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Elements, genomes and ecosystems: cascading nitrogen and phosphorus impacts across levels of biological organisation

Event

Starts:

June
012015

09:00

Ends:

June
022015

17:00

Location

Kavli Royal Society Centre, Chicheley Hall, Newport Pagnell, Buckinghamshire, MK16 9JJ

Overview

Theo Murphy international scientific meeting organised by Professor Andrew Leitch, Professor Maurine Neiman, Professor Dag Hessen, Professor Puni Jeyasingh, Professor Lawrence J. Weider and Dr Ilia Leitch

Centuries-old Daphnia pulicaria from South Center Lake (MN, U.S.A.). Photo courtesy of Dagmar Frisch.

Event details

This meeting will explore how environmental nitrogen (N) and phosphorus (P) impact the evolution and use of nucleic acids and how these effects, in turn, cascade through natural and agricultural ecosystems. It unites expertise in N and P metabolism, plant and animal genome evolution, ecology (including those interested in biodiversity and ecosystem functioning), and agriculture.

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Abstracts of the speakers will be available closer to the meeting. Recorded audio of the presentations will be available on this page after the event.

Attending this event

This is a residential conference, which allows for increased discussion and networking. It is free to attend, however participants need to cover their accommodation and catering costs if required.

Travel bursaries funded by the US National Science Foundation are available to assist attendance at this meeting for US graduate students and postdocs. Further details, and an application form, are available online. Deadline for applications is 15 December 2014. For information contact Puni Jeyasingh.

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Event organisers

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Schedule of talks

Stoichiometry of N and P and responses to environmental change

4 talks Show detail Hide detail

Polyploidy and environmental change: theory vs evidence

Professor Babara Mable, University of Glasgow, UK

Abstract

There are several long-standing theories that have been invoked to explain advantages that might be associated with polyploidy.  One that has been commonly cited is that polyploids should be able to tolerate or adapt to a wider range of environments than their diploid relatives, due to increased genetic buffering provided by having twice as many gene copies and so an increase in phenotypic flexibility.  While there is a strong theoretical basis for such predictions, there have been remarkably few direct experimental tests.  Correlational studies sometimes (but not always) have supported the theory but for most polyploid organisms, there has been no experimental demonstration of increased tolerance to changing environmental conditions.  The purpose of this talk is to review what we do and don’t know about the role that whole genome duplication plays in adaptation.

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StoichioMetaTranscriptomics of sea waters

Professor Claudia Acquisti, University of Munster, Germany

Abstract

The elucidation of the genetic basis of ecosystem processes is one of the open challenges in the metagenomics era. Current research indicates that the material costs of evolutionary change play a crucial role in constraining the evolution of proteins and genes in response to nutrient limitations in natural ecosystems. For example, the nitrogen content of molecular sequences has been established as a marker to trace connections between the genome and the eco-physiology of the organisms. However, these results have primarily relied on few well established genetic model organisms, leaving the question of the relevance of adaptation to nutrient availability in natural environments only partially addressed.

Recent advances in metagenomics allow to extend our understanding of the impact of the evolutionary history of nutrient limitation on molecular evolution in a biogeochemical framework, providing a major arena to directly quantify the allocation of nutrients from the abiotic habitat to genes and proteins in environmental samples. Following the biogeochemical cycling of nitrogen along the marine water column, here we evaluate the evolutionary consequences of environmental availability of nitrogen on the material costs of genetic change combining the power of metagenomics and biogeochemistry. The results suggest a pivotal role of nitrogen-limitation in shaping proteome and transcriptome composition within and between species in natural communities.

