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Omirou M, Stephanou C, Anastopoulos I, Philippot L, Ioannides IM. Differential response of N 2O emissions, N 2O-producing and N 2O-reducing bacteria to varying tetracycline doses in fertilized soil. ENVIRONMENTAL RESEARCH 2022; 214:114013. [PMID: 35964670 DOI: 10.1016/j.envres.2022.114013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Tetracyclines are the most widely used antibiotics worldwide. Their presence in soils could affect nutrient cycling, but our knowledge regarding how they affect soil microbial communities involved in greenhouse gas emissions is limited. The objective of the current study was to evaluate how tetracycline is affecting N2O emissions and the abundance of denitrifiers in fertilized soil. For this purpose, soil mesocosms were treated with only NH4NO3 (100 mg/kg) or NH4NO3 (100 mg/kg) plus three different doses of tetracycline (0.1, 0.5 and 2 mg/kg). Soils that did not receive tetracycline or NH4NO3 were used as controls. Nitrous oxide fluxes were monitored daily for 16 days. The total bacterial (16S rRNA), the abundance of N2O-reducing and -producing bacteria were quantified by qPCR at the end of the experiment. The application of NH4NO3 caused a significant increase of N2O emissions and AOB abundance but did not affect the abundance of denitrifiers and AOA compared to control soils. Different doses of tetracycline in fertilized soils did not mitigate these N2O emissions; instead, higher cumulative emissions were noticed in soils treated with the lowest dose. In these soils the total bacterial abundance was higher compared to soils received higher tetracycline concentration. The abundances of the N2O-producing and N2O-reducing communities were also differently affected by the addition of tetracycline, which was dose-dependent. Higher doses of tetracycline favored N2O-reducers within the total bacterial community, which could be important for mitigating N2O emissions in the long term.
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Affiliation(s)
- Michalis Omirou
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus.
| | - Coralea Stephanou
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus
| | - Ioannis Anastopoulos
- Department of Agriculture, University of Ioannina,UoI, Kostakii Campus, 47040 Arta, Greece
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000 Dijon, France
| | - Ioannis M Ioannides
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus
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2
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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] [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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3
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Ding L, Zhou J, Li Q, Tang J, Chen X. Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones. MICROBIAL ECOLOGY 2022; 83:393-407. [PMID: 33893533 DOI: 10.1007/s00248-021-01746-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.
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Affiliation(s)
- Lilian Ding
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Jingyi Zhou
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Qiyao Li
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Jianjun Tang
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China.
| | - Xin Chen
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China.
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4
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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. FRONTIERS IN PLANT SCIENCE 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] [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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5
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Kavehei A, Gore DB, Chariton AA, Hose GC. Characterizing the spatial distributions of soil biota at a legacy base metal mine using environmental DNA. CHEMOSPHERE 2022; 286:131899. [PMID: 34426292 DOI: 10.1016/j.chemosphere.2021.131899] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 05/20/2023]
Abstract
Characterizing the distribution of biota in response to contaminants is a critical element of site risk assessments. In this study we investigated the spatial distributions of biota and soil chemistry data in surface soil from Sunny Corner, a legacy base metal sulfide mine, Australia. Our results showed that copper (Cu), zinc (Zn), arsenic (As) and lead (Pb) in the surface soil exceeded Australian national soil quality guidelines and posed risks to the environment. Environmental (e)DNA metabarcoding of prokaryote and eukaryote composition confirmed the suggestion of environmental risk posed by these elements collectively explaining 72.9 % and 60.5 % of the total variation in the composition of soil prokaryotes and eukaryotes, respectively. Prokaryotic taxa from the phyla Gemmatimonadetes, Verrucomicrobia and Deinococcus-Thermus showed similar spatial patterns to As and Pb, and were positively correlated. Eukaryotic taxa from the phylum Chlorophyta had similar positive correlations with As and Pb in the soil. In contrast, Amoebozoa and Cercozoa, were sensitive to metals and metalloids, having higher relative abundances in soils with lower concentrations of contaminants. Our study shows that metabarcoding is a promising ecological approach for rapid, large scale assessment of contaminated and potentially impacted sites.
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Affiliation(s)
- Armin Kavehei
- Department of Earth and Environmental Sciences, Macquarie University, Sydney, 2109, Australia.
| | - Damian B Gore
- Department of Earth and Environmental Sciences, Macquarie University, Sydney, 2109, Australia
| | - Anthony A Chariton
- Department of Biological Sciences, Macquarie University, Sydney, 2109, Australia
| | - Grant C Hose
- Department of Biological Sciences, Macquarie University, Sydney, 2109, Australia
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6
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Saghaï A, Banjeree S, Degrune F, Edlinger A, García-Palacios P, Garland G, van der Heijden MGA, Herzog C, Maestre FT, Pescador DS, Philippot L, Rillig MC, Romdhane S, Hallin S. Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils. Environ Microbiol 2021; 24:341-356. [PMID: 34796612 DOI: 10.1111/1462-2920.15830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/28/2021] [Accepted: 10/27/2021] [Indexed: 01/04/2023]
Abstract
Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Florine Degrune
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Anna Edlinger
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gina Garland
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Soil Quality and Use Group, Agroscope, Zurich, Switzerland.,Department of Environmental System Sciences, Soil Resources Group, ETH Zurich, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Chantal Herzog
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Alicante, Spain.,Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | - David S Pescador
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnología, Móstoles, Spain
| | - Laurent Philippot
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Sana Romdhane
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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7
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Hu J, Zhao Y, Yao X, Wang J, Zheng P, Xi C, Hu B. Dominance of comammox Nitrospira in soil nitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146558. [PMID: 33765470 DOI: 10.1016/j.scitotenv.2021.146558] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/09/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
The first and limiting step of nitrification is catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recently, complete ammonia oxidizers (comammox Nitrospira) have been discovered to perform complete nitrification in one cell, yet their role in soil nitrification is still unclear. This study investigated the abundance and contribution of aerobic ammonia oxidizers in typical soil habitats, and assessed the role of comammox Nitrospira in ammonia-oxidizing communities. The results showed that comammox Nitrospira were dominant in 70% of the samples and their abundance displayed a significant positive correlation with nitrification potential. The median amoA gene transcription level of comammox Nitrospira exceeded that of AOA and AOB in in-situ soils. The abundance of comammox Nitrospira was negatively correlated with soil pH, dominating in 84% of soil samples with pH < 6.17. The results challenge the role of AOA and AOB in soils, highlighting the importance of comammox Nitrospira in soil nitrification, especially in acid soils. This work supports better understanding and regulation of the soil nitrogen cycle.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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8
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Maura D, Elmekki N, Goddard CA. The ammonia oxidizing bacterium Nitrosomonas eutropha blocks T helper 2 cell polarization via the anti-inflammatory cytokine IL-10. Sci Rep 2021; 11:14162. [PMID: 34238943 PMCID: PMC8266879 DOI: 10.1038/s41598-021-93299-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
The prevalence of atopic diseases has been steadily increasing since the mid twentieth century, a rise that has been linked to modern hygienic lifestyles that limit exposure to microbes and immune system maturation. Overactive type 2 CD4+ helper T (Th2) cells are known to be closely associated with atopy and represent a key target for treatment. In this study, we present an initial characterization of ammonia oxidizing bacteria (AOB) Nitrosomonas eutropha D23, an environmental microbe that is not associated with human pathology, and show AOB effectively suppress the polarization of Th2 cells and production of Th2-associated cytokines (IL-5, IL-13, and IL-4) by human peripheral blood mononuclear cells (PBMC). We show that AOB inhibit Th2 cell polarization not through Th1-mediated suppression, but rather through mechanisms involving the anti-inflammatory cytokine IL-10 and the potential inhibition of dendritic cells, as evidenced by a reduction in Major Histocompatibility Complex Class II (MHC II) and CD86 expression following AOB treatment. This is the first report of immunomodulatory properties of AOB, and provides initial support for the development of AOB as a potential therapeutic for atopic diseases.
