1
|
Sheridan PO, Meng Y, Williams TA, Gubry-Rangin C. Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae. Nat Commun 2023; 14:7305. [PMID: 37951938 PMCID: PMC10640624 DOI: 10.1038/s41467-023-43196-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023] Open
Abstract
Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.
Collapse
Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Yiyu Meng
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | |
Collapse
|
2
|
Mynard P, Algar A, Lancaster L, Bocedi G, Fahri F, Gubry-Rangin C, Lupiyaningdyah P, Nangoy M, Osborne O, Papadopulos A, Sudiana IM, Juliandi B, Travis J, Herrera-Alsina L. Impact of Phylogenetic Tree Completeness and Misspecification of Sampling Fractions on Trait Dependent Diversification Models. Syst Biol 2023; 72:106-119. [PMID: 36645380 DOI: 10.1093/sysbio/syad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 12/02/2022] [Accepted: 01/15/2023] [Indexed: 01/17/2023] Open
Abstract
Understanding the origins of diversity and the factors that drive some clades to be more diverse than others are important issues in evolutionary biology. Sophisticated SSE (state-dependent speciation and extinction) models provide insights into the association between diversification rates and the evolution of a trait. The empirical data used in SSE models and other methods is normally imperfect, yet little is known about how this can affect these models. Here, we evaluate the impact of common phylogenetic issues on inferences drawn from SSE models. Using simulated phylogenetic trees and trait information, we fitted SSE models to determine the effects of sampling fraction (phylogenetic tree completeness) and sampling fraction misspecification on model selection and parameter estimation (speciation, extinction, and transition rates) under two sampling regimes (random and taxonomically biased). As expected, we found that both model selection and parameter estimate accuracies are reduced at lower sampling fractions (i.e., low tree completeness). Furthermore, when sampling of the tree is imbalanced across subclades and tree completeness is ≤ 60%, rates of false positives increase and parameter estimates are less accurate, compared to when sampling is random. Thus, when applying SSE methods to empirical datasets, there are increased risks of false inferences of trait dependent diversification when some sub-clades are heavily under-sampled. Mis-specifying the sampling fraction severely affected the accuracy of parameter estimates: parameter values were over-estimated when the sampling fraction was specified as lower than its true value, and under-estimated when the sampling fraction was specified as higher than its true value. Our results suggest that it is better to cautiously under-estimate sampling efforts, as false positives increased when the sampling fraction was over-estimated. We encourage SSE studies where the sampling fraction can be reasonably estimated and provide recommended best practices for SSE modelling.
Collapse
Affiliation(s)
- Poppy Mynard
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Adam Algar
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Lesley Lancaster
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Greta Bocedi
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Fahri Fahri
- Department of Biology, Tadulako University, Palu, Indonesia
| | | | - Pungki Lupiyaningdyah
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, 16911, Indonesia
| | - Meis Nangoy
- Faculty of Animal Husbandry, Sam Ratulangi University, Kampus Bahu Street, Manado, 95115 Indonesia
| | - Owen Osborne
- School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - Alexander Papadopulos
- School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - I Made Sudiana
- Microbial Ecology Research Group, Research Center for Biology, Indonesian Institute of Sciences, Cibinong 19611, Indonesia
| | - Berry Juliandi
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia
| | - Justin Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | |
Collapse
|
3
|
Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. Environ Sci Technol 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
Collapse
Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| |
Collapse
|
4
|
Zhao J, Wang B, Zhou X, Alam MS, Fan J, Guo Z, Zhang H, Gubry-Rangin C, Zhongjun J. Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories. Microb Ecol 2022; 83:424-435. [PMID: 33970312 PMCID: PMC8891100 DOI: 10.1007/s00248-021-01763-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/21/2021] [Indexed: 06/01/2023]
Abstract
Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.