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Elevated nitrogen deposition and changed N:P-ratios: implications scaling from ecosystems to cells

Professor Dag Hessen, University of Oslo

Abstract

Due to fossil fuel combustion, fertilization industry and agricultural activity, the global N-cycle is strongly perturbed, with anthropogenic conversion of N2 to bioavailable N now exceeding natural N2-fixation. This causes an increased N-loading to many ecosystems with major changes in elemental ratios. For aquatic “pristine” ecosystems this has caused elevated N:P-ratios and shifts from N to P-limitation in autotrophs.  N-deposition impact in the catchment may be superimposed on the direct effects in lakes, as terrestrial autotrophs may profoundly affect retention and mineralization of elements. Increased forest growth caused by atmospheric N-fertilization will cause an increased demand for other elements like P. On the other hand, increased root-induced weathering can promote release of not only P, but also key elements from plant production like Si and Fe. The net effect will affect both the absolute and relative export of elements to lakes, and this will entail a suit of ecosystem impacts, from productivity to community composition, size structure and food-webs. This presentation will explore these issues from a large data-base of boreal lakes, demonstrating how elevated N-deposition profoundly impacts elemental ratios and ecosystem properties in these systems.

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From source to sea: transport and cycling of phosphorus and nitrogen in rivers

Professor Helen Jarvie, Centre for Ecology & Hydrology, UK

Abstract

Phosphorus (P) and nitrogen (N) are key limiting nutrients for food production, yet we face an overabundance of P and N entering aquatic systems, from agricultural production and food consumption.  This impairs water quality, undermines the health of aquatic ecosystems, and threatens water security.  Seventy-five year datasets from the Thames watershed, UK, will be used to demonstrate how increasing human population and changing agricultural practices have resulted in dramatic shifts in watershed inputs and outputs of P and N. Long-term accumulation of P and N within watersheds has resulted in large-scale nutrient ‘legacies’ stored in pools, with varying residence times, along the land-water continuum.  Case studies will explore the storage, recycling and transport of P and N along the continuum from groundwater, through headwater streams and rivers, to the watershed outlet.  These demonstrate how chronic release of P and N from legacy stores may continue to impair water quality for years or decades, masking the effects of nutrient management and conservation programmes.   Finally, the implications of changing anthropogenic pressures, climate change and agri-environment policy will be discussed, in relation to transfers of P and N between watershed pools, the draw-down in existing nutrient legacies, and achieving improvements in water quality and ecology.

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Genome and metabalome diversity

4 talks Show detail Hide detail

Adaptation at the genome level in haploid, diploid, and polyploid yeast

Dr Aleeza Gerstein, University of Minnesota, USA

Abstract

Asexual fungal microbes display incredible tolerance to karyotypic variation, with variation among individuals in both ploidy (the number of homologous chromosome sets) and aneuploidy (imbalance in the number of chromosomes). Such Variation may thus represent a form of epigenetic variation, as is it can be rapidly selected for or against depending on the environmental condition. Here we utilized the predominant human fungal pathogen Candida Albicans to assess the interplay between ploidy drive, which tends to push ploidy to the historical ploidy level (in this case diploidy), and environmental pressure, which may select for lower or higher genome sizes. We evolved three (initially) haploid, three diploid and three tetraploid strains for ~140 generations under phosphorus limitation, nitrogen limitation, and nutrient sufficient conditions, and measured genome size at the culmination of the experiment. Under nutrient sufficient conditions, we found selection for genome size reduction—haploid strains were able to maintain haploidy in spite of ploidy drive, while tetraploid strains showed a reduction in ploidy. Under nitrogen limitation, in contrast, we found selection towards an increased genome size—tetraploid strains were able to maintain tetraploidy, while haploid strains increased towards diploidy. The Influence of phosphorus limitation pointed towards the importance of initial genetic background, as some strains behaved more similarly to those evolved under nitrogen limitation, while others behaved more similarly to those evolved under nutrient sufficient conditions. Combined, this work demonstrates the influence of nutrient limitation on dictating evolutionary ploidy trajectories, as we found that environmental pressure can overwhelm the strong force of ploidy drive.

