOA and AOB amoA gene ranged from 5.28 × 108 gene copies (g-soil−1) to 2.23 × 108 gene copies (g-soil−1) and 5.45 × 108 gene copies (g-soil−1) to 3.30 × 107 gene copies (g-soil−1), respectively. Five environmental variables, namely, ORP, DO, NO\documentclass[12pt]{minimal}
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}{}${}_{4}^{+}$\end{document}4+ were played a major function in microbial communities of AOA and AOB in sediments. The T-RFLP profiles of AOA showed that 488 and 116 bp T-RFs were dominated. Overall, the results of this study showed that anthropogenic activities andenvironmental stress in rivers can alter the structure and function of microbes in their variable environment.
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Affiliation(s)
- Amjed Ginawi
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Faculty of Marine Science and Fisheries, Red Sea University, Port Sudan, Red Sea State, Sudan
| | - Lixiao Wang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huading Wang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bingbing Yu
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yan Yunjun
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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159
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Laffite A, Florio A, Andrianarisoa KS, Creuze des Chatelliers C, Schloter‐Hai B, Ndaw SM, Periot C, Schloter M, Zeller B, Poly F, Le Roux X. Biological inhibition of soil nitrification by forest tree species affectsNitrobacterpopulations. Environ Microbiol 2020; 22:1141-1153. [DOI: 10.1111/1462-2920.14905] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/25/2019] [Accepted: 12/18/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Amandine Laffite
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Alessandro Florio
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | | | - Charline Creuze des Chatelliers
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Brigitte Schloter‐Hai
- Research Unit for Comparative Microbiome AnalysisHelmholtz Zentrum München D‐85764 Ingolstädter Landstraße 1 Neuherberg Germany
| | - Sidy M. Ndaw
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Charlotte Periot
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Michael Schloter
- Research Unit for Comparative Microbiome AnalysisHelmholtz Zentrum München D‐85764 Ingolstädter Landstraße 1 Neuherberg Germany
| | - Bernd Zeller
- Biogéochimie des Ecosystèmes ForestiersINRA Grand‐EST Nancy UR 1138 Route d'Amance, 54280 Champenoux France
| | - Franck Poly
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne LEM, INRA UMR 1418, CNRS UMR 5557Université Lyon 1, Université de Lyon F‐69622 Villeurbanne Cedex France
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160
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Prosser JI, Hink L, Gubry-Rangin C, Nicol GW. Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies. GLOBAL CHANGE BIOLOGY 2020; 26:103-118. [PMID: 31638306 DOI: 10.1111/gcb.14877] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/30/2019] [Indexed: 05/02/2023]
Abstract
Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N2 O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N2 O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N2 O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N2 O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N2 O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N2 O emissions.
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Affiliation(s)
- James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Linda Hink
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | | | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Lyon, France
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161
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Sanders T, Fiencke C, Hüpeden J, Pfeiffer EM, Spieck E. Cold Adapted Nitrosospira sp.: A Potential Crucial Contributor of Ammonia Oxidation in Cryosols of Permafrost-Affected Landscapes in Northeast Siberia. Microorganisms 2019; 7:E699. [PMID: 31847402 PMCID: PMC6955795 DOI: 10.3390/microorganisms7120699] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 01/01/2023] Open
Abstract
Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols.
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Affiliation(s)
- Tina Sanders
- Helmholtz Zentrum Geesthacht, Institut für Küstenforschung, Max-Planck-Str. 1, 21502 Geesthacht, Germany
| | - Claudia Fiencke
- Universität Hamburg, Institut für Bodenkunde, Allende-Platz 2, 20146 Hamburg, Germany; (C.F.); (E.M.P.)
- Center for Earth System Research and Sustainability, Universität Hamburg, Allende-Platz 2, 20146 Hamburg, Germany
| | - Jennifer Hüpeden
- Universität Hamburg, Mikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany; (J.H.); (E.S.)
| | - Eva Maria Pfeiffer
- Universität Hamburg, Institut für Bodenkunde, Allende-Platz 2, 20146 Hamburg, Germany; (C.F.); (E.M.P.)
- Center for Earth System Research and Sustainability, Universität Hamburg, Allende-Platz 2, 20146 Hamburg, Germany
| | - Eva Spieck
- Universität Hamburg, Mikrobiologie und Biotechnologie, Ohnhorststr. 18, 22609 Hamburg, Germany; (J.H.); (E.S.)
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162
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Tu R, Jin W, Han SF, Zhou X, Wang T, Gao SH, Wang Q, Chen C, Xie GJ, Wang Q. Rapid enrichment and ammonia oxidation performance of ammonia-oxidizing archaea from an urban polluted river of China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113258. [PMID: 31669955 DOI: 10.1016/j.envpol.2019.113258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 09/07/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Ammonia oxidation is the rate-limiting step in nitrification process and dominated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). In the present study, a highly enriched culture of AOA was obtained from urban polluted water in Shahe River, Shenzhen, China. The optimum growth conditions were identified by orthogonal analysis as 37 °C, with pH 7.0 and initial ammonia concentration of 1.0 mM. Under these conditions, the highest abundance of AOA was obtained as 4.6 × 107 copies/ng DNA. Growth of AOA in polluted river water showed significant reduction in ammonia concentration in AOA-enriched cultures without antibiotics after 10 days of incubation, while synchronous increase in nitrate concentration was up to 12.7 mg/L. However, AOA-enriched by antibiotic showed insignificant changes in ammonia or nitrite concentration. This study showed that AOB play an important role in ammonia oxidation of polluted river water, and AOA alone showed insignificant changes in ammonia or nitrite concentrations. Therefore, the ammonia oxidation performance of natural water could not be improved by adding high concentration AOA bacterial liquid.
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Affiliation(s)
- Renjie Tu
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Wenbiao Jin
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Song-Fang Han
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Xu Zhou
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China.
| | - Tianqiang Wang
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Shu-Hong Gao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Qing Wang
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 150001, Harbin, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 150001, Harbin, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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163
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Herber J, Klotz F, Frommeyer B, Weis S, Straile D, Kolar A, Sikorski J, Egert M, Dannenmann M, Pester M. A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance. Environ Microbiol 2019; 22:212-228. [PMID: 31657089 DOI: 10.1111/1462-2920.14840] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022]
Abstract
Ammonia released during organic matter mineralization is converted during nitrification to nitrate. We followed spatiotemporal dynamics of the nitrifying microbial community in deep oligotrophic Lake Constance. Depth-dependent decrease of total ammonium (0.01-0.84 μM) indicated the hypolimnion as the major place of nitrification with 15 N-isotope dilution measurements indicating a threefold daily turnover of hypolimnetic total ammonium. This was mirrored by a strong increase of ammonia-oxidizing Thaumarchaeota towards the hypolimnion (13%-21% of bacterioplankton) throughout spring to autumn as revealed by amplicon sequencing and quantitative polymerase chain reaction. Ammonia-oxidizing bacteria were typically two orders of magnitude less abundant and completely ammonia-oxidizing (comammox) bacteria were not detected. Both, 16S rRNA gene and amoA (encoding ammonia monooxygenase subunit B) analyses identified only one major species-level operational taxonomic unit (OTU) of Thaumarchaeota (99% of all ammonia oxidizers in the hypolimnion), which was affiliated to Nitrosopumilus spp. The relative abundance distribution of the single Thaumarchaeon strongly correlated to an equally abundant Chloroflexi clade CL500-11 OTU and a Nitrospira OTU that was one order of magnitude less abundant. The latter dominated among recognized nitrite oxidizers. This extremely low diversity of nitrifiers shows how vulnerable the ecosystem process of nitrification may be in Lake Constance as Central Europe's third largest lake.
