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Govednik A, Eler K, Mihelič R, Suhadolc M. Mineral and organic fertilisation influence ammonia oxidisers and denitrifiers and nitrous oxide emissions in a long-term tillage experiment. Sci Total Environ 2024; 928:172054. [PMID: 38569950 DOI: 10.1016/j.scitotenv.2024.172054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Nitrous oxide (N2O) emissions from different agricultural systems have been studied extensively to understand the mechanisms underlying their formation. While a number of long-term field experiments have focused on individual agricultural practices in relation to N2O emissions, studies on the combined effects of multiple practices are lacking. This study evaluated the effect of different tillage [no-till (NT) vs. conventional plough tillage (CT)] in combination with fertilisation [mineral (MIN), compost (ORG), and unfertilised control (CON)] on seasonal N2O emissions and the underlying N-cycling microbial community in one maize growing season. Rainfall events after fertilisation, which resulted in increased soil water content, were the main triggers of the observed N2O emission peaks. The highest cumulative emissions were measured in MIN fertilisation, followed by ORG and CON fertilisation. In the period after the first fertilisation CT resulted in higher cumulative emissions than NT, while no significant effect of tillage was observed cumulatively across the entire season. A higher genetic potential for N2O emissions was observed under NT than CT, as indicated by an increased (nirK + nirS)/(nosZI + nosZII) ratio. The mentioned ratio under NT decreased in the order CON > MIN > ORG, indicating a higher N2O consumption potential in the NT-ORG treatment, which was confirmed in terms of cumulative emissions. The AOB/16S ratio was strongly affected by fertilisation and was higher in the MIN than in the ORG and CON treatments, regardless of the tillage system. Multiple regression has revealed that this ratio is one of the most important variables explaining cumulative N2O emissions, possibly reflecting the role of bacterial ammonia oxidisers in minerally fertilised soil. Although the AOB/16S ratio aligned well with the measured N2O emissions in our experimental field, the higher genetic potential for denitrification expressed by the (nirK + nirS)/(nosZI + nosZII) ratio in NT than CT was not realized in the form of increased emissions. Our results suggest that organic fertilisation in combination with NT shows a promising combination for mitigating N2O emissions; however, addressing the yield gap is necessary before incorporating it in recommendations for farmers.
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Affiliation(s)
- Anton Govednik
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Klemen Eler
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Rok Mihelič
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Marjetka Suhadolc
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
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Elrys AS, Abo El-Maati MF, Dan X, Wen Y, Mou J, Abdelghany AE, Uwiragiye Y, Shuirong T, Yanzheng W, Meng L, Zhang J, Müller C. Aridity creates global thresholds in soil nitrogen retention and availability. Glob Chang Biol 2024; 30:e17003. [PMID: 37943245 DOI: 10.1111/gcb.17003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023]
Abstract
Identifying tipping points in the relationship between aridity and gross nitrogen (N) cycling rates could show critical vulnerabilities of terrestrial ecosystems to climate change. Yet, the global pattern of gross N cycling response to aridity across terrestrial ecosystems remains unknown. Here, we collected 14,144 observations from 451 15 N-labeled studies and used segmented regression to identify the global threshold responses of soil gross N cycling rates and soil process-related variables to aridity index (AI), which decreases as aridity increases. We found on a global scale that increasing aridity reduced soil gross nitrate consumption but increased soil nitrification capacity, mainly due to reduced soil microbial biomass carbon (MBC) and N (MBN) and increased soil pH. Threshold response of gross N production and retention to aridity was observed across terrestrial ecosystems. In croplands, gross nitrification and extractable nitrate were inhibited with increasing aridity below the threshold AI ~0.8-0.9 due to inhibited ammonia-oxidizing archaea and bacteria, while the opposite was favored above this threshold. In grasslands, gross N mineralization and immobilization decreased with increasing aridity below the threshold AI ~0.5 due to decreased MBN, but the opposite was true above this threshold. In forests, increased aridity stimulated nitrate immobilization below the threshold AI ~1.0 due to increased soil C/N ratio, but inhibited ammonium immobilization above the threshold AI ~1.3 due to decreased soil total N and increased MBC/MBN ratio. Soil dissimilatory nitrate reduction to ammonium decreased with increasing aridity globally and in forests when the threshold AI ~1.4 was passed. Overall, we suggest that any projected increase in aridity in response to climate change is likely to reduce plant N availability in arid regions while enhancing it in humid regions, affecting the provision of ecosystem services and functions.
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Affiliation(s)
- Ahmed S Elrys
- College of Tropical Crops, Hainan University, Haikou, China
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- Liebig Centre for Agroecology and Climate Impact Research, Justus Liebig University, Giessen, Germany
| | - Mohamed F Abo El-Maati
- Agriculture Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Xiaoqian Dan
- College of Tropical Crops, Hainan University, Haikou, China
| | - YuHong Wen
- College of Tropical Crops, Hainan University, Haikou, China
| | - Jinxia Mou
- College of Tropical Crops, Hainan University, Haikou, China
| | - Ahmed Elsayed Abdelghany
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid, Areas of Ministry of Education, Northwest A&F University, Yangling, China
- Water Relation and Field Irrigation Department, Agriculture and Biological Institute, National Research Centre, Cairo, Egypt
| | - Yves Uwiragiye
- Department of Agriculture, Faculty of Agriculture, Environmental Management and Renewable Energy, University of Technology and Arts of Byumba, Byumba, Rwanda
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Tang Shuirong
- College of Tropical Crops, Hainan University, Haikou, China
| | - Wu Yanzheng
- College of Tropical Crops, Hainan University, Haikou, China
| | - Lei Meng
- College of Tropical Crops, Hainan University, Haikou, China
| | - JinBo Zhang
- College of Tropical Crops, Hainan University, Haikou, China
- Liebig Centre for Agroecology and Climate Impact Research, Justus Liebig University, Giessen, Germany
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Christoph Müller
- Liebig Centre for Agroecology and Climate Impact Research, Justus Liebig University, Giessen, Germany
- Institute of Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
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3
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Wang J, Shi L, Liu J, Deng J, Zou J, Zhang X, Shen Z, Chen Y. Earthworm-mediated nitrification and gut digestive processes facilitate the remobilization of biochar-immobilized heavy metals. Environ Pollut 2023; 322:121219. [PMID: 36746291 DOI: 10.1016/j.envpol.2023.121219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Earthworms and biochar tend to have opposite effects on heavy metal bioavailability in soil. However, the influence and controlling process of earthworms on the immobilisation effect of biochar remain poorly understood. Through the co-cultivation of earthworms with rice-husk biochar and sludge biochar in heavy metal-contaminated soil and desorption experiments involving simulated earthworm gut, we explored the factors that earthworms influence the heavy metal immobilisation ability of biochar. Our results showed that rice-husk biochar and sludge biochar effectively immobilized heavy metals in soil, whereas earthworm activity mobilised heavy metals in biochar-treated soil, which weakens the immobilisation of biochar. The soil pH reduction effect of earthworms by increasing the abundance of soil ammonia-oxidising bacteria to promote soil nitrification is an important mechanism through which earthworms mobilise heavy metals; however, this process did not occur within 10 days of incubation. Nitrification inhibitors effectively inhibit the mobilisation of heavy metals in soil by earthworms. In addition, the bioavailability of heavy metals in earthworm casts was significantly higher than those in the surrounding soil and earthworm-free soil. Moreover, simulated earthworm gut fluid promoted the re-release of heavy metals from the soil and biochar particles. These results suggest that the gut digestion of earthworms is another important mechanism by which earthworms mobilise soil heavy metals and weaken the immobilisation of biochar. Therefore, earthworms weakened the immobilisation effect of biochar mainly by promoting nitrification to reduce soil pH and through gut digestion.