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9
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Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States. MICROBIAL ECOLOGY 2020; 80:778-792. [PMID: 32535638 DOI: 10.1007/s00248-020-01534-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.
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Affiliation(s)
- Emily L Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA
| | - John R Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA.
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10
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Hu J, Zhao Y, Yang W, Wang J, Liu H, Zheng P, Hu B. Surface ammonium loading rate shifts ammonia-oxidizing communities in surface water-fed rapid sand filters. FEMS Microbiol Ecol 2020; 96:5899051. [PMID: 32860687 DOI: 10.1093/femsec/fiaa179] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/26/2020] [Indexed: 01/15/2023] Open
Abstract
Nitrification is important in drinking water treatment plants (DWTPs) for ammonia removal and is widely considered as a stepwise process mediated by ammonia- and nitrite-oxidizing microorganisms. The recent discovery of complete ammonia oxidizers (comammox) has challenged the long-held assumption that the division of metabolic labor in nitrification is obligate. However, little is known about the role of comammox Nitrospira in DWTPs. Here, we explored the relative importance of comammox Nitrospira, canonical ammonia-oxidizing archaea (AOA) and bacteria (AOB) in 12 surface water-fed rapid sand filters (RSFs). Quantitative PCR results showed that all the three ammonia-oxidizing guilds had the potential to dominate nitrification in DWTPs. Spearman's correlation and redundancy analysis revealed that the surface ammonium loading rate (SLR) was the key environmental factor influencing ammonia-oxidizing communities. Comammox Nitrospira were likely to dominate the nitrification under a higher SLR. PCR and phylogenetic analysis indicated that most comammox Nitrospira belonged to clade A, with clade B comammox Nitrospira almost absent. This work reveals obvious differences in ammonia-oxidizing communities between surface water-fed and groundwater-fed RSFs. The presence of comammox Nitrospira can support the stability of drinking water production systems under high SLR and warrants further investigation of their impact on drinking water quality.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Weiling Yang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China.,Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
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11
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Frąc M, Lipiec J, Usowicz B, Oszust K, Brzezińska M. Structural and functional microbial diversity of sandy soil under cropland and grassland. PeerJ 2020; 8:e9501. [PMID: 32953254 PMCID: PMC7474522 DOI: 10.7717/peerj.9501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Background Land use change significantly alters soil organic carbon content and the microbial community. Therefore, in the present study, the effect of changing cropland to grassland on structural and functional soil microbial diversity was evaluated. The specific aims were (i) to identify the most prominent members of the fungal communities and their relevant ecological guild groups; (ii) to assess changes in the diversity of ammonia-oxidizing archaea; (iii) to determine the relationships between microbial diversity and selected physical and chemical properties. Methods We investigated microbial diversity and activity indicators, bulk density and the water-holding capacity of sandy soil under both cropland and 25-year-old grassland (formerly cropland) in Trzebieszów, in the Podlasie Region, Poland. Microbial diversity was assessed by: the relative abundance of ammonia-oxidizing archaea, fungal community composition and functional diversity. Microbial activity was assessed by soil enzyme (dehydrogenase, β-glucosidase) and respiration tests. Results It was shown that compared to cropland, grassland has a higher soil organic carbon content, microbial biomass, basal respiration, rate of enzyme activity, richness and diversity of the microbial community, water holding capacity and the structure of the fungal and ammonia-oxidizing archaea communities was also altered. The implications of these results for soil quality and soil health are also discussed. The results suggest that grassland can have a significant phytosanitary capacity with regard to ecosystem services, due to the prominent presence of beneficial and antagonistic microbes. Moreover, the results also suggest that grassland use may improve the status of soil organic carbon and nitrogen dynamics, thereby increasing the relative abundance of fungi and ammonia-oxidizing archaea.
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Affiliation(s)
- Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Jerzy Lipiec
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Bogusław Usowicz
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Karolina Oszust
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
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12
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Chen C, Han H, Xu T, Lv Y, Hu K, Li XX, Qiao Y, Ding GC, Li J. Comparison of the Total, Diazotrophic and Ammonia-Oxidizing Bacterial Communities Between Under Organic and Conventional Greenhouse Farming. Front Microbiol 2020; 11:1861. [PMID: 32903338 PMCID: PMC7434936 DOI: 10.3389/fmicb.2020.01861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/15/2020] [Indexed: 12/15/2022] Open
Abstract
Organic greenhouse farming is an innovative system that may maintain a high yield and healthy agroecosystem. There have been no rigorous studies on the comparison of total and nitrogen-cycling bacterial community in vegetable soils between organic and conventional farming management at large scale. A survey of bacterial community and nitrogen cycles from soils under organic and conventional greenhouse farming was performed at 30 sites, covering seven soil types with 4 to 18 years of organic farming history. Communities of the total, diazotrophs and ammonia-oxidizing bacteria were studied with high-throughput sequencing of the 16S rRNA, nifH and amoA genes, respectively. Organic greenhouse farming did not influence alpha diversities. Beta diversities among the total (26/30) and diazotrophic (17/19) bacteria differed between farming systems, but compositional differences in ammonia-oxidizing bacteria between the two farming systems were only detected at 6 sites. Despite the effects of farming system on most bacterial genera were varied across different sites, organic greenhouse farming persistently selected for a few genera, possibly for the biodegradation of organic carbon with high molecular weight (Hyphomicrobium, Rubinisphaera, Aciditerrimonas, Planifilum, Phaselicystis, and Ohtaekwangia), but against putative ammonia oxidizing (Nitrosospira, Nitrosopumilus) and diazotrophic (Bradyrhizobium) bacterial genera, as determined by 16S rRNA analysis. Diazotrophic bacteria affiliated with nifH cluster 1J were preferentially associated with organic greenhouse farming, in contrast to Paenibacillus borealis. In summary, this study provides insights into the complex effects of organic greenhouse farming on the total, diazotrophic and ammonia oxidizing bacterial communities across different environmental context.
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Affiliation(s)
- Chen Chen
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Hui Han
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Ting Xu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheck Biotechnology Co., Ltd., Suzhou, China
| | - Yizhong Lv
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Kelin Hu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Xue Xian Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Yuhui Qiao
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guo-Chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheck Biotechnology Co., Ltd., Suzhou, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheck Biotechnology Co., Ltd., Suzhou, China
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13
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Brin LD, Goyer C, Zebarth BJ, Burton DL, Chantigny MH. Linking changes in snow cover with microbial nitrogen cycling functional gene abundance and expression in agricultural soil. FEMS Microbiol Ecol 2020; 95:5511778. [PMID: 31167230 DOI: 10.1093/femsec/fiz073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/04/2019] [Indexed: 11/12/2022] Open
Abstract
In eastern Canada, climate change-related warming and increased precipitation may alter winter snow cover, with potential consequences for soil conditions, nitrogen (N) cycling, and microbes. We conducted a 2-year field study aimed at determining the influence of snow removal, snow accumulation, and ambient snow in a potato-barley crop system on the abundance and expression of denitrifier (nirS, nirK, nosZ) and nitrifier (ammonium oxidizing archaeal (AOA) and bacterial (AOB) amoA) genes. Denitrifier and nitrifier abundance and expression results were compared to N2O production, soil atmosphere accumulation, and surface fluxes. In the first winter, nirK abundance was lowest while AOB abundance was greatest in snow accumulation treatments. In the second winter, greatest abundances were observed in the ambient snow treatment, which had greatest N2O accumulation and spring thaw fluxes, suggesting a link between microbial populations and biogeochemical functioning. Treatment effects on gene expression were limited, but greatest AOA, AOB, and nosZ expression was measured near 0°C and above 15°C, indicating that activity was promoted by freeze-thaw conditions and at summer temperatures. Overall, effects of changing snow depth on denitrifier and nitrifier abundance were not solely due to change in soil temperature, but also to soil moisture and/or interactions between these parameters.
