| 1. |
- Timmis, Kenneth, et al.
(författare)
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A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society
- 2024
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Ingår i: Microbial Biotechnology. - 1751-7907. ; 17:5
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Tidskriftsartikel (refereegranskat)abstract
- EXECUTIVE SUMMARY: Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative-the IMiLI-is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators-learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators-learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships-a global societally relevant microbiology education ecosystem-in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient.ABSTRACT: The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us-individuals/communities/nations/the human world-and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. HERE, WE PRESENT: our concept of how microbiology literacy may be achieved and the rationale underpinning it; the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091-1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge.
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| 2. |
- Baker, Kate L., et al.
(författare)
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Environmental and spatial characterisation of microbial community composition to inform sampling strategies
- 2009
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 41:11, s. 2292-2298
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Tidskriftsartikel (refereegranskat)abstract
- Soil physicochemical properties and microbial communities are highly heterogeneous and vary widely over spatial scales, necessitating careful consideration of sampling strategies to provide representative and reproducible soil samples across field sites. To achieve this, the study aimed to establish appropriate sampling methodology and to determine links between the variability of parameters, utilising two sampling strategies. The first (design 1) involved extracting 25 cores from random locations throughout the field and pooling them into five sets of five cores. The second (design 2) involved a further 25 cores within five 1 m2 sub-plots. Sub-samples from each sub-plot were pooled in order to determine between and within sub-plot variability. All samples were analysed independently and as pooled sub-samples. Results indicate that pooling spatially separated samples significantly reduced the variability in pH, compared to individual samples. Pooling samples from a small area resulted in lower within sub-plot variability than between sub-plots for pH and bacterial community composition assessed by terminal-restriction fragment length polymorphism analysis. Following multivariate statistical analysis, a large amount of variation in community composition was explained by soil pH, which is remarkable given the relatively small size of the sampling area and minor differences in pH. Moisture content was also important in determining bacterial communities in the random design (design 1). In the 1 m2 sub-plot design (design 2), the spatial location of the plots explained a large degree of the variation in bacterial community composition between plots, which was due to spatial autocorrelation of pH and possible additional environmental parameters. This study emphasises the importance of sampling design for obtaining representative samples from soil.
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| 3. |
- Elväng, Annelie, 1965-
(författare)
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Quantitative monitoring of microorganisms in environmental samples using biomarkers
- 1998
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The use of microorganisms in environmental biotechnology is an area of growing interest. Microorganisms have been used for diverse applications, such as biological fertilizers, biological pesticides and bioremediation of toxic chemicals. In many cases, the bacteria of interest have been genetically alterred to improve certain traits. Before large scale environmental release of genetically modified microorganisms is attempted, careful risk assessment of the fate and survival of the inoculum and potential effects on the ecosystem must be evaluated. In order to monitor the inocula in complex environmental samples among a large population of indigenous microorganisms, the methods for detection of the microbe must be very specific and sensitive. To achieve any reliable estimations of fate, survival and efficacy of the inocula the methods for detection also need to be quantitative.Bacteria of interest can be tagged with specific biomarkers of eukaryotic origin, such as the firefly luciferase gene, luc, or the Aequoria victoria green fluorescent protein gene, gfp. These biomarkers confer novel genotypes (the marker gene itself) and phenotypes (bioluminescence or fluorescence, respectively) that are absent in the natural microbial flora. For example, PCR amplification, with primers targeting the marker gene, can be used for sensitive detection of biomarked bacteria. Alternatively, the bioluminescent reaction of the firefly luciferase enzyme can be used as: 1) an in vivo indicator of metabolic activity of the cell since luciferase activity is dependent on cellular energy reserves, or 2) an in vitro assay (supplemented with ATP and substrate). The in vitro assay of luciferase activity is independent of the energy status of the cell. The in vivo fluorescence of the green fluorescent protein is also independent of cellular energy reserves or co-factors.Methods were developed for specific detection of bacteria with luc or gfp biomarkers in soil and sediment samples. Complementary methods were used for quantitative monitoring of bacteria based on: DNA sequence, cellular activity, cellular protein content and total numbers of cells. All methods developed were independent of traditional cultivation techniques.Different quantitative approaches were developed and applied for monitoring of specific bacteria with environmental relevance. For example, luc-tagged cyanobacteria were quantitated in Baltic Sea sediment by competitive PCR amplification of the luc biomarker. Luciferase activity, expressed by the luc biomarker, was quantitated by luminometry. In addition, Arthrobacter chlorophenolicus A6 cells were tagged with gfp or luc biomarkers and quantitated during degradation of high concentrations of 4-chlorophenol in soil. As the cells bioremediated the soil, the metabolic activity of the Arthrobacter population was monitored as bioluminescence by luminometry and the total number of fluorescent Arthrobacter cells were enumerated by flow cytometry. In conclusion, these quantitative approaches, based on biomarkers, were demonstrated to be useful for accurate monitoring of specific cells in environmental samples.
