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Prosser JI. How and why in microbial ecology: an appeal for scientific aims, questions, hypotheses and theories. Environ Microbiol 2022; 24:4973-4980. [PMID: 36151709 DOI: 10.1111/1462-2920.16221] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022]
Abstract
This article precedes a series of articles on the important questions, hypotheses and theories in microbial ecology. It considers why, as scientists, we ask questions and propose hypotheses and what makes them important, good or significant. Emphasis is placed on 'scientific' questions, the need for scientific aims and on possible reasons for, and inadequacy of aim-less studies and question-free. Current global issues surrounding the climate crisis, pandemics and antibiotic resistance focus attention on science and scientists. They exemplify the urgent need for greater understanding of the interactions between microbes and their biological and physicochemical environments, i.e. of microbial ecology. They also provide examples of reaction against science and scientists and highlight why we must be clear what defines (good) science, its power and limitations, and ensure that this is communicated to stakeholders and the general public. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- James I Prosser
- Institute of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, Scotland, UK
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2
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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.
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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.
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3
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Aigle A, Gubry-Rangin C, Thion C, Estera-Molina KY, Richmond H, Pett-Ridge J, Firestone MK, Nicol GW, Prosser JI. Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria. Environ Microbiol 2021; 22:4032-4045. [PMID: 32783333 DOI: 10.1111/1462-2920.15192] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/10/2020] [Indexed: 11/28/2022]
Abstract
Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.
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Affiliation(s)
- A Aigle
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Thion
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - K Y Estera-Molina
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - H Richmond
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - J Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, 94551, USA
| | - M K Firestone
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - G W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - J I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
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4
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Dini-Andreote F, Kowalchuk GA, Prosser JI, Raaijmakers JM. Towards meaningful scales in ecosystem microbiome research. Environ Microbiol 2020; 23:1-4. [PMID: 33047413 DOI: 10.1111/1462-2920.15276] [Citation(s) in RCA: 5] [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: 09/09/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - George A Kowalchuk
- Ecology & Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
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5
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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.
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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
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Abstract
Microbial ecology, the scientific study of interactions between natural microbial communities and their environments, has been facilitated by the application of molecular and 'omics'-based techniques that overcome some of the limitations of cultivation-based studies. This has increased emphasis on community ecology and 'microbiome' studies, but the majority address technical, rather than scientific challenges. Most are descriptive, do not address scientific aims or questions and are not designed to increase understanding or test hypotheses. The term 'hypothesis' is increasingly misused and critical testing of ideas or theory is restricted to a small minority of studies. This article discusses current microbial ecology research within the context of four approaches: description, induction, inference to the best explanation and deduction. The first three of these do not follow the established scientific method and are not based on scientific ecological questions. Observations are made and sometimes compared with published data, sometimes with attempts to explain findings in the context of existing ideas or hypotheses, but all lack objectivity and are biased by the observations made. By contrast, deductive studies address ecological questions and attempt to explain currently unexplained phenomena through the construction of hypotheses, from mechanism-based assumptions, that generate predictions that are then tested experimentally. Identification of key scientific questions, research driven by meaningful hypotheses and adoption of scientific method are essential for progress in microbial ecology, rather than the current emphasis on descriptive approaches that address only technical challenges. It is, therefore, imperative that we carefully consider and define the fundamental scientific questions that drive our own research and focus on ideas, concepts and hypotheses that can increase understanding, and only then consider which techniques are required for experimental testing. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- James I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
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7
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Affiliation(s)
- James I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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8
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Prosser JI, Hink L, Gubry-Rangin C, Nicol GW. Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies. 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.
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Affiliation(s)
- James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Linda Hink
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | | | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Lyon, France
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9
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Aigle A, Prosser JI, Gubry-Rangin C. The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers. Environ Microbiome 2019; 14:3. [PMID: 33902715 PMCID: PMC7989807 DOI: 10.1186/s40793-019-0342-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 06/06/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments in phylogenetic methodology, provides the potential for better analysis of microbial niche specialisation. This study aimed to develop an approach for sequencing of bacterial and archaeal amoA genes amplified from soil using bioinformatics pipelines developed for general analysis of functional genes and employed sequence data to reassess phylogeny and niche specialisation in terrestrial bacterial ammonia oxidisers. RESULTS amoA richness and community composition differed with bioinformatics approaches used but analysis of MiSeq sequences was reliable for both archaeal and bacterial amoA genes and was used for subsequent assessment of potential niche specialisation of soil bacteria ammonia oxidisers. Prior to ecological analysis, phylogenetic analysis of Nitrosospira, which dominates soil AOB, was revisited using a phylogenetic analysis of 16S rRNA and amoA genes in available AOB genomes. This analysis supported congruence between phylogenies of the two genes and increased previous phylogenetic resolution, providing support for additional gene clusters of potential ecological significance. Analysis of environmental sequences using these new sequencing, bioinformatics and phylogenetic approaches demonstrated, for the first time, similar niche specialisation in AOB to that in AOA, indicating pH as a key ecological factor controlling the composition of soil ammonia oxidiser communities. CONCLUSIONS This study presents the first bioinformatics pipeline for optimal analysis of Illumina MiSeq sequencing of a functional gene and is adaptable to any amplicon size (even genes larger than 500 bp). The pipeline was used to provide an up-to-date phylogenetic analysis of terrestrial betaproteobacterial amoA genes and to demonstrate the importance of soil pH for their niche specialisation and is broadly applicable to other ecosystems and diverse microbiomes.
