Luis Cunha

Luis Cunha

Research Associate

School of Biosciences

Research Overview

I am an environmental biologist/bioinformatician specialized in invertebrate biology, currently working as a Marie-Curie Fellow between Cardiff, UK and EMBRAPA in Brazil. I have been actively involved in several NGS-based genomic and transcriptomic projects to assemble and annotate several invertebrate genomes. I am also involved in projects related to evolutionary ecology, phylogenetics and population genetics and genomics, including functional genomics of organisms living in extreme environments. I am particularly amazed by the volcanic Pontoscolex corethrurus, which became the main subject of study during my Ph.D. research project. My current research projects focus on the study of biodiversity signatures in historical anthropogenic ecosystems, in particular the Amazonian Dark Earth. I am also using animals closely associated with human activity, in particular earthworms, to infer ancient human migrations across South America.

Researchgate news: Extreme earthworms, living at the volcano’s edge

Terra Preta de Indio Network

Division

Organisms and Environment

I am an environmental biologist who became a bioinformatician led by the demands of personal research interests mainly towards invertebrate ecotoxicology, genomics and adaptations to extreme aquatic and terrestrial environments. As a scientist, I always felt highly motivated and committed to the pursuit of a career as an independent research leader and inspirational teacher in biological sciences. I carry a boundless enthusiasm for my research subjects and a passion to communicate such enthusiasm to the public alike, factors which strength my confidence to contribute positively to the high-quality research-led priority of Cardiff University. Day-to-day involvement in the supervision of undergraduate research projects during my post-doctoral period at Cardiff confirmed my desire to integrate active research with effective teaching. The following is a brief resume of my personal achievements and technical skills.

My interest in biological sciences led me to pursue a degree in Biology in one of my favourite places on earth, the Azores Islands, Portugal. During my bachelor studies, I also had the opportunity to conduct research in the Mexican Caribbean region, where I participated in a short-term research programme about invertebrate larval nutritional and general physiology aspects. The research focused on invertebrate’s husbandry, mainly in an attempt of obtaining basic biological information for productive purposes. The success of my research project reinforced my conviction to pursue a career in research and allowed me to attain a First Class Honours degree. In September of 2005, I received an M.Sc. scholarship from the European Social Fund in order to attend the M.Sc. course in Shellfish Biology, Fisheries and Culture at Bangor University. Under the supervision of Dr. Lewis Le Vay, I was able to study the physiology of soft corals and the impact of standard husbandry practices. By the time, I had become interested in questions about how organisms respond and adapt to stressful conditions and I thought that the volcanic islands of Azores would be an appropriate “natural laboratory” to address such questions. I started collaborating with a research group at the Universidade dos Acores and after few months applied to the Science Foundation of the Regional Government of Azores (SRCT) for a Ph.D. scholarship with the project entitled “The effects of extreme environments of volcanic origin in organisms using earthworms as models” (Grant M3.1.2/F/029/2007-RTF/3). At the time I found that studying the particular and unique features of the reducing environments of geothermal biotopes (i.e. the combination of elevated soil, water, and atmospheric elemental composition, together with constant diffuse degassing and high temperatures) was most interesting because the ephemeral nature of the geothermal field is expected to favour the colonization by species with remarkable colonization abilities.

My period at Cardiff University has been marked by my involvement in research during my post-doctoral work, but also by my interaction with graduate and undergraduate students, whom I helped to advise in their research projects. The teaching experiences I collected in Portugal and the UK, as well as the workshops that I organised (e.g. 1st Workshop on “Volcanic environments and their impact on biological organisms” or the 1st Workshop on studies in Terra Preta de Indio (Amazonian Dark Earths)), have unambiguously underlined my commitment to pursuing an academic career. In fact, I consider that my knowledge and experience, coupled with my personal enthusiasm to understand the living world, serve as a key combination of personal traits necessary to carry on research into the future and transmit my biological knowledge and excitement to the future generations of researchers.

My Ph.D.

During my Ph.D. studies, the scale of my research changed from tissue and cell marker analyses to the molecular level, enabling the study of a population of earthworms living in what I like to describe as a volcanic furnace of evolution, a geothermal field in Sao Miguel Island. In order to increase the expertise, I initiated collaboration with Prof. John Morgan and Prof. Peter Kille at Cardiff University and together we wrote a research proposal that was graded as Excellent and successfully funded by the Portuguese Science Foundation (€120,000; Grant PTDC/AAC-AMB/115713/2009). With these funds, I was able to characterise genetically a population of earthworms living inside the geothermal field including among others the identification of various loci under positive selection which likely reflect the worm’s adaptation to the extreme volcanic environmental conditions.