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Affiliation(s)
- Janina Herber
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Franziska Klotz
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Benjamin Frommeyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Dietmar Straile
- Limnological Institute, University of Konstanz, Mainaustraße 252, Constance, 78464, Germany
| | - Allison Kolar
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Johannes Sikorski
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Michael Dannenmann
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany.,Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany.,Technical University of Braunschweig, Institute for Microbiology, Spielmannstrasse 7, Braunschweig, 38106, Germany
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164
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Mukhtar H, Lin YP, Lin CM, Lin YR. Relative Abundance of Ammonia Oxidizing Archaea and Bacteria Influences Soil Nitrification Responses to Temperature. Microorganisms 2019; 7:microorganisms7110526. [PMID: 31690001 PMCID: PMC6920900 DOI: 10.3390/microorganisms7110526] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/24/2019] [Accepted: 10/31/2019] [Indexed: 11/16/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB) are thought to contribute differently to soil nitrification, yet the extent to which their relative abundances influence the temperature response of nitrification is poorly understood. Here, we investigated the impact of different AOA to AOB ratios on soil nitrification potential (NP) across a temperature gradient from 4 °C to 40 °C in twenty different organic and inorganic fertilized soils. The temperature responses of different relative abundance of ammonia oxidizers for nitrification were modeled using square rate theory (SQRT) and macromolecular rate theory (MMRT) models. We found that the proportional nitrification rates at different temperatures varied among AOA to AOB ratios. Predicted by both models, an optimum temperature (Topt) for nitrification in AOA dominated soils was significantly higher than for soils where AOA and AOB abundances are within the same order of magnitude. Moreover, the change in heat capacity (ΔCP‡) associated with the temperature dependence of nitrification was positively correlated with Topt and significantly varied among the AOA to AOB ratios. The temperature ranges for NP decreased with increasing AOA abundance for both organic and inorganic fertilized soils. These results challenge the widely accepted approach of comparing NP rates in different soils at a fixed temperature. We conclude that a shift in AOA to AOB ratio in soils exhibits distinguished temperature-dependent characteristics that have an important impact on nitrification responses across the temperature gradient. The proposed approach benefits the accurate discernment of the true contribution of fertilized soils to nitrification for improvement of nitrogen management.
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Affiliation(s)
- Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Chiao-Ming Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan.
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165
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Pan KL, Gao JF, Li DC, Fan XY. The dominance of non-halophilic archaea in autotrophic ammonia oxidation of activated sludge under salt stress: A DNA-based stable isotope probing study. BIORESOURCE TECHNOLOGY 2019; 291:121914. [PMID: 31377507 DOI: 10.1016/j.biortech.2019.121914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/22/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Dynamics of nitrification activity, ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundance and active ammonia oxidizers of activated sludge were explored under different salinities. Results showed that specific ammonium oxidation rates were significantly negative with increasing salinity. The responses of AOA and AOB populations to salt stress were distinct. AOA abundance decreased at moderate salinities (2.5, 5 and 7 g L-1) and increased at high salinities (10, 15, 20 and 30 g L-1), while AOB abundance showed opposite tendency. DNA-based stable isotope probing assays indicated AOA exclusively dominated active ammonia oxidation of test samples under different salinities. The active AOA communities retrieved were all non-halophilic and regulated by salinities. Candidatus Nitrosocosmicus exaquare and Ca. Nitrosocosmicus franklandus were the predominantly active AOA in both salt-free and salt-containing microcosms, while 13C-labeled Nitrososphaera viennensis and Ca. Nitrososphaera gargensis were only retrieved from the microcosms amended with 0 and 30 g L-1 salinity, respectively.
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Affiliation(s)
- Kai-Ling Pan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jing-Feng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Ding-Chang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiao-Yan Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
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166
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Wang M, Chen S, Chen L, Wang D. Saline stress modifies the effect of cadmium toxicity on soil archaeal communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 182:109431. [PMID: 31301593 DOI: 10.1016/j.ecoenv.2019.109431] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/25/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
The objective of this study was to examine the response of soil archaeal communities to saline stress in different types of Cd-contaminated soils from the North China Plain. Increased soil salinity by addition of 0.5% sodium salts (NaCl: Na2SO4: NaHCO3: Na2CO3 = 1:9:9:1) increased available Cd concentration, resulting in decreased ratios of Cd2+/CdT and CdSO4/CdT and increased ratios of CdCln2-n/CdT in soil solution. Soil saline stress decreased archaeal abundance and diversity and changed major soil archaeal taxa. For example, increased saline stress enriched taxa in the archaeal phyla Thaumarchaeota and Euryarchaeota, and these enriched tolerant taxa had much stronger correlations with soil properties, such as soil pH, EC or Na+. In addition, some microbes with low abundances like Bathyarchaeia (no rank) and Candidatus Nitrosotenuis were found to closely correlate with soil pH, EC, Na+, and Cl-, indicating they might play disproportionate roles in regulating ecological functions in stressed habitats. These results suggest that saline stress modified the effect of Cd toxicity on soil archaeal communities in different types of Cd-contaminated soils.
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Affiliation(s)
- Meng Wang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs / Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Shibao Chen
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs / Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
| | - Li Chen
- Institute of Plant Protection and Environmental Protection, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, PR China
| | - Duo Wang
- College of Energy, Xiamen University, Xiamen, Fujian, 361102, PR China
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167
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Bale NJ, Palatinszky M, Rijpstra WIC, Herbold CW, Wagner M, Sinninghe Damsté JS. Membrane Lipid Composition of the Moderately Thermophilic Ammonia-Oxidizing Archaeon " Candidatus Nitrosotenuis uzonensis" at Different Growth Temperatures. Appl Environ Microbiol 2019; 85:e01332-19. [PMID: 31420340 PMCID: PMC6805073 DOI: 10.1128/aem.01332-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/12/2019] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Nitrosotenuis uzonensis" is the only cultured moderately thermophilic member of the thaumarchaeotal order Nitrosopumilales (NP) that contains many mesophilic marine strains. We examined its membrane lipid composition at different growth temperatures (37°C, 46°C, and 50°C). Its lipids were all membrane-spanning glycerol dialkyl glycerol tetraethers (GDGTs), with 0 to 4 cyclopentane moieties. Crenarchaeol (cren), the characteristic thaumarchaeotal GDGT, and its isomer (cren') were present in high abundance (30 to 70%). The GDGT polar headgroups were mono-, di-, and trihexoses and hexose/phosphohexose. The ratio of glycolipid to phospholipid GDGTs was highest in the cultures grown at 50°C. With increasing growth temperatures, the relative contributions of cren and cren' increased, while those of GDGT-0 to GDGT-4 (including isomers) decreased. TEX86 (tetraether index of tetraethers consisting of 86 carbons)-derived temperatures were much lower than the actual growth temperatures, further demonstrating that TEX86 does not accurately reflect the membrane lipid adaptation of thermophilic Thaumarchaeota As the temperature increased, specific GDGTs changed relative to their isomers, possibly representing temperature adaption-induced changes in cyclopentane ring stereochemistry. Comparison of a wide range of thaumarchaeotal core lipid compositions revealed that the "Ca Nitrosotenuis uzonensis" cultures clustered separately from other members of the NP order and the Nitrososphaerales (NS) order. While phylogeny generally seems to have a strong influence on GDGT distribution, our analysis of "Ca Nitrosotenuis uzonensis" demonstrates that its terrestrial, higher-temperature niche has led to a lipid composition that clearly differentiates it from other NP members and that this difference is mostly driven by its high cren' content.IMPORTANCE For Thaumarchaeota, the ratio of their glycerol dialkyl glycerol tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX86 proxy. "Ca Nitrosotenuis uzonensis" is a moderately thermophilic thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of "Ca Nitrosotenuis uzonensis" cultures was distinct from those of other members of its order and was more similar to those of other thermophilic, terrestrial Thaumarchaeota This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a thaumarchaeote inhabits also shapes its GDGT composition.
