Background and rationale
Soil microbes are central in terrestrial carbon cycling. They act as gatekeepers of soil-atmosphere carbon exchange by balancing the rate of organic matter decomposition and stabilisation. This balance can shift under altered environmental conditions. Climate change is making droughts more severe and frequent, particularly in Mediterranean ecosystems. Droughts reduce microbial activity and affect soil carbon cycling. The reduction in microbial activity may occur due to direct organismal physiological responses to water stress as well as due to indirect limitations to resource diffusion and transport.
Long-term climatic shifts like drought are known to change the composition of active members of the microbial community, as selective pressures enable some taxa to gain competitive advantage over others. Chronic drought stress is also likely to impose adaptive pressures on organisms to increase fitness in the changed environment. Microorganisms have the potential to acquire new genes through horizontal gene transfer. Such evolutionary processes could enable organisms under chronic drought to gain stress tolerance traits. However, how these ecological (selective) and evolutionary (adaptive) pressures impact community dynamics and their overall physiology in response to drought stress is not well understood.
Aims and objectives
This PhD project aims to understand the mechanisms of drought stress response in individual microbial populations and how it impacts overall community traits and soil carbon cycling processesin Mediterranean ecosystems from California and Spain. The aim is to study the ecological andevolutionary processes that shape communities under long-term drought. We will use a trait-based approach to explore population-level trade-offs between stress tolerance and physiological traits linked to growth.
A combination of microbial culture isolation-based and non-cultivation molecular-based population genomics will be used to study drought-tolerant microbes. Later on, targeted lab-mesocosm experiments will be conducted to understand the response of drought-tolerant and drought-sensitivepopulations to water stress and the consequences on their fitness. This population-level understanding will be used to assess community shifts in response to drought and predict ecosystem functions such as organic matter decomposition and storage.
Expected field locations
We will have access to soils from multiple sites with long-term drought treatments through ongoing and new collaborationsin California and Spain. These sites have field-scale long-term precipitation manipulations. Soils will be obtained from these sites for the detailed assessments planned in this PhD project, however field work will be minimal.
Essential and desirable skills
We seek an enthusiastic PhD student with microbiology, ecology or soil science background with interests in omics technologies. Statistics and bioinformatics experience are desirable.
Essential: Applicants are expected to hold (or be about to achieve) at least a 2:1 UK Honours degree (or Equivalent) in a relevant subject such as microbiology, ecology or soil science. Applicants with a 2:2 Honours degree (or Equivalent) may be considered providing they have a Distinction at Master’s level.
Desirable: We seek an enthusiastic PhD student with interests in omics technologies. Statistics and bioinformatics experience are desirable.
|Profile: Ashish Malik|
Institution: University of Aberdeen
Department/School: School of Biological Sciences
|Profile: Deepak Kumaresan|
Institution: Queen's University, Belfast
Department/School: School of Biological Sciences
|Profile: Cécile Gubry-Rangin|
Institution: University of Aberdeen
Department/School: School of Biological Sciences
J. P. Schimel, Life in dry soils: effects of drought on soil microbial communities and processes. Annu. Rev. Ecol. Evol. Syst. 49, 409-432 (2018).
S. Manzoni, J. P. Schimel, A. Porporato, Responses of soil microbial communities to water stress: Results from a meta-analysis. Ecology 93, 930-938 (2012).
A. A. Malik, et al., Drought and plant litter chemistry alter microbial gene expression and metabolite production. ISME J. (2020) https:/doi.org/10.1038/s41396-020-0683-6.
P.O. Sheridan, …, C. Gubry-Rangin. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat Commun 13, 4110 (2022). https://doi.org/10.1038/s41467-022-31847-7
E. Kröber, …, D. Kumaresan.Comparative genomics analyses indicate differential methylated amine utilization trait within members of the genus Gemmobacter. Environmental Microbiology Reports, 13: 195-208(2021) https://doi.org/10.1111/1758-2229.12927
Soils from multiple field-scale long-term drought experiments in Mediterranean ecosystems from California and Spainwill be used to understand population-and community-level drought stress tolerance mechanisms. This will be achieved using microbial culture isolation-based, and molecular-based population genomics, combined with targeted mesocosm experiments. Shotgun metagenomics will be used to decipher community-level physiological response to long-term drought. Culturing will be performed using diverse media with in situ substrate levels (including soil wash agar) to facilitate the recovery of slow growing taxa, which are often the most abundant groups in soil. The genomes of individual populations will be obtained through genomic sequencing of culture isolates. To mitigate potential difficulties in cultivating soil microbes, we will use a complementary molecular approach to determine the potential metabolism of uncultivated microbes using de novo assembly of individual genomes from shotgun metagenomics data (metagenomics-assembled genomes). A pipeline for de novo assembly of genomes is already developed and will be used to assess distributions of functional genes linked tostress tolerance across populations. 13C isotope tracing will be used to quantify traits like growth rate and growth yield for individual isolates. 13C-labelled plant litter dissolved organic matter will be used as a tracer and 13C in microbial DNA and respired CO2 will be measured on isotope ratio mass spectrometer and cavity ring-down spectrometer, respectively. Microbiome data generated will be integrated with ecosystem measures using rigorous ecological statistics tools. Such a combination of microbiological culturing, stable isotope tracing, genome assembly, bioinformatics and ecological statistics approaches will enable a detailed mechanistic understanding of microbial drought stress adaptation.