Metazoan Life Extreme Environments

I assisted Prof. Morgan and Prof. Peter Kille in the structuring of a grant application to NERC in order to extend my Ph.D. studies. The project entitled “Stress in a hot place” was seen as an attractive project and was successfully funded (NE/I026022/1). At the present moment, I am working a Marie Curie fellow research in Embrapa-Forestry (Curitiba, Brazil) & Cardiff University (UK)  under a collaboration project funded by the European Union.

Biodiversity Signatures in Anthropogenic Ecosystems

In this stage I am interested in the study of soil biodiversity signatures associated with ecosystems which were historically highly manipulated by humans, the denominated anthropogenic ecosystems, in particular, the Amazonian Dark Earths (please see our network web page http://tpinet.org). With the advent of next generation technologies (NGS), I had the opportunity to participate in the assembly of several invertebrate genomes, among which P. corethurus, one of the earthworms living in the neotropical South American rainforests. Using different sequencing strategies and coupling gene expression data, most of the times by writing my own software tools, I was able to understand better the complex genome of such invasive earthworm.

Projects

Networking project

“A Worm's Trail: Implementing a collaborative network for the study of Historical and Recent Land Use and Soil Management in Neotropical Rainforests” (Grant NE/M017656/1)

The main objective of the project is to establish a long term collaborative network between Cardiff University and EMBRAPA in order to gain knowledge about the functioning and potential role of soil ecosystem engineers, organic matter and nutrients to Amazon Dark Earth (ADE) formation; this novel approach will aid in understanding the origin and sustainable management of these soils as well as other highly weathered acidic soils under humid tropical conditions.

Network webpage:

http://tpinet.org/

Biodiversity signatures in Amazonia

Tracking Historical and Recent Human Settlement, Land use & Migration in Neotropical Rainforests using Ecosystem Engineers” (Grant NE/M017656/1)

The anthropologic and archaeological study of pre-Columbian people of the Amazon Basin has revealed sophisticated ecosystem modifications Notwithstanding the absence of historical written records, the biological evidence of these practices remains in the remarkable soils referred to as Amazonian 'dark earths' (ADEs), or “Terra Preta do Indio”, produced by these ancient civilisations to promote highly enriched environment. With increasing global demand for food, energy and carbon, it is crucial to understand and learn from past land management systems. We can also learn from the influence of these historical practices on the associated biodiversity in order to appropriately manage the current and plan the future land uses. This understanding is essential for both economic and environmental sustainability, and to provide for the needs and aspirations of current and future generations, while simultaneously conserving the ecological fidelity of the resource base on which they depend. This is particularly important with respect to soils and their intrinsic and diverse living organisms, because they sustain plant production (thus, they are at the base of the human food production chain), and have important consequences for water quality and availability. Furthermore, soils are a vast storehouse for biodiversity including many invertebrate species that contribute a number of essential ecosystem services, although most of these species remain mostly unknown, unseen and disregarded. By promoting the interdisciplinary connection between anthropology/archaeology, soil ecology and genomics, we will be able propose to integrate and harness the research expertise of internationally renowned scientists to investigate both the relationship of ADEs to the associated extant biodiversity, reveal details of past and current anthropogenic impact on the natural surroundings, as well as new clues regarding settlement dynamics over a large part of Brazil. Therefore, this project’s intention is to contribute to the knowledge of soil animal biodiversity and its relationship with soil fertility and land use changes in a mega-diverse biome (Amazonia). Our objectives will be accomplished by:

1. Assessing the current soil biodiversity assemblages to gain knowledge about the functioning and potential role of soil ecosystem engineers, organic matter and nutrients to the formation of these extremely fertile soils; this novel approach will aid in understanding the origin and sustainable management of ADEs as well as highly weathered and acid soils under humid tropical conditions.
2. Using DNA barcoding to describe the diversity of the ecosystem engineer community associated with past and recent settlements throughout the Amazonian Basin.
3. Using genomics of a peregrine species closely related with human landscape domestication to mirror the human exchanges and flow among the Neotropical rainforest associated with the migration of Amazonian Indians.