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| 4. |
- Gocht, Stephan, et al.
(författare)
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Certifying Solvers for Clique and Maximum Common (Connected) Subgraph Problems
- 2020
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Ingår i: Principles and Practice of Constraint Programming - 26th International Conference, CP 2020, Proceedings. - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. - 9783030584740 ; 12333, s. 338-357
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Konferensbidrag (refereegranskat)abstract
- An algorithm is said to be certifying if it outputs, together with a solution to the problem it solves, a proof that this solution is correct. We explain how state of the art maximum clique, maximum weighted clique, maximal clique enumeration and maximum common (connected) induced subgraph algorithms can be turned into certifying solvers by using pseudo-Boolean models and cutting planes proofs, and demonstrate that this approach can also handle reductions between problems. The generality of our results suggests that this method is ready for widespread adoption in solvers for combinatorial graph problems.
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| 5. |
- Graham, Emily B., et al.
(författare)
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Microbes as Engines of Ecosystem Function : When Does Community Structure Enhance Predictions of Ecosystem Processes?
- 2016
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.
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| 6. |
- James, Sarah-Naomi, et al.
(författare)
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A population-based study of head injury, cognitive function and pathological markers.
- 2021
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Ingår i: Annals of clinical and translational neurology. - : Wiley. - 2328-9503. ; 8:4, s. 842-856
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Tidskriftsartikel (refereegranskat)abstract
- To assess associations between head injury (HI) with loss of consciousness (LOC), ageing and markers of later-life cerebral pathology; and to explore whether those effects may help explain subtle cognitive deficits in dementia-free individuals.Participants (n=502, age=69-71) from the 1946 British Birth Cohort underwent cognitive testing (subtests of Preclinical Alzheimer Cognitive Composite), 18 F-florbetapir Aβ-PET and MR imaging. Measures include Aβ-PET status, brain, hippocampal and white matter hyperintensity (WMH) volumes, normal appearing white matter (NAWM) microstructure, Alzheimer's disease (AD)-related cortical thickness, and serum neurofilament light chain (NFL). LOC HI metrics include HI occurring: (i) >15years prior to the scan (ii) anytime up to age 71.Compared to those with no evidence of an LOC HI, only those reporting an LOC HI>15years prior (16%, n=80) performed worse on cognitive tests at age 69-71, taking into account premorbid cognition, particularly on the digit-symbol substitution test (DSST). Smaller brain volume (BV) and adverse NAWM microstructural integrity explained 30% and 16% of the relationship between HI and DSST, respectively. We found no evidence that LOC HI was associated with Aβ load, hippocampal volume, WMH volume, AD-related cortical thickness or NFL (all p>0.01).Having a LOC HI aged 50's and younger was linked with lower later-life cognitive function at age ~70 than expected. This may reflect a damaging but small impact of HI; explained in part by smaller BV and different microstructure pathways but not via pathology related to AD (amyloid, hippocampal volume, AD cortical thickness) or ongoing neurodegeneration (serum NFL).