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Affiliation(s)
- Nicole J Bale
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Texel, The Netherlands
| | - Marton Palatinszky
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - W Irene C Rijpstra
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Texel, The Netherlands
| | - Craig W Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
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168
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Moeller FU, Webster NS, Herbold CW, Behnam F, Domman D, Albertsen M, Mooshammer M, Markert S, Turaev D, Becher D, Rattei T, Schweder T, Richter A, Watzka M, Nielsen PH, Wagner M. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. Environ Microbiol 2019; 21:3831-3854. [PMID: 31271506 PMCID: PMC6790972 DOI: 10.1111/1462-2920.14732] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022]
Abstract
Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.
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Affiliation(s)
- Florian U. Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Nicole S. Webster
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Craig W. Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Daryl Domman
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Stephanie Markert
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Dmitrij Turaev
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Dörte Becher
- Institute of Microbiology, Microbial ProteomicsUniversity of GreifswaldGreifswaldGermany
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
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169
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Li W, Feng D, Yang G, Deng Z, Rui J, Chen H. Soil water content and pH drive archaeal distribution patterns in sediment and soils of water-level-fluctuating zones in the East Dongting Lake wetland, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:29127-29137. [PMID: 31392608 DOI: 10.1007/s11356-019-06109-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Archaea play a vital role in Earth's geochemical cycles, but the factors that drive their distribution between sediments and water-level-fluctuating zones in the East Dongting Lake (EDL) wetland are poorly understood. Here, we used Illumina MiSeq to investigate the variation in the soil archaeal community structure and diversity among sediments and four water-level-fluctuating zones (mudflat, sedge, sedge-Phragmites, and Phragmites) in the EDL wetland. Diverse archaeal assemblages were found in our study, Crenarchaeota, Euryarchaeota, and ammonia-oxidizing and methanogenic subset were the dominant groups, and all their abundances shifted from sediment to water-level-fluctuating zones. The principal coordinates analysis and cluster analysis showed that the overall archaeal community structure was separated into two clusters: cluster I contained nine samples from sediment, mudflat, and sedge zones, whereas cluster II contained six samples from sedge-Phragmites and Phragmites zones. Archaeal diversity was significantly highest in sediment and lowest in Phragmites zone soils. The Mantel test showed that the variation in archaeal community structure was significantly positively correlated with soil water content and pH. The relative abundances of Crenarchaeota and Nitrososphaerales decreased with soil water content, while Euryarchaeota and Methanomicrobiales increased with soil water content. The relative abundance of Methanomicrobiales significantly decreased with pH (R2 = 0.34-0.48). Chao 1, observed operational taxonomic units, Shannon index, and Simpson index all correlated significantly positively with water content (R2 = 0.40-0.60), while Shannon and Simpson indexes both correlated significantly negatively with pH (R2 = 0.20-0.37). Our results demonstrated that the variations in the archaeal community structure were markedly driven by soil water content and pH in the EDL wetland. Our findings suggested that archaeal communities shifted among sediment and four water-level-fluctuating zones, highlighting that the spatiotemporal heterogeneity of greenhouse gas flux in small scale should be taken into account for accurate prediction of greenhouse gas emissions in the Dongting Lake area, especially on the background of climate change and human activities.
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Affiliation(s)
- Wei Li
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, 650091, China
| | - Defeng Feng
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, 650224, China
| | - Gang Yang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Zhengmiao Deng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Hunan, 410125, China
| | - Junpeng Rui
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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170
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Fang J, Zhao R, Cao Q, Quan Q, Sun R, Liu J. Effects of emergent aquatic plants on nitrogen transformation processes and related microorganisms in a constructed wetland in northern China. PLANT AND SOIL 2019; 443:473-492. [DOI: 10.1007/s11104-019-04249-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/01/2019] [Indexed: 06/14/2024]
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171
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Vera A, Moreno JL, García C, Morais D, Bastida F. Boron in soil: The impacts on the biomass, composition and activity of the soil microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 685:564-573. [PMID: 31181533 DOI: 10.1016/j.scitotenv.2019.05.375] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 06/09/2023]
Abstract
The high boron (B) content in desalinated seawater is a concern for crop development. However, in spite of the importance of the soil microbial community in soil fertility, the below-ground impacts of B are still unknown. Here, in a soil-ryegrass model system, the activity, biomass and diversity of the soil microbial community were evaluated in response to irrigation with: i) 0.3 mg B L-1; ii) 1 mg B L-1; and iii) 50 mg B L-1. We assessed two different compounds of boron: boric acid (H3BO3) and disodium tetraborate decahydrate (Na2B4O7·10H2O). Overall, the 1 mg B L-1 dose was identified as the threshold limit that did not irreversibly harm soil sustainability. In contrast, the highest B dose had a noticeable impact on the nitrogen (N) cycle of the soil, as demonstrated by an increase in the water-soluble N content and a decrease in urease activity. Analysis of the phospholipid fatty acids (PLFAs) revealed that the effect of B on the soil microbial biomass was dependent on the chemical form used. High B doses reduced soil microbial respiration and influenced the composition of the bacterial and fungal communities, with fungal diversity being diminished, as revealed by sequencing approaches.
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Affiliation(s)
- A Vera
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain.
| | - J L Moreno
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - C García
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - D Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, Praha 4 14220, Czech Republic
| | - F Bastida
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain
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172
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Mukhtar H, Lin YP, Lin CM, Petway JR. Assessing thermodynamic parameter sensitivity for simulating temperature responses of soil nitrification. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:1596-1608. [PMID: 31414689 DOI: 10.1039/c9em00310j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Soil nitrification responses to temperature have major implications for the global nitrogen cycle. Temperature sensitivity of soil nitrification has been modeled using several mathematical models, yet the extent to which model-generated thermodynamic parameters are accurate and sensitive in describing temperature sensitivity is unclear. In this study, we performed global sensitivity analysis to identify the key thermodynamic parameters that are most influential when simulating the temperature response of the soil nitrification potential (NP) across two different temperature gradients (4-40 °C and 20-45 °C) which are imposed upon sixteen different soils with square root growth (SQRT) and macromolecular rate theory (MMRT) models. We found that two thermodynamic parameters stand out as moderately to highly sensitive, and are uniquely identifiable in each model, regardless of the temperature range. The minimum and maximum measured temperatures seem to have no impact on the list of sensitive parameters but do influence the parameter ranges, especially for the SQRT model. However, parameters that control the minimum temperature and curvature of the NP response curve (Tmin and ΔC‡P) were found to have little to no sensitivity to SQRT and MMRT model outputs, respectively. We show that the parameter sensitivity and range of measured temperatures influence the complementary model's ability to describe the temperature sensitivity of soil nitrification. Our proposed framework enhances the accurate interpretation of existing thermodynamic parameters that explain the temperature sensitivity of soil biochemical processes, and provides methodological recommendations for future temperature sensitivity studies.
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Affiliation(s)
- Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
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173
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Lehtovirta-Morley LE. Ammonia oxidation: Ecology, physiology, biochemistry and why they must all come together. FEMS Microbiol Lett 2019; 365:4931719. [PMID: 29668934 DOI: 10.1093/femsle/fny058] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/09/2018] [Indexed: 12/31/2022] Open
Abstract
Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 -) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation.
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Affiliation(s)
- Laura E Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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174
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Norton J, Ouyang Y. Controls and Adaptive Management of Nitrification in Agricultural Soils. Front Microbiol 2019; 10:1931. [PMID: 31543867 PMCID: PMC6728921 DOI: 10.3389/fmicb.2019.01931] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.