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Affiliation(s)
- Axel Aigle
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, St. Machar Drive, Aberdeen, AB24 3UU UK
| | - James I. Prosser
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, St. Machar Drive, Aberdeen, AB24 3UU UK
| | - Cécile Gubry-Rangin
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, St. Machar Drive, Aberdeen, AB24 3UU UK
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Merbt SN, Proia L, Prosser JI, Martí E, Casamayor EO, von Schiller D. Stream drying drives microbial ammonia oxidation and first-flush nitrate export. Ecology 2018; 97:2192-2198. [PMID: 27859084 DOI: 10.1002/ecy.1486] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 04/15/2016] [Accepted: 05/25/2016] [Indexed: 11/09/2022]
Abstract
Stream microbial communities and associated processes are influenced by environmental fluctuations that may ultimately dictate nutrient export. Discharge fluctuations caused by intermittent stream flow are increasing worldwide in response to global change. We examined the impact of flow cessation and drying on in-stream nitrogen cycling. We determined archaeal (AOA) and bacterial ammonia oxidizer (AOB) abundance and ammonia oxidation activity in surface and deep sediments from different sites along the Fuirosos stream (Spain) subjected to contrasting hydrological conditions (i.e., running water, isolated pools, and dry streambeds). AOA were more abundant than AOB, with no major changes across hydrological conditions or sediment layers. However, ammonia oxidation activity and sediment nitrate content increased with the degree of stream drying, especially in surface sediments. Upscaling of our results shows that ammonia oxidation in dry streambeds can contribute considerably (~50%) to the high nitrate export typically observed in intermittent streams during first-flush events following flow reconnection. Our study illustrates how the dry channels of intermittent streams can be potential hotspots of ammonia oxidation. Consequently, shifts in the duration, spatial extent and severity of intermittent flow can play a decisive role in shaping nitrogen cycling and export along fluvial networks in response to global change.
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Affiliation(s)
- Stephanie N Merbt
- Eawag-Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Toxicology, Überlandstrasse 133 Postfach 611, 8600, Dübendorf, Switzerland
| | - Lorenzo Proia
- Catalan Institute for Water Research, Emili Grahit 101, 17003, Girona, Spain.,Ecology of Aquatic Systems, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, United Kingdom
| | - Eugènia Martí
- Integrative Freshwater Ecology Group, Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés a la Cala St. Francesc 14, 17300, Blanes, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés a la Cala St. Francesc 14, 17300, Blanes, Spain
| | - Daniel von Schiller
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, PO Box 644, 48080, Bilbao, Spain
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11
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Catão ECP, Thion C, Krüger RH, Prosser JI. Ammonia oxidisers in a non-nitrifying Brazilian savanna soil. FEMS Microbiol Ecol 2018; 93:4209577. [PMID: 29029046 DOI: 10.1093/femsec/fix122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Low nitrification rates in Brazilian savanna (Cerrado) soils have puzzled researchers for decades. Potential mechanisms include biological inhibitors, low pH, low microbial abundance and low soil moisture content, which hinders microbial activity, including ammonia oxidation. Two approaches were used to evaluate these potential mechanisms: (i) manipulation of soil moisture and pH in microcosms containing Cerrado soil and (ii) assessment of nitrification inhibition in slurries containing mixtures of Cerrado soil and an actively nitrifying agricultural soil. Despite high ammonium concentration in Cerrado soil microcosms, little NO3- accumulation was observed with increasing moisture or pH, but in some Cerrado soil slurries, ammonia-oxidising archaea (AOA) amoA transcripts were detected after 14 days. In mixed soil slurries, the final NO3- concentration reflected the initial proportions of agricultural and Cerrado soils in the mixture, providing no evidence of nitrification inhibitors in Cerrado soil. AOA community denaturing gradient gel electrophoresis profiles were similar in the mixed and nitrifying soils. These results suggest that nitrification in Cerrado soils is not constrained by water availability, ammonium availability, low pH or biological inhibitors, and alternative potential explanations for low nitrification levels are discussed.
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Affiliation(s)
- Elisa C P Catão
- Cellular Biology Department, Instituto Central de Ciencias Sul, Universidade de Brasilia (UnB), 700910-900 Brasilia, DF, Brazil.,Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, UK
| | - Cécile Thion
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, UK.,Laboratoire Ampère, UMR CNRS 5005, École Centrale de Lyon, 34 avenue Guy de Collongue, 69130 Ecully, France
| | - R H Krüger
- Cellular Biology Department, Instituto Central de Ciencias Sul, Universidade de Brasilia (UnB), 700910-900 Brasilia, DF, Brazil
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, UK
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12
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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.
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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.
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13
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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.
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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
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14
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Liu S, Han P, Hink L, Prosser JI, Wagner M, Brüggemann N. Abiotic Conversion of Extracellular NH 2OH Contributes to N 2O Emission during Ammonia Oxidation. Environ Sci Technol 2017; 51:13122-13132. [PMID: 29039187 DOI: 10.1021/acs.est.7b02360] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Abiotic processes involving the reactive ammonia-oxidation intermediates nitric oxide (NO) or hydroxylamine (NH2OH) for N2O production have been indicated recently. The latter process would require the availability of substantial amounts of free NH2OH for chemical reactions during ammonia (NH3) oxidation, but little is known about extracellular NH2OH formation by the different clades of ammonia-oxidizing microbes. Here we determined extracellular NH2OH concentrations in culture media of several ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as one complete ammonia oxidizer (comammox) enrichment (Ca. Nitrospira inopinata) during incubation under standard cultivation conditions. NH2OH was measurable in the incubation media of Nitrosomonas europaea, Nitrosospira multiformis, Nitrososphaera gargensis, and Ca. Nitrosotenuis uzonensis, but not in media of the other tested AOB and AOA. NH2OH was also formed by the comammox enrichment during NH3 oxidation. This enrichment exhibited the largest NH2OH:final product ratio (1.92%), followed by N. multiformis (0.56%) and N. gargensis (0.46%). The maximum proportions of NH4+ converted to N2O via extracellular NH2OH during incubation, estimated on the basis of NH2OH abiotic conversion rates, were 0.12%, 0.08%, and 0.14% for AOB, AOA, and Ca. Nitrospira inopinata, respectively, and were consistent with published NH4+:N2O conversion ratios for AOB and AOA.