Expected Training Provision
Research training will be available in technical skills linked to molecular biology tools, culturing, bioinformatics, stable isotope tracing and ecological statistics. The Centre for Genome Enabled Biology and Medicine at University of Aberdeen houses DNA sequencing platforms like Illumina NextSeq500 and Oxford Nanopore GridION which will be available to the project including training. The genomes of individual populations will be obtained through genomic sequencing of culture isolates. The supervisory teamis experienced in microbiological tools and will provide guidance and training. De novo assembly of individual genomes from shotgun metagenomics data will be done using an established pipeline. UoA has state-of-the-art molecular facilities and bioinformatic and computational biology support required for downstream analyses of the generated sequence data, e.g. genome assembly, polishing of contigs and functional annotations. Analytical facilities for gas and compound-specific 13C isotope analysis will be available to the student to quantify traits like growth rate and growth yield for individual isolates using stable isotope tracers. There will be full access to the stable isotope facilities at UoA including IRMS supported by a dedicated analytical technician who will help with the measurements. Student will be trained in using and applying these cutting-edge tools and to integrate the microbiome data with ecosystem measures. Student will be encouraged to attend university-based and external courses on acquiring various technical skills, especially bioinformatics (e.g. Strategies and Techniques for Analysing Microbial Population Structures STAMPS course at Marine Biological Laboratory, US). We also have established systems for training and skills development, monitoring progress and other support.
The proposed project not only aims at advancing the field of fundamental microbial ecology but will also significantly advance knowledge on physiological mechanisms of soil microbes under long-term drought and their links to soil carbon cycling. This will generate new knowledge and theoretical concepts for future work, which will directly benefit thewider research community. Timely publication of results in peer-reviewed journals and presentation at national and international scientific conferences will enable the student to disseminate the new understanding generated to other researchers in the field. Audiences of journals and conferences will be in the field of microbial ecology but also general ecology and environmental as well as other sections ofmicrobiology, biogeochemistry and soil science. The methodological or theoretical advances made in the project will be applicable to these fields.There is a lack of mechanistic understanding of drought effects on microbial physiological adaptation and the subsequent microbial control on soil C cycling. Such knowledge is essential to assess the sensitivity of the soil C pool to future changes in soil moisture and to better predict changes in its pool size. The findings of this project will therefore enable earth system climate-carbon modellers to improve the prognosis of climate change feedbacks in response to changes in precipitation. Such projections will help policy-makers at different governance levels and relevant NGOs in making key decisions relevant to mitigation of climate change effects.
The student will primarily be based at University of Aberdeen under the supervision of Dr. Ashish A.Malik (AAM) with access to lab and facilities for research and training at the School of Biological Sciences. AAM’s research focusses on understanding soil microbial processes and the underlying mechanisms from population and community to ecosystem scales. To address the challenge of translating the immense taxonomic and metabolic diversity of microbes into ecologically meaningful information, he has developed trait-based approaches to study microbial distribution across environmental gradients which will be applied in this PhD project. This would build on his past work on understanding the physiological constraints facing microbes under drought and the consequences for plant litter decomposition in Californian grasslands.
Co-supervisors Dr Deepak Kumaresan (DK) at Queen’s University Belfast and Prof. Cecile Gubry-Rangin (CGR) at University of Aberdeen will be involved in providing advice and guidance as well as monitoring project progress through periodic meetings. DK’sworks on using eco-genomics tools to elucidate eco-physiological mechanisms in microbial systems that underpin ecosystem servicesand his insight will be highly valuable to the project. CGR’s research is directed toward understanding ecological, physiological and evolutionary adaptation of microbial populations. Her research is performed at the ecological level throughanalysis of community response to environmental perturbations and over the longer-term evolutionary scales through analysis of genetic diversification. The supervisory team with highly relevant expertise and technical skills will make a valued contribution to the project.
In Year 1, the student will complete induction process at UoA and get familiarised with the research environment and available facilities. This period will be used by the student to review the literature relevant topics, choose the key focus area within the broader theme, gain technical skills and hands-on experience in using the relevant analytical systems, and make field visits to sample soils that will be tested in the project. Some initial analytical trials will be performed to assess the suitability and success of the measurements planned. The student will present their project objectives with some preliminary results at a relevant national conference (e.g. BSSS Early career researchers meeting, MMEG). During this period, the student will also prepare for their first PhD progression interview.
Once the planned methods and approaches are deemed appropriate through initial trials and assessments, the student can proceed to perform the full suite of analysis on the entire sample set in the second year. This will include culturing, metagenomics, stable isotope analysis, and bioinformatics. The large amount of data that will be generated through various analyses will then be processed through a rigorous statistical framework. At the end of this period, the student will present initial results atan international conference (BESS, ISME) and will also prepare for the second PhD progression interview. In the third year, data analysis will be completed and the student will begin drafting a manuscript for publication. This will also help the student prepare their thesis. The plan is to submit at least one high profile manuscript to a journal before thesis submission.
Not applicable at this time.