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Affiliation(s)
- Jeanette Norton
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
| | - Yang Ouyang
- Department of Microbiology and Plant Biology, Institute of Environmental Genomics, University of Oklahoma, Norman, OK, United States
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175
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Wang B, Qin W, Ren Y, Zhou X, Jung MY, Han P, Eloe-Fadrosh EA, Li M, Zheng Y, Lu L, Yan X, Ji J, Liu Y, Liu L, Heiner C, Hall R, Martens-Habbena W, Herbold CW, Rhee SK, Bartlett DH, Huang L, Ingalls AE, Wagner M, Stahl DA, Jia Z. Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. ISME JOURNAL 2019; 13:3067-3079. [PMID: 31462715 PMCID: PMC6863869 DOI: 10.1038/s41396-019-0493-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/01/2019] [Accepted: 07/29/2019] [Indexed: 01/04/2023]
Abstract
Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is tightly linked to the acquisition of a variant of the energy-yielding ATPases via horizontal transfer. Whereas the ATPase genealogy of neutrophilic Thaumarchaeota is congruent with their organismal genealogy inferred from concatenated conserved proteins, a common clade of V-type ATPases unites phylogenetically distinct clades of acidophilic/acid-tolerant and piezophilic/piezotolerant species. A presumptive function of pumping cytoplasmic protons at low pH is consistent with the experimentally observed increased expression of the V-ATPase in an acid-tolerant thaumarchaeote at low pH. Consistently, heterologous expression of the thaumarchaeotal V-ATPase significantly increased the growth rate of E. coli at low pH. Its adaptive significance to growth in ocean trenches may relate to pressure-related changes in membrane structure in which this complex molecular machine must function. Together, our findings reveal that the habitat expansion of Thaumarchaeota is tightly correlated with extensive horizontal transfer of atp operons.
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Affiliation(s)
- Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Yi Ren
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Xue Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Man-Young Jung
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ping Han
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Emiley A Eloe-Fadrosh
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.,Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Lu Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xin Yan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Junbin Ji
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Linmeng Liu
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | | | | | - Willm Martens-Habbena
- Department of Microbiology and Cell Science & Fort Lauderdale Research and Education Center, University of Florida, Gainesville, FL, USA
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
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176
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Zhang S, Song W, Wemheuer B, Reveillaud J, Webster N, Thomas T. Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota. mSystems 2019; 4:e00288-19. [PMID: 31409660 PMCID: PMC6697440 DOI: 10.1128/msystems.00288-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/22/2019] [Indexed: 01/25/2023] Open
Abstract
Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "Candidatus UNitrosopumilus hexadellus," "Candidatus UNitrosopumilus detritiferus," and "Candidatus UCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "Ca UCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca UNitrosopumilus detritiferus" and "Ca UNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.
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Affiliation(s)
- Shan Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Weizhi Song
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Julie Reveillaud
- ASTRE, INRA, CIRAD, University of Montpellier, Montpellier, France
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Torsten Thomas
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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177
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Lablab Purpureus Influences Soil Fertility and Microbial Diversity in a Tropical Maize-Based No-Tillage System. SOIL SYSTEMS 2019. [DOI: 10.3390/soilsystems3030050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There are multiple mechanisms by which enhanced diversity of plant communities improves soil structure and function. One critical pathway mediating this relationship is through changes to soil prokaryotic communities. Here, nine different cropping systems were studied to evaluate how legume and grass cover crops influence soil fertility and microbial communities in a maize-based no tillage system. The soil’s bacterial and archaeal communities were sequenced (Illumina GAIIx, 12 replicates for treatment) and correlated with eight different soil features. The microbial community composition differed widely between planting treatments, with three primary “community types” emerging in multivariate space: (1) A community type associated with bare soil linked with low P, low pH, and high aluminum [Al]; (2) a community type associated with Lablab beans linked with high soil N, total organic carbon and other base cation concentrations, and high pH; and (3) a community type of all other non-lablab planting arrangements linked with higher soil P (relative to bare soil), but lower soil fertility (N and base cations). Lablab-based arrangements also expressed the highest microbial richness and alpha diversity. The inclusion of Lablab in maize-based cropping systems represents a potential alternative to reduce the use of chemical fertilizers and increase the chemical and biological quality in agricultural soils under the no-tillage system.
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178
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Nguyen LTT, Broughton K, Osanai Y, Anderson IC, Bange MP, Tissue DT, Singh BK. Effects of elevated temperature and elevated CO 2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:81-89. [PMID: 31026646 DOI: 10.1016/j.scitotenv.2019.04.181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Rising global air temperature and atmospheric CO2 are expected to have considerable effects on soil nutrient cycling and plant productivity. Soil nitrification controlled by ammonia-oxidizing bacteria and archaea (AOB and AOA) communities plays a key role in contributing to plant nitrogen (N) availability; however, response of soil nitrification and functional microbial communities to climate change and subsequent consequences for crop yields remain largely unknown. Cotton productivity is a function of temperature and N availability under well-watered conditions. In general, cotton growth responds positively to elevated CO2, but simultaneous warming may offset benefits of rising CO2. In this study, cotton was used as a model system to elucidate the short-term response of soil nitrification and ammonia-oxidizing communities to elevated temperature and elevated CO2 using field-based environmentally-controlled chambers. Elevated temperature (ambient + 1.1 °C) altered the AOA community, while elevated temperature and elevated CO2 (ambient + 132 ppm) significantly increased soil nitrification rate and shifted AOB and AOA communities, but these effects depended on cotton developmental stages. Ammonia-oxidizing community abundance and structure were statistically correlated with nitrifying activity. Our findings suggest that climate change will positively affect soil nitrifying communities, leading to an increase in process rates and subsequent N availability, which is directly linked to crop productivity.
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Affiliation(s)
- Linh T T Nguyen
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Katie Broughton
- CSIRO Agriculture and Food, Australian Cotton Research Institute, Locked Bag 59, Narrabri, NSW 2390, Australia
| | - Yui Osanai
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Michael P Bange
- CSIRO Agriculture and Food, Australian Cotton Research Institute, Locked Bag 59, Narrabri, NSW 2390, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia; Global Centre for Land-Based Innovation, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
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179
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Alves RJE, Kerou M, Zappe A, Bittner R, Abby SS, Schmidt HA, Pfeifer K, Schleper C. Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures. Front Microbiol 2019; 10:1571. [PMID: 31379764 PMCID: PMC6657660 DOI: 10.3389/fmicb.2019.01571] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Climate change is causing arctic regions to warm disproportionally faster than those at lower latitudes, leading to alterations in carbon and nitrogen cycling, and potentially higher greenhouse gas emissions. It is thus increasingly important to better characterize the microorganisms driving arctic biogeochemical processes and their potential responses to changing conditions. Here, we describe a novel thaumarchaeon enriched from an arctic soil, Candidatus Nitrosocosmicus arcticus strain Kfb, which has been maintained for seven years in stable laboratory enrichment cultures as an aerobic ammonia oxidizer, with ammonium or urea as substrates. Genomic analyses show that this organism harbors all genes involved in ammonia oxidation and in carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle, characteristic of all AOA, as well as the capability for urea utilization and potentially also for heterotrophic metabolism, similar to other AOA. Ca. N. arcticus oxidizes ammonia optimally between 20 and 28°C, well above average temperatures in its native high arctic environment (-13-4°C). Ammonia oxidation rates were nevertheless much lower than those of most cultivated mesophilic AOA (20-45°C). Intriguingly, we repeatedly observed apparent faster growth rates (based on marker gene counts) at lower temperatures (4-8°C) but without detectable nitrite production. Together with potential metabolisms predicted from its genome content, these observations indicate that Ca. N. arcticus is not a strict chemolithotrophic ammonia oxidizer and add to cumulating evidence for a greater metabolic and physiological versatility of AOA. The physiology of Ca. N. arcticus suggests that increasing temperatures might drastically affect nitrification in arctic soils by stimulating archaeal ammonia oxidation.