Collapse
Affiliation(s)
- Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, UK
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Zhou
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China
| | - Mohammad Saiful Alam
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Department of Soil Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Jianbo Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhiying Guo
- Soil Subcenter of Chinese Ecological Research Network, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Huimin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, UK.
| | - Jia Zhongjun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| |
Collapse
|
5
|
Pan H, Feng H, Liu Y, Lai CY, Zhuge Y, Zhang Q, Tang C, Di H, Jia Z, Gubry-Rangin C, Li Y, Xu J. Correction to: Grazing weakens competitive interactions between active methanotrophs and nitrifiers modulating greenhouse-gas emissions in grassland soils. ISME Commun 2022; 2:7. [PMID: 37938267 PMCID: PMC9723542 DOI: 10.1038/s43705-022-00090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Affiliation(s)
- Hong Pan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an City, Shandong, 271018, China
| | - Haojie Feng
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an City, Shandong, 271018, China
| | - Yaowei Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Chun-Yu Lai
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Yuping Zhuge
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an City, Shandong, 271018, China
| | - Qichun Zhang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Hongjie Di
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
| | - Yong Li
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
6
|
Harris BJ, Sheridan PO, Davín AA, Gubry-Rangin C, Szöllősi GJ, Williams TA. Rooting Species Trees Using Gene Tree-Species Tree Reconciliation. Methods Mol Biol 2022; 2569:189-211. [PMID: 36083449 DOI: 10.1007/978-1-0716-2691-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Interpreting phylogenetic trees requires a root, which provides the direction of evolution and polarizes ancestor-descendant relationships. But inferring the root using genetic data is difficult, particularly in cases where the closest available outgroup is only distantly related, which are common for microbes. In this chapter, we present a workflow for estimating rooted species trees and the evolutionary history of the gene families that evolve within them using probabilistic gene tree-species tree reconciliation. We illustrate the pipeline using a small dataset of prokaryotic genomes, for which the example scripts can be run using modest computer resources. We describe the rooting method used in this work in the context or other rooting strategies and discuss some of the limitations and opportunities presented by probabilistic gene tree-species tree reconciliation methods.
Collapse
Affiliation(s)
- Brogan J Harris
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Paul O Sheridan
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Adrián A Davín
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Gergely J Szöllősi
- Dept. of Biological Physics, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK.
| |
Collapse
|
7
|
Herrera-Alsina L, Mynard P, Sudiana IM, Juliandi B, Travis JMJ, Gubry-Rangin C. Reconstruction of State-Dependent Diversification: Integrating Phenotypic Traits into Molecular Phylogenies. Methods Mol Biol 2022; 2569:305-326. [PMID: 36083455 DOI: 10.1007/978-1-0716-2691-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The relative contribution of speciation and extinction into current diversity is certainly unknown, but mathematical frameworks that use genetic information have been developed to provide estimates of these processes. To that end, it is necessary to reconstruct molecular phylogenetic trees which summarize ancestor-descendant relationships as well as the timing of evolutionary events (i.e., rates). Nevertheless, diversification models show poor fit when assuming that single rate of speciation/extinction is constant over time and across lineages: species exhibit such a great variation in features that it is unlikely they give birth and die at the same pace. The state-dependent diversification framework (SSE) reconciles the species phenotypic variation with heterogeneous rates of diversification observed in a clade. This family of models allows testing contrasting hypotheses on mode of speciation, trait evolution, and its influence on speciation/extinction regimes. Although microbial species richness outnumbers diversity in plants and animals, diversification models are underused in microbiology. Here, we introduce microbiologists to models that estimate diversification rates and provide a detailed description of SSE models. Besides theoretical principles underlying the method, we also show how SSE analysis should be set up in R. We use pH evolution in Thaumarchaeota to explain its evolutionary dynamic in the light of SSE model. We hope this chapter spurs the study of trait evolution and evolutionary outcomes in microorganisms.