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Affiliation(s)
- Jie Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liang Shi
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China; National Joint Local Engineering Research Center for Rural Land Resources Use and Consolidation, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaqiang Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jia Deng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianwen Zou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaokai Zhang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China; National Joint Local Engineering Research Center for Rural Land Resources Use and Consolidation, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China; National Joint Local Engineering Research Center for Rural Land Resources Use and Consolidation, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China.
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Diao M, Balkema C, Suárez-Muñoz M, Huisman J, Muyzer G. Succession of bacteria and archaea involved in the nitrogen cycle of a seasonally stratified lake. FEMS Microbiol Lett 2023; 370:7043454. [PMID: 36796795 PMCID: PMC9990978 DOI: 10.1093/femsle/fnad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Human-driven changes affect nutrient inputs, oxygen solubility, and the hydrodynamics of lakes, which affect biogeochemical cycles mediated by microbial communities. However, information on the succession of microbes involved in nitrogen cycling in seasonally stratified lakes is still incomplete. Here, we investigated the succession of nitrogen-transforming microorganisms in Lake Vechten over a period of 19 months, combining 16S rRNA gene amplicon sequencing and quantification of functional genes. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) and anammox bacteria were abundant in the sediment during winter, accompanied by nitrate in the water column. Nitrogen-fixing bacteria and denitrifying bacteria emerged in the water column in spring when nitrate was gradually depleted. Denitrifying bacteria containing nirS genes were exclusively present in the anoxic hypolimnion. During summer stratification, abundances of AOA, AOB, and anammox bacteria decreased sharply in the sediment, and ammonium accumulated in hypolimnion. After lake mixing during fall turnover, abundances of AOA, AOB, and anammox bacteria increased and ammonium was oxidized to nitrate. Hence, nitrogen-transforming microorganisms in Lake Vechten displayed a pronounced seasonal succession, which was strongly determined by the seasonal stratification pattern. These results imply that changes in stratification and vertical mixing induced by global warming are likely to alter the nitrogen cycle of seasonally stratified lakes.
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Affiliation(s)
- Muhe Diao
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Cherel Balkema
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - María Suárez-Muñoz
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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Tang S, Rao Y, Huang S, Xu Y, Zeng K, Liang X, Ling Q, Liu K, Ma J, Yu F, Li Y. Impact of environmental factors on the ammonia-oxidizing and denitrifying microbial community and functional genes along soil profiles from different ecologically degraded areas in the Siding mine. J Environ Manage 2023; 326:116641. [PMID: 36343494 DOI: 10.1016/j.jenvman.2022.116641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/08/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Ammonia oxidizers (ammonia-oxidizing bacteria (AOB amoA) and ammonia-oxidizing archaea (AOA amoA)) and denitrifiers (encoded by nirS, nirK and nosZ) in the soil nitrogen cycle exist in a variety of natural ecosystems. However, little is known about the contribution of these five N-related functional genes to nitrification and denitrification in the soil profile in severely ecologically degraded areas. Therefore, in the present study, the abundance, diversity and community composition of AOA, AOB, nirS, nirK and nosZ were investigated in the soil profiles of different ecologically degraded areas in the Siding mine. The results indicated that, at the phylum level, the dominant archaea were Crenarchaeota and Thaumarchaeota and the dominant bacteria were Proteobacteria. Heavy metal contents had a great impact on AOA amoA, nirS and nirK gene abundances. AOA amoA contributed more during the ammonia oxidation process and was better adapted for survival in heavy metal-contaminated environments. In addition to heavy metals, the soil organic matter (SOM) content and C/N ratio had strong effects on the AOA and AOB community diversity and structure. In addition, variations in the net ammonification and nitrification rates were proportional to AOA amoA abundance along the soil profile. The soil C/N ratio, soil available phosphorus content and soil moisture influenced the denitrification process. Both soil available phosphorus and moisture were more strongly related to nosZ than to nirS and nirK. In addition, nosZ presented a higher correlation with the nosZ/(nirS + nirK) ratio. Moreover, nosZ/(nirS + nirK) was the key functional gene group that drove the major processes for NH4+-N and NO3--N transformation. This study demonstrated the role and importance of soil property impacts on N-related microbes in the soil profile and provided a better understanding of the role and importance of N-related functional genes and their contribution to soil nitrification and denitrification processes in highly degraded areas in the Siding mine.
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Affiliation(s)
- Shuting Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Yin Rao
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Shulian Huang
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Yue Xu
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Kaiyue Zeng
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Xin Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Qiujie Ling
- College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China
| | - Kehui Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, 541004, Guilin, China; College of Life Science, Guangxi Normal University, 541004, Guilin, China
| | - Jiangming Ma
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, 541004, Guilin, China; College of Life Science, Guangxi Normal University, 541004, Guilin, China
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, 541004, Guilin, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China.
| | - Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, 541004, Guilin, China; College of Environment and Resources, Guangxi Normal University, 541004, Guilin, China.
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6
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Bhaduri D, Sihi D, Bhowmik A, Verma BC, Munda S, Dari B. A review on effective soil health bio-indicators for ecosystem restoration and sustainability. Front Microbiol 2022; 13:938481. [PMID: 36060788 PMCID: PMC9428492 DOI: 10.3389/fmicb.2022.938481] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.
