Copy of Sequencing the meiofaunal metagenome of the marine/freshwater interface in key estuarine ecosystems

Lead Research Organisation: The Natural History Museum
Department Name: Life Sciences

Abstract

Estuaries are key transitional habitats that are significantly affected by local and global human activities (ie they are main centres of habitation, industrialization, pollution and recreation). Estuaries are typically considered to be low biodiversity systems; probably due to the presence of low alpha diversity of macrofauna. In contrast, meiofaunal diversity (animals smaller than 45um, dominated by nematodes) is substantial, with most estuaries estimated to be inhabited by approximately 200 species of nematodes, with numbers ranging from a staggering 106-108 animals/m2, contributing to between 50-90% of the metazoan faunal species richness (the total numbers of species present). Meiofaunal biodiversity plays a very important role in sediment ecosystem processes, contributing to the regulation of carbon, nitrogen, and sulphur cycling, water column processes, pollutant distribution, secondary production, food chain processes, and stability of sediments. Meiofauna are clearly key components of ecosystem functioning, but studying meiofaunal communities using standard morphological approaches requires highly-skilled taxonomists and is incredibly time consuming. Not only does this restrict the analysis of meaningful sample sizes in ecological studies, but the small size and morphological similarities of different species of meiofaunal organisms have led to severe doubts regarding the reliability of morphological taxonomic approaches. As a result of these constraints, combinations of morphological approaches and new molecular genetic methods are being developed for nematode biodiversity assessments. Perhaps the most exciting development in this field is the potential to apply massively parallel sequencing (MPS), to elucidate the molecular community composition of microbial, or meiofaunal samples. This brand new technology has the ability to simultaneously sequence hundreds of thousands of short strands of DNA (in four hours), that can be used as species identification tags. To date, this has never been possible using standard cloning and sequencing methods and MPS also represents incredible value for money, with each sequence in this type of application costing less than 5p. The availability of MPS technology, in addition to recent significant advances in the knowledge of the phylogenetic and ecological relationships of nematode taxa, now offers a molecular and bioinformatic framework that can be used to accurately characterise meiofaunal biodiversity in real time. Such advances allow hypotheses to be developed and tested to elucidate relationships between meiofaunal biodiversity and biotic/abiotic processes. Moreover, these methods will facilitate the development of hydrodynamic models that can be used to predict the spatial and temporal composition of meiofaunal communities according to the relationships between flow rates and sediment composition. The current proposal seeks to create novel biodiversity genome sequence resources for ecologically important estuarine species throughout a range of substrate types in estuarine ecosystems characterized by ongoing (Mersey) and recovering (Thames) industrial and municipal pollutant regimes. The data will be used to address biotic- and abiotic-focused ecological hypotheses, and will generate a predicted c. 320,000 novel sequence reads, effectively characterizing a significant component of the UK's estuarine meiofauna, thus providing a platform for understanding ecosystem functioning in marine sediments. These data can then be combined with complimentary datasets derived from sandy sediments and be used to develop cost-effective, time-saving, DNA chip-based meiofaunal community identification tools (e.g. for biomonitoring and ecotoxicology studies), thus, driving forward research (academic and commercial) into biodiversity-ecosystem functioning in marine sediments.
 
Description This project underpinned a larger body of work that developed a novel method of biodiversity identification, using second generation sequencing, specifically tailored to microbial metazoan taxa. The project quantified the richness of approximately 21 phyla from across the full salinity range of both the Thames and the Mersey estuaries. The River Thames was more biodiverse than the River Mersey and we were also able to identify very different factors affecting the biodiversity of the microbial metazoan communities across disparate taxonomic groups and also the different river basins.
Exploitation Route The approaches can be used for biomonitoring in environmental and industrial contexts, for regulatory bodies and end-users. The principal investigator is currently working on optimising similar protocols to be used for freshwater monitoring purposes with the Environment Agency. The novel method of biodiversity identification can be used as a cost-effective and accurate approach for routine biomonitoring and also for identifying species that are likely to be bioindicators for various environmental pollutants for which monitoring species currently do not exist.
Sectors Agriculture, Food and Drink,Chemicals,Education,Environment,Other