Collapse
Affiliation(s)
| | - Poppy Mynard
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - I Made Sudiana
- Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Berry Juliandi
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, Indonesia
| | | | | |
Collapse
|
8
|
Pan H, Feng H, Liu Y, Lai CY, Zhuge Y, Zhang Q, Tang C, Di H, Jia Z, Gubry-Rangin C, Li Y, Xu J. Grazing weakens competitive interactions between active methanotrophs and nitrifiers modulating greenhouse-gas emissions in grassland soils. ISME Commun 2021; 1:74. [PMID: 36765259 PMCID: PMC9723554 DOI: 10.1038/s43705-021-00068-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 11/09/2022]
Abstract
Grassland soils serve as a biological sink and source of the potent greenhouse gases (GHG) methane (CH4) and nitrous oxide (N2O). The underlying mechanisms responsible for those GHG emissions, specifically, the relationships between methane- and ammonia-oxidizing microorganisms in grazed grassland soils are still poorly understood. Here, we characterized the effects of grazing on in situ GHG emissions and elucidated the putative relations between the active microbes involving in methane oxidation and nitrification activity in grassland soils. Grazing significantly decreases CH4 uptake while it increases N2O emissions basing on 14-month in situ measurement. DNA-based stable isotope probing (SIP) incubation experiment shows that grazing decreases both methane oxidation and nitrification processes and decreases the diversity of active methanotrophs and nitrifiers, and subsequently weakens the putative competition between active methanotrophs and nitrifiers in grassland soils. These results constitute a major advance in our understanding of putative relationships between methane- and ammonia-oxidizing microorganisms and subsequent effects on nitrification and methane oxidation, which contribute to a better prediction and modeling of future balance of GHG emissions and active microbial communities in grazed grassland ecosystems.
Collapse
Affiliation(s)
- Hong Pan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an City, Shandong, 271018, China
| | - Haojie Feng
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an City, Shandong, 271018, China
| | - Yaowei Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Chun-Yu Lai
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Yuping Zhuge
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Daizong Road, Tai'an City, Shandong, 271018, China
| | - Qichun Zhang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Hongjie Di
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
| | - Yong Li
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
9
|
Aigle A, Gubry-Rangin C, Thion C, Estera-Molina KY, Richmond H, Pett-Ridge J, Firestone MK, Nicol GW, Prosser JI. Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria. Environ Microbiol 2021; 22:4032-4045. [PMID: 32783333 DOI: 10.1111/1462-2920.15192] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/10/2020] [Indexed: 11/28/2022]
Abstract
Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.
Collapse
Affiliation(s)
- A Aigle
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Thion
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - K Y Estera-Molina
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - H Richmond
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - J Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, 94551, USA
| | - M K Firestone
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - G W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - J I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| |
Collapse
|
10
|
Sheridan PO, Raguideau S, Quince C, Holden J, Zhang L, Williams TA, Gubry-Rangin C. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat Commun 2020; 11:5494. [PMID: 33127895 PMCID: PMC7603488 DOI: 10.1038/s41467-020-19132-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022] Open
Abstract
Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.
Collapse
Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Christopher Quince
- Warwick Medical School, University of Warwick, Coventry, UK
- Organisms and Ecosystems, Earlham Institute, Norwich, UK
- Gut Microbes and Health, Quadram Institute, Norwich, UK
| | - Jennifer Holden
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Lihong Zhang
- European Centre for Environment and Human Health, Medical School, University of Exeter, Exeter, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | |
Collapse
|
11
|
Zhao J, Meng Y, Drewer J, Skiba UM, Prosser JI, Gubry-Rangin C. Differential Ecosystem Function Stability of Ammonia-Oxidizing Archaea and Bacteria following Short-Term Environmental Perturbation. mSystems 2020; 5:e00309-20. [PMID: 32546672 PMCID: PMC7300361 DOI: 10.1128/msystems.00309-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/29/2020] [Indexed: 11/20/2022] Open
Abstract
Rapidly expanding conversion of tropical forests to oil palm plantations in Southeast Asia leads to soil acidification following intensive nitrogen fertilization. Changes in soil pH are predicted to have an impact on archaeal ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete (comammox) ammonia oxidizers and, consequently, on nitrification. It is therefore critical to determine whether the predicted effects of pH on ammonia oxidizers and nitrification activity apply in tropical soils subjected to various degrees of anthropogenic activity. This was investigated by experimental manipulation of pH in soil microcosms from a land-use gradient (forest, riparian, and oil palm soils). The nitrification rate was greater in forest soils with native neutral pH than in converted acidic oil palm soils. Ammonia oxidizer activity decreased following acidification of the forest soils but increased after liming of the oil palm soils, leading to a trend of a reversed net nitrification rate after pH modification. AOA and AOB nitrification activity was dependent on pH, but AOB were more sensitive to pH modification than AOA, which demonstrates a greater stability of AOA than AOB under conditions of short-term perturbation. In addition, these results predict AOB to be a good bioindicator of nitrification response following pH perturbation during land-use conversion. AOB and/or comammox species were active in all soils along the land-use gradient, even, unexpectedly, under acidic conditions, suggesting their adaptation to native acidic or acidified soils. The present study therefore provided evidence for limited stability of soil ammonia oxidizer activity following intensive anthropogenic activities, which likely aggravates the vulnerability of nitrogen cycle processes to environmental disturbance.IMPORTANCE Physiological and ecological studies have provided evidence for pH-driven niche specialization of ammonia oxidizers in terrestrial ecosystems. However, the functional stability of ammonia oxidizers following pH change has not been investigated, despite its importance in understanding the maintenance of ecosystem processes following environmental perturbation. This is particularly true after anthropogenic perturbation, such as the conversion of tropical forest to oil palm plantations. This study demonstrated a great impact of land-use conversion on nitrification, which is linked to changes in soil pH due to common agricultural practices (intensive fertilization). In addition, the different communities of ammonia oxidizers were differently affected by short-term pH perturbations, with implications for future land-use conversions but also for increased knowledge of associated global nitrous oxide emissions and current climate change concerns.