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Affiliation(s)
- Lindsay D Brin
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Claudia Goyer
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Bernie J Zebarth
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - David L Burton
- Department of Environmental Sciences, Dalhousie University, Agricultural Campus, PO Box 550, Truro, Nova Scotia, B2N 5E3, Canada
| | - Martin H Chantigny
- Québec Research and Development Centre, Agriculture and Agri-Food Canada, 2560 Hochelaga Boulevard, Québec, Québec, G1V 2J3, Canada
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14
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Mukhtar H, Lin YP, Lin CM, Lin YR. Relative Abundance of Ammonia Oxidizing Archaea and Bacteria Influences Soil Nitrification Responses to Temperature. Microorganisms 2019; 7:microorganisms7110526. [PMID: 31690001 PMCID: PMC6920900 DOI: 10.3390/microorganisms7110526] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/24/2019] [Accepted: 10/31/2019] [Indexed: 11/16/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB) are thought to contribute differently to soil nitrification, yet the extent to which their relative abundances influence the temperature response of nitrification is poorly understood. Here, we investigated the impact of different AOA to AOB ratios on soil nitrification potential (NP) across a temperature gradient from 4 °C to 40 °C in twenty different organic and inorganic fertilized soils. The temperature responses of different relative abundance of ammonia oxidizers for nitrification were modeled using square rate theory (SQRT) and macromolecular rate theory (MMRT) models. We found that the proportional nitrification rates at different temperatures varied among AOA to AOB ratios. Predicted by both models, an optimum temperature (Topt) for nitrification in AOA dominated soils was significantly higher than for soils where AOA and AOB abundances are within the same order of magnitude. Moreover, the change in heat capacity (ΔCP‡) associated with the temperature dependence of nitrification was positively correlated with Topt and significantly varied among the AOA to AOB ratios. The temperature ranges for NP decreased with increasing AOA abundance for both organic and inorganic fertilized soils. These results challenge the widely accepted approach of comparing NP rates in different soils at a fixed temperature. We conclude that a shift in AOA to AOB ratio in soils exhibits distinguished temperature-dependent characteristics that have an important impact on nitrification responses across the temperature gradient. The proposed approach benefits the accurate discernment of the true contribution of fertilized soils to nitrification for improvement of nitrogen management.
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Affiliation(s)
- Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Chiao-Ming Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan.
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15
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Martínez-Olivas MA, Jiménez-Bueno NG, Hernández-García JA, Fusaro C, Luna-Guido M, Navarro-Noya YE, Dendooven L. Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale. PeerJ 2019; 7:e6127. [PMID: 31249729 PMCID: PMC6587938 DOI: 10.7717/peerj.6127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 11/17/2018] [Indexed: 11/20/2022] Open
Abstract
Background A great number of studies have shown that the distribution of microorganisms in the soil is not random, but that their abundance changes along environmental gradients (spatial patterns). The present study examined the spatial variability of the physicochemical characteristics of an extreme alkaline saline soil and how they controlled the archaeal and bacterial communities so as to determine the main spatial community drivers. Methods The archaeal and bacterial community structure, and soil characteristics were determined at 13 points along a 211 m transect in the former lake Texcoco. Geostatistical techniques were used to describe spatial patterns of the microbial community and soil characteristics and determine soil properties that defined the prokaryotic community structure. Results A high variability in electrolytic conductivity (EC) and water content (WC) was found. Euryarchaeota dominated Archaea, except when the EC was low. Proteobacteria, Bacteroidetes and Actinobacteria were the dominant bacterial phyla independent of large variations in certain soil characteristics. Multivariate analysis showed that soil WC affected the archaeal community structure and a geostatistical analysis found that variation in the relative abundance of Euryarchaeota was controlled by EC. The bacterial alpha diversity was less controlled by soil characteristics at the scale of this study than the archaeal alpha diversity. Discussion Results indicated that WC and EC played a major role in driving the microbial communities distribution and scale and sampling strategies were important to define spatial patterns.
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Affiliation(s)
| | | | - Juan Alfredo Hernández-García
- Laboratory of Biological Variation and Evolution, Department of Zoology, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - Carmine Fusaro
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Tlaxcala, Mexico
| | | | | | - Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City, Mexico
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16
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Li S, Peng C, Cheng T, Wang C, Guo L, Li D. Nitrogen-cycling microbial community functional potential and enzyme activities in cultured biofilms with response to inorganic nitrogen availability. J Environ Sci (China) 2019; 76:89-99. [PMID: 30528038 DOI: 10.1016/j.jes.2018.03.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 05/03/2023]
Abstract
Biofilms mediate crucial biochemical processes in aquatic ecosystems. It was hypothesized that eutrophication may promote the growth of biofilms, resulting in larger numbers of functional genes. However, the metabolic activity and the roles of biofilms in N cycling will be affected by ambient inorganic nitrogen availability, not by the abundance of functional genes. Biofilms were cultured either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def) in a flow incubator, and the N-cycling gene abundances (nifH, N2 fixation; amoA, ammonia oxidation, archaea and bacteria; nirS and nirK, denitrification) and enzyme activities (nitrogenase and nitrate reductase) were analyzed. The results showed that, comparing the N-def and N-rep biofilms, the former contained lower nifH gene abundance, but higher nitrogenase activity (NA), while the latter contained higher nifH gene abundance, but lower NA. Different patterns of NA diel variations corresponded to the dynamic microbial community composition and different stages of biofilm colonization. Ammonia oxidizing bacteria (AOB), detected only in N-def biofilms, were responsible for nitrification in biofilms. N-rep biofilms contained high nirS and nirK gene abundance and high denitrification enzyme activity, but N-def biofilms contained significantly lower denitrification gene abundance and activity. In general, the strong N2 fixation in N-def biofilms and strong denitrification in N-rep biofilms assured the balance of aquatic ecosystems. The results suggested that evaluation of the functional processes of N cycling should not only focus on genetic potential, but also on the physiological activity of biofilms.
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Affiliation(s)
- Shuangshuang Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Hebei Engineering Research Center for Water Pollution Control and Water Ecological Remediation, College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Chengrong Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Taisheng Cheng
- National University of Tainan, Department of Biological Sciences and Technology, Tainan 70005, China
| | - Chun Wang
- Environmental Simulation and Pollution Control State Key Joint Laboratory and State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 10084, China
| | - Liangliang Guo
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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17
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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] [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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18
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Song M, Peng W, Zeng F, Du H, Peng Q, Xu Q, Chen L, Zhang F. Spatial Patterns and Drivers of Microbial Taxa in a Karst Broadleaf Forest. Front Microbiol 2018; 9:1691. [PMID: 30093895 PMCID: PMC6070632 DOI: 10.3389/fmicb.2018.01691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/06/2018] [Indexed: 11/13/2022] Open
Abstract
Spatial patterns and drivers of soil microbial communities have not yet been well documented. Here, we used geostatistical modeling and Illumina sequencing of 16S rRNA genes to explore how the main microbial taxa at the phyla level are spatially distributed in a 25-ha karst broadleaf forest in southwest China. Proteobacteria, dominated by Alpha- and Deltaproteobacteria, was the most abundant phylum (34.51%) in the karst forest soils. Other dominating phyla were Actinobacteria (30.73%), and Acidobacteria (12.24%). Soil microbial taxa showed spatial dependence with an autocorrelation range of 44.4-883.0 m, most of them within the scope of the study plots (500 m). An increasing trend was observed for Alphaproteobacteria, Deltaproteobacteria, and Chloroflexi from north to south in the study area, but an opposite trend for Actinobacteria, Acidobacteira, and Firmicutes was observed. Thaumarchaeota, Bacteroidetes, Gemmatimonadetes, and Verrucomicrobia had patchy patterns, Nitrospirae had a unimodal pattern, and Latescibacteria had an intermittent pattern with low and high value strips. Location, soil total phosphorus, elevation, and plant density were significantly correlated with main soil bacterial taxa in the karst forest. Moreover, the total variation in soil microbial communities better explained by spatial factors than environmental variables. Furthermore, a large part of variation (76.8%) was unexplained in the study. Therefore, our results suggested that dispersal limitation was the primary driver of spatial pattern of soil microbial taxa in broadleaved forest in karst areas, and other environmental variables (i.e., soil porosity and temperature) should be taken into consideration.