 
Description The research findings have been employed by a large number of groups globally to investigate the biodiversity of microscopic communities and has provided a research framework that could be used for stakeholder relevance by monitoring approaches.
First Year Of Impact 2010
Sector Agriculture, Food and Drink,Chemicals,Education,Environment,Manufacturing, including Industrial Biotechology,Other
Impact Types Societal,Economic,Policy & public services

 
Description Marie Curie Incoming Fellowship
Amount € 174,000 (EUR)
Organisation Marie Sklodowska-Curie Actions 
Sector Academic/University
Country Global
Start 10/2010 
End 10/2011
 
Description Marie Curie Outgoing Fellowship
Amount € 290,000 (EUR)
Organisation Marie Sklodowska-Curie Actions 
Sector Academic/University
Country Global
Start 10/2012 
End 10/2015
 
Description NBAF small grant round 2007-2008
Amount £4,750 (GBP)
Funding ID MGF 167 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 02/2007 
End 02/2008
 
Description NBAF small grant round 2013-2014
Amount £4,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 02/2013 
End 12/2014
 
Description NERC AFI Collaborative Gearing Scheme
Amount £15,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 02/2010 
End 02/2012
 
Description NERC Highlight Topic
Amount £1,250,000 (GBP)
Funding ID NE/N006216/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 12/2015 
End 02/2020
 
Description NERC Standard Grant
Amount £1,200,000 (GBP)
Funding ID NE/N003756/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 03/2016 
End 02/2019
 
Title The metagenetic/metabarcoding identification of meiobenthic biodiversity 
Description Soils and sediments are preserved upon collection and brought back to the lab for bulk extraction of environmental DNA. Marker genes (e.g. rRNA) are amplified from genomic extracts using barcoded, conserved primer pairs. Following high-throughput sequencing (typically conducted on 454 or Illumina platforms), data sets are processed and clustered into operational taxonomic units (OTUs) under a range of pairwise identity cutoffs. OTUs are subsequently used to conduct a- and b-diversity analyses, summarize community taxonomy and interpret assemblages in a phylogenetic context. 
Type Of Material Biological samples 
Year Produced 2010 
Provided To Others? Yes  
Impact The development of this highly cited methodology has created a new field of research in the identification of microscopic eukaryotic biodiversity from sediment matrices. Moreover, stakeholder groups are increasingly interested in the molecular genetic en masse community identification of biological complexity to enhance existing biomonitoring programs that are undertaken to adhere to (e.g.) the European Union Water Framework Directive. 
 
Title High throughput sequencing datasets 
Description All of the sequencing data generated from the NERC grants have been deposited in the NCBI short read archive, therefore making them publicly available for all to use. 
Type Of Material Database/Collection of data 
Year Produced 2010 
Provided To Others? Yes  
Impact The sharing of our data has created many synergies, including data mining by other researchers for related uses and the development of novel analytical approaches. 
 
Description Hosting Swedish FORMAS funded Fellow Francisco Nascimento 
Organisation Stockholm University
Country Sweden 
Sector Academic/University 
PI Contribution Francisco Nascimento is an ecologist working on marine benthic ecosystems and wanted to further his knowledge and experience by engaging with DNA sequencing-based methodologies to assess biodiversity in a number of study systems as part of his ongoing research portfolio. He has been a regular visitor to the group, whereby we have trained him with the appropriate skill sets and set up numerous collaborations throughout our research network.
Collaborator Contribution Members of the group and my wider collaborative network are collaborating with Francisco on grant applications and papers.
Impact There are no manuscript outputs currently, but these will be forthcoming. Nevertheless, Francisco has been successful in winning independent funding in Sweden to support his ongoing research and these will be detailed in the appropriate sections.
Start Year 2014
 