Collapse
Affiliation(s)
- Jun Zhao
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Yiyu Meng
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Julia Drewer
- Centre for Ecology and Hydrology, Penicuik, United Kingdom
| | - Ute M Skiba
- Centre for Ecology and Hydrology, Penicuik, United Kingdom
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| |
Collapse
|
12
|
Prosser JI, Hink L, Gubry-Rangin C, Nicol GW. Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies. Glob Chang Biol 2020; 26:103-118. [PMID: 31638306 DOI: 10.1111/gcb.14877] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/30/2019] [Indexed: 05/02/2023]
Abstract
Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N2 O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N2 O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N2 O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N2 O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N2 O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N2 O emissions.
Collapse
Affiliation(s)
- James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Linda Hink
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | | | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Lyon, France
| |
Collapse
|
13
|
Aigle A, Prosser JI, Gubry-Rangin C. The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers. Environ Microbiome 2019; 14:3. [PMID: 33902715 PMCID: PMC7989807 DOI: 10.1186/s40793-019-0342-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 06/06/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments in phylogenetic methodology, provides the potential for better analysis of microbial niche specialisation. This study aimed to develop an approach for sequencing of bacterial and archaeal amoA genes amplified from soil using bioinformatics pipelines developed for general analysis of functional genes and employed sequence data to reassess phylogeny and niche specialisation in terrestrial bacterial ammonia oxidisers. RESULTS amoA richness and community composition differed with bioinformatics approaches used but analysis of MiSeq sequences was reliable for both archaeal and bacterial amoA genes and was used for subsequent assessment of potential niche specialisation of soil bacteria ammonia oxidisers. Prior to ecological analysis, phylogenetic analysis of Nitrosospira, which dominates soil AOB, was revisited using a phylogenetic analysis of 16S rRNA and amoA genes in available AOB genomes. This analysis supported congruence between phylogenies of the two genes and increased previous phylogenetic resolution, providing support for additional gene clusters of potential ecological significance. Analysis of environmental sequences using these new sequencing, bioinformatics and phylogenetic approaches demonstrated, for the first time, similar niche specialisation in AOB to that in AOA, indicating pH as a key ecological factor controlling the composition of soil ammonia oxidiser communities. CONCLUSIONS This study presents the first bioinformatics pipeline for optimal analysis of Illumina MiSeq sequencing of a functional gene and is adaptable to any amplicon size (even genes larger than 500 bp). The pipeline was used to provide an up-to-date phylogenetic analysis of terrestrial betaproteobacterial amoA genes and to demonstrate the importance of soil pH for their niche specialisation and is broadly applicable to other ecosystems and diverse microbiomes.