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Affiliation(s)
- Ricardo J Eloy Alves
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Anna Zappe
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Romana Bittner
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Sophie S Abby
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Heiko A Schmidt
- Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, Medical University of Vienna, University of Vienna, Vienna, Austria
| | - Kevin Pfeifer
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Institute for Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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180
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Zhang H, Sun H, Zhou S, Bai N, Zheng X, Li S, Zhang J, Lv W. Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems. Sci Rep 2019; 9:9367. [PMID: 31249385 PMCID: PMC6597706 DOI: 10.1038/s41598-019-45877-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/11/2019] [Indexed: 01/27/2023] Open
Abstract
Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.
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Affiliation(s)
- Hanlin Zhang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Huifeng Sun
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Sheng Zhou
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Naling Bai
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Xianqing Zheng
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Shuangxi Li
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Juanqin Zhang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Weiguang Lv
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China. .,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China. .,Shanghai Key Laboratory of Horticultural Technology, Shanghai, 201403, China. .,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China.
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181
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Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium. mSystems 2019; 4:4/4/e00181-19. [PMID: 31239395 PMCID: PMC6593220 DOI: 10.1128/msystems.00181-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms. Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2. However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii. We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments. IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.
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182
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Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, Grosch R, Pühler A, Sczyrba A, Schlüter A. Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes (Basel) 2019; 10:E424. [PMID: 31163637 PMCID: PMC6627896 DOI: 10.3390/genes10060424] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 11/24/2022] Open
Abstract
To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe-plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant-growth-promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.
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Affiliation(s)
- Johanna Nelkner
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Christian Henke
- Center for Biotechnology (CeBiTec), Bielefeld University, Computational Metagenomics Group, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Timo Wentong Lin
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Wiebke Pätzold
- Center for Biotechnology (CeBiTec), Bielefeld University, Computational Metagenomics Group, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Sebastian Jaenicke
- Justus-Liebig-University Gießen, Bioinformatics & Systems Biology, Heinrich-Buff-Ring 58, 35392 Gießen, Germany.
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ) Großbeeren/Erfurt eV, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Computational Metagenomics Group, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
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183
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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: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [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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184
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Miranda ARL, Mendes LW, Lemos LN, Antunes JEL, Amorim MR, Melo VMM, de Melo WJ, Van den Brink PJ, Araujo ASF. Dynamics of archaeal community in soil with application of composted tannery sludge. Sci Rep 2019; 9:7347. [PMID: 31089146 PMCID: PMC6517401 DOI: 10.1038/s41598-019-43478-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/25/2019] [Indexed: 01/08/2023] Open
Abstract
Application of composted tannery sludge (CTS) could promote a shift in the structure of soil microbial communities. Although the effect of CTS on bacterial community has been studied, it is unclear how the composition and diversity of archaeal community respond to CTS amendment and which environmental factors drive the community over time. Here, we hypothesize that the Archaea structure and composition respond to CTS amendment over the time. CTS had been previously applied annually along 6 years and this assessment occurred for 180 days following the application in the 7th year by using different rates (0, 2.5, 5, 10 and 20 ton ha−1). We used amplicon 16S rRNA sequencing to assess the changes in the structure of the archaeal community. Thaumarchaeota and Euryarchaeota were the most abundant phyla found in soils with application of CTS, with Thaumarchaeota dominating the sequences in all samples with relative abundances of >98%. We observed a decreasing trend on the archaeal diversity over the time with increasing CTS application rate, together with an increase in the community similarity. The redundancy analyses (RDA) explained 43% of the total variation in operational taxonomic units and identified Na, pH, Cr and P as the main drivers of the archaeal community over time after application of highest CTS rates. CTS application changes the structure of Archaea community, with significant increase of Thaumarchaeota and Aenigmarchaeota groups, which can be further explored for its biotechnological use in contaminated soils.
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Affiliation(s)
- Ana Roberta Lima Miranda
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil.
| | | | | | - Jadson Emanuel Lopes Antunes
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil
| | - Marineide Rodrigues Amorim
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil
| | | | - Wanderley Jose de Melo
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Path of Access Prof. Paulo Donato Castellane, Km 5, Postal Code: 14884-900, Jaboticabal, SP, Brazil.,University of Brazil: University campus Descalvado - Hilário da Silva Passos Avenue, 950 - University park, Descalvado, SP, Brazil
| | - Paul J Van den Brink
- Wageningen University, Aquatic Ecology and Water Quality Management Group, P.O. Box 47, 6700 AA, Wageningen, The Netherlands.,Wageningen Environmental Research, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
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185
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Luo J, Liu Y, Tao Q, Hou Q, Wu K, Song Y, Liu Y, Guo X, Li J, Hashmi MLUR, Liang Y, Li T. Successive phytoextraction alters ammonia oxidation and associated microbial communities in heavy metal contaminated agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:616-625. [PMID: 30763842 DOI: 10.1016/j.scitotenv.2019.01.315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
Phytoextraction is an attractive strategy for remediation of soils contaminated by heavy metal (HM), yet the effects of this practice on biochemical processes involved in soil nutrient cycling remain unknown. Here we investigated the impact of successive phytoextraction with a Cd/Zn co-hyperaccumulator Sedum alfredii (Crassulaceae) on potential nitrification rates (PNRs), abundance and composition of nitrifying communities and functional genes associated with nitrification using archaeal and bacterial 16S rRNA gene profiling and quantitative real-time PCR. The PNRs in rhizosphere were significantly (P < 0.05) lower than in the unplanted soils, and decreased markedly with planting time. The decrease of PNR was more paralleled by changes in numbers of copy and transcript of archaeal amoA gene than the bacterial counterpart. Phylogenetic analysis revealed that phytoextraction induced shifts in community structure of soil group 1.1b lineage-dominated ammonia-oxidizing archaea (AOA), Nitrosospira cluster 3-like ammonia-oxidizing bacteria (AOB) and Nitrospira-like nitrite-oxidizing bacteria (NOB). A strong positive correlation was observed between amoA gene transcript numbers and PNRs, whereas root exudates showed negative effect on PNR. This effect was further corroborated by incubation test with the concentrated root exudates of S. alfredii. Partial least squares path model demonstrated that PNR was predominantly controlled by number of AOA amoA gene transcripts which were strongly influenced by root exudation and HM level in soil. Our result reveals that successive phytoextraction of agricultural soil contaminated by HMs using S. alfredii could inhibit ammonia oxidation and thereby reduce nitrogen loss.