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Affiliation(s)
- Shurong Liu
- Institute of Bio- and Geosciences-Agrosphere (IBG-3), Forschungszentrum Jülich GmbH , 52425 Jülich, Germany
| | - Ping Han
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna , Althanstrasse 14, 1090 Vienna, Austria
| | - Linda Hink
- School of Biological Sciences, University of Aberdeen , Cruickshank Building, Aberdeen AB24 3UU, United Kingdom
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen , Cruickshank Building, Aberdeen AB24 3UU, United Kingdom
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna , Althanstrasse 14, 1090 Vienna, Austria
| | - Nicolas Brüggemann
- Institute of Bio- and Geosciences-Agrosphere (IBG-3), Forschungszentrum Jülich GmbH , 52425 Jülich, Germany
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15
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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] [What about the content of this article? (0)] [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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16
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Prosser JI. Spotlight on… Jim Prosser. FEMS Microbiol Lett 2017; 364:4110318. [PMID: 28922843 DOI: 10.1093/femsle/fnx183] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 08/23/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- James I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen AB24 3UU, United Kingdom
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17
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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.
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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
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18
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Elling FJ, Könneke M, Nicol GW, Stieglmeier M, Bayer B, Spieck E, de la Torre JR, Becker KW, Thomm M, Prosser JI, Herndl GJ, Schleper C, Hinrichs KU. Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environ Microbiol 2017; 19:2681-2700. [PMID: 28419726 DOI: 10.1111/1462-2920.13759] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/28/2022]
Abstract
Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the phylum Thaumarchaeota. Here, we comprehensively describe the core and intact polar lipid (IPL) inventory of ten ammonia-oxidising thaumarchaeal cultures representing all four characterized phylogenetic clades. IPLs of these thaumarchaeal strains are generally similar and consist of membrane-spanning, glycerol dibiphytanyl glycerol tetraethers with monoglycosyl, diglycosyl, phosphohexose and hexose-phosphohexose headgroups. However, the relative abundances of these IPLs and their core lipid compositions differ systematically between the phylogenetic subgroups, indicating high potential for chemotaxonomic distinction of thaumarchaeal clades. Comparative lipidomic analyses of 19 euryarchaeal and crenarchaeal strains suggested that the lipid methoxy archaeol is synthesized exclusively by Thaumarchaeota and may thus represent a diagnostic lipid biomarker for this phylum. The unprecedented diversity of the thaumarchaeal lipidome with 118 different lipids suggests that membrane lipid composition and adaptation mechanisms in Thaumarchaeota are more complex than previously thought and include unique lipids with as yet unresolved properties.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany.,Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | | | - Barbara Bayer
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria
| | - Eva Spieck
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, 22609, Germany
| | - José R de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, 93053, Germany
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Gerhard J Herndl
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, The Netherlands
| | | | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
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19
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Cotton CM, Prosser JI. Editorial: FEMS Letters: investing in science for 40 years. FEMS Microbiol Lett 2017; 364:3854958. [PMID: 30052911 DOI: 10.1093/femsle/fnx095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- C M Cotton
- CEO, Federation of European Microbiological Societies, Delftechpark 37A, 2628 XJ Delft, The Netherlands. E-mail:
| | - J I Prosser
- OBE FRS FRSE FRSB FAAM, Institute of Biological and Environmental Sciences, University of Aberdeen
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20
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Auffret MD, Karhu K, Khachane A, Dungait JAJ, Fraser F, Hopkins DW, Wookey PA, Singh BK, Freitag TE, Hartley IP, Prosser JI. The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature. PLoS One 2016; 11:e0165448. [PMID: 27798702 PMCID: PMC5087920 DOI: 10.1371/journal.pone.0165448] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/12/2016] [Indexed: 11/19/2022] Open
Abstract
Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.
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Affiliation(s)
- Marc D. Auffret
- University of Aberdeen, Cruickshank Building St Machar Drive, Aberdeen AB24 3UU, United Kingdom
- * E-mail:
| | - Kristiina Karhu
- University of Exeter Amory Building, Rennes Drive, Exeter EX4 4RJ, United Kingdom
| | - Amit Khachane
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith 2751 NSW, Australia
| | - Jennifer A. J. Dungait
- Sustainable Soils and Grassland Systems Department, Rothamsted Research North Wyke, Okehampton, EX20 2SB, United Kingdom
| | - Fiona Fraser
- School of Energy, Environment and Agrifood, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, United Kingdom
| | - David W. Hopkins
- The Royal Agricultural University, Cirencester, Gloucestershire, GL7 6JS, United Kingdom
| | - Philip A. Wookey
- Institute of Life & Earth Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, United Kingdom
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith 2751 NSW, Australia
| | - Thomas E. Freitag
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, United Kingdom
| | - Iain P. Hartley
- University of Exeter Amory Building, Rennes Drive, Exeter EX4 4RJ, United Kingdom
| | - James I. Prosser
- University of Aberdeen, Cruickshank Building St Machar Drive, Aberdeen AB24 3UU, United Kingdom
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21
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Affiliation(s)
- James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, UK
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22
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Hink L, Nicol GW, Prosser JI. Archaea produce lower yields of N2O than bacteria during aerobic ammonia oxidation in soil. Environ Microbiol 2016; 19:4829-4837. [DOI: 10.1111/1462-2920.13282] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/24/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Linda Hink
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive; Aberdeen AB24 3UU UK
| | - Graeme W. Nicol
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive; Aberdeen AB24 3UU UK
| | - James I. Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive; Aberdeen AB24 3UU UK
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23
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Thion CE, Poirel JD, Cornulier T, De Vries FT, Bardgett RD, Prosser JI. Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance. FEMS Microbiol Ecol 2016; 92:fiw091. [DOI: 10.1093/femsec/fiw091] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2016] [Indexed: 01/03/2023] Open
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24
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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.