Collapse
Affiliation(s)
- Axel Aigle
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, St. Machar Drive, Aberdeen, AB24 3UU UK
| | - James I. Prosser
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, St. Machar Drive, Aberdeen, AB24 3UU UK
| | - Cécile Gubry-Rangin
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, St. Machar Drive, Aberdeen, AB24 3UU UK
| |
Collapse
|
14
|
Potts LD, Perez Calderon LJ, Gontikaki E, Keith L, Gubry-Rangin C, Anderson JA, Witte U. Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates. FEMS Microbiol Ecol 2019; 94:5047303. [PMID: 29982504 PMCID: PMC6166136 DOI: 10.1093/femsec/fiy127] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022] Open
Abstract
Oil reserves in deep-sea sediments are currently subject to intense exploration, with associated risks of oil spills. Previous research suggests that microbial communities from deep-sea sediment (>1000m) can degrade hydrocarbons (HCs), but have a lower degradation ability than shallow (<200m) communities, probably due to in situ temperature. This study aimed to assess the effect of marine origin on microbial HC degradation potential while separating the influence of temperature, and to characterise associated HC-degrading bacterial communities. Microbial communities from 135 and 1000 m deep sediments were selectively enriched on crude oil at in situ temperatures and both consortia were subsequently incubated for 42 days at 20°C with two HC mixtures: diesel fuel or model oil. Significant HC biodegradation occurred rapidly in the presence of both consortia, especially of low molecular weight HCs and was concomitant with microbial community changes. Further, oil degradation was higher with the shallow consortium than with the deep one. Dominant HC-degrading bacteria differed based on both spatial origin of the consortia and supplemented HC types. This study provides evidence for influence of sediment spatial origin and HC composition on the selection and activity of marine HC-degrading bacterial communities and is relevant for future bioremediationdevelopments.
Collapse
Affiliation(s)
- Lloyd D Potts
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom.,Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Luis J Perez Calderon
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom.,Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Evangelia Gontikaki
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - Lehanne Keith
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - James A Anderson
- Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Ursula Witte
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| |
Collapse
|
15
|
Hink L, Gubry-Rangin C, Nicol GW, Prosser JI. The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions. ISME J 2018; 12:1084-1093. [PMID: 29386627 PMCID: PMC5864188 DOI: 10.1038/s41396-017-0025-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/09/2017] [Accepted: 11/15/2017] [Indexed: 11/09/2022]
Abstract
High and low rates of ammonium supply are believed to favour ammonia-oxidising bacteria (AOB) and archaea (AOA), respectively. Although their contrasting affinities for ammonium are suggested to account for these differences, the influence of ammonia concentration on AOA and AOB has not been tested under environmental conditions. In addition, while both AOB and AOA contribute to nitrous oxide (N2O) emissions from soil, N2O yields (N2O-N produced per NO2--N generated from ammonia oxidation) of AOA are lower, suggesting lower emissions when AOA dominate ammonia oxidation. This study tested the hypothesis that ammonium supplied continuously at low rates is preferentially oxidised by AOA, with lower N2O yield than expected for AOB-dominated processes. Soil microcosms were supplied with water, urea or a slow release, urea-based fertiliser and 1-octyne (inhibiting only AOB) was applied to distinguish AOA and AOB activity and associated N2O production. Low ammonium supply, from mineralisation of organic matter, or of the fertiliser, led to growth, ammonia oxidation and N2O production by AOA only, with low N2O yield. High ammonium supply, from free urea within the fertiliser or after urea addition, led to growth of both groups, but AOB-dominated ammonia oxidation was associated with twofold greater N2O yield than that dominated by AOA. This study therefore demonstrates growth of both AOA and AOB at high ammonium concentration, confirms AOA dominance during low ammonium supply and suggests that slow release or organic fertilisers potentially mitigate N2O emissions through differences in niche specialisation and N2O production mechanisms in AOA and AOB.
Collapse
Affiliation(s)
- Linda Hink
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK.,Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Graeme W Nicol
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK.,Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK.
| |
Collapse
|
16
|
Herbold CW, Lehtovirta-Morley LE, Jung MY, Jehmlich N, Hausmann B, Han P, Loy A, Pester M, Sayavedra-Soto LA, Rhee SK, Prosser JI, Nicol GW, Wagner M, Gubry-Rangin C. Ammonia-oxidising archaea living at low pH: Insights from comparative genomics. Environ Microbiol 2017; 19:4939-4952. [PMID: 29098760 PMCID: PMC5767755 DOI: 10.1111/1462-2920.13971] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/22/2017] [Indexed: 01/08/2023]
Abstract
Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.