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Affiliation(s)
- Jipeng Luo
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuying Liu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Tao
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiong Hou
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Keren Wu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuchao Song
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuankun Liu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinyu Guo
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinxing Li
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Laeeq Ur Rehman Hashmi
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tingqiang Li
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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186
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Ren M, Feng X, Huang Y, Wang H, Hu Z, Clingenpeel S, Swan BK, Fonseca MM, Posada D, Stepanauskas R, Hollibaugh JT, Foster PG, Woyke T, Luo H. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME JOURNAL 2019; 13:2150-2161. [PMID: 31024152 DOI: 10.1038/s41396-019-0418-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/07/2019] [Accepted: 04/03/2019] [Indexed: 11/09/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in marine and terrestrial habitats, playing a major role in the global nitrogen cycle. However, their evolutionary history remains unexplored, which limits our understanding of their adaptation mechanisms. Here, our comprehensive phylogenomic tree of Thaumarchaeota supports three sequential events: origin of AOA from terrestrial non-AOA ancestors, colonization of the shallow ocean, and expansion to the deep ocean. Careful molecular dating suggests that these events coincided with the Great Oxygenation Event around 2300 million years ago (Mya), and oxygenation of the shallow and deep ocean around 800 and 635-560 Mya, respectively. The first transition was likely enabled by the gain of an aerobic pathway for energy production by ammonia oxidation and biosynthetic pathways for cobalamin and biotin that act as cofactors in aerobic metabolism. The first transition was also accompanied by the loss of dissimilatory nitrate and sulfate reduction, loss of oxygen-sensitive pyruvate oxidoreductase, which reduces pyruvate to acetyl-CoA, and loss of the Wood-Ljungdahl pathway for anaerobic carbon fixation. The second transition involved gain of a K+ transporter and of the biosynthetic pathway for ectoine, which may function as an osmoprotectant. The third transition was accompanied by the loss of the uvr system for repairing ultraviolet light-induced DNA lesions. We conclude that oxygen availability drove the terrestrial origin of AOA and their expansion to the photic and dark oceans, and that the stressors encountered during these events were partially overcome by gene acquisitions from Euryarchaeota and Bacteria, among other sources.
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Affiliation(s)
- Minglei Ren
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.,Shenzhen Research Institute, The Chinese University of Hong Kong, 518000, Shenzhen, China
| | - Xiaoyuan Feng
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yongjie Huang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.,Shenzhen Research Institute, The Chinese University of Hong Kong, 518000, Shenzhen, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, 515063, Shantou, China
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, 515063, Shantou, China
| | | | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA.,National Biodefense Analysis and Countermeasures Center, Frederick, MD, 21702, USA
| | - Miguel M Fonseca
- CINBIO and Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - David Posada
- CINBIO and Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | | | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Shenzhen Research Institute, The Chinese University of Hong Kong, 518000, Shenzhen, China.
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187
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Liu L, Li S, Han J, Lin W, Luo J. A Two-Step Strategy for the Rapid Enrichment of Nitrosocosmicus-Like Ammonia-Oxidizing Thaumarchaea. Front Microbiol 2019; 10:875. [PMID: 31105671 PMCID: PMC6491936 DOI: 10.3389/fmicb.2019.00875] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/04/2019] [Indexed: 12/03/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are widely distributed on the earth and play a significant role in the global nitrogen cycle. Although dozens of AOA strains were obtained in the last 13 years, it is still necessary to obtain more AOA strains for the entire exploration of their ecology, physiology, and underlying biochemistry in different environments. In this study, we designed a two-step strategy for the rapid enrichment of Nitrosocosmicus–like AOA from soils. Firstly, combination of kanamycin and ampicillin was chosen as the selective stress for bacteria and quartz sands were used as the attachment of AOA cells during the first step cultivation; only after 40–75 days cultivation, AOA enrichments with abundance >20% were obtained. Secondly, combination of ciprofloxacin and azithromycin was chosen as the selective stress for the following cultivation; it is able to penetrate the biofilms and kill the bacterial cells inside the aggregate, contributing to the AOA enrichments reached high abundances (90%) only after one-time cultivation. Basing on this strategy, three AOA strains were obtained from agricultural soils only after 90–150 days cultivation. Phylogenetic analysis suggested these AOA belong to the soil group I.1b Thaumarchaeota and are closely related to the genus Nitrosocosmicus. In general, AOA enrichment or isolation is very difficult and time-consuming (an average of 2–3 years). Here, we provide a new strategy for the rapid enrichment of high abundance of Nitrosocosmicus-like AOA from soil, which gives a new solution to the AOA enrichment and cultivation in a short period.
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Affiliation(s)
- Liangting Liu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Surong Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jiamin Han
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Weitie Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianfei Luo
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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188
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Bayer B, Vojvoda J, Reinthaler T, Reyes C, Pinto M, Herndl GJ. Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria. Int J Syst Evol Microbiol 2019; 69:1892-1902. [PMID: 30938665 DOI: 10.1099/ijsem.0.003360] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two mesophilic, neutrophilic and aerobic marine ammonia-oxidizing archaea, designated strains NF5T and D3CT, were isolated from coastal surface water of the Northern Adriatic Sea. Cells were straight small rods 0.20-0.25 µm wide and 0.49-2.00 µm long. Strain NF5T possessed archaella as cell appendages. Glycerol dibiphytanyl glycerol tetraethers with zero to four cyclopentane moieties (GDGT-0 to GDGT-4) and crenarchaeol were the major core lipids. Menaquinone MK6 : 0 was the major respiratory quinone. Both isolates gained energy by oxidizing ammonia (NH3) to nitrite (NO2-) and used bicarbonate as a carbon source. Strain D3CT was able use urea as a source of ammonia for energy production and growth. Addition of hydrogen peroxide (H2O2) scavengers (catalase or α-keto acids) was required to sustain growth. Optimal growth occurred between 30 and 32 °C, pH 7.1 and 7.3 and between 34 and 37‰ salinity. The cellular metal abundance ranking of both strains was Fe>Zn>Cu>Mn>Co. The genomes of strains NF5T and D3CT have a DNA G+C content of 33.4 and 33.8 mol%, respectively. Phylogenetic analyses of 16S rRNA gene sequences revealed that both strains are affiliated with the class Nitrososphaeria, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. The two isolates are separated by phenotypic and genotypic characteristics and are assigned to distinct species within the genus Nitrosopumilus gen. nov. according to average nucleotide identity thresholds of their closed genomes. Isolates NF5T (=JCM 32270T =NCIMB 15114T) and D3CT (=JCM 32271T =DSM 106147T =NCIMB 15115T) are type strains of the species Nitrosopumilusadriaticus sp. nov. and Nitrosopumiluspiranensis sp. nov., respectively.
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Affiliation(s)
- Barbara Bayer
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Jana Vojvoda
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Thomas Reinthaler
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Carolina Reyes
- 2Department of Environmental Geosciences, Environmental Science Research Network, University of Vienna, Vienna, Austria
| | - Maria Pinto
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- 1Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria.,3Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
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189
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Affinity informs environmental cooperation between ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (Anammox) bacteria. ISME JOURNAL 2019; 13:1997-2004. [PMID: 30936420 DOI: 10.1038/s41396-019-0408-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/18/2019] [Accepted: 03/15/2019] [Indexed: 11/08/2022]
Abstract
Anaerobic ammonia-oxidizing (Anammox) bacteria (AnAOB) rely on nitrite supplied by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Affinities for ammonia and oxygen play a crucial role in AOA/AOB competition and their association with AnAOB. In this work we measured the affinity constants for ammonia and oxygen (half-saturation; km) of two freshwater AOA enrichments, an AOA soil isolate (N. viennensis), and a freshwater AnAOB enrichment. The AOA enrichments had similar kinetics (μmax ≈ 0.36 d-1, km,NH4 ≈ 0.78 µM, and km,O2 ≈ 2.9 µM), whereas N. viennensis had similar km values but lower μmax (0.23 d-1). In agreement with the current paradigm, these AOA strains showed a higher affinity for ammonia (lower km,NH4; 0.34-1.27 µM) than published AOB measurements (>20 µM). The slower growing AnAOB (μmax ≈ 0.16 d-1) had much higher km values (km,NH4 ≈ 132 µM, km,NO2 ≈ 48 µM) and were inhibited by oxygen at low levels (half-oxygen inhibition; ki,O2 ≈ 0.092 µM). The higher affinity of AOA for ammonia relative to AnAOB, suggests AOA/AnAOB cooperation is only possible where AOA do not outcompete AnAOB for ammonia. Using a biofilm model, we show that environments of ammonia/oxygen counter diffusion, such as stratified lakes, favors this cooperation.