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Affiliation(s)
- Debarati Bhaduri
- ICAR-National Rice Research Institute, Cuttack, India
- *Correspondence: Debarati Bhaduri
| | - Debjani Sihi
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States
| | - Arnab Bhowmik
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
- Arnab Bhowmik
| | - Bibhash C. Verma
- Central Rainfed Upland Rice Research Station (ICAR-NRRI), Hazaribagh, India
| | | | - Biswanath Dari
- Agriculture and Natural Resources, Cooperative Extension at North Carolina Agricultural and Technical State University, Greensboro, NC, United States
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Farooq MS, Uzair M, Maqbool Z, Fiaz S, Yousuf M, Yang SH, Khan MR. Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers. Front Plant Sci 2022; 13:913204. [PMID: 35769304 PMCID: PMC9234532 DOI: 10.3389/fpls.2022.913204] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 05/22/2023]
Abstract
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4 +-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4 +, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
- *Correspondence: Seung Hwan Yang,
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
- Muhammad Ramzan Khan,
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Madegwa YM, Uchida Y. Liming improves the stability of soil microbial community structures against the application of digestate made from dairy wastes. J Environ Manage 2021; 297:113356. [PMID: 34311257 DOI: 10.1016/j.jenvman.2021.113356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/16/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Lime is used to reduce soil acidification in agricultural soils. However, its effects on the soil microbial community are not well understood. Additionally, the soil microbial community is known to be influenced by fertilizers. However, the question remains whether liming influences the magnitude of fertilizers' impact on soil microbial communities. Therefore, an incubation experiment was performed to understand the effect of lime application (pH = 6.5 and 5.5 for the soils with and without lime, respectively) and fertilizer (digestate, urea and control) on the soil microbial community structures, stability and gene functions. Soils were sampled weekly after the application of fertilizers for a month. For microbial community analysis, DNA was extracted and sequenced targeting 16 S rRNA region. For gene abundances i.e 16 S rRNA, ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB), nitrous oxide reductase (nosZ) and nitrite reductase (nirS) quantitative PCR was conducted. In results, the relative abundance of Actinobacteria was influenced more strongly by digestate in lime soils, while Alphaproteobacteria was influenced more strongly by digestate in the no lime soil. In NL treatments, digestate had a significant effect on more operational taxonomic units (146) compared to lime (127), indicating that lime application increased soil microbial community's stability. Liming and fertilizer had a significant effect on 16 S rRNA gene copy numbers with the highest values observed in lime plus digestate treatments. Soil pH had a significant effect on AOA, nosZ and nirS gene copy numbers with the highest values observed in lime treatments. In the lime treatments digestate application had a positive impact on AOB gene copy numbers but this was not the case for soils without liming treatments. These results indicate that soil pH and fertilizer type should be taken into consideration for the management of functional gene abundance in agricultural soils.
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Affiliation(s)
| | - Yoshitaka Uchida
- Global Center for Food, Land and Water Resources, Research Faculty of Agriculture, Hokkaido University, Japan.
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9
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Wei H, Lin X. Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum. Sci Total Environ 2021; 771:144824. [PMID: 33545473 DOI: 10.1016/j.scitotenv.2020.144824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g-1 d-1, mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 106 and 2.4 ± 3.54 × 106 copies g-1, respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4+) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4+ consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.
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Affiliation(s)
- Hengchen Wei
- The University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Xianbiao Lin
- Laboratory of Microbial Ecology and Matter Cycles, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; School of Geographic Sciences, Key Laboratory of Geographic Information Science of the Ministry of Education, East China Normal University, Shanghai 200241, China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai 519000, China.
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10
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Wang X, Wang Y, Zhu F, Zhang C, Wang P, Zhang X. Effects of Different Land Use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils. Appl Environ Microbiol 2021; 87:e0009221. [PMID: 33837020 DOI: 10.1128/AEM.00092-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Land use types with different disturbance gradients show many variations in soil properties, but the effects of different land use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in soils under three land use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.
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Aigle A, Gubry-Rangin C, Thion C, Estera-Molina KY, Richmond H, Pett-Ridge J, Firestone MK, Nicol GW, Prosser JI. Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria. Environ Microbiol 2021; 22:4032-4045. [PMID: 32783333 DOI: 10.1111/1462-2920.15192] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/10/2020] [Indexed: 11/28/2022]
Abstract
Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.
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Affiliation(s)
- A Aigle
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Thion
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - K Y Estera-Molina
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - H Richmond
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - J Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, 94551, USA
| | - M K Firestone
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - G W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - J I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
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Liu X, Shao Y, Dong Y, Dong M, Xu Z, Hu X, Liu A. Response of ammonia-oxidizing archaea and bacteria to sulfadiazine and copper and their interaction in black soils. Environ Sci Pollut Res Int 2021; 28:11357-11368. [PMID: 33123879 DOI: 10.1007/s11356-020-11356-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
The large-scale development of animal husbandry and the wide agricultural application of livestock manure lead to more and more serious co-pollution of heavy metals and antibiotics in soil. In this study, two common feed additives, copper (Cu) and sulfadiazine (SDZ), were selected as target pollutants to evaluate the toxicity and interaction of antibiotics and heavy metals on ammonia oxidizers diversity, potential nitrification rate (PNR), and enzymatic activity in black soils. The results showed that soil enzyme activity was significantly inhibited by single Cu pollution, but the toxicity could be reduced by introducing low-concentration SDZ (5 mg · kg-1), which showed an antagonistic effect between Cu and SDZ (5 mg · kg-1), while the combined toxicity of high-concentration SDZ (10 mg · kg-1) and Cu were strengthened compared with the single Cu contamination on soil enzymes. In contrast, soil PNR was more sensitive to single Cu pollution and its combined pollution with SDZ than the enzyme activity. Real-time fluorescence quota PCR and Illumina Hiseq/Miseq sequencing results showed that ammonia-oxidizing archaea (AOA) was decreased in C2 (200 mg · kg-1 Cu treatment) and ammonia-oxidizing bacteria (AOB) was obviously stimulated in soil contaminated in C2, while in S5 (5 mg · kg-1 SDZ treatment), AOB was decreased; both AOA and AOB were significantly decreased at gene level in soils with combined pollutants (C2S5, 200 mg · kg-1 Cu combined with 5 mg · kg-1 SDZ). So, it can be concluded that combined pollution can cause more serious toxicity on the enzymatic activity, PNR, and ammonia-oxidizing microorganisms in soil through the synergistic effect between heavy metals and antibiotics pollutants.
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Affiliation(s)
- Xijuan Liu
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Yifei Shao
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Yuanpeng Dong
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Mengyang Dong
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Ziwen Xu
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Xinxin Hu
- College of Resources and Environmental engineering, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Aiju Liu
- College of Resources and Environmental engineering, Shandong University of Technology, Zibo, 255049, People's Republic of China.
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Liu L, Liu M, Jiang Y, Lin W, Luo J. Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon " Candidatus Nitrosocosmicus agrestis". mSystems 2021; 6:e01003-20. [PMID: 33594004 DOI: 10.1128/mSystems.01003-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ammonia tolerance is a universal characteristic among the ammonia-oxidizing bacteria (AOB); in contrast, the known species of ammonia-oxidizing archaea (AOA) have been regarded as ammonia sensitive, until the identification of the genus “Candidatus Nitrosocosmicus.” However, the mechanism of its ammonia tolerance has not been reported. In this study, the AOA species “Candidatus Nitrosocosmicus agrestis,” obtained from agricultural soil, was determined to be able to tolerate high concentrations of NH3 (>1,500 μM). In the genome of this strain, which was recovered from metagenomic data, a full set of genes for the pathways of polysaccharide metabolism, urea hydrolysis, arginine synthesis, and polyamine synthesis was identified. Among them, the genes encoding cytoplasmic carbonic anhydrase (CA) and a potential polyamine transporter (drug/metabolite exporter [DME]) were found to be unique to the genus “Ca. Nitrosocosmicus.” When “Ca. Nitrosocosmicus agrestis” was grown with high levels of ammonia, the genes that participate in CO2/HCO3− conversion, glutamate/glutamine syntheses, arginine synthesis, polyamine synthesis, and polyamine excretion were significantly upregulated, and the polyamines, including putrescine and spermidine, had significant levels of production. Based on genome analysis, gene expression quantification, and polyamine determination, we propose that the production and excretion of polyamines is probably one of the reasons for the ammonia tolerance of “Ca. Nitrosocosmicus agrestis,” and even of the genus “Ca. Nitrosocosmicus.” IMPORTANCE Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global N2O emission. Recently, some AOA species from the genus “Ca. Nitrosocosmicus” were also found to have high ammonia tolerance. However, the reported mechanism for the ammonia tolerance is very rare and indeterminate for AOB and for AOA species. In this study, an ammonia-tolerant AOA strain of the species “Ca. Nitrosocosmicus agrestis” was identified and its potential mechanisms for ammonia tolerance were explored. This study will be of benefit for determining more of the ecological role of AOA in agricultural soils or other environments.
