Stress in a hot place: Ecogenomics and phylogeography in a pantropical sentinel inhabiting multi-stressor volcanic soils

Lead Research Organisation: Cardiff University
Department Name: School of Biosciences

Abstract

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).

Furnas, a rural parish on São Miguel in the Azores, is situated inside a caldera of an active volcano. Persistent volcanic activity at Furnas creates a soil presenting three formidable life-threatening challenges: locally low O2 (10%) and high CO2 levels (54%), high temperatures (37oC), and elevated metal concentrations rendered bioavailable due to soil acidification (pH 5.8). It is astounding that this extreme soil supports a viable population of A. gracilis. [It is noteworthy that CO2 concentrations greater than 17% leads death within 1 minute in exposed humans.] The aim of this project is to investigate specific functional aspects of how this soil-dwelling multi-cellular animal tolerates the inhospitable conditions of active volcanic soils.

We will investigate the molecular and physiological responses of populations of A. gracilis under three discrete scenarios:i) earthworms sampled directly from inactive and actively volcanic soils;ii) earthworms transplanted from volcanically active to microcosms located in non-active soils, and vice versa; and iii) a series of laboratory 'exposures' representing every combination of the three chemical/physical challenges encountered in the field (i.e. singular or combinatorial). Our observations will encompass the following:

- Comprehensive soil analyses to allow modeling of metal availability for uptake by the earthworms.
- Profiling gene expression to reveal how the earthworm regulates its transcriptome enabling it to tolerate the severe challenges presented by active volcanism.
- Computational interrogation of genetic data to identify mutations in functionally significant target genes involved in metal stress, thermo-tolerance, CO2 metabolism, and hypoxia.
- Measuring the expression level of a conserved gene known as "Hypoxia-Induced Factor" (HIF) which previous studies indicate is paramount in regulating responses to hypoxia, thermal stress, and metal toxicity in vertebrates.
- Measuring the expression of genes belonging to the 'heat-shock' superfamily of stress-response chaperones.
- Biochemical and physiological measurements to determine the efficiency of O2 transport across the body wall, and the amount and O2-affinity properties of the haemoglobin.
- Measuring diurnal changes in the O2 consumption and ATP production rates of Amynthas to establish whether behavior and physiology are modified in active volcanic soils.

In parallel, we propose to support a PhD student to determine the genetic structure of A. gracilis populations in the Azores, and (through collaboration) in Asia (Laos, Korea, Thailand, South China), the region of origin of the cosmopolitan species. The studentship will also study the organism's reproduction, reported to be predominately asexual (parthenogenetic), and the implications of this for a species that is a successful invasive colonizer across a wide circum-tropical range.

Planned Impact

The project's impact will be felt through: its core academic findings related to tolerance to individual & combinatorial stress; increased understanding of active volcanic soils; through the development of novel tools for monitoring geogenic & anthropogenic stress; knowledge of how reproduction strategies underpin species invasion; personnel training & technology transfer. These individual outcomes are described below with a transparent justification of how they map onto NERC science themes (ST) & theme action plans.

Knowledge of the mechanistic basis of metazoan extremophile adaptations.

The project will investigate the underlying mechanistic basis of tolerance to O2 deprivation (anoxia), CO2 exposure (hypercapnia), elevated temperature & increased metal tolerance. The knowledge thus derived from the earthworm may provide understanding of clinical anoxia & hypercapnia events e.g. brain ischemia. In addition, understanding thermal adaptation has transparent implications for understanding how ecosystem will respond to long term climate change (ST:Climate System). Elevated soil metal availability, stemming from geogenic or anthropogenic sources, has important implications for the interaction between the environment & human health (ST:Environment, pollution & human health).

Understanding post-volcanic soil processes & risk management.