Metazoans Living on a Volcanic Edge

“Stress in a hot place: Characterising the ecogenomics of a pantropical sentinel inhabiting multi-stressor volcanic soils” (Grant NE/I026022/1)
“Understanding of how any metazoan organism tolerates an extreme environment comprised of multiple stressors may help to predict the impacts of current and future multifaceted global change on biodiversity and ecological function. Active volcanic soils represent extreme environments with unique features: elevated metal-ion concentrations, constant degassing over a wide area, and high temperature. Elevated soil temperature, as well as low O2, high CO2, and acidified soil are inhospitable challenges to the resident biota. The present proposal will derive a mechanistic understanding of the adaptation of an ecologically-relevant, ecosytem engineering, soil-dwelling  invasive earthworm species (Amynthas gracilis) to cocktails of physico-chemical stressors of natural origin. Furthermore, the observations on this metazoan life-form with extremophile traits will have applications in the bioeconomy (biotechnology, agriculture and vermicomposting), medicine (models for anoxia & hypercapnia), and environmental management (ecotoxicology, risk assessment, land reclamation).”

Grants

2015: Marie Curie Global Fellowship H2020-MSCA-IF-2014 Grant Number 660378 (209,279£)

2015: Co-I in NERC-IOF Grant NE/M017656/1 entitled “Hook a Worm to Catch a Man: Tracking Historical and Recent Human Settlement, Land use & Migration in Neotropical Rainforests using Ecosystem Engineers” (269,691£)

2015: Co-I in NERC-DIR Grant NE/M017656/1 entitled “A Worm's Trail: Implementing a collaborative network for the study of Historical and Recent Land Use and Soil Management in Neotropical Rainforests” (37,718£)

2012: 4rd Place for the best Business Idea with the project “GEOMARTEC – The use of renewable energies in shrimp aquaculture” at the Concurso Regional de Empreendedorismo e ao Prémio Millenium BCP/CE UAC Melhor Ideia de Negócio.

2011: Team Member of a Standard NERC Grant NE/I026022/1 entitled “Stress in a hot place: Characterising the ecogenomics of a pantropical sentinel inhabiting multi-stressor volcanic soils” (380,000£)

2011: Grant PTDC/AAC-AMB/115713/2009 funded by Portuguese Science Foundation: Research Project entitled “An Azorean furnace of evolution: honing molecular-genetic tools for phylogeography and ecotoxicogenomics in a pantropical sentinel inhabiting multi-stressor volcanic soil” (120,000€).

2011-2012: Mexican Government Scholarship for advanced postgraduate studies to be conducted at Centro de Investigacion y Estudios Avanzados (CINVESTAV).

2010: Grant M3.2.4/I/003A/2010 funded by the Regional Government of Azores, for the organization of the Scientific Meeting “A volcanic furnace of Evolution” (4,740€).

2008-2012: PhD Scholarship Entitled M3.1.2/F/029/2007 “The Effects of the extreme environment of volcanic origin in organisms using earthworms as models”.

2008: Best Poster Award received during the “Fourth International Conference on Metals and Genetics. Paris (France).

2005-2006: 2005-2006: M.Sc. Scholarship funded by the European Social Fund.

Collaborations

During my period associated with Cardiff University I was also able to establish strong collaboration links that have led to the development of new research proposals and innovative science ideas, in particular, the collaboration with Dr. Dave Spurgeon (Centre for Ecology & Hydrology), Prof. Mark Hodson (York University), but also within my own School with Profs Mike Bruford, Kille, Weightman and Dr. Pablo Orozco-terWengel. Old overseas collaboration links were also refreshed, in particular with Prof. Rafael Montiel (LANGEBIO, Mexico), together they were able to assembly and described a new entomopathogenic nematode genome (to be submitted to Genome Research during 2016 summer). Also sourced in a strong collaboration with my Mexican partners, in particular with Dr. Barois (INECOL, Mexico), I was able to describe the associated microbiomes of the earthworms living in the geothermal field. I am also starting to collaborate with Prof. Barbara Plytycz (Jagiellonian University, Krakow, Poland) and Prof. Laszlo Molnar (University of Pecs, Hungary) in a fascinating subject concerning the evolution of the neural-immune axis as exemplified by cerebral and caudal regeneration in earthworms.