Collapse
Affiliation(s)
- Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Laura E Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK
| | - Man-Young Jung
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 362-763, South Korea
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Ping Han
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Inhoffenstr. 7B, Braunschweig 38124, Germany
| | - Luis A Sayavedra-Soto
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 362-763, South Korea
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, L'Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully CEDEX, France
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK
| |
Collapse
|
17
|
Hink L, Lycus P, Gubry-Rangin C, Frostegård Å, Nicol GW, Prosser JI, Bakken LR. Kinetics of NH 3 -oxidation, NO-turnover, N 2 O-production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers. Environ Microbiol 2017; 19:4882-4896. [PMID: 28892283 DOI: 10.1111/1462-2920.13914] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/26/2017] [Indexed: 11/28/2022]
Abstract
Ammonia oxidising bacteria (AOB) are thought to emit more nitrous oxide (N2 O) than ammonia oxidising archaea (AOA), due to their higher N2 O yield under oxic conditions and denitrification in response to oxygen (O2 ) limitation. We determined the kinetics of growth and turnover of nitric oxide (NO) and N2 O at low cell densities of Nitrosomonas europaea (AOB) and Nitrosopumilus maritimus (AOA) during gradual depletion of TAN (NH3 + NH4+) and O2 . Half-saturation constants for O2 and TAN were similar to those determined by others, except for the half-saturation constant for ammonium in N. maritimus (0.2 mM), which is orders of magnitudes higher than previously reported. For both strains, cell-specific rates of NO turnover and N2 O production reached maxima near O2 half-saturation constant concentration (2-10 μM O2 ) and decreased to zero in response to complete O2 -depletion. Modelling of the electron flow in N. europaea demonstrated low electron flow to denitrification (≤1.2% of the total electron flow), even at sub-micromolar O2 concentrations. The results corroborate current understanding of the role of NO in the metabolism of AOA and suggest that denitrification is inconsequential for the energy metabolism of AOB, but possibly important as a route for dissipation of electrons at high ammonium concentration.
Collapse
Affiliation(s)
- Linda Hink
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Pawel Lycus
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully CEDEX 69134, France
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| |
Collapse
|
18
|
Viollet A, Pivato B, Mougel C, Cleyet-Marel JC, Gubry-Rangin C, Lemanceau P, Mazurier S. Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities. Mycorrhiza 2017; 27:23-33. [PMID: 27549437 DOI: 10.1007/s00572-016-0730-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/11/2016] [Indexed: 05/20/2023]
Abstract
Type three secretion systems (T3SSs) mediate cell-to-cell interactions between Gram-negative bacteria and eukaryotes. We hypothesized that fluorescent pseudomonads harboring T3SS (T3SS+) would be beneficial to arbuscular mycorrhizal symbiosis because non-pathogenic fluorescent pseudomonads have been previously shown to be much more abundant in mycorrhizal than in non-mycorrhizal roots. We tested this hypothesis by comparing mycorrhization and the associated rhizosphere microbial communities of Medicago truncatula grown in a non-sterile soil inoculated with either the T3SS+ mycorrhiza helper bacterium Pseudomonas fluorescens (C7R12) or a T3SS- mutant of the strain. Results showed that the bacterial secretion system was responsible for the promotion of mycorrhization because root colonization by arbuscular mycorrhizal fungi was not promoted by the T3SS- mutant. The observed T3SS-mediated promotion of mycorrhization was associated with changes in the rhizosphere bacterial communities and the increased occurrence of Claroidoglomeraceae within the intraradical arbuscular mycorrhizal fungi. Furthermore, both pseudomonad strains promoted the host-free growth of a model arbuscular mycorrhizal fungus in vitro, suggesting that T3SS-mediated promotion of mycorrhization occurs during plant-fungal interactions rather than during the pre-symbiotic phase of fungal growth. Taken together, these data provide evidence for the involvement of T3SS in promoting arbuscular mycorrhization by a model fluorescent pseudomonad and suggest the implication of interactions between the bacterium and mycorrhizas.