The high fertility of volcanic soils often attracts high-density human habitation, thus creating critical risk scenarios. Development of robust bio-monitoring is essential since the potential risk cannot be assessed purely through chemical composition since toxicology is mitigated through the soil's physical characteristics. Therefore deployment of a terrestrial sentinel presents a viable option when informing risk models. Since the target organism, A. gracilis, is a highly invasive species it represents a viable tool for these risk assessments (ST:Environment, pollution & human health).
The project will also determine the geochemistry of active volcanic soils & their relation to those from surrounding non-active locations. By characterising the impact of prolonged exposure or removal of physical stressor (diffuse gassing/increased temperature) better predictions for the consequence of the expansion or reduction of volcanic activity may be determined (ST:Earth System Science).

Parthenogenesis as a strategy for invasion of Island habitats, defined by both physical & chemical barriers.

Determining the implications of a parthenogenetic reproductive strategy for species dispersal, genetic diversity & invasive success has significant global implications for biodiversity (ST:Biodiversity). The project will consider these questions in the context of invasion of physical islands (those surrounded by water) & chemical islands (those created by changing soil chemistry).

Developing a molecular tool kit for a pantropical sentinel species.
All molecular genetic data & resources will be made available through the appropriate public repositories & this can then be exploited by researcher world-wide. A. gracilis is a cosmopolitan, pantropical, peregrine & invasive species. It has been described in India, Asia, Africa, Australia & Pacific/Atlantic Islands. This distribution makes it an ideal candidate for monitoring soil quality & ecotoxicity in developing countries.

Development & technical approach.

This project will deploy cutting edge 'omics' approaches, & requires significant informatics support from NBAF-E. It will develop & apply novel technological & analytical approaches that will have utility in a much wider environment sciences context (ST:Technology).

Training & technology transfer.

Specific training & technology transfer will occur between the Cardiff group & the collaborating laboratory based in the Azores. This will be achieved through data sharing but also specifically by reciprocal research visits by staff based at the two institutions.
 
Description Determined the phylogeography of earthworm species through the Azores.
Sequenced and assembled the genome of a species of earthworm adapted to a volcanic caldera.
Identification of the population independent and population specific transcript response to the multiple stressor associated with living on a active volcanic soil.
Derived the first global methalome for an annalid.
Described the global miRNA of an annelid and the spatial expression pattern of a series of annelid specific miRNAs.
Determined the epigenetic modifications (miRNAs and methylation changes) associated with the multiple stressor associated with living on a active volcanic soils.
Exploitation Route The resources and observations have profound implication for understanding the fundamental relationship between the environmental the its impact of gene control through influence the epigenome. There are additional specific finding associated with physiological adaptation to heat and CO2 which have wide ranging implications in other fields.
Sectors Environment,Healthcare,Manufacturing, including Industrial Biotechology

 
Description Epiworm: Finding the ghost in the genome: Assessing the contribution of epigenetics to environmental plasticity in the soil sentinel Lumbricus rubellus
Amount € 221,606 (EUR)
Funding ID 329690 
Organisation Marie Sklodowska-Curie Actions 
Sector Charity/Non Profit
Country Global
Start 08/2013 
End 08/2015
 
Description Microsatellite marker development for an invasive earthworm species adapted to volcanic soils
Amount £1,360 (GBP)
Organisation Cardiff University 
Sector Academic/University
Country United Kingdom
Start 06/2014 
End 09/2014
 
Description Untangling the Volcanic Earthworm Genome
Amount $5,237 (USD)
Organisation Pacific Biosciences of California, Inc. 
Sector Private
Country United States
Start 08/2016 
End 08/2017
 
