State of the Science Stories: Genomics Observatories | Assemble+

State-of-the-Science Stories: Genomics Observatories

What is a Genomics Observatory?

A Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.

In ASSEMBLE Plus' Genomics Observatories joint research activity, coordinated genomics observations of planktonic and benthic communities will be performed and optimised. Building on the long-term investment, infrastructure, expertise, and traditions of more than 20 ASSEMBLE Plus marine stations, ASSEMBLE Plus will also produce a roadmap for our marine genomic observatories, to optimise their outputs and to ensure their longevity.

 

What is a ASSEMBLE Plus doing that is different?

1. ASSEMBLE Plus is coordinating the Ocean Sampling Day

The Ocean Sampling Day (OSD) is a world-wide sampling programme: one day every year hundreds of scientists and citizens collect water samples from the ocean in a coordinated and controlled manner. These samples are sequenced at HCMR in Greece, to extract the DNA of whatever is in the water, telling us what was living at that sampling site the time. Each yearly OSD dataset can tell us the compositiion of the ocean as sampled from hundreds of sites accross the world. Taken together with the in-situ meaurements of the physical (temperature, etc) and chemical (salinity, etc) conditions, the OSD data over the years can tell us how climate change is affecting life in the oceans. 

OSD challenges are genomics observatory challenges. OSD takes place at every summer solstice (21st June). Each year, new stations register, and contribute to that year's OSD event and to the subsequent OSD events. In each station, environmental and genomic data are produced following standardised sampling and experimental procedures for reproducibility and comparability. Samples are centralised for further processing (biobanking, high molecular weight DNA extraction, DNA metabarcoding of prokaryotic and eukaryotic microbial communities) to avoid biases between individual laboratories.

OSD in 2018 and 2019 delivered high-quality genomic DNA for 65 stations, which are being amplicon* sequenced and will soon be jointly submitted to shotgun** metagenomics sequencing. All data and metadata, genomics and environmental, will be made publicly available via the ASSEMBLE Plus data collection. OSD events are a great exercise in acquainting the community with the production and value of high-quality Findable, Accessible, Interoperable and Reusable (FAIR) data, which until now has been more of a wish than of a practice. 

2. ASSEMBLE Plus is participiating in the ARMS project 

The Autonomous Reef Monitoring Structures (ARMS) are units made up of eight connected and stacked plates. A unit is placed on the sea floor, and over a period of time it gets colonised by whatever is living there. Because of their three-dimensional structure, mimicking the complexity of hard bottom marine substrates, they attract encrusting species (corals, algae, etc.) and motile organisms (crustaceans, mollusks, polychaetes, etc.). The key innovation of the ARMS is their ability to sample marine communities over precisely the same area and in the exact same manner providing a standardised and quantifiable measure of biodiversity over time and location. The ARMS-MBON project (Marine Biodiversity Observation Network for genetic monitoring of hard-bottom communities) which has a focus on Europe and the polar regions, is part of ASSEMBLE Plus.

Unlike the water column that is sampled by OSD, the nature of benthic habitats presents a huge diversity which it makes it difficult – if not impossible – to standardise the sampling methods to allow a comparison of the biodiversities from different sites and from different times. This is where the ARMS come in: as passive collectors that can be deployed in any type of benthic habitat, they sample the marine benthic fauna in a standarised and repeatable way.

ARMS deployment has been taking place in two phases. The exploratory phase in 2018 aimed to train our practicioners, benchmark the sampling and analysis methods, and decide on deployment periods. This phase has completed and the data are in process of analysis, and will be archived in our ASSEMBLE Plus data collection. The second phase began in 2019, during which specific scientific questions were addressed, for example we focussed on determining the capacity of the ARMS to detect non-indigenous species (NIS) around ports. ARMS units have been deployed in 19 sampling areas at ASSEMBLE Plus sites in European coastal waters and Antarctica, in triplicates whenever possible. Once brought up, each ARMS plate is treated separately (high-resolution photographs are taken, and DNA metabarcoding of eukaryotic communities are produced). ARMS can be used for a broad range of questions including long-term ecological research, monitoring, and inventory (LTER). 

3. ASSEMBLE Plus is working on barcoding reference databases 

Finally, ASSEMBLE Plus aims to enrich the local DNA barcoding reference databases (Guillou et al., 2013; Glöckner et al., 2017; Herbert et al., 2003), so that DNA metabarcoding (Ruppert et al., 2019) captures taxonomically well-annotated biodiversity data. Indeed, DNA metabarcoding is a high-throughput, effective, and relatively cheap method for assessing biodiversity. Despite that, a high percentage of biodiveristy that could be captured by DNA metabaroding method remains unkown, mainly because of the relatively poor reference databases that exist for DNA barcoding.  ASSEMBLE Plus’ work is working towards improving this shortcoming.

 

What Next? 

  • Monthly OSD sampling will be undertaken (2020) at some of ASSEMBLE Plus’ stations
  • The ARMS data will be uploaded to nd GeoME
  • All OSD and ARMS data and metadata will will be added to the ASSEMBLE Plus data collection in 2020

 

Potential Impact

At the international level, we are at present far from being able to produce long-term genomic data that can allow for a deep understanding of biodiversity dynamics in terms of structure and function across geographical areas and ecosystem types. Such data are simply not produced. ASSEMBLE plus is building the elements of an infrastructure that will allow the production of such data, and making FAIR and publicly available. OSD and ARMS are such examples involving broader international collaborations. ASSEMBLE Plus is now in the process of moving from the test level to the operational level. Once completed, ASSEMBLE Plus will deliver a roadmap for long-term observations of marine ecosystems by combining standardised methods for genomics and environmental data, and by integrating new technologies and data types.

 

* "Amplicon" works by amplifying the strands of DNA in the sample, and extracts  marker genes to identify the population/community composition of the sample.

** "Shotgun" involves breaking the genome collected from the sample into a collection of small DNA fragments that are sequenced (i.e. the ATCG patterns are read and digitised) individually. A computer program looks for overlaps in the DNA sequences and uses them to place the individual fragments in their correct order to reconstitute the genome. Thus, shotgun metagenomics is to comprehensively sample all genes in all organisms present in a given complex sample.

References

Davies, N., Meyer, C., Gilbert, J.A., et al. (2014) A call for an international network of genomic observatories (GOs). GigaScience, 1(1): 5.
Davies, N., Field, D., Amaral-Zettler, L., et al. (2014) The founding charter of the Genomic Observatories Network. GigaScience, 3(1): 2.
Guillou, L. Bachar, D., Audic, S., et al. (2013) The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41(D1): 597-604.
Glöckner, F.O., Yilmaz, P., Quast, C., et al. (2017) 25 years of serving the community with ribosomal RNA gene reference databases and tools. J Biotechnol., 10(261): 169-176.
Hebert, P.D., Cywinska, A. and Ball, S.L. (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci., 270: 313–21.
Ransome, E., Geller, J.B., Timmers, M., et al. (2017) The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia. PLOS ONE 12(4): e017506.
Ruppert, K. M., Kline, R. J., and Rahman, M. S. (2019) Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA. Global Ecol. Conser. 17:e00547. doi: 10.1016/j.gecco.2019.e00547
Wilkinson, M.D., Dumontier M., Aalbersberg I.J., et al. (2016) The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3: 160018.

 

 

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