iOES Poster: Using metagenomics to assess soil microbial diversity under future climate scenarios

Joseph Jenkins, Prof. Gail Taylor, Dr. Rich Edwards.

1st International Environmental Omics Synthesis (iEOS) Conference, Cardiff, UK (Sept 11-13, 2013). Poster CE-3.

Abstract:

Soil microbes are responsible for the function of biogeochemical cycles, which are essential to maintain soil quality. Anthropogenic climate change is resulting in variation of the soil habitat, through alteration of a multitude of soil variables. In particular, prevalence of drought and use of geoengineering methods to sequester carbon (such as biochar) are expected to increase.

To test the implications of drought and biochar amendment in soil habitats, soil samples were collected from two long term experimental sites, and shotgun metagenomic sequencing undertaken to determine changes in soil microbial diversity. Furthermore, analysis of the method itself will be undertaken to determine potential issues with the technique, and to improve the methodology for future studies.

Future work will attempt to compare results of shotgun and amplicon metagenomic methods, and sequencing of additional biochar treated samples from a range of European sites undertaken. This will provide a means to compare changes in microbial diversity after biochar incorporation under a variety of field conditions, providing insight into its likely effects for soil microbial ecology.

iOES Poster: Using Next Generation Sequencing to Understand Plant Acclimation and Adaptation to the Changing Environment

Alex Watson-Lazowski, Yunan Lin, Jennifer DeWoody, Richard Edwards and Gail Taylor.

1st International Environmental Omics Synthesis (iEOS) Conference, Cardiff, UK (Sept 11-13, 2013). Poster EcO-15.

Abstract:

Plant adaptation to elevated atmospheric carbon dioxide (CO2) is of great interest, as the concentration of this gas in the atmosphere has risen by more than 30% to 388 μmol mol-1 since the industrial revolution. On average there has been a rise of 3 ppm per year. Plant fossil samples suggest that atmospheric CO2 may be acting as a selective agent driving evolution, but limited evidence is available to support this idea for plants subjected to future predicted concentrations. Studying evolutionary responses to this aspect of environmental change is difficult, but here we use a CO2 spring site where plants have been exposed for multiple generations to concentrations of CO2 predicted for 2050. From this, detailed phenotyping data was collected, including data for stomatal patterning. Considerable evidence exists to show that stomatal numbers have declined across geological time and that this is linked to CO2 concentration, but few CO2-sensitive stomatal patterning genes have ever been identified. When grown under elevated CO2 concentrations P. lanceolata (the narrow leaf plantain), seeds collected from the spring site showed a counter-intuitive change in stomatal index and density. Here, in this non- model plant we have investigated the gene expression changes underlying this stomatal patterning response to elevated CO2.

RNA-Seq allows for in depth analysis of plant species with no previous information required, enabling rapid evaluation of any of novel plant acclimations and adaptions. Using this approach we have identified a set of novel genes for stomatal patterning in high CO2 and confirmed previously observed acclimation responses.

RNA-Seq refers to the use of high-throughput deep-sequencing technologies to sequence cDNA in order to get information about the transcriptome of a given biological sample.

1st International Environmental Omics Synthesis (iEOS) Conference

The lab has a couple of posters at the 1st International Environmental Omics Synthesis (iEOS) Conference conference in Cardiff this week (Sept 11-13), so come and say hello to Joe and/or Alex if you are in Cardiff.

Poster EcO-15:

UNDERSTANDING PLANT ADAPTATION TO THE CHANGING ENVIRONMENT USING NEXT GENERATION RNA TRANSCRIPTOME SEQUENCING

Alex Watson-Lazowski, Yunan Lin, Jennifer DeWoody, Richard Edwards and Gail Taylor. Centre for Biological Sciences, University of Southampton.

Plant adaptation to elevated atmospheric carbon dioxide (CO2) is of great interest, as the concentration of this gas in the atmosphere has risen by more than 30% to 388 μmol mol-1 since the industrial revolution. On average there has been a rise of 3 ppm per year. Plant fossil samples suggest that atmospheric CO2 may be acting as a selective agent driving evolution, but limited evidence is available to support this idea for plants subjected to future predicted concentrations. Studying evolutionary responses to this aspect of environmental change is difficult, but here we use a CO2 spring site where plants have been exposed for multiple generations to concentrations of CO2 predicted for 2050. From this, detailed phenotyping data was collected, including data for stomatal patterning. Considerable evidence exists to show that stomatal numbers have declined across geological time and that this is linked to CO2 concentration, but few CO2-sensitive stomatal patterning genes have ever been identified. When grown under elevated CO2 concentrations P. lanceolata (the narrow leaf plantain), seeds collected from the spring site showed a counter-intuitive change in stomatal index and density. Here, in this non- model plant we have investigated the gene expression changes underlying this stomatal patterning response to elevated CO2.

RNA-Seq allows for in depth analysis of plant species with no previous information required, enabling rapid evaluation of any of novel plant acclimations and adaptions. Using this approach we have identified a set of novel genes for stomatal patterning in high CO2 and confirmed previously observed acclimation responses.

RNA-Seq refers to the use of high-throughput deep-sequencing technologies to sequence cDNA in order to get information about the transcriptome of a given biological sample.

Poster CE-3:

USING METAGENOMICS TO ASSESS SOIL MICROBIAL DIVERSITY UNDER FUTURE CLIMATE SCENARIOS

Joseph Jenkins, Prof. Gail Taylor, Dr. Rich Edwards. University of Southampton, ExpeER, EuroChar.