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Modrzyński JJ, Aamand J, Wittorf L, Badawi N, Hubalek V, Canelles A, Hallin S, Albers CN. Combined removal of organic micropollutants and ammonium in reactive barriers developed for managed aquifer recharge. Water Res 2021; 190:116669. [PMID: 33279750 DOI: 10.1016/j.watres.2020.116669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/11/2020] [Accepted: 11/22/2020] [Indexed: 06/12/2023]
Abstract
Groundwater is an important drinking water resource. To ensure clean drinking water, managed aquifer recharge (MAR) could be an attractive solution when recharging with treated wastewater. The installation of reactive barriers, e.g. with compost or other organic materials at MAR facilities, may improve pollutant removal. To link pollutant transformation processes and microbiology in reactive barriers, we simulated infiltration through different sand-compost mixtures using laboratory columns with depth-specific sampling of water and barrier material. We also evaluated the effect of inoculation with activated sludge. Our focus was on the simultaneous removal of organic micropollutants and nitrogen species, with parallel monitoring of the development of microbial communities. During 17 weeks of operation, the columns were fed with synthetic wastewater containing five organic micropollutants (1-2 µg/L each) and ammonium (2 mg N/L). Unique communities developed in the columns in relation to barrier material, with high effects of compost addition and minor effect of inoculation. Removal of the micropollutant paracetamol (acetaminophen) occurred in all columns, while sulfamethoxazole was only removed in columns with 50% compost. By contrast, limited removal was observed for sulfadiazine, carbamazepine and diuron, with the latter two displaying transient removal, attributed sorption. Oxygen was depleted within the top few cm of the columns when compost was present, but this was sufficient to remove all ammonium through nitrification. The fate of accumulated nitrate at deeper layers depended on the fraction of compost, with more compost leading to removal of nitrate by denitrification, but also by dissimilatory nitrate reduction to ammonium, hampering the overall nitrogen removal efficiency. Introducing compost as reactive barrier in MAR facilities has a large effect on the microbial communities and processes, but whether it will provide overall cleaner water to the underlying aquifer is uncertain and will depend very much on the type of pollutant.
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Affiliation(s)
- Jakub J Modrzyński
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark
| | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark
| | - Lea Wittorf
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, 750 07 Uppsala, Sweden
| | - Nora Badawi
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark
| | - Valerie Hubalek
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, 750 07 Uppsala, Sweden
| | - Arnau Canelles
- Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, 750 07 Uppsala, Sweden
| | - Christian N Albers
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark.
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Xia WW, Zhao J, Zheng Y, Zhang HM, Zhang JB, Chen RR, Lin XG, Jia ZJ. Active Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope Probing. Appl Environ Microbiol 2020; 86:e01807-20. [PMID: 32978127 PMCID: PMC7657639 DOI: 10.1128/aem.01807-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/17/2020] [Indexed: 01/19/2023] Open
Abstract
Long-term nitrogen field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes in communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to those of 13C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimens for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N-fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable-isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and Nitrosospira viennensis-like AOA, despite the strong advantage of AOB over AOA in the N-fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was the opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidence that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in 13C-labeled microcosms.IMPORTANCE The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.
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Affiliation(s)
- Wei-Wei Xia
- Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yan Zheng
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - Hui-Min Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jia-Bao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Rui-Rui Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xian-Gui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhong-Jun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Ke Y, Tong T, Chen J, Huang J, Xie S. Influences of hexafluoropropylene oxide (HFPO) homologues on soil microbial communities. Chemosphere 2020; 259:127504. [PMID: 32650170 DOI: 10.1016/j.chemosphere.2020.127504] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/05/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
Hexafluoropropylene oxide (HFPO) homologues, as emerging perfluoroalkyl substances (PFASs) to replace legacy PFASs, have wide applications in the organofluorine industry and have been detected in the global environment. However, it is still unclear what effect HFPO homologues will exert on microbial abundance, community structure and function. The objective of this study was to assess potential impacts of HFPO homologue acids on archaea, bacteria, and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the soil environment. Grassland soil microcosms were supplemented with low (0.1 mg/kg) or high (10 mg/kg) dosages of dimer, trimer and tetramer acids of HFPO (HFPO-DA, HFPO-TA, and HFPO-TeA), respectively. The amendment of HFPO homologues acids initially decreased the abundance of archaea and bacteria but increased them in the later period. The addition of HFPO homologues acids raised AOA abundance but restrained AOB growth during the whole incubation. AOA and AOB community structures showed considerable variations. Potential nitrifying rate (PNR) showed an increase in the initial period followed by a decline in the later period. HFPO-DA had a lasting and suppressive effect on AOB and PNR even at a nearly environmental level. Overall, HFPO homologues with different carbon chain lengths had different impacts on soil microbial community and ammonia oxidation.
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Affiliation(s)
- Yanchu Ke
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tianli Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jun Huang
- School of Environment, Beijing Key Laboratory for Emerging Organic Contaminants Control (BKLEOC), State Key Joint Laboratory of Environment Simulation and Pollution Control (SKLESPC), Tsinghua University, Beijing, 100084, China.
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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Hernández-Del Amo E, Dolinová I, la Ramis-Jorba G, Gich F, Bañeras L. Limited effect of radial oxygen loss on ammonia oxidizers in Typha angustifolia root hairs. Sci Rep 2020; 10:15694. [PMID: 32973299 DOI: 10.1038/s41598-020-72653-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/31/2020] [Indexed: 11/11/2022] Open
Abstract
The benefits of plant–microbe interactions have been exploited extensively for nutrient removal. Radial oxygen loss in aquatic macrophytes potentially promotes nitrification and accelerates nitrogen removal through coupled nitrification–denitrification process. Nitrification is likely the limiting activity for an effective nitrogen removal in wetlands. In this work, we have quantified the effect of radial oxygen losses in Typha angustifolia plants in environments of contrasting salinities, including a temporary lagoon, a constructed wetland, and a river estuary. In all sites, radial oxygen diffusion occurred mainly at a narrow band, from 1 to 5 cm from the root tip, and were almost absent at the tip and basal sections of the root (> 5 cm). Root sections with active oxygen diffusion tended to show higher bacterial and archaeal densities in the rhizoplane according to 16S rRNA gene abundance data, except at higher salinities. Archaeal amoA /bacterial amoA gene ratios were highly variable among sites. Archaeal nitrifiers were only favoured over bacteria on the root surface of Typha collected from the constructed wetland. Collectively, radial oxygen loss had little effect on the nitrifying microbial community at the smaller scale (differences according to root-section), and observed differences were more likely related to prevailing physicochemical conditions of the studied environments or to long-term effects of the root microenvironment (root vs sediment comparisons).