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Genome size variation across micro-algae

Professor Bente Edvardsen, University of Oslo, Norway

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The wondrous cycles of polyploidy in plants

Professor Jonathan. F. Wendel, Iowa State University, USA

Abstract

One of the signal realizations of the genomics era is that all plants have experienced multiple rounds of whole genome doubling. This history involves an array of novel genomic interactions and fractionation processes that result in deletion of much, but not all, of the duplicated chromatin. These possibilities are illustrated using the model genus Gossypium (cotton), which includes classic allopolyploids arising from a biological reunion 1-2 MYA of divergent diploids from different hemispheres. This serendipitous merger generated a spectrum of genomic responses, including gene silencing, intergenomic gene conversion, and genome-wide disruption and modification of ancestral expression patterns. Allopolyploid formation induces massive alteration in gene expression and complex transcriptomic responses, including genomic expression dominance and bias, transgressive expression, and novel cytonuclear interactions. Duplicate gene (homoeolog) expression modulations are temporally partitioned into alterations arising immediately as a consequence of genomic merger and secondarily as a result of long-term evolutionary change, the latter reflecting long-term evolutionary forces such as duplicate gene neofunctionalization and subfunctionalization. Homoeolog expression varies even at the level of development and maturation of the single-celled cotton fibre. Polyploid plants provide insights into the genetic and network architecture underlying the evolution of morphology, as well as several evolutionary dimensions of a prominent mode of plant speciation. Attention is drawn to the episodic and cyclic nature of whole genome doubling in plants, and the many unexplored questions concerning the relationships among DNA, RNA, and protein levels, and the possibility of selection on N and P.

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Animal genomes large and small

Dr. T. Ryan Gregory, University of Guelph, Canada

Abstract

The extraordinary diversity in genome sizes (haploid nuclear DNA contents, or “C-values”) among eukaryote species has remained a major puzzle in genetics for over 60 years.  The size of a genome bears no relationship to the number of coding genes it contains or to the complexity of the organism in which it is found, a finding so surprising to early researchers that it became known as the “C-value paradox”.  While the discovery of non-coding DNA has solved this paradox, it has raised a series of new questions regarding the origins, mechanisms of spread and loss, phenotypic consequences, and reasons for differential abundance of non-coding DNA in different species.  This seminar explores these questions, with a particular emphasis on the connection between genome size and such important phenotypic characteristics as cell size, body size, metabolism, and development in animals.

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Diversity of the genomic responses to N and P stress in the environment

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Plant genome diversity and evolution in response to environmental N and P

Professor Andrew Leitch, Queen Mary University of London, UK
Dr Ilia Leitch, Royal Botanic Gardens, Kew, UK

Abstract

Angiosperm genome sizes (GS) range c. 2,400-fold, but are strongly skewed towards small values despite having an abundance of repetitive DNA and, in most lineages, multiple rounds of polyploidy in their ancestry. Such observations suggest selection against large GSs. One potential source of selection is nutrient availability, particularly phosphorous (P) and nitrogen (N), since large genomes are costly to build in terms of N and P needed to make nucleic acids, elements that are frequently limiting. To test the hypothesis that N and P availability limits GS, we analysed the impact of different nutrient regimes on the above-ground biomass of angiosperm species with different GS, ploidy level, and Grime’s C-S-R plant strategies growing in the world’s longest running ecological experiment, Park Grass (Rothamsted, UK), established 1856. The biomass-weighted GS of species growing on plots where both N and P were added in fertilizer treatments were significantly higher than plants growing on control plots and plots where either N or P (but not both) were added. Polyploids with a large GS and a strong C (competitor) strategy increased most significantly when both N and P were added together. These results are consistent with the long-term Rengen Grassland experiment recently published by Šmarda et al. (2013) and are consistent with the hypothesized effect of N and P limiting biomass on plots in species dependant on GS. The data also point to polyploids with large genomes being strong competitors but only in the presence of both N and P. Overall these data support the suggestion that nucleic acids are indeed biochemically costly, influencing plant community and ecosystem composition. In addition to the Park Grass plots, we have analysed the Silwood Park (UK) field experiment, set up over the last 24 years. These plots were also established to see the effects of fertilizer and pH on species composition, but with a design that enables a much greater power of statistical analysis. In addition, they allow the effects of rabbit, insect and mollusc herbivory on biomass to be investigated. We will therefore present the impact of GS in relation to the plants growing on these plots as well.