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Affiliation(s)
- Min Song
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Agricultural College, Hunan Agricultural University, Changsha, China
| | - Wanxia Peng
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Fuping Zeng
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Hu Du
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Qin Peng
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Qingguo Xu
- Agricultural College, Hunan Agricultural University, Changsha, China
| | - Li Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Fang Zhang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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Yang W, Wang Y, Tago K, Tokuda S, Hayatsu M. Comparison of the Effects of Phenylhydrazine Hydrochloride and Dicyandiamide on Ammonia-Oxidizing Bacteria and Archaea in Andosols. Front Microbiol 2017; 8:2226. [PMID: 29184545 PMCID: PMC5694480 DOI: 10.3389/fmicb.2017.02226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/30/2017] [Indexed: 11/13/2022] Open
Abstract
Dicyandiamide, a routinely used commercial nitrification inhibitor (NI), inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO). Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO). The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.
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Affiliation(s)
- Wenjie Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, China
| | - Yong Wang
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kanako Tago
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Shinichi Tokuda
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Kyoto, Japan
| | - Masahito Hayatsu
- Division of Biogeochemical Cycles, Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
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20
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Nacke H, Schöning I, Schindler M, Schrumpf M, Daniel R, Nicol GW, Prosser JI. Links between seawater flooding, soil ammonia oxidiser communities and their response to changes in salinity. FEMS Microbiol Ecol 2017; 93:4563574. [DOI: 10.1093/femsec/fix144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 10/23/2017] [Indexed: 11/13/2022] Open
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21
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Jiang X, Wu Y, Liu G, Liu W, Lu B. The effects of climate, catchment land use and local factors on the abundance and community structure of sediment ammonia-oxidizing microorganisms in Yangtze lakes. AMB Express 2017; 7:173. [PMID: 28905318 PMCID: PMC5597559 DOI: 10.1186/s13568-017-0479-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/05/2017] [Indexed: 11/30/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in regulating the nitrification process in lake ecosystems. However, the relative effects of climate, catchment land use and local conditions on the sediment ammonia-oxidizing communities in lakes remain unclear. In this study, the diversity and abundance of AOA and AOB communities were investigated in ten Yangtze lakes by polymerase chain reaction (PCR), clone library and quantitative PCR techniques. The results showed that the abundances of both AOA and AOB in bare sediments were considerably but not significantly higher than those in vegetated sediments. Interestingly, AOB communities were more sensitive to changes in local environmental factors and vegetation characteristics than were AOA communities. Amongst climate and land use variables, mean annual precipitation, percentage of agriculture and percentage of vegetation were the key determinants of AOB abundance and diversity. Additionally, total organic carbon and chlorophyll-a concentrations in lake water were significantly related to AOB abundance and diversity. The results of the ordination analysis indicated that 81.2 and 84.3% of the cumulative variance for the species composition of AOA and AOB communities could be explained by the climate, land use and local factors. The climate and local environments played important roles in shaping AOA communities, whereas catchment agriculture and water chlorophyll-a concentration were key influencing factors of AOB communities. Our findings suggest that the composition and structure of sediment ammonia-oxidizing communities in Yangtze lakes are strongly influenced by different spatial scale factors.
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23
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He Y, Hu W, Ma D, Lan H, Yang Y, Gao Y. Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland. Can J Microbiol 2017; 63:573-582. [DOI: 10.1139/cjm-2016-0492] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H′), Phragmites australis (samples R and R′), and Karelinia caspia (samples K and K′) to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 104 to 2.94 × 105 gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 105 and 1.05 × 106 gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH4+-N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB’s higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.
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Affiliation(s)
- Yuan He
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
| | - Wenge Hu
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
| | - Decao Ma
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
| | - Hongzhu Lan
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
| | - Yang Yang
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
| | - Yan Gao
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
- College of Life Science, Shihezi University, Shihezi, Xinjiang, People’s Republic of China, 832000
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Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling. ISME JOURNAL 2017; 11:2102-2111. [PMID: 28534876 DOI: 10.1038/ismej.2017.75] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/14/2017] [Accepted: 03/23/2017] [Indexed: 11/08/2022]
Abstract
As climate cooling is increasingly regarded as important natural variability of long-term global warming trends, there is a resurging interest in understanding its impact on biodiversity and ecosystem functioning. Here, we report a soil transplant experiment from lower to higher elevations in a Tibetan alpine grassland to simulate the impact of cooling on ecosystem community structure and function. Three years of cooling resulted in reduced plant productivity and microbial functional potential (for example, carbon respiration and nutrient cycling). Microbial genetic markers associated with chemically recalcitrant carbon decomposition remained unchanged despite a decrease in genes associated with chemically labile carbon decomposition. As a consequence, cooling-associated changes correlated with a decrease in soil organic carbon (SOC). Extrapolation of these results suggests that for every 1 °C decrease in annual average air temperature, 0.1 Pg (0.3%) of SOC would be lost from the Tibetan plateau. These results demonstrate that microbial feedbacks to cooling have the potential to differentially impact chemically labile and recalcitrant carbon turnover, which could lead to strong, adverse consequences on soil C storage. Our findings are alarming, considering the frequency of short-term cooling and its scale to disrupt ecosystems and biogeochemical cycling.
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Jenkins SN, Murphy DV, Waite IS, Rushton SP, O'Donnell AG. Ancient landscapes and the relationship with microbial nitrification. Sci Rep 2016; 6:30733. [PMID: 27480661 PMCID: PMC4969748 DOI: 10.1038/srep30733] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/06/2016] [Indexed: 11/09/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB) drive nitrification and their population dynamics impact directly on the global nitrogen cycle. AOA predominate in the majority of soils but an increasing number of studies have found that nitrification is largely attributed to AOB. The reasons for this remain poorly understood. Here, amoA gene abundance was used to study the distribution of AOA and AOB in agricultural soils on different parent materials and in contrasting geologic landscapes across Australia (n = 135 sites). AOA and AOB abundances separated according to the geologic age of the parent rock with AOB higher in the more weathered, semi-arid soils of Western Australia. AOA dominated the younger, higher pH soils of Eastern Australia, independent of any effect of land management and fertilization. This differentiation reflects the age of the underlying parent material and has implications for our understanding of global patterns of nitrification and soil microbial diversity. Western Australian soils are derived from weathered archaean laterite and are acidic and copper deficient. Copper is a co-factor in the oxidation of ammonia by AOA but not AOB. Thus, copper deficiency could explain the unexpectedly low populations of AOA in Western Australian soils.