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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
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25
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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.
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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
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26
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Abstract
Technological advances are enabling the sequencing of environmental DNA and RNA at increasing depth and with decreasing costs. Metagenomic and transcriptomic analysis of soil microbial communities and the assembly of 'population genomes' from soil DNA are therefore now feasible. Although the value of such 'omic' approaches is limited by the associated technical and bioinformatic difficulties, even if these obstacles were eliminated and 'perfect' metagenomes and metatranscriptomes were available, important conceptual challenges remain. This Opinion article considers these conceptual challenges in the context of the current use of omics in soil microbiology, but the main arguments presented are also relevant to the application of omics to marine, freshwater, gut or other environments.
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Affiliation(s)
- James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, UK
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27
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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.
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Affiliation(s)
- Barbara Stempfhuber
- Environmental Genomics, Helmholtz Zentrum München, German Research Centre for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
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28
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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.
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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
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Thion C, Prosser JI. Differential response of nonadapted ammonia-oxidising archaea and bacteria to drying-rewetting stress. FEMS Microbiol Ecol 2014; 90:380-9. [PMID: 25070168 DOI: 10.1111/1574-6941.12395] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 04/23/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 11/30/2022] Open
Abstract
Climate change is expected to increase the frequency of severe drought events followed by heavy rainfall, which will influence growth and activity of soil microorganisms, through osmotic stress and changes in nutrient concentration. There is evidence of rapid recovery of processes and adaptation of communities in soils regularly experiencing drying/rewetting and lower resistance and resilience in nonadapted soils. A microcosm-based study of ammonia-oxidising archaea (AOA) and bacteria (AOB), employing a grassland soil that rarely experiences drought, was used to test this hypothesis and also whether AOB were more resistant and resilient, through greater tolerance of high ammonia concentrations produced during drought and rewetting. Treated soils were dried, incubated for 3 weeks, rewetted, incubated for a further 3 weeks and compared to untreated soils, maintained at a constant moisture content. Nitrate accumulation and AOA and AOB abundance (abundance of respective amoA genes) and community composition (DGGE analysis of AOA amoA and AOB 16S rRNA genes) were poorly adapted to drying-rewetting. AOA abundance and community composition were less resistant than AOB during drought and less resilient after rewetting, at times when ammonium concentration was higher. Data provide evidence for poor adaptation of microbial communities and processes to drying-rewetting in soils with no history of drought and indicate niche differentiation of AOA and AOB associated with high ammonia concentration.
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Affiliation(s)
- Cécile Thion
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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30
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Lehtovirta-Morley LE, Ge C, Ross J, Yao H, Nicol GW, Prosser JI. Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds. FEMS Microbiol Ecol 2014; 89:542-52. [PMID: 24909965 PMCID: PMC4261999 DOI: 10.1111/1574-6941.12353] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 05/02/2014] [Accepted: 05/02/2014] [Indexed: 12/02/2022] Open
Abstract
Autotrophic ammonia oxidation is performed by two distinct groups of microorganisms: ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB). AOA outnumber their bacterial counterparts in many soils, at times by several orders of magnitude, but relatively little is known of their physiology due to the lack of cultivated isolates. Although a number of AOA have been cultivated from soil, Nitrososphaera viennensis was the sole terrestrial AOA in pure culture and requires pyruvate for growth in the laboratory. Here, we describe isolation in pure culture and characterisation of two acidophilic terrestrial AOA representing the Candidatus genus Nitrosotalea and their responses to organic acids. Interestingly, despite their close phylogenetic relatedness, the two Nitrosotalea strains exhibited differences in physiological features, including specific growth rate, temperature preference and to an extent, response to organic compounds. In contrast to N. viennensis, both Nitrosotalea isolates were inhibited by pyruvate but their growth yield increased in the presence of oxaloacetate. This study demonstrates physiological diversity within AOA species and between different AOA genera. Different preferences for organic compounds potentially influence the favoured localisation of ammonia oxidisers within the soil and the structure of ammonia-oxidising communities in terrestrial ecosystems.
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Prosser JI, Cole JA, Nielsen J, Bavoil PM, Häggblom MM. Most influential FEMS publications. FEMS Microbiol Lett 2014; 354:83-4. [PMID: 24842770 DOI: 10.1111/1574-6968.12444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A selection of influential FEMS publications to celebrate the 40th anniversary of FEMS.
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Affiliation(s)
- James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.
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33
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Freitag TE, Klenke T, Krumbein WE, Gerdes G, Prosser JI. Effect of anoxia and high sulphide concentrations on heterotrophic microbial communities in reduced surface sediments (Black Spots) in sandy intertidal flats of the German Wadden Sea. FEMS Microbiol Ecol 2012; 44:291-301. [PMID: 19719610 DOI: 10.1016/s0168-6496(03)00076-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Abstract Black reduced sediment surfaces (Black Spots) in sandy intertidal flats of the German Wadden Sea (southern North Sea) are characterised by elevated sulphide concentrations (up to 20 mM) and low redox potentials. It is assumed that the appearance of Black Spots is linked to elevated levels of organic matter content within the sediments. In order to establish the effect of high substrate and sulphide concentrations on the heterotrophic microbial communities in Black Spot sediments, bacterial abundances and the potential C-source utilisation patterns of microbial communities were compared in natural and artificially induced Black Spots and unaffected control sites. Bacterial numbers were estimated by direct counts and the most probable number technique for different physiological groups, while patterns of C-substrate utilisation of entire aerobic microbial communities were assessed using the Biolog sole-carbon-source-catabolism assay. Bacterial abundances at Black Spot sites were increased, with increases in mean cell numbers, more disperse data distributions and more extreme values. Substrate utilisation patterns of aerobic microbial communities were significantly different in Black Spot sediment slurries, showing diminished richness (number of C-sources catabolised) and substrate diversity (Shannon diversity index) in comparison to unaffected sites. Principal component analysis clearly discriminated Black Spot utilisation patterns from controls and indicated that microbial communities in individual Black Spot sites are functionally diverse and differ from communities in oxidised surface sediments and reduced subsurface sediments at control sites. This work suggests that potentially negative effects on microbial communities in Black Spot sediments, through anoxia and high sulphide concentrations, are balanced by the stimulating influence of substrate availability, leading to comparable or higher bacterial numbers, but lower functional microbial diversity of aerobic microbial communities.