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| 7. |
- Langenheder, Silke, et al.
(författare)
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Bacterial biodiversity-ecosystem function relations are modified by environmental complexity
- 2010
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 5:5, s. e10834-
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundWith 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 FindingsHere 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/SignificanceOur 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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| 8. |
- Langenheder, Silke, et al.
(författare)
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Resource availability influences the diversity of a functional group of heterotrophic soil bacteria.
- 2008
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 10:9, s. 2245-2256
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Tidskriftsartikel (refereegranskat)abstract
- Resource availability is a key factor regulating biodiversity and ecosystem functioning, but the relationship between resource availability and diversity has only been rarely investigated in microbial communities. The aim of this study was to determine how diversity and community structure of a functional group of soil bacteria are influenced by resource concentration. To achieve this, we used soil microcosms to investigate degradation of benzoate, which served as a model compound, by soil bacterial communities. Microcosms were supplied with 13C-labelled benzoate at four concentrations and RNA-stable isotope probing followed by molecular fingerprinting analysis of 16S rRNA genes was employed to identify bacteria able to assimilate benzoate at different concentrations. The composition of the benzoate degrader community differed at different concentrations and there was a significant decrease in taxa evenness at the highest substrate concentration. Active organisms could be grouped into generalists, occurring at all substrate concentrations, specialists, active at one particular benzoate concentration only, and taxa that were active at either the two lowest or two highest concentrations. The study comprises the first explicit demonstration that resource availability has an effect on the diversity of a functional group of heterotrophic soil bacteria.
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| 9. |
- Langenheder, Silke, et al.
(författare)
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Role of functionally dominant species in varying environmental regimes : evidence for the performance-enhancing effect of biodiversity
- 2012
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Ingår i: BMC Ecology. - : Springer Science and Business Media LLC. - 1472-6785. ; 12, s. 14-
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Tidskriftsartikel (refereegranskat)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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| 10. |
- Philippot, Laurent, et al.
(författare)
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The ecological coherence of high bacterial taxonomic ranks
- 2010
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Ingår i: Nature Reviews Microbiology. - : Springer Science and Business Media LLC. - 1740-1526 .- 1740-1534. ; 8:7, s. 523-529
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Forskningsöversikt (refereegranskat)abstract
- The species is a fundamental unit of biological organization, but its relevance for Bacteria and Archaea is still hotly debated. Even more controversial is whether the deeper branches of the ribosomal RNA-derived phylogenetic tree, such as the phyla, have ecological importance. Here, we discuss the ecological coherence of high bacterial taxa in the light of genome analyses and present examples of niche differentiation between deeply diverging groups in terrestrial and aquatic systems. The ecological relevance of high bacterial taxa has implications for bacterial taxonomy, evolution and ecology.
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| 11. |
- Rütting, Tobias, 1977, et al.
(författare)
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The contribution of ammonia-oxidizing archaea and bacteria to gross nitrification under different substrate availability
- 2021
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717. ; 160
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Tidskriftsartikel (refereegranskat)abstract
- The first step of autotrophic nitrification is performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recent studies show that their relative contributions are determined by the substrate sources and availability, yet evidence provided by quantification of their respective gross activities in soil is lacking. Here, we conducted a microcosm study with agricultural soil with high (50 μg N g−1) and low (5 μg N g−1) ammonium application, and quantified gross nitrification rates using 15N-tracers. AOA and AOB activities were distinguished using the bacterial inhibitor 1-octyne and acetylene, which inhibits both AOA and AOB. Under low ammonium supply, AOA and AOB contributed equally to gross ammonia oxidation, but AOB outcompeted AOA under higher ammonium supply. These results provide the first direct evidence that substrate availability affects the relative contribution of AOA and AOB to gross nitrification.
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