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Affiliation(s)
- Sasha N Jenkins
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Daniel V Murphy
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Ian S Waite
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Steven P Rushton
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, England, UK
| | - Anthony G O'Donnell
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
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Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation. Appl Microbiol Biotechnol 2016; 100:9331-9341. [DOI: 10.1007/s00253-016-7736-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/04/2016] [Accepted: 07/10/2016] [Indexed: 11/29/2022]
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Reverchon F, Bai SH, Liu X, Blumfield TJ. Tree Plantation Systems Influence Nitrogen Retention and the Abundance of Nitrogen Functional Genes in the Solomon Islands. Front Microbiol 2015; 6:1439. [PMID: 26733978 PMCID: PMC4686685 DOI: 10.3389/fmicb.2015.01439] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
Tree mono-plantations are susceptible to soil nutrient impoverishment and mixed species plantations have been proposed as a way of maintaining soil fertility while enhancing biodiversity. In the Solomon Islands, mixed species plantations where teak (Tectona grandis) is inter-planted with a local tree species (Flueggea flexuosa) have been used as an alternative to teak mono-plantations and are expected to increase soil microbial diversity and modify microbial biogeochemical processes. In this study, we quantified the abundance of microbial functional genes involved in the nitrogen (N) cycle from soil samples collected in teak, flueggea, and mixed species plantations. Furthermore, we measured soil properties such as pH, total carbon (C) and total N, stable N isotope composition (δ(15)N), and inorganic N pools. Soil pH and δ(15)N were higher under teak than under flueggea, which indicates that intercropping teak with flueggea may decrease bacterial activities and potential N losses. Higher C:N ratios were found under mixed species plantations than those under teak, suggesting an enhancement of N immobilization that would help preventing fast N losses. However, inorganic N pools remained unaffected by plant cover. Inter-planting teak with flueggea in mixed species plantations generally increased the relative abundance of denitrification genes and promoted the enrichment of nosZ-harboring denitrifiers. However, it reduced the abundance of bacterial amoA (ammonia monooxygenase) genes compared to teak mono-plantations. The abundance of most denitrification genes correlated with soil total N and C:N ratio, while bacterial and archeal nitrification genes correlated positively with soil NH4 (+) concentrations. Altogether, these results show that the abundance of bacterial N-cycling functional guilds vary under teak and under mixed species plantations, and that inter-planting teak with flueggea may potentially alleviate N losses associated with nitrification and denitrification and favor N retention. Mixed plantations could also allow an increase in soil C and N stocks without losing the source of income that teak trees represent for local communities.
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Affiliation(s)
- Frédérique Reverchon
- Instituto de Ecología A.C., Red de Estudios Moleculares AvanzadosXalapa, México
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, NathanQLD, Australia
| | - Shahla H. Bai
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, NathanQLD, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, MaroochydoreQLD, Australia
| | - Xian Liu
- Environmental Futures Research Institute, School of Environment, Griffith University, NathanQLD, Australia
- Forestry College, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Timothy J. Blumfield
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, NathanQLD, Australia
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Gan XH, Zhang FQ, Gu JD, Guo YD, Li ZQ, Zhang WQ, Xu XY, Zhou Y, Wen XY, Xie GG, Wang YF. Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China. Antonie van Leeuwenhoek 2015; 109:237-51. [DOI: 10.1007/s10482-015-0627-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
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Sterngren AE, Hallin S, Bengtson P. Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil. Front Microbiol 2015; 6:1350. [PMID: 26648926 PMCID: PMC4663241 DOI: 10.3389/fmicb.2015.01350] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/16/2015] [Indexed: 12/02/2022] Open
Abstract
Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil.
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Affiliation(s)
- Anna E Sterngren
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
| | - Sara Hallin
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Per Bengtson
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
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Spatial distribution patterns of ammonia-oxidizing archaea abundance in subtropical forests at early and late successional stages. Sci Rep 2015; 5:16587. [PMID: 26565069 PMCID: PMC4643239 DOI: 10.1038/srep16587] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/15/2015] [Indexed: 11/17/2022] Open
Abstract
Characterizing the spatial distribution patterns of soil microorganisms is helpful in understanding the biogeochemical processes they perform, but has been less studied relative to those of macroorganisms. In this study, we investigated and compared the spatially explicit distribution patterns of ammonia-oxidizing archaea (AOA) abundance and the influential factors between an early (ES) and a late successional (LS) subtropical forest stand. The average AOA abundance, vegetational attributes, and soil nutrient contents were mostly greater in the LS than the ES stand (P = 0.085 or smaller), but their spatial variations were more pronounced in the ES than the LS stand. The spatial distribution patches of AOA abundance were smaller and more irregular in the ES stand (patch size <50 m) than in the LS stand (patch size about 120 m). Edaphic and vegetational variables contributed more to the spatial variations of AOA abundance for the ES (9.3%) stand than for LS stand, whereas spatial variables (MEMs) were the main contributors (62%) for the LS stand. These results suggest that environmental filtering likely influence the spatial distribution of AOA abundance at early successional stage more than that at late successional stage, while spatial dispersal is dominant at late successional stage.
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Environmental Filtering of Microbial Communities in Agricultural Soil Shifts with Crop Growth. PLoS One 2015; 10:e0134345. [PMID: 26226508 PMCID: PMC4520589 DOI: 10.1371/journal.pone.0134345] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 07/08/2015] [Indexed: 11/19/2022] Open
Abstract
Plant and soil properties cooperatively structure soil microbial communities, with implications for ecosystem functioning. However, the extent to which each factor contributes to community structuring is not fully understood. To quantify the influence of plants and soil properties on microbial diversity and composition in an agricultural context, we conducted an experiment within a corn-based annual cropping system and a perennial switchgrass cropping system across three topographic positions. We sequenced barcoded 16S ribosomal RNA genes from whole soil three times throughout a single growing season and across two years in July. To target the belowground effects of plants, we also sampled rhizosphere soil in July. We hypothesized that microbial community α-diversity and composition (β-diversity) would be more sensitive to cropping system effects (annual vs. perennial inputs) than edaphic differences among topographic positions, with greater differences occurring in the rhizosphere compared to whole soil. We found that microbial community composition consistently varied with topographic position, and cropping system and the rhizosphere influenced α-diversity. In July, cropping system and rhizosphere structured a small but specific group of microbes implying a subset of microbial taxa, rather than broad shifts in community composition, may explain previously observed differences in resource cycling between treatments. Using rank abundance analysis, we detected enrichment of Saprospirales and Actinomycetales, including cellulose and chitin degraders, in the rhizosphere soil and enrichment of Nitrospirales, Syntrophobacterales, and MND1 in the whole soil. Overall, these findings support environmental filtering for the soil microbial community first by soil and second by the rhizosphere. Across cropping systems, plants selected for a general rhizosphere community with evidence for plant-specific effects related to time of sampling.
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Constancias F, Terrat S, Saby NPA, Horrigue W, Villerd J, Guillemin JP, Biju-Duval L, Nowak V, Dequiedt S, Ranjard L, Chemidlin Prévost-Bouré N. Mapping and determinism of soil microbial community distribution across an agricultural landscape. Microbiologyopen 2015; 4:505-17. [PMID: 25833770 PMCID: PMC4475391 DOI: 10.1002/mbo3.255] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 02/23/2015] [Accepted: 03/02/2015] [Indexed: 11/13/2022] Open
Abstract
Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity.