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Evolutionary ecology of phosphorus use in a freshwater zooplankter

Professor Puni Jeyasingh, Oklahoma State University, USA
Professor Lawrence Weider, University of Oklahoma, USA

Abstract

Compared to producers, we know little about the physiological and evolutionary consequences of variation in phosphorus (P) supply in consumers. Because consumers impart strong control on P supply, information on the physiological and evolutionary consequences of altered P supply is needed for a better understanding of ecosystem responses to nutrient pollution (i.e. eutrophication). Work on the keystone freshwater consumer, Daphnia, has revealed complex physiological and evolutionary consequences to altered inorganic P supply. There is substantial variation in genotype X P-environment interactions in Daphnia P-use. Such G x E interactions appear to be largely driven by differential expression of pathways mitigating the biochemical responses of algae to altered P supply. By exploiting the unique biology of daphniids that produce diapausing “resting eggs”, we compared eggs laid before and after the onset of cultural eutrophication. We reconstructed not only the population genetic history by analyzing resting egg DNA over a ~1600-year-period, but also the transcriptomic and physiological differences on a few experimentally hatched (“resurrected”) eggs. Striking shifts in frequency of neutral markers, transcriptomes, and P-use were closely correlated with the onset of anthropogenic eutrophication. Radiotracer assays revealed unique effects of ancient and extant genotypes on the quality and quantity of algae via differential recycling. Such effects are unlikely to be a simple function of differences in P-recycling, because we found significant differences between ancient and extant genotypes in the content of several other elements (e.g., potassium, iron).

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Consequences of polyploidy for a New Zealand snail

Professor Maurine Neiman, University of Iowa, USA

Abstract

Maurine will start by surveying some of the potential costs and benefits associated with polyploidy and will then explain why her New Zealand “mud snail” system is such a great model for the study of ploidy elevation (and sex!). After a brief foray into the genomic consequences of polyploidy, she will then consider whether phenotypic costs associated with polyploidy can help to explain why diploidy generally prevails in animals. Maurine will present data from her snail system indicating that while these phenotypic costs are likely to exist, they might only be evident under stressful conditions. She will focus on evaluating connections between costs of polyploidy associated with building additional chromosomes when the environmental availability of the nutrients (e.g., phosphorus) of which nucleic acids are comprised is low.

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P selection and genome size variation in plants

Dr Petr Šmarda, Masaryk University, Czech Republic

Abstract

DNA in the cell nuclei is very rich in phosphorus (P) and therefore it is expected that organisms with large genome (nuclei) sizes may be selectively disadvantaged (limited in growths and occurrence) in the phosphorus limited environments. During the past four years we have made several observational and manipulative experiments testing this hypothesis. In one experiment we observed differences in genome sizes spectra of species in a vegetation that have established on plots with different nitrogen (N) and P treatment in a >70-years continuing grassland fertilizer experiment. In other experiments we have compared genome size spectra of species in eight radiating genera of the Cape flora adapted for soils that sharply differ in the total-rock and the plant-available N and P contents and in plots with various nutrient contents in Svalbard, a high arctic area known for extraordinarily high frequency of polyploids. In several manipulative experiments we have observed effects of increased N and P on differences in germination speed, germination and emergence success, and total biomass between polyploids and their diploid progenitors (12–14 pairs). Our results allow to detect some effect of increased or low nutrients on the success of polyploids and species with increased genome size, though neither P nor N seem to be the primary reasons for their success in a particular habitat or environment. Maybe a better understanding on the role of nutrients on success of species with different genome size could be obtained with exact knowledge of their genome size-associated nutrient demands.