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Affiliation(s)
- Thomas E Freitag
- Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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34
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Langenheder S, Bulling MT, Prosser JI, Solan M. Role of functionally dominant species in varying environmental regimes: evidence for the performance-enhancing effect of biodiversity. BMC Ecol 2012; 12:14. [PMID: 22846071 PMCID: PMC3480835 DOI: 10.1186/1472-6785-12-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [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: 04/13/2012] [Accepted: 06/26/2012] [Indexed: 11/30/2022] Open
Abstract
Background Theory suggests that biodiversity can act as a buffer against disturbances and environmental variability via two major mechanisms: Firstly, a stabilising effect by decreasing the temporal variance in ecosystem functioning due to compensatory processes; and secondly, a performance enhancing effect by raising the level of community response through the selection of better performing species. Empirical evidence for the stabilizing effect of biodiversity is readily available, whereas experimental confirmation of the performance-enhancing effect of biodiversity is sparse. Results Here, we test the effect of different environmental regimes (constant versus fluctuating temperature) on bacterial biodiversity-ecosystem functioning relations. We show that positive effects of species richness on ecosystem functioning are enhanced by stronger temperature fluctuations due to the increased performance of individual species. Conclusions Our results provide evidence for the performance enhancing effect and suggest that selection towards functionally dominant species is likely to benefit the maintenance of ecosystem functioning under more variable conditions.
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Affiliation(s)
- Silke Langenheder
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 UU3, UK.
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35
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Prosser JI. Ecosystem processes and interactions in a morass of diversity. FEMS Microbiol Ecol 2012; 81:507-19. [PMID: 22715974 DOI: 10.1111/j.1574-6941.2012.01435.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 06/14/2012] [Accepted: 06/15/2012] [Indexed: 11/27/2022] Open
Abstract
High diversity in natural communities is indicated by both traditional, cultivation-based methods and molecular techniques, but the latter have significantly increased richness estimates. The increased ease and reduced cost associated with molecular analysis of microbial communities have fuelled interest in the links between richness, community composition and ecosystem function, and raise questions about our ability to understand mechanisms controlling interactions in highly complex communities. High-throughput sequencing is increasing the depth of sequencing but the relevance of such studies to important ecological questions is often unclear. This article discusses, and challenges, some of the often implicit assumptions made in community studies. It suggests greater focus on ecological questions, more critical analysis of accepted concepts and consideration of the fundamental mechanisms controlling microbial processes and interactions in situ. These considerations indicate that many questions do not require deeper sequence analysis and increased phylogenetic resolution but, rather, require analysis at smaller spatial scale, determination of phenotypic diversity and temporal, rather than snapshot, studies. Increasing realisation of the high richness of microbial communities, and potentially high physiological diversity, also require new conceptual approaches.
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Affiliation(s)
- James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.
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36
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Gilbertson WW, Solan M, Prosser JI. Differential effects of microorganism-invertebrate interactions on benthic nitrogen cycling. FEMS Microbiol Ecol 2012; 82:11-22. [PMID: 22533682 DOI: 10.1111/j.1574-6941.2012.01400.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/16/2012] [Accepted: 04/20/2012] [Indexed: 11/30/2022] Open
Abstract
Infaunal invertebrate activity can fundamentally alter physicochemical conditions in sediments and influence nutrient cycling. However, despite clear links between invertebrate activity and microbially mediated processes such as nitrification, the mechanisms by which bioturbating macrofauna affect microbial communities have received little attention. This study provides strong evidence for differential stimulation of microbial nitrogen transformations by three functionally contrasting species of macrofauna (Hediste diversicolor, Corophium volutator, Hydrobia ulvae). Despite increased nitrification, abundance of ammonia-oxidising bacteria (AOB) and ammonia-oxidising archaea (AOA) at the sediment-water interface did not significantly change in the presence of macrofauna. However, species-specific differences in macrofaunal activity did influence ammonia oxidiser community structure, increasing AOB abundance relative to AOA in the presence of C. volutator or H. ulvae, but with no change in H. diversicolor and no-macrofauna treatments. Denaturing gradient gel electrophoresis profiles were similar between macrofaunal treatments, although one AOB band increased in relative intensity in the presence of C. volutator, decreased in the H. diversicolor treatment and was unchanged in the H. ulvae treatment. These data suggest that links between bioturbating macrofauna and nutrient cycling are not expressed through changes in the abundance of ammonia oxidisers in surface sediments, but are associated with changes in the AOA : AOB ratio depending on the invertebrate species.
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Affiliation(s)
- William W Gilbertson
- Oceanlab, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeenshire, UK.