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Tang HM, Xiao XP, Li C, Shi LH, Cheng KK, Wen L, Li WY, Wang K. Influences of different manure N input on soil ammonia-oxidizing archaea and bacterial activity and community structure in a double-cropping rice field. J Appl Microbiol 2020; 130:937-947. [PMID: 32852144 DOI: 10.1111/jam.14830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/24/2020] [Accepted: 08/18/2020] [Indexed: 11/28/2022]
Abstract
AIMS The short-term effects of different organic manure nitrogen (N) input on soil ammonia-oxidizing archaea (AOA) and bacterial (AOB) activity and community structure at maturity stages of early rice and late rice were investigated in the present paper, in a double-cropping rice system in southern China. METHODS AND RESULTS A field experiment was done by applying five different organic and inorganic N input treatments: (i) 100% N of chemical fertilizer (M0), (ii) 30% N of organic manure and 70% N of chemical fertilizer (M30), (iii) 50% N of organic manure and 50% N of chemical fertilizer (M50), (iv) 100% N of organic manure (M100) and (v) without N fertilizer input as control (CK). Microbial community changes were assessed using fatty acid methyl esters, and ammonia oxidizer (AO) changes were followed using quantitative PCR. The results showed that AOA were higher than that of AOB based upon amoA gene copy at maturity stages of early rice and late rice. Also, the abundance of AOB and AOA with M30, M50 and M100 treatments was significantly higher than that of CK treatment. Manure N input treatments had significant effect on AOB and AOA abundance, and a higher correlation between AOB and manure N input was observed. AOB correlated moderately with soil organic carbon content, and AOA correlated moderately with water-filled pore space. CONCLUSIONS This study found that abundance of AOB and AOA was increased under the given organic N conditions, and the soil AOB and AOA community and diversity were changed by different short-term organic manure N input treatments. SIGNIFICANCE AND IMPACT OF THE STUDY Soil microbial community and specific N-utilizing microbial groups were affected by organic manure N input practices.
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Affiliation(s)
- H M Tang
- Hunan Soil and Fertilizer Institute, Changsha, PR China
| | - X P Xiao
- Hunan Soil and Fertilizer Institute, Changsha, PR China
| | - C Li
- Hunan Soil and Fertilizer Institute, Changsha, PR China
| | - L H Shi
- Hunan Soil and Fertilizer Institute, Changsha, PR China
| | - K K Cheng
- Hunan Soil and Fertilizer Institute, Changsha, PR China
| | - L Wen
- Hunan Soil and Fertilizer Institute, Changsha, PR China
| | - W Y Li
- Hunan Soil and Fertilizer Institute, Changsha, PR China
| | - K Wang
- Hunan Soil and Fertilizer Institute, Changsha, PR China
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Alori ET, Emmanuel OC, Glick BR, Babalola OO. Plant-archaea relationships: a potential means to improve crop production in arid and semi-arid regions. World J Microbiol Biotechnol 2020; 36:133. [PMID: 32772189 DOI: 10.1007/s11274-020-02910-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
Crop production in arid and semi-arid regions of the world is limited by several abiotic factors, including water stress, temperature extremes, low soil fertility, high soil pH, low soil water-holding capacity, and low soil organic matter. Moreover, arid and semi-arid areas experience low levels of rainfall with high spatial and temporal variability. Also, the indiscriminate use of chemicals, a practice that characterizes current agricultural practice, promotes crop and soil pollution potentially resulting in serious human health and environmental hazards. A reliable and sustainable alternative to current farming practice is, therefore, a necessity. One such option includes the use of plant growth-promoting microbes that can help to ameliorate some of the adverse effects of these multiple stresses. In this regard, archaea, functional components of the plant microbiome that are found both in the rhizosphere and the endosphere may contribute to the promotion of plant growth. Archaea can survive in extreme habitats such as areas with high temperatures and hypersaline water. No cases of archaea pathogenicity towards plants have been reported. Archaea appear to have the potential to promote plant growth, improve nutrient supply and protect plants against various abiotic stresses. A better understanding of recent developments in archaea functional diversity, plant colonizing ability, and modes of action could facilitate their eventual usage as reliable components of sustainable agricultural systems. The research discussed herein, therefore, addresses the potential role of archaea to improve sustainable crop production in arid and semi-arid areas.
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Yang X, Ni K, Shi Y, Yi X, Ji L, Ma L, Ruan J. Heavy nitrogen application increases soil nitrification through ammonia-oxidizing bacteria rather than archaea in acidic tea (Camellia sinensis L.) plantation soil. Sci Total Environ 2020; 717:137248. [PMID: 32084690 DOI: 10.1016/j.scitotenv.2020.137248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/09/2020] [Accepted: 02/09/2020] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) fertilizer is widely used in agricultural ecosystems and influences N transformation processes in the soil such as nitrification. However, whether nitrification is primarily dominated by ammonia-oxidizing bacteria (AOB) or archaea (AOA) under heavy N application is still under debate. In the present work, the effect of long-term (12 years) N fertilization on soil nitrification and the key influencing factors were investigated in acidic tea plantation soil that received four different rates of N application (0, 119, 285, and 569 kg N ha-1 yr-1). Nitrification potential was measured and partitioned using chemical inhibitors. The abundance of functional genes involved in ammonia oxidation was quantified using quantitative polymerase chain reaction (qPCR). Ammonia-oxidizing communities were identified by shotgun metagenome sequencing. Potential nitrification rate in tea plantation soil was mainly dominated by autotrophic nitrification (PNRA) (71-79%). PNRA and heterotrophic nitrification (PNRH) were both significantly increased by heavy N (569 kg ha-1) application. Moreover, PNRA was mainly due to the contribution of AOB (52-66%) in N-treated soils, and N569 significantly increased the AOB contribution without affecting the AOA contribution. N569 increased the functional gene abundance of AOB and TAO100 (a non-halophilic γ-AOB) but decreased that of AOA. The dominant AOB (Nitrosomonas, Nitrosospira, and Nitrosococcus), AOA (Nitrososphaera and Nitrosopumilus) and commamox (Nitrospira) groups were profoundly altered by long-term N application rates. Partial least squares regression showed that total nitrification (PNRT), PNRA, and PNRAOB were primarily explained by the functional gene abundance of nitrifiers whereas PNRH and PNRAOA were closely associated with soil and pruned litter properties. Moreover, structural equation modeling (SEM) revealed that long-term N application significantly and indirectly affected nitrification potential by directly influencing soil properties, pruned litter properties, and functional gene abundance. Understanding the relative contribution of AOA and AOB to nitrification may help to better regulate N fertilizer use in agricultural ecosystems.