Title Volcanic Earthworm Reciprocal Transplantation - Genomic, Transcriptomic and miRNA data 
Description Volcanic Earthworm Reciprocal Transplantation: NCBI Bioproject Accession: PRJNA513445 The objective of this dataset is to evidence the molecular origins of the remarkable environmental plasticity displayed by the peregrine species Amynthas gracilis. This earthworm exhibits different morphotypes which vary with the soil attributes. Biosamples: 1. Macela->Macela 3 Identifiers: BioSample: SAMN10712943; Sample name: MM_3; SRA: SRS4229215 Organism: Amynthas gracilis isolate: MM_3 Package: Invertebrate; version 1.0 Accession: SAMN10712943 ID: 10712943 2. Macela->Macela 2 Identifiers: BioSample: SAMN10712942; Sample name: MM_2; SRA: SRS4229222 Organism: Amynthas gracilis isolate: MM_2 Package: Invertebrate; version 1.0 Accession: SAMN10712942 ID: 10712942 3. Macela->Macela 1 Identifiers: BioSample: SAMN10712941; Sample name: MM_1; SRA: SRS4229219 Organism: Amynthas gracilis isolate: MM_1 Package: Invertebrate; version 1.0 Accession: SAMN10712941 ID: 10712941 4. Macela->Volcanic 3 Identifiers: BioSample: SAMN10712940; Sample name: MV_3; SRA: SRS4229220 Organism: Amynthas gracilis isolate: MV_3 Package: Invertebrate; version 1.0 Accession: SAMN10712940 ID: 10712940 5. Macela->Volcanic 2 Identifiers: BioSample: SAMN10712939; Sample name: MV_2; SRA: SRS4229213 Organism: Amynthas gracilis isolate: MV_2 Package: Invertebrate; version 1.0 Accession: SAMN10712939 ID: 10712939 6. Macela->Volcanic 1 Identifiers: BioSample: SAMN10712938; Sample name: MV_1; SRA: SRS4229214 Organism: Amynthas gracilis isolate: MV_1 Package: Invertebrate; version 1.0 Accession: SAMN10712938 ID: 10712938 7. Volcanic->Macela 3 Identifiers: BioSample: SAMN10712937; Sample name: VM_3; SRA: SRS4229211 Organism: Amynthas gracilis isolate: VM_3 Package: Invertebrate; version 1.0 Accession: SAMN10712937 ID: 10712937 8. Volcanic->Macela 2 Identifiers: BioSample: SAMN10712936; Sample name: VM_2; SRA: SRS4229212 Organism: Amynthas gracilis isolate: VM_2 Package: Invertebrate; version 1.0 Accession: SAMN10712936 ID: 10712936 9. Volcanic->Macela 1 Identifiers: BioSample: SAMN10712935; Sample name: VM_1; SRA: SRS4229217 Organism: Amynthas gracilis isolate: VM_1 Package: Invertebrate; version 1.0 Accession: SAMN10712935 ID: 10712935 10. Volcanic->Volcanic 3 Identifiers: BioSample: SAMN10712934; Sample name: VV_3; SRA: SRS4229218 Organism: Amynthas gracilis isolate: VV_3 Package: Invertebrate; version 1.0 Accession: SAMN10712934 ID: 10712934 11. Volcanic->Volcanic 2 Identifiers: BioSample: SAMN10712933; Sample name: VV_2; SRA: SRS4229221 Organism: Amynthas gracilis isolate: VV_2 Package: Invertebrate; version 1.0 Accession: SAMN10712933 ID: 10712933 12. Volcanic->Volcanic 1 Identifiers: BioSample: SAMN10712932; Sample name: VV_1; SRA: SRS4229216 Organism: Amynthas gracilis isolate: VV_1 Package: Invertebrate; version 1.0 Accession: SAMN10712932 ID: 10712932 SRA raw data: Experiment Accession Experiment Title Organism Name Instrument Submitter Study Accession Study Title Sample Accession Sample Title Total Size, Mb Total RUNs Total Spots Total Bases Library Name Library Strategy Library Source Library Selection SRX5257084 MeDIP-Seq of Amynthas gracilis, mixed tissue Amynthas gracilis Illumina HiSeq 2500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229219 341.97 1 14632622 728275327 Input MeDIP-Seq GENOMIC 5-methylcytidine antibody SRX5257083 MeDIP-Seq of Amynthas gracilis, mixed tissue Amynthas gracilis Illumina HiSeq 2500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229214 275.84 1 12703975 634936805 MV MeDIP-Seq GENOMIC 5-methylcytidine antibody SRX5257082 MeDIP-Seq of Amynthas gracilis, mixed tissue Amynthas gracilis Illumina HiSeq 2500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229219 335.47 1 15477553 773081930 MM MeDIP-Seq GENOMIC 5-methylcytidine antibody SRX5257081 MeDIP-Seq of Amynthas gracilis, mixed tissue Amynthas gracilis Illumina HiSeq 2500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229216 199.73 1 9150071 456456089 VV MeDIP-Seq GENOMIC 5-methylcytidine antibody SRX5257080 MeDIP-Seq of Amynthas gracilis, mixed tissue Amynthas gracilis Illumina HiSeq 2500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229217 308.16 1 14175950 708635147 VM MeDIP-Seq GENOMIC 5-methylcytidine antibody SRX5256970 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229218 829.81 1 13094271 1309427100 VV_3 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256969 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229217 476.43 1 7539407 753940700 VM_1 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256968 