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Affiliation(s)
| | - Sébastien Terrat
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
- Université de Bourgogne, UMR1347 AgroecologieBP 86510, F-21000 Dijon, France
| | | | - Walid Horrigue
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | - Jean Villerd
- INRA, UMR1121 Universite de Lorraine (Ensaia)F-54518, Vandoeuvre-les-Nancy, France
| | | | - Luc Biju-Duval
- INRA, UMR1347 AgroécologieBP 86510, F-21000, Dijon, France
| | - Virginie Nowak
- INRA, UMR1347 AgroécologieBP 86510, F-21000, Dijon, France
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | - Samuel Dequiedt
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
| | - Lionel Ranjard
- INRA, UMR1347 AgroécologieBP 86510, F-21000, Dijon, France
- INRA, UMR1347 Agroécologie-Plateforme GenoSolBP 86510, F-21000, Dijon, France
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Corbel S, Mougin C, Martin-Laurent F, Crouzet O, Bru D, Nélieu S, Bouaïcha N. Evaluation of phytotoxicity and ecotoxicity potentials of a cyanobacterial extract containing microcystins under realistic environmental concentrations and in a soil-plant system. CHEMOSPHERE 2015; 128:332-40. [PMID: 25754013 DOI: 10.1016/j.chemosphere.2015.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 10/20/2014] [Accepted: 02/03/2015] [Indexed: 06/04/2023]
Abstract
The impact of a crude extract of Microcystis aeruginosa (PCC7820) containing 14 microcystin variants was investigated on seeds germination and radicles development of four agricultural plants: two tomato varieties Solanum lycopersicum (MicroTom and Saint-Pierre), the wheat Triticum aestivum and the lettuce Lactuca sativa. In addition, the effect of 14 d-exposure to irrigation water containing realistic concentrations of microcystins (0-0.1 mg eq. microcystin-LRL(-1)) on the tomato MicroTom seedling growth was further evaluated on roots and aerial part biomasses. Impacts on soil bacterial parameters, as such extracellular enzymatic activities, nitrification activity and abundances of ammonia-oxidizing microorganisms were also investigated. In germination-test, the cyanobacterial extract inhibited only the germination of the wheat seeds, with an EC50 of 11 mg eq. microcystin-LRL(-1); which is 13 times lower than that of the cadmium chloride (EC50 of 145 mg L(-1)). Moreover, the cyanobacterial extract containing low concentrations of microcystins increased the growth of primary roots; however, high concentrations decreased it for all plants except for the wheat. In the soil-plant approach, only aerial part biomass of the tomato MicroTom was enhanced significantly. In addition, only soil nitrification potential and ammonia-oxidizing bacterial abundances were consistently impacted. A significant positive correlation (r=0.56) was found between the increase of nitrification potential and abundances of ammonia-oxidizing bacteria. This work suggested, that exposure to a cyanobacterial extract containing realistic environmental microcystins concentrations could affect seed germination, depending plant species. It was also highlighted, for the first time, disturbances in soil bacteria functioning, evidences on soil nitrification process.
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Affiliation(s)
- Sylvain Corbel
- INRA, UMR1402 ECOSYS, F-78026 Versailles, France; Laboratoire Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud/CNRS/AgroParisTech, Université Paris-Sud, F-91405 Orsay, France
| | - Christian Mougin
- INRA, UMR1402 ECOSYS, F-78026 Versailles, France; AgroParisTech, UMR1402 ECOSYS, F-78026 Versailles cedex, France
| | | | - Olivier Crouzet
- INRA, UMR1402 ECOSYS, F-78026 Versailles, France; AgroParisTech, UMR1402 ECOSYS, F-78026 Versailles cedex, France
| | - David Bru
- INRA, UMR1347 Agroécologie, F-21000 Dijon, France
| | - Sylvie Nélieu
- INRA, UMR1402 ECOSYS, F-78026 Versailles, France; AgroParisTech, UMR1402 ECOSYS, F-78026 Versailles cedex, France
| | - Noureddine Bouaïcha
- Laboratoire Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud/CNRS/AgroParisTech, Université Paris-Sud, F-91405 Orsay, France.
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Tsiknia M, Paranychianakis NV, Varouchakis EA, Nikolaidis NP. Environmental drivers of the distribution of nitrogen functional genes at a watershed scale. FEMS Microbiol Ecol 2015; 91:fiv052. [PMID: 25962763 DOI: 10.1093/femsec/fiv052] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2015] [Indexed: 11/14/2022] Open
Abstract
To date only few studies have dealt with the biogeography of microbial communities at large spatial scales, despite the importance of such information to understand and simulate ecosystem functioning. Herein, we describe the biogeographic patterns of microorganisms involved in nitrogen (N)-cycling (diazotrophs, ammonia oxidizers, denitrifiers) as well as the environmental factors shaping these patterns across the Koiliaris Critical Zone Observatory, a typical Mediterranean watershed. Our findings revealed that a proportion of variance ranging from 40 to 80% of functional genes abundance could be explained by the environmental variables monitored, with pH, soil texture, total organic carbon and potential nitrification rate being identified as the most important drivers. The spatial autocorrelation of N-functional genes ranged from 0.2 to 6.2 km and prediction maps, generated by cokriging, revealed distinct patterns of functional genes. The inclusion of functional genes in statistical modeling substantially improved the proportion of variance explained by the models, a result possibly due to the strong relationships that were identified among microbial groups. Significant relationships were set between functional groups, which were further mediated by land use (natural versus agricultural lands). These relationships, in combination with the environmental variables, allow us to provide insights regarding the ecological preferences of N-functional groups and among them the recently identified clade II of nitrous oxide reducers.
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Affiliation(s)
- Myrto Tsiknia
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis 73100 Chania, Greece
| | - Nikolaos V Paranychianakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis 73100 Chania, Greece
| | - Emmanouil A Varouchakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis 73100 Chania, Greece
| | - Nikolaos P Nikolaidis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis 73100 Chania, Greece
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Cheeke TE, Schütte UM, Hemmerich CM, Cruzan MB, Rosenstiel TN, Bever JD. Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes. Mol Ecol 2015; 24:2580-93. [PMID: 25827202 DOI: 10.1111/mec.13178] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/28/2015] [Accepted: 03/18/2015] [Indexed: 02/06/2023]
Abstract
Maize, genetically modified with the insect toxin genes of Bacillus thuringiensis (Bt), is widely cultivated, yet its impacts on soil organisms are poorly understood. Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots and may be uniquely sensitive to genetic changes within a plant host. In this field study, the effects of nine different lines of Bt maize and their corresponding non-Bt parental isolines were evaluated on AMF colonization and community diversity in plant roots. Plants were harvested 60 days after sowing, and data were collected on plant growth and per cent AMF colonization of roots. AMF community composition in roots was assessed using 454 pyrosequencing of the 28S rRNA genes, and spatial variation in mycorrhizal communities within replicated experimental field plots was examined. Growth responses, per cent AMF colonization of roots and AMF community diversity in roots did not differ between Bt and non-Bt maize, but root and shoot biomass and per cent colonization by arbuscules varied by maize cultivar. Plot identity had the most significant effect on plant growth, AMF colonization and AMF community composition in roots, indicating spatial heterogeneity in the field. Mycorrhizal fungal communities in maize roots were autocorrelated within approximately 1 m, but at greater distances, AMF community composition of roots differed between plants. Our findings indicate that spatial variation and heterogeneity in the field has a greater effect on the structure of AMF communities than host plant cultivar or modification by Bt toxin genes.
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Affiliation(s)
- Tanya E Cheeke
- Department of Biology, Portland State University, PO Box 751, Portland, OR, 97207, USA; Department of Biology, Indiana University, Bloomington, IN, 47405, USA; Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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36
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Zhang Y, Chen L, Dai T, Sun R, Wen D. Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms. Appl Microbiol Biotechnol 2015; 99:6481-91. [PMID: 25797330 DOI: 10.1007/s00253-015-6524-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 12/14/2022]
Abstract
Ammonia was observed as a potential significant factor to manipulate the abundance and activity of ammonia-oxidizing microorganisms (AOMs) in water environments. For the first time, this study confirmed this phenomenon by laboratory cultivation. In a series of estuarine sediment-coastal water microcosms, we investigated the AOM's phylogenetic composition and activity change in response to ammonia concentration. Increase of ammonia concentration promoted bacterial amoA gene abundance in a linear pattern. The ratio of transcribed ammonia-oxidizing bacteria (AOB) amoA gene/ammonia-oxidizing archaea (AOA) amoA gene increased from 0.1 to 43 as NH4 (+)-N increased from less than 0.1 to 12 mg L(-1), and AOA amoA transcription was undetected under 20 mg NH4 (+)-N L(-1). The incubation of stable isotope probing (SIP) microcosms revealed a faster (13)C-NaHCO3 incorporation rate of AOA amoA gene under 0.1 mg NH4 (+)-N L(-1) and a sole (13)C-NaHCO3 utilization of the AOB amoA gene under 20 mg NH4 (+)-N L(-1). Our results indicate that ammonia concentration manipulates the structure of AOM. AOA prefers to live and perform higher amoA transcription activity than AOB in ammonia-limited water environments, and AOB tends to take the first contributor place in ammonia-rich ones.