Description NSF EUKHits Research Catalysis network 
Organisation National Science Foundation (NSF)
Country United States 
Sector Public 
PI Contribution Co-ordinating member of the NSF EUKHits Research Catalysis network - workshop participation/organization in USA and Europe.
Collaborator Contribution Leaders and members of the NSF EUKHits Research Catalysis network - workshop participation/organization in USA and Europe.
Impact SMBE UC Davis Eukaryotic sequencing workshop, CA USA. USA ESA Eukaryotic sequencing workshop, Sacramento.
Start Year 2012
 
Description Hosted Special -omic biodiversity session at iEOS meeting, Liverpool 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Chaired special session at 2nd iEOS Meeting, Liverpool
Year(s) Of Engagement Activity 2014
 
Description Hosted Symposium at BES/SFE meeting, Lille, France 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact As part of NSF Catalysis Network EUKHits, hosted biodiversity focused symposium at the BES/SFE Lille conference
Year(s) Of Engagement Activity 2014
 
Description Invited speaker ar ECOFINDERS EU Consortium meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact SC Invited by Large EU consortium to talk about metabarcoding analyses.
Year(s) Of Engagement Activity 2014
 
Description Invited summer school lecturer Roscoff evoutionary genomics course 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Each year, I teach at an International Summer school in the CNRS Marine Research Station, Roscoff, disseminating knowledge regaridng these grants findings, amongst others. The teaching always sparks many discussions with global reach/training.
Year(s) Of Engagement Activity 2009,2010,2011,2012,2013
 
Description NERC Planet Earth Online article 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Raised awareness of NERC funded research.

Increased the profile of using molecular genetic analyses to identify biodiversity and understand macro ecological patterns in the Marine biosphere and potential implications of environmental change.
Year(s) Of Engagement Activity 2014
URL http://planetearth.nerc.ac.uk/news/story.aspx?id=1765
 
Description NERC Planet Earth Online article 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Showcasedwork in an easily understandable format to the general public.

Increased awareness of NERC funded research and raise the profile of the use of molecular ecology in the identification of biodiversity.
Year(s) Of Engagement Activity 2010
URL http://planetearth.nerc.ac.uk/news/story.aspx?id=867
 
Description NESCENT Eukaryotic environmental sequencing meeting, Durham USA 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Participation accelerated synergies in this field, including databasing data and public accessibility and resulted in peer reviewed publication (Bik et al. TREE, 2012).

Global audience were made aware of work via research groups and engagement with stakeholders.
Year(s) Of Engagement Activity 2011
 
Description Scientific advisor to the International SeaBed Authority 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Third sector organisations
Results and Impact Invited as part of expert panel to provide deep sea biodiversity assessment advice to the ISA in relation to deep sea miniong activities.
Year(s) Of Engagement Activity 2015
 
Description Sixth form College visit (Wrexham) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Talk sparked questions and discussion afterwards

Talk stimulated interest in Molecular Ecology
Year(s) Of Engagement Activity 2012
 
Description Speaker at the U.K.'s first and second and third environmental DNA stakeholder meeting (York; DEFRA, Hull, Bangor); hosting from Bangor event 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Third sector organisations
Results and Impact The talk sparked many questions and extensive discussions afterwards in relation to stakeholder related issues and future use of these technologies in environmental monitoring. All England, Wales and Scotland stakeholder groups were in attendance (approximately 80 people from numerous organisations).

As a consequence of this line of work, I have been contacted by environmental consultancies and also formulated sub working committees, in order to progress work in this particular research area.
Year(s) Of Engagement Activity 2014,2015
 
Description Wales Gene Park presentation at local School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Schools
Results and Impact Talk sparked questions and discussion afterwards and interest in Molecular Ecology

Pupils were interested in visiting the lab.
Year(s) Of Engagement Activity 2013
 
Description Wales Gene Park, Ysgol Sir Thomas Jones 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact This popular science talk was delivered to approximately 40 students from the science stream from year 10 and 6th form groups. The Wales Gene Park organisation promotes the integration of research and STEM style subjects and in particular genetic work throughout national schools to increase the profile of the subject matter and encourage pupils to become engaged with molecular genetic research.
Year(s) Of Engagement Activity 2016