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229216 814.31 1 12873567 1287356700 VV_1 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256967 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229221 537.5 1 8490577 849057700 VV_2 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256966 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229214 651.79 1 10323043 1032304300 MV_1 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256965 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229213 695.51 1 11008134 1100813400 MV_2 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256964 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229221 685.71 1 10736310 1073631000 VM_2 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256963 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229211 650.08 1 10317342 1031734200 VM_3 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256962 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229220 708.27 1 11192393 1119239300 MV_3 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256961 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229219 654.21 1 10436188 1043618800 MM_1 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256960 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229222 787.23 1 12485424 1248542400 MM_2 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5256959 miRNA-Seq of Amynthas gracilis: mixed tissue sample Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229215 901.83 1 14278896 1427889600 MM_3 miRNA-Seq TRANSCRIPTOMIC cDNA SRX5225357 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229222 1822.72 1 17126781 3406693517 MM_RNA_2 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225356 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229221 1610.25 1 15012683 2985388168 VV_RNA_2 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225355 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229220 1555.67 1 14531521 2889557512 MV_RNA_3 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225354 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229219 1930.02 1 17993591 3578918437 MM_RNA_1 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225353 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229218 1654.32 1 15365875 3058133259 VV_RNA_3 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225352 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229217 1502.43 1 13930927 2768790547 VM_RNA_1 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225351 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229216 1107.37 1 10333151 2055956553 VV_RNA_1 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225350 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229215 2048.54 1 19274320 3832782011 MM_RNA_3 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225349 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229214 1462.31 1 13697278 2726074723 MV_RNA_1 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225348 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229213 1727.98 1 16182012 3220670158 MV_RNA_2 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225347 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229212 1687.13 1 15736040 3128986277 VM_RNA_2 RNA-Seq TRANSCRIPTOMIC size fractionation SRX5225346 RNA-Seq of Amynthas gracilis mixed tissue Amynthas gracilis NextSeq 500 Cardiff University SRP176610 Volcanic Earthworm Reciprocal Transplantation SRS4229211 2148.87 1 20037808 3985631118 VM_RNA_3 RNA-Seq TRANSCRIPTOMIC size fractionation 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact First Earthworm epigenome described. Most complete Earthworm miRNA collection to date Transcript responses elicited by exposure to extreme environment associated with residence to a volcanic caldera 
URL https://www.ncbi.nlm.nih.gov/bioproject?LinkName=biosample_bioproject&from_uid=10712943
 
Description Review of the sequencing technology, it's strengths and Weaknesses / Sequencing technology and its impact on experimental design 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact NERC-­-MDIBL Environmental Genomics and Metabolomics Training course
Year(s) Of Engagement Activity 2016
URL http://www.birmingham.ac.uk/schools/biosciences/news/2016/06Mar-NERC-MDIBL-Environmental-Genomics-Me...
 
Description iEOS2014 Hot but not too hot to handle: persistence of an earthworm under extreme volcanic conditions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Stimulated discussion and refined thinking

Stimulated additional collaboration
Year(s) Of Engagement Activity 2014
URL http://environmentalomics.org/ieos2014-agenda/