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World problems: Ecosystems and agriculture under N and P limitation

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Managing agriculture in the face of phosphorus scarcity

Dr Alan Richardson, CSIRO Agriculture, Canberra, Australia

Abstract

The productivity of agriculture on phosphorus (P) deficient soils is improved by application of P fertilizers. Low P soils arise after ecosystem development over geological timescales. Plants evolved on such soils often acclimate by growing slowly but agriculture demands fast-growing species, often with relatively high critical external P requirements.  P is initially applied to build and, subsequently, to maintain levels of P ‘availability’ in soil that can support optimal plant growth.  However, soils being fertilised to alleviate P deficiency accumulate some of the P in forms that are only sparingly-available to plants. This sink for P must be covered by fertilizer applications until, over long periods, the P-sorption capacity of the soil is saturated. P inputs must also cover P export from farming systems in products.  These are minimum requirements for sustainable agriculture or soil P resources will be degraded.  Unfortunately, P fertiliser use is often accompanied by damaging leakage of P to the wider environment, especially when fertilisers are applied in excess.  Excessive use is unnecessary and can be addressed by better agronomic practices.  However, where P inputs need to be greater than P exports to maintain production there is a ‘technical’ inefficiency that is difficult to avoid. Reducing this imbalance can provide economic and resource conservation opportunities.  Development of farming systems that operate at lower critical levels of ‘available’ soil P would address inefficiencies associated with P accumulation in soil and will also help to reduce P losses from fertile systems where P inputs only need to equal outputs.

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Three things about P sustainability and what we're trying to do about it

Professor James Elser, Arizona State University, USA

Abstract

Phosphorus is essential for all living things, including crops and livestock, and thus increased P inputs have been essential for the Green Revolution. However, concerns about rising prices for phosphate rock as well as about the water quality impacts of increasing P inputs from cities and farms have raised serious questions about the long term sustainability of the modern food system. Here I illustrate some dimensions of the P sustainability challenge in three dimensions: 1. rising global demand for P due to changing diets, 2. non-linear dynamics and regime shifts in phosphate rock prices, and 3. large-scale accumulation of "legacy P" in three global catchments. Lest anyone despair, I will also describe some recent efforts to advance understanding, awareness, and solutions to the P sustainability challenge, including the new North American Partnership for Phosphorus Sustainability and its counterpart European Sustainable Phosphorus Platform.

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Roots of the second green revolution

Professor Jonathan Lynch, Penn State University, USA

Abstract

The historical Green Revolution was an input intensification strategy combining fertilizers with fertilizer responsive crop genotypes. The second Green Revolution will improve crop productivity with limited nutrient supply. Low phosphorus availability is a primary constraint to food production in developing nations. Several root phenes under genetic control can improve crop growth in low P soils, by improving topsoil foraging and by reducing the metabolic costs of soil exploration.  These phenes include root hair length and density, basal root growth angle, and basal root whorl number. Selection for these root phenotypes in common bean breeding has resulted in new P efficient lines with 50-150% greater yield in low P soils of Africa and Latin America.  In addition to greater productivity, these new P efficient lines reduce soil P loss through erosion, improve biological nitrogen fixation, and improve responsiveness to locally available rock P resources.  Improved bean production can improve household nutrition but may also have unexpected social effects depending on the seed class being improved. This case study demonstrates the value of improving the productivity and nutrient economy of low input production systems by genetic selection for root phenotypes, even in the absence of input intensification.

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Elements, genomes and ecosystems: cascading nitrogen and phosphorus impacts across levels of biological organisation Kavli Royal Society Centre, Chicheley Hall Newport Pagnell Buckinghamshire MK16 9JJ