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Affiliation(s)
- Yan Zhang
- School of Environment, Tsinghua University, Beijing, 100084, China
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37
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Wood SA, Almaraz M, Bradford MA, McGuire KL, Naeem S, Neill C, Palm CA, Tully KL, Zhou J. Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture. Front Microbiol 2015; 6:90. [PMID: 25926815 PMCID: PMC4396515 DOI: 10.3389/fmicb.2015.00090] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/24/2015] [Indexed: 11/13/2022] Open
Abstract
Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.
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Affiliation(s)
- Stephen A Wood
- Department of Ecology, Evolution and Environmental Biology, Columbia University New York, NY, USA ; Agriculture and Food Security Center, The Earth Institute, Columbia University New York, NY, USA
| | - Maya Almaraz
- Department of Ecology and Evolutionary Biology, Brown University Providence, RI, USA
| | - Mark A Bradford
- School of Forestry and Environmental Studies, Yale University New Haven, CT, USA
| | - Krista L McGuire
- Department of Ecology, Evolution and Environmental Biology, Columbia University New York, NY, USA ; Department of Biology, Barnard College of Columbia University New York, NY, USA
| | - Shahid Naeem
- Department of Ecology, Evolution and Environmental Biology, Columbia University New York, NY, USA
| | - Christopher Neill
- Department of Ecology and Evolutionary Biology, Brown University Providence, RI, USA ; The Ecosystems Center, Marine Biological Laboratory Woods Hole, MA, USA
| | - Cheryl A Palm
- Agriculture and Food Security Center, The Earth Institute, Columbia University New York, NY, USA
| | - Katherine L Tully
- Agriculture and Food Security Center, The Earth Institute, Columbia University New York, NY, USA ; Department of Plant Science and Landscape Architecture, University of Maryland College Park, MD, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA ; Earth Science Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing, China
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Hirsch PR, Mauchline TH. The Importance of the Microbial N Cycle in Soil for Crop Plant Nutrition. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:45-71. [PMID: 26505688 DOI: 10.1016/bs.aambs.2015.09.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Nitrogen is crucial for living cells, and prior to the introduction of mineral N fertilizer, fixation of atmospheric N2 by diverse prokaryotes was the primary source of N in all ecosystems. Microorganisms drive the N cycle starting with N2 fixation to ammonia, through nitrification in which ammonia is oxidized to nitrate and denitrification where nitrate is reduced to N2 to complete the cycle, or partially reduced to generate the greenhouse gas nitrous oxide. Traditionally, agriculture has relied on rotations that exploited N fixed by symbiotic rhizobia in leguminous plants, and recycled wastes and manures that microbial activity mineralized to release ammonia or nitrate. Mineral N fertilizer provided by the Haber-Bosch process has become essential for modern agriculture to increase crop yields and replace N removed from the system at harvest. However, with the increasing global population and problems caused by unintended N wastage and pollution, more sustainable ways of managing the N cycle in soil and utilizing biological N2 fixation have become imperative. This review describes the biological N cycle and details the steps and organisms involved. The effects of various agricultural practices that exploit fixation, retard nitrification, and reduce denitrification are presented, together with strategies that minimize inorganic fertilizer applications and curtail losses. The development and implementation of new technologies together with rediscovering traditional practices are discussed to speculate how the grand challenge of feeding the world sustainably can be met.
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Affiliation(s)
- Penny R Hirsch
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Tim H Mauchline
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
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39
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Impact of carbon source amendment on ammonia-oxidizing microorganisms in reservoir riparian soil. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0979-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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40
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Mukherjee S, Juottonen H, Siivonen P, Lloret Quesada C, Tuomi P, Pulkkinen P, Yrjälä K. Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site. ISME JOURNAL 2014; 8:2131-42. [PMID: 25105905 DOI: 10.1038/ismej.2014.151] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/16/2014] [Accepted: 05/21/2014] [Indexed: 11/09/2022]
Abstract
Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.
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Affiliation(s)
- Shinjini Mukherjee
- Department of Biosciences, MEM Group, University of Helsinki, Helsinki, Finland
| | - Heli Juottonen
- Department of Biosciences, MEM Group, University of Helsinki, Helsinki, Finland
| | - Pauli Siivonen
- Department of Biosciences, MEM Group, University of Helsinki, Helsinki, Finland
| | | | | | | | - Kim Yrjälä
- Department of Biosciences, MEM Group, University of Helsinki, Helsinki, Finland
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41
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Latitudinal distribution of ammonia-oxidizing bacteria and archaea in the agricultural soils of eastern China. Appl Environ Microbiol 2014; 80:5593-602. [PMID: 25002421 DOI: 10.1128/aem.01617-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients.
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42
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Xu W, Li M, Ding JF, Gu JD, Luo ZH. Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean. Appl Microbiol Biotechnol 2014; 98:7993-8004. [DOI: 10.1007/s00253-014-5833-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 01/29/2023]
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Wang C, Shan B, Zhang H, Zhao Y. Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals. J Environ Sci (China) 2014; 26:502-511. [PMID: 25079261 DOI: 10.1016/s1001-0742(13)60443-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/04/2013] [Accepted: 06/08/2013] [Indexed: 06/03/2023]
Abstract
The Haihe River is characterized by high ammonia pollution. Therefore, it is necessary to determine how environmental factors, such as heavy metals in the river limit the spatial distribution of ammonia-oxidizing microorganisms. In this study, the relationships between five heavy metals and ammonia-oxidizing microorganisms were studied. The results showed that under high ammonia, low oxygen and high concentrations of suspended particles, ammonia-oxidizing bacteria (AOB) ranged from 10(1.3) to 10(4.8) gene copies/mL and ammonia-oxidizing archaea (AOA) ranged from 10(2.7) to 10(4.9) gene copies/mL. The average metal concentrations in water were 23.57 (Cr), 21.58 (Ni), 65.09 (Cu), 622.03 (Zn) and 10.16 (As) μg/L, with those of Zn, Cu and Cr being higher than the US EPA criteria. Scatter plots of microbial abundance and metals indicated that both AOA and AOB were limited by heavy metals, but in different ways. As had an inhibitory effect on AOB, while Ni and Zn promoted AOA, and the other metals investigated showed no significant correlation with microbial abundance. Overall, our results indicated that the effects of heavy metals on ammonia-oxidizing microorganisms in water are complex, and that the final effect is determined by the physiological role of each element in the microorganisms, as well as environmental conditions such as complexation of organic matter, not simply the total metal concentration.
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Affiliation(s)
- Chao Wang
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Baoqing Shan
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Hong Zhang
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu Zhao
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Impacts of edaphic factors on communities of ammonia-oxidizing archaea, ammonia-oxidizing bacteria and nitrification in tropical soils. PLoS One 2014; 9:e89568. [PMID: 24586878 PMCID: PMC3938500 DOI: 10.1371/journal.pone.0089568] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022] Open
Abstract
Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (ca. 105 to 106 copies archaeal amoA g−1 soil), but AOB levels were low and bacterial amoA was infrequently detected. AOA abundance showed a significant negative correlation (p<0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by amoA terminal restriction fragment (TRF) analysis, differed significantly between soils (p<0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (p<0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (p<0.01). In clone libraries, phylotypes of archaeal amoA (predominantly Nitrososphaera) and bacterial amoA (predominanatly Nitrosospira) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (p<0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity.
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45
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Alves RJE, Wanek W, Zappe A, Richter A, Svenning MM, Schleper C, Urich T. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea. THE ISME JOURNAL 2013; 7:1620-31. [PMID: 23466705 PMCID: PMC3721107 DOI: 10.1038/ismej.2013.35] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 11/09/2022]
Abstract
The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota-AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.