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Affiliation(s)
- Xiangde Yang
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China
| | - Kang Ni
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Yuanzhi Shi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Xioayun Yi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Lingfei Ji
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Lifeng Ma
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Jianyun Ruan
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
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Diao T, Peng Z, Niu X, Yang R, Ma F, Guo L. Changes of Soil Microbes Related with Carbon and Nitrogen Cycling after Long-Term CO2 Enrichment in a Typical Chinese Maize Field. Sustainability 2020; 12:1250. [DOI: 10.3390/su12031250] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Elevated atmospheric CO2 concentration (eCO2) has been the most important driving factor and characteristic of climate change. To clarify the effects of eCO2 on the soil microbes and on the concurrent status of soil carbon and nitrogen, an experiment was conducted in a typical summer maize field based on a 10-year mini FACE (Free Air Carbon Dioxide Enrichment) system in North China. Both rhizospheric and bulk soils were collected for measurement. The soil microbial carbon (MBC), nitrogen (MBN), and soil mineral N were measured at two stages. Characteristics of microbes were assayed for both rhizospheric soil and bulk soils at the key stage. We examined the plasmid copy numbers, diversities, and community structures of bacteria (in terms of 16s rRNA), fungi (in terms of ITS-internal transcribed spacer), ammonia oxidizing bacteria (AOB) and denitrifiers including nirK, nirS, and nosZ using the Miseq sequencing technique. Results showed that under eCO2 conditions, both MBC and MBN in rhizospheric soil were increased significantly. The quantity of ITS was increased in the eCO2 treatment compared with that in the ambient CO2 (aCO2) treatment, while the quantity of 16s rRNA in rhizospheric soil showed decrease in the rhizospheric soil in the eCO2 treatment. ECO2 changed the relative abundance of microbes in terms of compositional proportion of some orders or genera particularly in the rhizospheric soil-n particular, Chaetomium increased for ITS, Subgroups 4 and 6 increased for 16s rRNA, Nitrosospira decreased for AOB, and some genera showed increase for nirS, nirK, and nosZ. Nitrate N was the main inorganic nitrogen form at the tasseling stage and both quantities of AOB and denitrifiers, as well as the nosZ/(nirS+nirK) showed an increase under eCO2 conditions particularly in the rhizospheric soil. The Nitrosospira decreased in abundance under eCO2 conditions in the rhizospheric soil and some genera of denitrifiers also showed differences in abundance. ECO2 did not change the diversities of microbes significantly. In general, results suggested that 10 years of eCO2 did affect the active component of C and N pools (such as MBC and MBN) and both the quantities and relative abundance of microbes which are involved in carbon and nitrogen cycling, possibly due to the differences in both the quantities and component of substrate for relevant microbes in the rhizospheric soils.
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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. Sci Total Environ 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Beule L, Corre MD, Schmidt M, Göbel L, Veldkamp E, Karlovsky P. Conversion of monoculture cropland and open grassland to agroforestry alters the abundance of soil bacteria, fungi and soil-N-cycling genes. PLoS One 2019; 14:e0218779. [PMID: 31246995 PMCID: PMC6597161 DOI: 10.1371/journal.pone.0218779] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 06/10/2019] [Indexed: 01/15/2023] Open
Abstract
Integration of trees in agroforestry systems can increase the system sustainability compared to monocultures. The resulting increase in system complexity is likely to affect soil-N cycling by altering soil microbial community structure and functions. Our study aimed to assess the abundance of genes encoding enzymes involved in soil-N cycling in paired monoculture and agroforestry cropland in a Phaeozem soil, and paired open grassland and agroforestry grassland in Histosol and Anthrosol soils. The soil fungi-to-bacteria ratio was greater in the tree row than in the crop or grass rows of the monoculture cropland and open grassland in all soil types, possibly due to increased input of tree residues and the absence of tillage in the Phaeozem (cropland) soil. In the Phaeozem (cropland) soil, gene abundances of amoA indicated a niche differentiation between archaeal and bacterial ammonia oxidizers that distinctly separated the influence of the tree row from the crop row and monoculture system. Abundances of nitrate (napA and narG), nitrite (nirK and nirS) and nitrous oxide reductase genes (nosZ clade I) were largely influenced by soil type rather than management system. The soil types’ effects were associated with their differences in soil organic C, total N and pH. Our findings show that in temperate regions, conversion of monoculture cropland and open grassland to agroforestry systems can alter the abundance of soil bacteria and fungi and soil-N-cycling genes, particularly genes involved in ammonium oxidation.
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Affiliation(s)
- Lukas Beule
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, Goettingen, Germany
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
- * E-mail:
| | - Marife D. Corre
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Marcus Schmidt
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Leonie Göbel
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Edzo Veldkamp
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Goettingen, Germany
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, Goettingen, Germany
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Cassman NA, Soares JR, Pijl A, Lourenço KS, van Veen JA, Cantarella H, Kuramae EE. Nitrification inhibitors effectively target N 2 O-producing Nitrosospira spp. in tropical soil. Environ Microbiol 2019; 21:1241-1254. [PMID: 30735001 PMCID: PMC6850170 DOI: 10.1111/1462-2920.14557] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/09/2019] [Accepted: 02/04/2019] [Indexed: 01/01/2023]
Abstract
The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2 O-producing AOB Nitrosospira with N2 O, NO3 - , NH4 + , water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3 - , NH4 + and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4 + , which suggests different drivers. These results support the co-occurrence of non-N2 O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2 O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.
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Affiliation(s)
- Noriko A. Cassman
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Johnny R. Soares
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Agata Pijl
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Késia S. Lourenço
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Johannes A. van Veen
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Heitor Cantarella
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Eiko E. Kuramae
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
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Sidhu H, O'Connor G, Ogram A, Kumar K. Bioavailability of biosolids-borne ciprofloxacin and azithromycin to terrestrial organisms: Microbial toxicity and earthworm responses. Sci Total Environ 2019; 650:18-26. [PMID: 30195128 DOI: 10.1016/j.scitotenv.2018.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/29/2018] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
Information on bioavailability of two antibiotic TOrCs, ciprofloxacin (CIP) and azithromycin (AZ), to terrestrial organisms is severely limited, especially in the biosolids context. Responses of two terrestrial organisms, earthworms and microbes, to a range of environmentally relevant concentrations of biosolids-borne CIP and AZ were assessed in laboratory incubation studies involving 3H-labeled compounds. Earthworm assessments were based on the Earthworm Sub-chronic Toxicity Test (OCSPP 850.3100). Microbial impacts were assessed using respiration and reverse transcriptase-quantitative PCR (mRNA) analyses of nutrient (N and P) cycling genes as toxicity markers. Antibiotic extractability and stability during incubations were assessed using sequential extractions with CaCl2, methanol:water, and accelerated solvent extraction and analyses using thin layer chromatography. Subsample combustion, in addition to sequential extraction, recovered nearly 100% of the added antibiotic. The two compounds persisted (estimated half-lives ≥ 3 y), but extractable fractions (especially of CIP) decreased over time. Neither biosolids-borne antibiotic significantly impacted overall respiration or N and P cycling. Microbial toxicity responses were minimal; complementary DNA (cDNA) concentrations of ammonia oxidizing bacterial genes were affected, but only initially. Similarly, earthworms showed no apparent response related to toxicity to environmentally relevant (and much greater) concentrations of biosolids-borne CIP and AZ. Earthworms, however, accumulated both compounds, and the bioaccumulation factor (BAF) values (dry weight basis) were ~4 (CIP) and ~7 (AZ) in depurated worms and ~20 (CIP and AZ) in un-depurated worms. The microbial and earthworm responses strongly to moderately correlated with "bioaccessible" fractions of the target TOrCs. The results suggest that biosolids-borne CIP and AZ toxicity to terrestrial microbes and earthworms is minimal, but there is a potential for target TOrC entry into ecological food web.