Soil microbes are responsible for the function of biogeochemical cycles, which are essential to maintain soil quality. Anthropogenic climate change is resulting in variation of the soil habitat, through alteration of a multitude of soil variables. In particular, prevalence of drought and use of geoengineering methods to sequester carbon (such as biochar) are expected to increase.

To test the implications of drought and biochar amendment in soil habitats, soil samples were collected from two long term experimental sites, and shotgun metagenomic sequencing undertaken to determine changes in soil microbial diversity. Furthermore, analysis of the method itself will be undertaken to determine potential issues with the technique, and to improve the methodology for future studies.

Future work will attempt to compare results of shotgun and amplicon metagenomic methods, and sequencing of additional biochar treated samples from a range of European sites undertaken. This will provide a means to compare changes in microbial diversity after biochar incorporation under a variety of field conditions, providing insight into its likely effects for soil microbial ecology.

New website under construction

Welcome to the new Edwards Lab website. The site is currently under construction, so content should appear over the next few weeks. In the meantime, you can visit my old webpage for research and software, or the University of Southampton Centre for Biological Sciences and Computational Modelling Group websites for more on lab members and research projects.

Responses of the Emiliania huxleyi proteome to ocean acidification

Jones BM, Iglesias-Rodriguez MD, Skipp PJS, Edwards RJ, Greaves MJ, Young JR, Elderfield H & O’Connor CD (2013): Responses of the Emiliania huxleyi proteome to ocean acidification. PLoS One 8(4): e61868.

Abstract

Ocean acidification due to rising atmospheric CO2 is expected to affect the physiology of important calcifying marine organisms, but the nature and magnitude of change is yet to be established. In coccolithophores, different species and strains display varying calcification responses to ocean acidification, but the underlying biochemical properties remain unknown. We employed an approach combining tandem mass-spectrometry with isobaric tagging (iTRAQ) and multiple database searching to identify proteins that were differentially expressed in cells of the marine coccolithophore species Emiliania huxleyi (strain NZEH) between two CO2 conditions: 395 (∼current day) and ∼1340 p.p.m.v. CO2. Cells exposed to the higher CO2 condition contained more cellular particulate inorganic carbon (CaCO3) and particulate organic nitrogen and carbon than those maintained in present-day conditions. These results are linked with the observation that cells grew slower under elevated CO2, indicating cell cycle disruption. Under high CO2 conditions, coccospheres were larger and cells possessed bigger coccoliths that did not show any signs of malformation compared to those from cells grown under present-day CO2 levels. No differences in calcification rate, particulate organic carbon production or cellular organic carbon: nitrogen ratios were observed. Results were not related to nutrient limitation or acclimation status of cells. At least 46 homologous protein groups from a variety of functional processes were quantified in these experiments, of which four (histones H2A, H3, H4 and a chloroplastic 30S ribosomal protein S7) showed down-regulation in all replicates exposed to high CO2, perhaps reflecting the decrease in growth rate. We present evidence of cellular stress responses but proteins associated with many key metabolic processes remained unaltered. Our results therefore suggest that this E. huxleyi strain possesses some acclimation mechanisms to tolerate future CO2 scenarios, although the observed decline in growth rate may be an overriding factor affecting the success of this ecotype in future oceans.

PMID: 23593500

Nicolas Palopoli (Postdoctoral Research Fellow)

Nico Palopoli started training in Computational Biology with his undergraduate thesis project on the structural modeling and characterization of starch-synthase III from Arabidopsis thaliana, under the guidance of Dr. Gustavo Parisi at the Structural Bioinformatics Group from Universidad Nacional de Quilmes (Argentina). He stayed at the group to fulfill his PhD thesis on the validation of protein 3D models using a structurally constrained protein evolution model.

While still a PhD student, Nico was awarded an Erasmus Mundus Sandwich PhD fellowship to spend an 8-month stay at Dr. Rita Casadio's Biocomputing Group from University of Bologna (Italy) where he started to develop structurally constrained, evolutionary-simulated Hidden Markov Models of protein families. His first Postdoctoral fellowship was awarded to take part in PhasIbeAm, the common bean genome sequencing project. Most of his work was conducted at the Protein Physiology Lab from Universidad de Buenos Aires (Argentina), where he also collaborated with Dr. Ignacio Sanchez on the application of information theory-based methods to study protein interactions by linear motifs.

Nico moved to the University of Southampton in October 2012 to work as a Research Fellow in the Edwards Lab on the project 'Integrated in silico prediction of protein-protein interaction motifs'. He left the lab in late 2014.

Employment History

• 2012-2014: Research Fellow. Centre for Biological Sciences, University of Southampton (UoS), Southampton, UK.
• 2011-2012: Postdoctoral Research Fellow. Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina.

Summary of Academic Qualifications

• 2011: PhD, "Development of an evolutionary-based method for the validation of protein tertiary structure and its application to starch-synthase type III from Arabidopsis thaliana." Structural Bioinformatics Group, Universidad Nacional de Quilmes (UNQ), Bernal, Buenos Aires, Argentina.
• 2006: Licentiate in Biotechnology. UNQ.

Main Funding History

• 2012-2014: Research Fellowship, UoS
• 2011-2012: Postdoctoral Fellowship, National Agency of Scientific and Technological Promotion (ANPCyT)
• 2010: Sandwich PhD Fellowship, Erasmus Mundus External Cooperation Window Lot 16
• 2008-2010: PhD Fellowship Type II, National Council for Scientific and Technical Research (CONICET)
• 2006-2008: PhD Fellowship Type I, ANPCyT

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ & Edwards RJ (2012): SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Research 40(21):10628-41.

Abstract

Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.

PMID: 22977176