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190
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Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests. Appl Microbiol Biotechnol 2019; 103:4229-4240. [PMID: 30923872 DOI: 10.1007/s00253-019-09721-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
Abstract
Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al3+, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.
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191
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Wang Z, Wang W, Li Y, Yang Q. Co-metabolic degradation of naphthalene and pyrene by acclimated strain and competitive inhibition kinetics. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2019; 54:505-513. [PMID: 30909840 DOI: 10.1080/03601234.2019.1586033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A dominant strain named Ochrobactrum sp. was isolated from soils contaminated with coal tar. The batch experiments were carried out to study the co-metabolic degradation of pyrene by Ochrobactrum MB-2 with naphthalene as the main substrate and the effects of several significant parameters such as naphthalene concentration, pH and temperature on removal efficiency were explored. The results showed that Ochrobactrum MB-2 effectively degraded naphthalene and that the addition of naphthalene favored the degradation of pyrene. The maximum elimination efficiency of naphthalene (10 mg L-1) and pyrene (1 mg L-1) was achieved at pH 7 and 25 °C, and the corresponding values were 99 and 41%, respectively. A competitive inhibition model based on the Michaelis-Menten equation was used to characterize the inhibitory effect of pyrene on naphthalene degradation. The values of the half-saturation coefficient for naphthalene (KS) and dissociation constant of enzyme-inhibitor complex (KC) were determined to be 4.93 and 1.38 mg L-1, respectively.
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Affiliation(s)
- Zhen Wang
- a School of Water Resources and Environment , China University of Geosciences , Beijing , China
- b Beijing Key Laboratory of Water Resource & Environmental Engineering , China University of Geosciences , Beijing , China
| | - Wenjing Wang
- a School of Water Resources and Environment , China University of Geosciences , Beijing , China
- b Beijing Key Laboratory of Water Resource & Environmental Engineering , China University of Geosciences , Beijing , China
| | - Yalong Li
- a School of Water Resources and Environment , China University of Geosciences , Beijing , China
- b Beijing Key Laboratory of Water Resource & Environmental Engineering , China University of Geosciences , Beijing , China
| | - Qi Yang
- a School of Water Resources and Environment , China University of Geosciences , Beijing , China
- b Beijing Key Laboratory of Water Resource & Environmental Engineering , China University of Geosciences , Beijing , China
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192
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Krupovic M, Makarova KS, Wolf YI, Medvedeva S, Prangishvili D, Forterre P, Koonin EV. Integrated mobile genetic elements in Thaumarchaeota. Environ Microbiol 2019; 21:2056-2078. [PMID: 30773816 PMCID: PMC6563490 DOI: 10.1111/1462-2920.14564] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/10/2019] [Accepted: 02/13/2019] [Indexed: 12/20/2022]
Abstract
To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence-like transposons, (iv) integrative-conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly-roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I-B CRISPR-Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Sofia Medvedeva
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Sorbonne Université, Collège doctoral, 75005, Paris, France
| | - David Prangishvili
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France
| | - Patrick Forterre
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris- Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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193
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Kong Y, Ling N, Xue C, Chen H, Ruan Y, Guo J, Zhu C, Wang M, Shen Q, Guo S. Long-term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing. Environ Microbiol 2019; 21:1224-1240. [PMID: 30724443 DOI: 10.1111/1462-2920.14553] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/19/2018] [Accepted: 01/02/2019] [Indexed: 11/28/2022]
Abstract
Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira-like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long-term fertilization shifted the composition of active Nitrospira-like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential.
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Affiliation(s)
- Yali Kong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chao Xue
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huan Chen
- Crop Research Institute, Anhui Academy of Agricultural Science, Hefei, 230031, China
| | - Yang Ruan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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194
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Meng J, Li J, He J, Li J, Deng K, Nan J. Nutrient removal from high ammonium swine wastewater in upflow microaerobic biofilm reactor suffered high hydraulic load. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 233:69-75. [PMID: 30557752 DOI: 10.1016/j.jenvman.2018.12.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/07/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
To understand the ability of an upflow microaerobic biofilm reactor (UMBR) to remove nutrient from manure-free swine wastewater rich in NH4+ with a COD/TN ratio less than 1.00, effect of hydraulic loading rate (HLR) on the microaerobic process was evaluated with a constant reflux ratio of 25 at 25 °C. The results showed that changes in HLR had a remarkable effect on the performance of the UMBR in nutrient removal from the wastewater. With the favorable HLR 3.0 m3/(m3·d) (Hydraulic Retention Time (HRT) 8 h), average removal of COD, NH4+ and TN in the microaerobic process reached 59.3%, 87.7% and 84.7%, respectively, though the COD/TN ratio was as low as 0.84. With an over HLR of 4.0 m3/(m3·d) (HRT decreased to 6 h), bad performance of the UMBR was observed with an average removal of COD, NH4+ and TN as low as 45.0%, 59.0% and 57.5%, respectively. Since the HLR was decreased to 2.4 m3/(m3·d) (HRT 10 h), the microaerobic process regained the efficiency in nutrient removal with a removal of COD, NH4+ and TN averaged 59.0%, 95.3% and 87.8%, respectively. The microaerobic condition allowed anammox bacteria, ammonia-oxidizing bacteria and archaea, nitrite-oxidizing bacteria and denitrifiers to all thrive in the UMBR, resulting in the efficient synchronous removal of organic carbon and nitrogen. As the dominant approach to nitrogen removal, anaerobic ammonium oxidation (anammox) pathway contributing to the TN removal in the microaerobic process exceeded 59.5% at HLR 3.0 m3/(m3·d). The results demonstrated that the UMBR can remove nitrogen and carbon from swine wastewater, with a suitable HLR.
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Affiliation(s)
- Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China; Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Jiuling Li
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jiamin He
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China.
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
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195
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Cockell CS, Harrison JP, Stevens AH, Payler SJ, Hughes SS, Kobs Nawotniak SE, Brady AL, Elphic R, Haberle CW, Sehlke A, Beaton KH, Abercromby AF, Schwendner P, Wadsworth J, Landenmark H, Cane R, Dickinson AW, Nicholson N, Perera L, Lim DS. A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars. ASTROBIOLOGY 2019; 19:284-299. [PMID: 30840501 PMCID: PMC6442273 DOI: 10.1089/ast.2018.1870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A major objective in the exploration of Mars is to test the hypothesis that the planet hosted life. Even in the absence of life, the mapping of habitable and uninhabitable environments is an essential task in developing a complete understanding of the geological and aqueous history of Mars and, as a consequence, understanding what factors caused Earth to take a different trajectory of biological potential. We carried out the aseptic collection of samples and comparison of the bacterial and archaeal communities associated with basaltic fumaroles and rocks of varying weathering states in Hawai'i to test four hypotheses concerning the diversity of life in these environments. Using high-throughput sequencing, we found that all these materials are inhabited by a low-diversity biota. Multivariate analyses of bacterial community data showed a clear separation between sites that have active fumaroles and other sites that comprised relict fumaroles, unaltered, and syn-emplacement basalts. Contrary to our hypothesis that high water flow environments, such as fumaroles with active mineral leaching, would be sites of high biological diversity, alpha diversity was lower in active fumaroles compared to relict or nonfumarolic sites, potentially due to high-temperature constraints on microbial diversity in fumarolic sites. A comparison of these data with communities inhabiting unaltered and weathered basaltic rocks in Idaho suggests that bacterial taxon composition of basaltic materials varies between sites, although the archaeal communities were similar in Hawai'i and Idaho. The taxa present in both sites suggest that most of them obtain organic carbon compounds from the atmosphere and from phototrophs and that some of them, including archaeal taxa, cycle fixed nitrogen. The low diversity shows that, on Earth, extreme basaltic terrains are environments on the edge of sustaining life with implications for the biological potential of similar environments on Mars and their exploration by robots and humans.