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Affiliation(s)
- Harmanpreet Sidhu
- Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States of America.
| | - George O'Connor
- Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States of America
| | - Andrew Ogram
- Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States of America
| | - Kuldip Kumar
- Metropolitan Water Reclamation District, Chicago, IL 60611, United States of America
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Jones CM, Hallin S. Geospatial variation in co-occurrence networks of nitrifying microbial guilds. Mol Ecol 2018; 28:293-306. [PMID: 30307658 PMCID: PMC6905385 DOI: 10.1111/mec.14893] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/20/2018] [Accepted: 10/01/2018] [Indexed: 01/07/2023]
Abstract
Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.
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Affiliation(s)
- Christopher M Jones
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
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Sauder LA, Engel K, Lo CC, Chain P, Neufeld JD. "Candidatus Nitrosotenuis aquarius," an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter. Appl Environ Microbiol 2018; 84:e01430-18. [PMID: 29959256 DOI: 10.1128/AEM.01430-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 06/27/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia is a metabolic waste product excreted by aquatic organisms that causes toxicity when it accumulates. Aquaria and aquaculture systems therefore use biological filters that promote the growth of nitrifiers to convert ammonia to nitrate. Ammonia-oxidizing bacteria (AOB) have been isolated from aquarium biofilters and are available as commercial supplements, but recent evidence suggests that ammonia-oxidizing archaea (AOA) are abundant in aquarium biofilters. In this study, we report the cultivation and closed genome sequence of the novel AOA representative "Candidatus Nitrosotenuis aquarius," which was enriched from a freshwater aquarium biofilter. "Ca Nitrosotenuis aquarius" oxidizes ammonia stoichiometrically to nitrite with a concomitant increase in thaumarchaeotal cells and a generation time of 34.9 h. "Ca Nitrosotenuis aquarius" has an optimal growth temperature of 33°C, tolerates up to 3 mM NH4Cl, and grows optimally at 0.05% salinity. Transmission electron microscopy revealed that "Ca Nitrosotenuis aquarius" cells are rod shaped, with a diameter of ∼0.4 μm and length ranging from 0.6 to 3.6 μm. In addition, these cells possess surface layers (S-layers) and multiple proteinaceous appendages. Phylogenetically, "Ca Nitrosotenuis aquarius" belongs to the group I.1a Thaumarchaeota, clustering with environmental sequences from freshwater aquarium biofilters, aquaculture systems, and wastewater treatment plants. The complete 1.70-Mbp genome contains genes involved in ammonia oxidation, bicarbonate assimilation, flagellum synthesis, chemotaxis, S-layer production, defense, and protein glycosylation. Incubations with differential inhibitors indicate that "Ca Nitrosotenuis aquarius"-like AOA contribute to ammonia oxidation within the aquarium biofilter from which it originated.IMPORTANCE Nitrification is a critical process for preventing ammonia toxicity in engineered biofilter environments. This work describes the cultivation and complete genome sequence of a novel AOA representative enriched from a freshwater aquarium biofilter. In addition, despite the common belief in the aquarium industry that AOB mediate ammonia oxidation, the present study suggests an in situ role for "Ca Nitrosotenuis aquarius"-like AOA in freshwater aquarium biofilters.
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Hellwig N, Gómez-brandón M, Ascher-jenull J, Bardelli T, Anschlag K, Fornasier F, Pietramellara G, Insam H, Broll G. Humus Forms and Soil Microbiological Parameters in a Mountain Forest: Upscaling to the Slope Scale. Soil Syst 2018; 2:12. [DOI: 10.3390/soilsystems2010012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Domeignoz-Horta LA, Philippot L, Peyrard C, Bru D, Breuil MC, Bizouard F, Justes E, Mary B, Léonard J, Spor A. Peaks of in situ N 2 O emissions are influenced by N 2 O-producing and reducing microbial communities across arable soils. Glob Chang Biol 2018; 24:360-370. [PMID: 28752605 DOI: 10.1111/gcb.13853] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/03/2017] [Indexed: 05/22/2023]
Abstract
Agriculture is the main source of terrestrial N2 O emissions, a potent greenhouse gas and the main cause of ozone depletion. The reduction of N2 O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only known biological process eliminating this greenhouse gas. Recent studies showed that a previously unknown clade of N2 O-reducers (nosZII) was related to the potential capacity of the soil to act as a N2 O sink. However, little is known about how this group responds to different agricultural practices. Here, we investigated how N2 O-producers and N2 O-reducers were affected by agricultural practices across a range of cropping systems in order to evaluate the consequences for N2 O emissions. The abundance of both ammonia-oxidizers and denitrifiers was quantified by real-time qPCR, and the diversity of nosZ clades was determined by 454 pyrosequencing. Denitrification and nitrification potential activities as well as in situ N2 O emissions were also assessed. Overall, greatest differences in microbial activity, diversity, and abundance were observed between sites rather than between agricultural practices at each site. To better understand the contribution of abiotic and biotic factors to the in situ N2 O emissions, we subdivided more than 59,000 field measurements into fractions from low to high rates. We found that the low N2 O emission rates were mainly explained by variation in soil properties (up to 59%), while the high rates were explained by variation in abundance and diversity of microbial communities (up to 68%). Notably, the diversity of the nosZII clade but not of the nosZI clade was important to explain the variation of in situ N2 O emissions. Altogether, these results lay the foundation for a better understanding of the response of N2 O-reducing bacteria to agricultural practices and how it may ultimately affect N2 O emissions.