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Affiliation(s)
| | - Wolfgang Wanek
- Department of Terrestrial Ecosystem Research, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Anna Zappe
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Department of Terrestrial Ecosystem Research, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, University of Tromsø, Tromsø, Norway
| | - Christa Schleper
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
| | - Tim Urich
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
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46
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Yao H, Campbell CD, Chapman SJ, Freitag TE, Nicol GW, Singh BK. Multi-factorial drivers of ammonia oxidizer communities: evidence from a national soil survey. Environ Microbiol 2013; 15:2545-56. [PMID: 23635043 DOI: 10.1111/1462-2920.12141] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/18/2013] [Accepted: 04/05/2013] [Indexed: 11/27/2022]
Abstract
The factors driving the abundance and community composition of soil microbial communities provide fundamental knowledge on the maintenance of biodiversity and the ecosystem services they underpin. Several studies have suggested that microbial communities are spatially organized, including functional groups and much of the observed variation is explained by geographical location or soil pH. Soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) are excellent models for such study due to their functional, agronomic and environmental importance and their relative ease of characterization. To identify the dominant drivers of different ammonia oxidizers, we used samples (n = 713) from the National Soil Inventory of Scotland (NSIS). Our results indicate that 40-45% of the variance in community compositions can be explained by 71 environmental variables. Soil pH and substrate, which have been regarded as the two main drivers, only explained 13-16% of the total variance. We provide strong evidence of multi-factorial drivers (land use, soil type, climate and N deposition) of ammonia-oxidizing communities, all of which play a significant role in the creation of specific niches that are occupied by unique phylotypes. For example, one AOA phylotype was strongly linked to woodland/semi-natural grassland, rainfall and N deposition. Some soil typologies, namely regosols, have a novel AOA community composition indicating typology as one of the factors which defines this ecological niche. AOA abundance was high and strongly linked the rate of potential nitrification in the highly acidic soils supporting the argument that AOA are main ammonia oxidizers in acidic soils. However, for AOB, soil pH and substrate (ammonia) were the main drivers for abundance and community composition. These results highlight the importance of multiple drivers of microbial niche formation and their impact on microbial biogeography that have significant consequences for ecosystem functioning.
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Affiliation(s)
- Huaiying Yao
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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Zhalnina K, de Quadros PD, Gano KA, Davis-Richardson A, Fagen JR, Brown CT, Giongo A, Drew JC, Sayavedra-Soto LA, Arp DJ, Camargo FAO, Daroub SH, Clark IM, McGrath SP, Hirsch PR, Triplett EW. Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Front Microbiol 2013; 4:104. [PMID: 23641242 PMCID: PMC3640186 DOI: 10.3389/fmicb.2013.00104] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/12/2013] [Indexed: 01/19/2023] Open
Abstract
Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial signatures of the agricultural land-use. The three sites included in this study are the Broadbalk Experiment at Rothamsted Research, UK, the Everglades Agricultural Area, Florida, USA, and the Kellogg Biological Station, Michigan, USA. The effects of agricultural management on the abundance and diversity of bacteria and archaea were determined using high throughput, barcoded 16S rRNA sequencing. In addition, the relative abundance of these organisms was correlated with soil features. Two groups of microorganisms involved in nitrogen cycle were highly correlated with land use at all three sites. The ammonia oxidizing-archaea, dominated by Ca. Nitrososphaera, were positively correlated with agriculture while a ubiquitous group of soil bacteria closely related to the diazotrophic symbiont, Bradyrhizobium, was negatively correlated with agricultural management. Analysis of successional plots showed that the abundance of ammonia oxidizing-archaea declined and the abundance of bradyrhizobia increased with time away from agriculture. This observation suggests that the effect of agriculture on the relative abundance of these genera is reversible. Soil pH and NH3 concentrations were positively correlated with archaeal abundance but negatively correlated with the abundance of Bradyrhizobium. The high correlations of Ca. Nitrososphaera and Bradyrhizobium abundances with agricultural management at three long-term experiments with different edaphoclimatic conditions allowed us to suggest these two genera as signature microorganisms for agricultural land use.
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Affiliation(s)
- Kateryna Zhalnina
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
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48
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Delgado-Baquerizo M, Gallardo A, Wallenstein MD, Maestre FT. Vascular plants mediate the effects of aridity and soil properties on ammonia-oxidizing bacteria and archaea. FEMS Microbiol Ecol 2013; 85:273-82. [PMID: 23550964 DOI: 10.1111/1574-6941.12119] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 12/31/2022] Open
Abstract
An integrated perspective of the most important factors driving the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in natural ecosystems is lacking, especially in drylands. We evaluated how different climatic, abiotic, and nutrient-related factors determine AOA and AOB abundance in bare and vegetated microsites from grasslands throughout the Mediterranean Basin. We found a strong negative relationship between the abundance of AOA genes and soil fertility (availability of C, N, and P). Aridity and other abiotic factors (pH, sand content, and electrical conductivity) were more important than soil fertility in modulating the AOA/AOB ratio. AOB were more abundant under vegetated microsites, while AOA, highly resistant to stressful conditions, were more abundant in bare ground areas. These results suggest that AOA may carry out nitrification in less fertile microsites, while AOB predominate under more fertile conditions. Our results indicate that the influence of aridity and pH on the relative dominance of AOA and AOB genes is ultimately determined by local-scale environmental changes promoted by perennial vegetation. Thus, in spatially heterogeneous ecosystems such as drylands, there is a mutual exclusion and niche division between these microorganisms, suggesting that they may be functionally complementary.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Departamento Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain.
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49
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Krause S, Meima-Franke M, Hefting MM, Bodelier PLE. Spatial patterns of methanotrophic communities along a hydrological gradient in a riparian wetland. FEMS Microbiol Ecol 2013; 86:59-70. [PMID: 23397906 DOI: 10.1111/1574-6941.12091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/06/2013] [Accepted: 02/06/2013] [Indexed: 11/30/2022] Open
Abstract
Microbial communities display a variety of biogeographical patterns mainly driven by large-scale environmental gradients. Here, we analysed the spatial distribution of methane-oxidizing bacteria (MOB) and methane oxidation in a strongly fluctuating environment. We investigated whether the spatial variability of the MOB community can be explained by an environmental gradient and whether this changes with different plot sizes. We applied a pmoA-specific microarray to detect MOB, measured methane oxidation, methane emissions and soil properties. All variables were measured in a 10 × 10 m, 1 × 1 m and 20 × 20 cm plot and interpreted using a geostatistical approach. Methane oxidation as well as MOB displayed spatial patterns reflected in the underlying flooding gradient. Overlapping and contrasting spatial patterns for type I and type II MOB suggested different ecological life strategies. With smaller plot size, the environmental gradient could not explain the variability in the data and local factors became more important. In conclusion, environmental gradients can generally explain variability in microbial spatial patterns; however, we think that this does not contribute to a mechanistic explanation for microbial diversity because the relevant scales for microorganisms are much smaller than those normally measured.
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Affiliation(s)
- Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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Cao H, Auguet JC, Gu JD. Global ecological pattern of ammonia-oxidizing archaea. PLoS One 2013; 8:e52853. [PMID: 23468838 PMCID: PMC3585293 DOI: 10.1371/journal.pone.0052853] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 11/22/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent. METHODOLOGY AND RESULTS We conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus) and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats. CONCLUSION AND SIGNIFICANCE Based on an up-to-date amoA phylogeny, this analysis provided insights into the possible evolutionary mechanisms and environmental parameters that shape AOA community assembly at global scale.
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Affiliation(s)
- Huiluo Cao
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Jean-Christophe Auguet
- Equipe Environnement et Microbiologie, UMR CNRS-IPREM 5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, China
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