Collapse
Affiliation(s)
- Amandine Viollet
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Barbara Pivato
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Christophe Mougel
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
- INRA, UMR1349 IGEPP, 35653, Le Rheu, France
| | - Jean-Claude Cleyet-Marel
- INRA, UMR 113 'Laboratoire des Symbioses Tropicales et Méditerranéennes', Campus International de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Cécile Gubry-Rangin
- INRA, UMR 113 'Laboratoire des Symbioses Tropicales et Méditerranéennes', Campus International de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Sylvie Mazurier
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France.
| |
Collapse
|
19
|
Macqueen DJ, Gubry-Rangin C. Molecular adaptation of ammonia monooxygenase during independent pH specialization in Thaumarchaeota. Mol Ecol 2016; 25:1986-99. [DOI: 10.1111/mec.13607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/24/2016] [Accepted: 03/02/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel J. Macqueen
- Institute of Biological and Environmental Sciences; University of Aberdeen; Aberdeen AB24 2TZ UK
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences; University of Aberdeen; Aberdeen AB24 2TZ UK
| |
Collapse
|
20
|
Lehtovirta-Morley LE, Ross J, Hink L, Weber EB, Gubry-Rangin C, Thion C, Prosser JI, Nicol GW. Isolation of 'Candidatus Nitrosocosmicus franklandus', a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiol Ecol 2016; 92:fiw057. [PMID: 26976843 PMCID: PMC4830249 DOI: 10.1093/femsec/fiw057] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2016] [Indexed: 11/13/2022] Open
Abstract
Studies of the distribution of ammonia oxidising archaea (AOA) and bacteria (AOB) suggest distinct ecological niches characterised by ammonia concentration and pH, arising through differences in substrate affinity and ammonia tolerance. AOA form five distinct phylogenetic clades, one of which, the 'Nitrososphaera sister cluster', has no cultivated isolate. A representative of this cluster, named 'Candidatus Nitrosocosmicus franklandus', was isolated from a pH 7.5 arable soil and we propose a new cluster name:'Nitrosocosmicus' While phylogenetic analysis of amoA genes indicates its association with the Nitrososphaera sister cluster, analysis of 16S rRNA genes provided no support for a relative branching that is consistent with a 'sister cluster', indicating placement within a lineage of the order Nitrososphaerales 'Ca.N. franklandus' is capable of ureolytic growth and its tolerances to nitrite and ammonia are higher than in other AOA and similar to those of typical soil AOB. Similarity of other growth characteristics of 'Ca.N. franklandus' with those of typical soil AOB isolates reduces support for niche differentiation between soil AOA and AOB and suggests that AOA have a wider physiological diversity than previously suspected. In particular, the high ammonia tolerance of 'Ca.N. franklandus' suggests potential contributions to nitrification in fertilised soils.
Collapse
Affiliation(s)
- Laura E Lehtovirta-Morley
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Jenna Ross
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Linda Hink
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Eva B Weber
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Cécile Thion
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - James I Prosser
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Graeme W Nicol
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen AB24 3UU, UK
| |
Collapse
|
21
|
Oton EV, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. ISME J 2015; 10:85-96. [PMID: 26140533 PMCID: PMC4604658 DOI: 10.1038/ismej.2015.101] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/13/2015] [Accepted: 05/08/2015] [Indexed: 11/09/2022]
Abstract
Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.
Collapse
Affiliation(s)
- Eduard Vico Oton
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK.,School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | | | - Graeme W Nicol
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK.,Laboratoire Ampère UMR CNRS 5005, École Centrale de Lyon, Université de Lyon, Ecully CEDEX, France
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK
| |
Collapse
|
22
|
Stempfhuber B, Engel M, Fischer D, Neskovic-Prit G, Wubet T, Schöning I, Gubry-Rangin C, Kublik S, Schloter-Hai B, Rattei T, Welzl G, Nicol GW, Schrumpf M, Buscot F, Prosser JI, Schloter M. pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils. Microb Ecol 2015; 69:879-883. [PMID: 25501889 DOI: 10.1007/s00248-014-0548-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/27/2014] [Indexed: 06/04/2023]
Abstract
In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.