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Affiliation(s)
| | - Laurent Philippot
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | | | - David Bru
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Florian Bizouard
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Eric Justes
- AGIR, INPT, INP-PURPAN, INRA, Université de Toulouse, Toulouse, France
| | | | | | - Ayme Spor
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
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Fang Y, Hu Z, Zou Y, Zhang J, Zhu Z, Zhang J, Nie L. Improving nitrogen utilization efficiency of aquaponics by introducing algal-bacterial consortia. Bioresour Technol 2017; 245:358-364. [PMID: 28898831 DOI: 10.1016/j.biortech.2017.08.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Aquaponics is a promising technology combining aquaculture with hydroponics. In this study, algal-bacterial consortia were introduced into aquaponics, i.e., algal-bacterial based aquaponics (AA), to improve the nitrogen utilization efficiency (NUE) of aquaponics. The results showed that the NUE of AA was 13.79% higher than that of media-based aquaponics (MA). In addition, higher NO3- removal by microalgae assimilation led to better water quality in AA, which made up for the deficiencies of poor aquaponic management of nitrate. As a result of lower NO3- concentrations and dramatically higher dissolved oxygen (DO) concentrations caused by microalgae photosynthesis in the photobioreactor, the N2O emission of AA was 89.89% lower than that of MA, although nosZ gene abundance in MA's hydroponic bed was approximately 30 times over that in AA. Considering the factors mentioned above, AA would improve the sustainability of aquaponics and have a good application foreground.
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Affiliation(s)
- Yingke Fang
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Zhen Hu
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong 250100, China.
| | - Yina Zou
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Jian Zhang
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Zhuoran Zhu
- School of Environmental Science and Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Jianda Zhang
- College of Resources and Environment Science, Hebei Normal University, 20# East Road of Southern 2nd Ring, Shijiazhuang 050024, China
| | - Lichao Nie
- Geotechnical and Structural Engineering Research Center, Shandong University, Jinan, Shandong 250061, China
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Samad MS, Johns C, Richards KG, Lanigan GJ, de Klein CAM, Clough TJ, Morales SE. Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria. Mol Ecol 2017; 26:5500-5514. [DOI: 10.1111/mec.14275] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/22/2017] [Accepted: 07/24/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Md Sainur Samad
- Department of Microbiology and Immunology; Otago School of Medical Sciences; University of Otago; Dunedin New Zealand
| | - Charlotte Johns
- Department of Soil and Physical Sciences; Lincoln University; Lincoln New Zealand
| | | | | | | | - Timothy J. Clough
- Department of Soil and Physical Sciences; Lincoln University; Lincoln New Zealand
| | - Sergio E. Morales
- Department of Microbiology and Immunology; Otago School of Medical Sciences; University of Otago; Dunedin New Zealand
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Clough TJ, Lanigan GJ, de Klein CAM, Samad MS, Morales SE, Rex D, Bakken LR, Johns C, Condron LM, Grant J, Richards KG. Influence of soil moisture on codenitrification fluxes from a urea-affected pasture soil. Sci Rep 2017; 7:2185. [PMID: 28526821 DOI: 10.1038/s41598-017-02278-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/10/2017] [Indexed: 11/23/2022] Open
Abstract
Intensively managed agricultural pastures contribute to N2O and N2 fluxes resulting in detrimental environmental outcomes and poor N use efficiency, respectively. Besides nitrification, nitrifier-denitrification and heterotrophic denitrification, alternative pathways such as codenitrification also contribute to emissions under ruminant urine-affected soil. However, information on codenitrification is sparse. The objectives of this experiment were to assess the effects of soil moisture and soil inorganic-N dynamics on the relative contributions of codenitrification and denitrification (heterotrophic denitrification) to the N2O and N2 fluxes under a simulated ruminant urine event. Repacked soil cores were treated with 15N enriched urea and maintained at near saturation (−1 kPa) or field capacity (−10 kPa). Soil inorganic-N, pH, dissolved organic carbon, N2O and N2 fluxes were measured over 63 days. Fluxes of N2, attributable to codenitrification, were at a maximum when soil nitrite (NO2−) concentrations were elevated. Cumulative codenitrification was higher (P = 0.043) at −1 kPa. However, the ratio of codenitrification to denitrification did not differ significantly with soil moisture, 25.5 ± 15.8 and 12.9 ± 4.8% (stdev) at −1 and −10 kPa, respectively. Elevated soil NO2− concentrations are shown to contribute to codenitrification, particularly at −1 kPa.
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Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, Neufeld JD. Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. ISME J 2017; 11:1142-1157. [PMID: 28195581 PMCID: PMC5398378 DOI: 10.1038/ismej.2016.192] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 11/10/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023]
Abstract
Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1–2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown metabolism.
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Affiliation(s)
- Laura A Sauder
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Jasmin Schwarz
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Rodrigues T, Belmok A, Catão E, Kyaw CM. Archaea in Natural and Impacted Brazilian Environments. Archaea 2016; 2016:1259608. [PMID: 27829818 DOI: 10.1155/2016/1259608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/08/2016] [Indexed: 11/26/2022]
Abstract
In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.
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Dini-Andreote F, Brossi MJDL, van Elsas JD, Salles JF. Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem. Front Microbiol 2016; 7:902. [PMID: 27379042 PMCID: PMC4908922 DOI: 10.3389/fmicb.2016.00902] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/26/2016] [Indexed: 11/25/2022] Open
Abstract
Coastal ecosystems are considered buffer zones for the discharge of land-derived nutrients without accounting for potential negative side effects. Hence, there is an urgent need to better understand the ecological assembly and dynamics of the microorganisms that are involved in nitrogen (N) cycling in such systems. Here, we employed two complementary methodological approaches (i.e., shotgun metagenomics and quantitative PCR) to examine the distribution and abundance of selected microbial genes involved in N transformations. We used soil samples collected along a well-established pristine salt marsh soil chronosequence that spans over a century of ecosystem development at the island of Schiermonnikoog, The Netherlands. Across the examined soil successional stages, the structure of the populations of genes involved in N cycling processes was strongly related to (shifts in the) soil nitrogen levels (i.e., NO3−, NH4+), salinity and pH (explaining 73.8% of the total variation, R2 = 0.71). Quantification of the genes used as proxies for N fixation, nitrification and denitrification revealed clear successional signatures that corroborated the taxonomic assignments obtained by metagenomics. Notably, we found strong evidence for niche partitioning, as revealed by the abundance and distribution of marker genes for nitrification (ammonia-oxidizing bacteria and archaea) and denitrification (nitrite reductase nirK, nirS and nitrous oxide reductase nosZ clades I and II). This was supported by a distinct correlation between these genes and soil physico-chemical properties, such as soil physical structure, pH, salinity, organic matter, total N, NO3−, NH4+ and SO42−, across four seasonal samplings. Overall, this study sheds light on the successional trajectories of microbial N cycle genes along a naturally developing salt marsh ecosystem. The data obtained serve as a foundation to guide the formulation of ecological models that aim to effectively monitor and manage pristine and impacted salt marsh areas. Such models should account for the ecology as well as the historical contingency of N cycling communities.
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Affiliation(s)
- Francisco Dini-Andreote
- Microbial Ecology Group, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Maria Julia de L Brossi
- Microbial Ecology Group, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology Group, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Joana F Salles
- Microbial Ecology Group, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
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Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière; 47 Boulevard de l'Hôpital 75013 Paris France
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