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37
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Levičnik-Höfferle S, Nicol GW, Ausec L, Mandić-Mulec I, Prosser JI. Stimulation of thaumarchaeal ammonia oxidation by ammonia derived from organic nitrogen but not added inorganic nitrogen. FEMS Microbiol Ecol 2012; 80:114-23. [PMID: 22150211 DOI: 10.1111/j.1574-6941.2011.01275.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 11/21/2011] [Accepted: 11/29/2011] [Indexed: 11/29/2022] Open
Abstract
Ammonia oxidation, the first step in nitrification, is performed by autotrophic bacteria and thaumarchaea, whose relative contributions vary in different soils. Distinctive environmental niches for the two groups have not been identified, but evidence from previous studies suggests that activity of thaumarchaea, unlike that of bacterial ammonia oxidizers, is unaffected by addition of inorganic N fertilizer and that they preferentially utilize ammonia generated from the mineralization of organic N. This hypothesis was tested by determining the influence of both inorganic and organic N sources on nitrification rate and ammonia oxidizer growth and community structure in microcosms containing acidic, forest soil in which ammonia oxidation was dominated by thaumarchaea. Nitrification rate was unaffected by the incubation of soil with inorganic ammonium but was significantly stimulated by the addition of organic N. Oxidation of ammonia generated from native soil organic matter or added organic N, but not added inorganic N, was accompanied by increases in abundance of the thaumarchaeal amoA gene, a functional gene for ammonia oxidation, but changes in community structure were not observed. Bacterial amoA genes could not be detected. Ammonia oxidation was completely inhibited by 0.01% acetylene in all treatments, indicating ammonia monooxygenase-dependent activity. The findings have implications for current models of soil nitrification and for nitrification control strategies to minimize fertilizer loss and nitrous oxide production.
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Affiliation(s)
- Spela Levičnik-Höfferle
- Department of Food Science and Technology, Chair of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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38
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Schmidt B, Mulder IE, Musk CC, Aminov RI, Lewis M, Stokes CR, Bailey M, Prosser JI, Gill BP, Pluske JR, Kelly D. Establishment of normal gut microbiota is compromised under excessive hygiene conditions. PLoS One 2011; 6:e28284. [PMID: 22164261 PMCID: PMC3229561 DOI: 10.1371/journal.pone.0028284] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 11/04/2011] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Early gut colonization events are purported to have a major impact on the incidence of infectious, inflammatory and autoimmune diseases in later life. Hence, factors which influence this process may have important implications for both human and animal health. Previously, we demonstrated strong influences of early-life environment on gut microbiota composition in adult pigs. Here, we sought to further investigate the impact of limiting microbial exposure during early life on the development of the pig gut microbiota. METHODOLOGY/PRINCIPAL FINDINGS Outdoor- and indoor-reared animals, exposed to the microbiota in their natural rearing environment for the first two days of life, were transferred to an isolator facility and adult gut microbial diversity was analyzed by 16S rRNA gene sequencing. From a total of 2,196 high-quality 16S rRNA gene sequences, 440 phylotypes were identified in the outdoor group and 431 phylotypes in the indoor group. The majority of clones were assigned to the four phyla Firmicutes (67.5% of all sequences), Proteobacteria (17.7%), Bacteroidetes (13.5%) and to a lesser extent, Actinobacteria (0.1%). Although the initial maternal and environmental microbial inoculum of isolator-reared animals was identical to that of their naturally-reared littermates, the microbial succession and stabilization events reported previously in naturally-reared outdoor animals did not occur. In contrast, the gut microbiota of isolator-reared animals remained highly diverse containing a large number of distinct phylotypes. CONCLUSIONS/SIGNIFICANCE The results documented here indicate that establishment and development of the normal gut microbiota requires continuous microbial exposure during the early stages of life and this process is compromised under conditions of excessive hygiene.
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Affiliation(s)
- Bettina Schmidt
- Gut Immunology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Imke E. Mulder
- Gut Immunology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Corran C. Musk
- Gut Immunology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Rustam I. Aminov
- Gut Immunology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Marie Lewis
- Veterinary Pathology, Infection and Immunity, School of Clinical Veterinary Science, University of Bristol, Bristol, United Kingdom
| | - Christopher R. Stokes
- Veterinary Pathology, Infection and Immunity, School of Clinical Veterinary Science, University of Bristol, Bristol, United Kingdom
| | - Mick Bailey
- Veterinary Pathology, Infection and Immunity, School of Clinical Veterinary Science, University of Bristol, Bristol, United Kingdom
| | - James I. Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Bhupinder P. Gill
- Agricultural and Horticultural Development Board, Milton Keynes, United Kingdom
| | - John R. Pluske
- School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Denise Kelly
- Gut Immunology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
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Merbt SN, Stahl DA, Casamayor EO, Martí E, Nicol GW, Prosser JI. Differential photoinhibition of bacterial and archaeal ammonia oxidation. FEMS Microbiol Lett 2011; 327:41-6. [PMID: 22093004 DOI: 10.1111/j.1574-6968.2011.02457.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 10/14/2011] [Accepted: 11/06/2011] [Indexed: 11/30/2022] Open
Abstract
Inhibition by light potentially influences the distribution of ammonia oxidizers in aquatic environments and is one explanation for nitrite maxima near the base of the euphotic zone of oceanic waters. Previous studies of photoinhibition have been restricted to bacterial ammonia oxidizers, rather than archaeal ammonia oxidizers, which dominate in marine environments. To compare the photoinhibition of bacterial and archaeal ammonia oxidizers, specific growth rates of two ammonia-oxidizing archaea (Nitrosopumilus maritimus and Nitrosotalea devanaterra) and bacteria (Nitrosomonas europaea and Nitrosospira multiformis) were determined at different light intensities under continuous illumination and light/dark cycles. All strains were inhibited by continuous illumination at the highest intensity (500 μE m(-2) s(-1)). At lower light intensities, archaeal growth was much more photosensitive than bacterial growth, with greater inhibition at 60 μE m(-2) s(-1) than at 15 μE m(-2) s(-1), where bacteria were unaffected. Archaeal ammonia oxidizers were also more sensitive to cycles of 8-h light/16-h darkness at two light intensities (60 and 15 μE m(-2) s(-1)) and, unlike bacterial strains, showed no evidence of recovery during dark phases. The findings provide evidence for niche differentiation in aquatic environments and reduce support for photoinhibition as an explanation of nitrite maxima in the ocean.