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Affiliation(s)
- Charles S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- Address correspondence to: Charles S. Cockell, School of Physics and Astronomy, University of Edinburgh, King's Buildings, Edinburgh EH9 3JZ, UK
| | - Jesse P. Harrison
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Adam H. Stevens
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Samuel J. Payler
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Scott S. Hughes
- Department of Geosciences, Idaho State University, Pocatello, Idaho, USA
| | | | - Allyson L. Brady
- School of Geography and Earth Sciences, McMaster University, Hamilton, Canada
| | - R.C. Elphic
- NASA Ames Research Center, Mountain View, California, USA
| | | | | | | | - Andrew F.J. Abercromby
- Biomedical Research & Environmental Sciences Division (SK), NASA Johnson Space Center, Houston, Texas, USA
| | - Petra Schwendner
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Jennifer Wadsworth
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Hanna Landenmark
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Rosie Cane
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Andrew W. Dickinson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Natasha Nicholson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Liam Perera
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Darlene S.S. Lim
- NASA Ames Research Center, Mountain View, California, USA
- Bay Area Environmental Research Institute (BAERI), Moffett Field, California, USA
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196
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Song K, Sawayanagi K, Numano T, Taniichi Y, Kikuchi T, Takeda T, Kanou H, Riya S, Hori T, Hosomi M, Terada A. High-rate partial nitrification of semiconductor wastewater: Implications of online monitoring and microbial community structure. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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197
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Duan P, Fan C, Zhang Q, Xiong Z. Overdose fertilization induced ammonia-oxidizing archaea producing nitrous oxide in intensive vegetable fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:1787-1794. [PMID: 30278423 DOI: 10.1016/j.scitotenv.2018.09.341] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their differential contribution to nitrous oxide (N2O) production, particularly in greenhouse based high N input vegetable soils. Six N treatments (N1, N2, N3, N4, N5 and N6 representing 0, 293, 587, 880, 1173 and 1760 kg N ha-1 yr-1, respectively) were continuously managed for three years in a typically intensified vegetable field in China. The aerobic incubation experiment involving these field-treated soils was designed to evaluate the relative contributions of AOA and AOB to N2O production by using acetylene or 1-octyne as inhibitors. The results showed that the soil pH and net nitrification rate gradually declined with increasing the fertilizer N application rates. The AOA were responsible for 44-71% of the N2O production with negligible N2O from AOB in urea unamended control soils. With urea amendment, the AOA were responsible for 48-53% of the N2O production in the excessively fertilized soils, namely the N5-N6 soils, while the AOB were responsible for 42-55% in the conventionally fertilized soils, namely the N1-N4 soils. Results indicated that overdose fertilization induced higher AOA-dependent N2O production than AOB, whereas urea supply led to higher AOB-dependent N2O production than AOA in conventionally fertilized soils. Additionally, a positive relationship existed between N2O production and NO2- accumulation during the incubation. Further mechanisms for NO2--dependent N2O production in intensive vegetable soils therefore deserve urgent attention.
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Affiliation(s)
- Pengpeng Duan
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Changhua Fan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan 571737, China
| | - Qianqian Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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198
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Jiao S, Xu Y, Zhang J, Lu Y. Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems. MICROBIOME 2019; 7:15. [PMID: 30709414 PMCID: PMC6359761 DOI: 10.1186/s40168-019-0630-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/17/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Understanding the spatial distributions and ecological diversity of soil archaeal communities in agricultural ecosystems is crucial for improvements in crop productivity. Here, we conducted a comprehensive, continental-scale survey of soil archaeal communities in adjacent pairs of maize (dryland) and rice (wetland) fields in eastern China. RESULTS We revealed the consequential roles of environmental filtering in driving archaeal community assembly for both maize and rice fields. Rice fields, abundant with Euryarchaeota, had higher archaeal diversity and steeper distance-decay slopes than maize fields dominated by Thaumarchaeota. Dominant soil archaea showed distinct continental atlases and niche differentiation between dryland and wetland habitats, where they were associated with soil pH and mean annual temperature, respectively. After identifying their environmental preferences, we grouped the dominant archaeal taxa into different ecological clusters and determined the unique co-occurrence patterns within each cluster. Using this empirical dataset, we built a continental atlas of soil archaeal communities to provide reliable estimates of their spatial distributions in agricultural ecosystems. CONCLUSIONS Environmental filtering plays a crucial role in driving the distinct continental atlases of dominant soil archaeal communities between dryland and wetland, with contrasting strategies of archaeal-driven nutrient cycling within these two agricultural ecosystems. These findings improve our ability to predict how soil archaeal communities respond to environmental changes and to manage soil archaeal communities for provisioning of agricultural ecosystem services.
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Affiliation(s)
- Shuo Jiao
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Yiqin Xu
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Jie Zhang
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, People's Republic of China.
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199
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Szukics U, Grigulis K, Legay N, Kastl EM, Baxendale C, Bardgett RD, Clément JC, Lavorel S, Schloter M, Bahn M. Management versus site effects on the abundance of nitrifiers and denitrifiers in European mountain grasslands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:745-753. [PMID: 30134212 DOI: 10.1016/j.scitotenv.2018.08.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/03/2018] [Accepted: 08/03/2018] [Indexed: 06/08/2023]
Abstract
It is well established that the abundances of nitrogen (N) transforming microbes are strongly influenced by land-use intensity in lowland grasslands. However, their responses to management change in less productive and less fertilized mountain grasslands are largely unknown. We studied eight mountain grasslands, positioned along gradients of management intensity in Austria, the UK, and France, which differed in their historical management trajectories. We measured the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as nitrite-reducing bacteria using specific marker genes. We found that management affected the abundance of these microbial groups along each transect, though the specific responses differed between sites, due to different management histories and resulting variations in environmental parameters. In Austria, cessation of management caused an increase in nirK and nirS gene abundances. In the UK, intensification of grassland management led to 10-fold increases in the abundances of AOA and AOB and doubling of nirK gene abundance. In France, ploughing of previously mown grassland caused a 20-fold increase in AOA abundance. Across sites the abundance of AOB was most strongly related to soil NO3--N availability, and AOA were favored by higher soil pH. Among the nitrite reducers, nirS abundance correlated most strongly with N parameters, such as soil NO3--N, microbial N, leachate NH4+-N, while the abundance of nirK-denitrifiers was affected by soil total N, organic matter (SOM) and water content. We conclude that alteration of soil environmental conditions is the dominant mechanism by which land management practices influence the abundance of each group of ammonia oxidizers and nitrite reducers.
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Affiliation(s)
- Ute Szukics
- Universität Innsbruck, Institut für Ökologie, Sternwartestr. 15, Innsbruck, Austria
| | - Karl Grigulis
- Laboratoire d'Ecologie Alpine, UMR 5553 CNRS, Université Joseph Fourier, Grenoble, France
| | - Nicolas Legay
- École de la Nature et du Paysage, INSA Centre Val de Loire, 9 Rue Chocolaterie, 41000 Blois, France; CNRS, CITERES, UMR 7324, 37200 Tours, France
| | - Eva-Maria Kastl
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, 85758 Oberschleissheim, Germany
| | | | - Richard D Bardgett
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | | | - Sandra Lavorel
- Laboratoire d'Ecologie Alpine, UMR 5553 CNRS, Université Joseph Fourier, Grenoble, France
| | - Michael Schloter
- Helmholtz Zentrum München GmbH, Research Unit for Comparative Microbiome Analysis, 85758 Oberschleissheim, Germany
| | - Michael Bahn
- Universität Innsbruck, Institut für Ökologie, Sternwartestr. 15, Innsbruck, Austria.
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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