Collapse
Affiliation(s)
- Barbara Stempfhuber
- Environmental Genomics, Helmholtz Zentrum München, German Research Centre for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
Thaumarchaeota are among the most abundant organisms on Earth and are ubiquitous. Within this phylum, all cultivated representatives of Group 1.1a and Group 1.1b Thaumarchaeota are ammonia oxidizers, and play a key role in the nitrogen cycle. While Group 1.1c is phylogenetically closely related to the ammonia-oxidizing Thaumarchaeota and is abundant in acidic forest soils, nothing is known about its physiology or ecosystem function. The goal of this study was to perform in situ physiological characterization of Group 1.1c Thaumarchaeota by determining conditions that favour their growth in soil. Several acidic grassland, birch and pine tree forest soils were sampled and those with the highest Group 1.1c 16S rRNA gene abundance were incubated in microcosms to determine optimal growth temperature, ammonia oxidation and growth on several organic compounds. Growth of Group 1.1c Thaumarchaeota, assessed by qPCR of Group 1.1c 16S rRNA genes, occurred in soil, optimally at 30°C, but was not associated with ammonia oxidation and the functional gene amoA could not be detected. Growth was also stimulated by addition of organic nitrogen compounds (glutamate and casamino acids) but not when supplemented with organic carbon alone. This is the first evidence for non-ammonia oxidation associated growth of Thaumarchaeota in soil. Uncultivated soil Group 1.1c Thaumarchaeota are abundant, but have no known function. We report their growth without ammonia oxidation, unlike thaumarchaeal relatives, and stimulation by organic C.
Collapse
Affiliation(s)
- Eva B Weber
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Laura E Lehtovirta-Morley
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - James I Prosser
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, Cruickshank Building, St Machar Drive, University of Aberdeen, Aberdeen, AB24 3UU, UK
| |
Collapse
|
24
|
Gubry-Rangin C, Béna G, Cleyet-Marel JC, Brunel B. Definition and evolution of a new symbiovar, sv. rigiduloides, among Ensifer meliloti efficiently nodulating Medicago species. Syst Appl Microbiol 2013; 36:490-6. [DOI: 10.1016/j.syapm.2013.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/04/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
|
25
|
Abstract
Nitrification is a central component of the global nitrogen cycle. Ammonia oxidation, the first step of nitrification, is performed in terrestrial ecosystems by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Published studies indicate that soil pH may be a critical factor controlling the relative abundances of AOA and AOB communities. In order to determine the relative contributions of AOA and AOB to ammonia oxidation in two agricultural acidic Scottish soils (pH 4.5 and 6), the influence of acetylene (a nitrification inhibitor) was investigated during incubation of soil microcosms at 20 °C for 1 month. High rates of nitrification were observed in both soils in the absence of acetylene. Quantification of respective amoA genes (a key functional gene for ammonia oxidizers) demonstrated significant growth of AOA, but not AOB. A significant positive relationship was found between nitrification rate and AOA, but not AOB growth. AOA growth was inhibited in the acetylene-containing microcosms. Moreover, AOA transcriptional activity decreased significantly in the acetylene-containing microcosms compared with the control, whereas no difference was observed for the AOB transcriptional activity. Consequently, growth and activity of only archaeal but not bacterial ammonia oxidizer communities strongly suggest that AOA, but not AOB, control nitrification in these two acidic soils.
Collapse
Affiliation(s)
- Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.
| | | | | |
Collapse
|
26
|
Abstract
In nitrogen-fixing symbiosis, plant sanctions against ineffective bacteria have been demonstrated in previous studies performed on soybean and yellow bush lupin, both developing determinate nodules with Bradyrhizobium sp. strains. In this study, we focused on the widely studied symbiotic association Medicago truncatula-Sinorhizobium meliloti, which forms indeterminate nodules. Using two strains isolated from the same soil and displaying different nitrogen fixation phenotypes on the same fixed plant line, we analysed the existence of both partner choice and plant sanctions by performing split-root experiments. By measuring different parameters such as the nodule number, the nodule biomass per nodule and the number of viable rhizobia per nodule, we showed that M. truncatula is able to select rhizobia based on recognition signals, both before and after the nitrogen fixation step. However, no sanction mechanism, described as a decrease in rhizobia fitness inside the nodules, was detected. Consequently, even if partner choice seems to be widespread among legumes, sanction of non-effective rhizobia might not be universal.
Collapse
Affiliation(s)
- Cécile Gubry-Rangin
- IRD, UMR 113, Laboratoire des Symbioses Tropicales et Méditerranéennes, Campus International de Baillarguet TA A-82/J, 34398 Montpellier Cedex 5, France.
| | | | | |
Collapse
|