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Affiliation(s)
- Stephanie N Merbt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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40
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology; Institute of Microbiology of the ASCR; Prague; Czech Republic
| | - Ian M. Head
- School of Civil Engineering and Geosciences; University of Newcastle upon Tyne; Newcastle; UK
| | - James I. Prosser
- Institute of Biological and Environmental Sciences; University of Aberdeen; Aberdeen; UK
| | - Michael Schloter
- Department of Terrestrial Ecogenetics; Helmholtz Zentrum München; Oberschleissheim; Germany
| | - Kornelia Smalla
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants (JKI); Institute for Epidemiology and Pathogen Diagnostics; Munich; Germany
| | - Christoph C. Tebbe
- Institute of Biodiversity; Johann Heinrich von Thünen-Institut; Braunschweig; Germany
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Offre P, Nicol GW, Prosser JI. Community profiling and quantification of putative autotrophic thaumarchaeal communities in environmental samples. Environ Microbiol Rep 2011; 3:245-253. [PMID: 23761257 DOI: 10.1111/j.1758-2229.2010.00217.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Growth of thaumarchaea with ammonia as a sole energy source has been demonstrated but their mode(s) of carbon metabolism remain uncertain, with evidence for autotrophy, heterotrophy and mixotrophy. Understanding the role played by autotrophy in thaumarchaeal growth strategies has been hindered by the lack of an adequate marker gene and PCR primers. The aim of this study was to develop PCR-based approaches to determine the prevalence of autotrophy associated with thaumarchaea. Primer pairs were designed specifically targeting hcd genes, encoding putative 4-hydroxybutyryl-CoA dehydratase, a key functional enzyme in thaumarchaeal autotrophy. Phylogenetic analysis of hcd gene sequences amplified from soils and sediments indicated the existence of environment-specific sequence clusters and hcd abundance in soil was 10(5) -10(6) g(-1) soil, as assessed by quantitative PCR. Abundance and diversity of hcd genes were also determined in soil microcosms incubated with and without acetylene, a known inhibitor of nitrification. Nitrification was accompanied by increases in hcd gene abundance and in the relative abundance of two bands in denaturing gradient gel electrophoresis profiles. Nitrification, growth and community changes were inhibited by acetylene and the findings are consistent with active autotrophic ammonia oxidation by archaea in soil.
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Affiliation(s)
- Pierre Offre
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, UK
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Höfferle Š, Nicol GW, Pal L, Hacin J, Prosser JI, Mandić-Mulec I. Ammonium supply rate influences archaeal and bacterial ammonia oxidizers in a wetland soil vertical profile. FEMS Microbiol Ecol 2011; 74:302-15. [PMID: 21039647 DOI: 10.1111/j.1574-6941.2010.00961.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Oxidation of ammonia, the first step in nitrification, is carried out in soil by bacterial and archaeal ammonia oxidizers and recent studies suggest possible selection for the latter in low-ammonium environments. In this study, we investigated the selection of ammonia-oxidizing archaea and bacteria in wetland soil vertical profiles at two sites differing in terms of the ammonium supply rate, but not significantly in terms of the groundwater level. One site received ammonium through decomposition of organic matter, while the second, polluted site received a greater supply, through constant leakage of an underground septic tank. Soil nitrification potential was significantly greater at the polluted site. Quantification of amoA genes demonstrated greater abundance of bacterial than archaeal amoA genes throughout the soil profile at the polluted site, whereas bacterial amoA genes at the unpolluted site were below the detection limit. At both sites, archaeal, but not the bacterial community structure was clearly stratified with depth, with regard to the soil redox potential imposed by groundwater level. However, depth-related changes in the archaeal community structure may also be associated with physiological functions other than ammonia oxidation.
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Affiliation(s)
- Špela Höfferle
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Verhamme DT, Prosser JI, Nicol GW. Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J 2011; 5:1067-71. [PMID: 21228892 DOI: 10.1038/ismej.2010.191] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH(4)(+)-N per gram of soil) and high (200 μg NH(4)(+)-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil.
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Affiliation(s)
- Daniel T Verhamme
- Institute of Biological and Environmental Sciences, University of Aberdeen, UK
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Abstract
Ecological studies of soil microorganisms require reliable techniques for assessment of microbial community composition, abundance, growth, and activity. Soil structure and physicochemical properties seriously limit the applicability and value of methods involving direct observation, and ecological studies have focused on communities and populations, rather than single cells or microcolonies. Although ammonia-oxidizing archaea were discovered 5 years ago, there are still no cultured representatives from soil and there remains a lack of knowledge regarding their genomic composition, physiology, or functional diversity. Despite these limitations, however, significant insights into their distribution, growth characteristics, and metabolism have been made through the use of a range of molecular methodologies. As well as the analysis of taxonomic markers such as 16S rRNA genes, the development of PCR primers based on a limited number of (mostly marine) sequences has enabled the analysis of homologues encoding proteins involved in energy and carbon metabolism. This chapter will highlight the range of molecular methodologies available for examining the diversity, growth, and activity of ammonia-oxidizing archaea in the soil environment.
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Affiliation(s)
- Graeme W Nicol
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
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Barnes RJ, van der Gast CJ, Riba O, Lehtovirta LE, Prosser JI, Dobson PJ, Thompson IP. The impact of zero-valent iron nanoparticles on a river water bacterial community. J Hazard Mater 2010; 184:73-80. [PMID: 20810211 DOI: 10.1016/j.jhazmat.2010.08.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/20/2010] [Accepted: 08/02/2010] [Indexed: 05/29/2023]
Abstract
Zero-valent iron (ZVI) nanoparticles are of interest because of their many potential biomedical and environmental applications. However, these particles have recently been reported to be cytotoxic to bacterial cells. The overall objective of this study was to determine the impact of 100mg/L ZVI nanoparticles on the diversity and structure of an indigenous river water bacterial community. Response during exposure for 36 days was determined by denaturing gel gradient electrophoresis (DGGE) analysis of bacterial 16S rRNA genes, amplified from extracted DNA, and viable and total cell abundances were determined by plate counting and fluorescent microscopy of DAPI-stained cells. Changes in river water chemistry were also monitored. Addition of ZVI nanoparticles led to a rapid decrease in oxidation-reduction potential (ORP) (+196 to -281 mV) and dissolved oxygen (DO) concentration (8.2-0.6 mg/L), both of which stabilized during the experiment. Interestingly, both viable and total bacterial cell abundances increased and pH decreased, characteristic of an active microbial community. Total community structure was visualized using rank-abundance plots fitted with linear regression models. The slopes of the regression models were used as a descriptive statistic of changes in evenness over time. Importantly, despite bacterial growth, addition of ZVI nanoparticles did not influence bacterial community structure.
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Affiliation(s)
- Robert J Barnes
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ, UK
| | | | - Olga Riba
- Interface Analysis Centre, University of Bristol, 121 St. Michael's Hill, Bristol BS2 8BS, UK
| | - Laura E Lehtovirta
- Institute of Biological and Environmental Sciences, University of Aberdeen, St. Machar Drive, AB24 3UU, UK
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, St. Machar Drive, AB24 3UU, UK
| | - Peter J Dobson
- Begbroke Directorate, Oxford University Begbroke Science Park, Sandy Lane, OX5 1PF, UK
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ, UK.
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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.
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Affiliation(s)
- Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.
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48
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Abstract
Inhibition of growth of axenic cultures of Nitrosomonas europaea by nitrapyrin was investigated in liquid culture and in soil. In liquid culture, exponentially growing cells were more sensitive than stationary-phase cells, possibly due to a requirement for uptake of nitrapyrin, metabolism of nitrapyrin, or both before inhibition. Differences in sensitivity were observed between the parent strain and two strains, sp1 and sp2, that were selected through repeated subculturing. These differences were reflected in the length of the lag period induced by nitrapyrin and in the specific growth rate and were due to different bactericidal and bacteriostatic effects. Soil provided significant protection from inhibition, with concentrations of nitrapyrin approximately one order of magnitude greater than those required for equivalent inhibition in liquid culture. The data show that strain differences alone do not explain differences in sensitivity between nitrification in soil and in liquid culture and suggest that the inhibitor may be more effective against actively nitrifying soils.
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Affiliation(s)
- S J Powell
- Department of Microbiology, University of Aberdeen, Marischal College, Aberdeen AB9 1AS, Scotland
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49
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Silcock DJ, Waterhouse RN, Glover LA, Prosser JI, Killham K. Detection of a single genetically modified bacterial cell in soil by using charge coupled device-enhanced microscopy. Appl Environ Microbiol 2010; 58:2444-8. [PMID: 16348749 PMCID: PMC195801 DOI: 10.1128/aem.58.8.2444-2448.1992] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genes encoding bioluminescence from Vibrio harveyi were cloned into Pseudomonas syringae pv. phaseoli-cola, resulting in high levels of bioluminescence. After inoculation of sterile and nonsterile soil slurries with bioluminescent P. syringae, cells could not be identified by conventional light microscopy. However, when we used charge coupled device-enhanced microscopy, bioluminescent single cells were detected easily in dark fields despite masking by soil particulate matter, and in addition, the extent of competition from indigenous soil bacteria could be monitored. The technique which we describe offers great potential for tracking and determining the spatial distribution of genetically marked microorganisms in the environment.
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Affiliation(s)
- D J Silcock
- Departments of Plant and Soil Science and Molecular and Cell Biology, University of Aberdeen, Aberdeen AB9 2UE, Scotland
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50
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Langenheder S, Bulling MT, Solan M, Prosser JI. Bacterial biodiversity-ecosystem functioning relations are modified by environmental complexity. PLoS One 2010; 5:e10834. [PMID: 20520808 PMCID: PMC2877076 DOI: 10.1371/journal.pone.0010834] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 04/19/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND With the recognition that environmental change resulting from anthropogenic activities is causing a global decline in biodiversity, much attention has been devoted to understanding how changes in biodiversity may alter levels of ecosystem functioning. Although environmental complexity has long been recognised as a major driving force in evolutionary processes, it has only recently been incorporated into biodiversity-ecosystem functioning investigations. Environmental complexity is expected to strengthen the positive effect of species richness on ecosystem functioning, mainly because it leads to stronger complementarity effects, such as resource partitioning and facilitative interactions among species when the number of available resource increases. METHODOLOGY/PRINCIPAL FINDINGS Here we implemented an experiment to test the combined effect of species richness and environmental complexity, more specifically, resource richness on ecosystem functioning over time. We show, using all possible combinations of species within a bacterial community consisting of six species, and all possible combinations of three substrates, that diversity-functioning (metabolic activity) relationships change over time from linear to saturated. This was probably caused by a combination of limited complementarity effects and negative interactions among competing species as the experiment progressed. Even though species richness and resource richness both enhanced ecosystem functioning, they did so independently from each other. Instead there were complex interactions between particular species and substrate combinations. CONCLUSIONS/SIGNIFICANCE Our study shows clearly that both species richness and environmental complexity increase ecosystem functioning. The finding that there was no direct interaction between these two factors, but that instead rather complex interactions between combinations of certain species and resources underlie positive biodiversity ecosystem functioning relationships, suggests that detailed knowledge of how individual species interact with complex natural environments will be required in order to make reliable predictions about how altered levels of biodiversity will most likely affect ecosystem functioning.
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Affiliation(s)
- Silke Langenheder
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.
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