Symposium: High throughput methods for application in marine biodiversity time series: Addressing their challenges to fulfil their promises
October 11-13 2017, Schloss Herrenhausen, Hannover
Goals:
Imaging and molecular high throughput tools have the potential to greatly increase the taxonomic resolution and accuracy of biodiversity time series but they might also be difficult to integrated consistently with more traditionally time series based on manual counts and analyses. High throughput techqueniques also hold additional challenges in terms of the complex associated metadata, IT and data management needs. The prime meeting goal is therefore to bring together the respective research communities to discuss biological, technical and management needs for these novel techniques to be used in routine susained biological ocean observations.
The meeting takes place at Schloss Herrenhausen near Hannover. This historic building complex does not only comprise the castle and gardens themselves but also hosts one of the most modern conference centres in Europe.
Meetings funded by the Volkswagenstiftung are regularly hosted here,
Onward travel to Hannover and the conference venue
1. From Hannover
The closest Airport is Hannover-Langenhagen. See Information below “How to get to the Grand Palace Hotel” to find further information.
2. From Hamburg
From Hamburg airport you have several options to ´get to Hannover': you can take a car, bus or train. The airport at Hamburg is directly connected to car rentals (www.sixt.de) or public transport (S-Bahn) and there are direct trains from the airport to Hamburg's main train station. From there you can easily reach Hannover. Train tickets can be booked at http://bahn.de for about 19,90€. If you would like to book over www.trainline.de you can directly get from Hamburg Airport to Hannover main train station for around 13,50€. The cheapest, but longest way to reach Hannover is by bus. Many companies like www.flixbus.de drive 16x daily for around 8€.
3. From Bremen
From Bremen airport you have the same options to ´get to Hannover': you can take a car, bus or train. The airport at Bremen is directly connected to car rentals (www.sixt.de) or public transport (S-Bahn) and there are direct trains from the airport to Bremen's main train station. From there you can easily reach Hannover. Take tram No 6 from the airport to Bremen Main station (Hauptbahnhof). From there take the local train to Hannover. Again, train tickets can be booked online at bahn.de or at the station for also about 19,90€. If you would like to book over www.trainline.de you can directly get from Bremen Airport to Hannover main train station for also around 13,50€.
The cheapest, but longest way to reach Hannover is again by bus. Many companies like www.flixbus.de drive 4x daily for around 5€.
In case of problems just let us know and we will make the booking by phone.
While in Hannover you will likely have to use public transport at some point. To make things easier for you we have booked so-called 'Congress cards' which can be used anywhere on Hannover's public transport system. These are covered by the meeting budget.
Congress cards for all participants will be placed at reception in the Grand Palace hotel and will be handed out upon arrival.
You will not need to book hotel rooms. All symposium participants will be accomodated in the Grand Palace Hotel in Hannover: http://grand-palace-hannover.de/. Rooms have already been blocked and we just need to update arrival and departure times as needed.
How to get to the Grand Palace Hotel
The Grand Palace Hotel is located in the city centre, very close to the train station (Hannover Hauptbahnhof). There are several ways how you can get to the Grand Palace Hotel.
1. From Hannover Airport
From Hannover Airport you have to go outside to the train station. Take Train “S5 Bad Pyrmont”. You will need a ticket you get from www.bahn.de. After 6 stops you will reach the Hannover main train station. See further information below.
2. From Hannover train station
The Hotel is just a 450 m walk away from the main train station.
Upon exiting the station via the main entrance you are on Ernst-August-Platz, go southwest (left) in the direction of Joachimstraße (23m). Turn left into the Joachimstraße (210m). Walk along Joachimstraße until you reach Lavesstraße (210m). The Hotel is on the left side. See map below.
The generation of reliable and comparable time series data is an important aspect of environmental monitoring and is carried out with a variety of methodologies. In Marine Biology/Oceanography there has been an increasing degree of automation of data generation. Instead of individual measurement intervals of days, weeks or months, modern sensors can generate data oceanographic data at frequencies of minutes or even seconds and at remote locations such as the open ocean and the deep sea. While these sensors were originally designed to measure physical parameters such as temperature, salinity and pH. they are increasingly being developed for the assessment of biological diversity in the water column and marine sediments. Novel technologies include automated sample collection, genetic sequencing and other molecular assays, as well as methods that combine flow cytometry with imaging techniques and automated species identification algorithms applied to digital images.
The different types of sensors used for biodiversity assessments are often at an early stage of development and lack technical and analytical standardization. Consequently, the comparability of data sets generated by different sensors is limited. The extent to which these numerous and diverse datasets can be integrated into existing time series sites has not yet been evaluated.
In the proposed symposium we will therefore invite key developers of these new techniques, biodiversity experts and taxonomists, as well as potential users and technical experts (for instance IT technicians) to discuss these novel technologies in marine biodiversity research and develop mechanisms for standardization and intercalibration. We will also identify possible projects that can be used to evaluate the applicability of sensors in a time series context specifically to investigate long-term changes in marine ecosystems
Scientific Background
Marine biodiversity is of fundamental importance for human well-being because it is vital for the functioning of the earth biosphere through processes such as oxygen production, carbon fixation, and the transfer of energy and recycling of matter in marine food webs. Climate change (e.g., ocean warming, acidification, changes in hydrography, etc.) is expected to have severe impacts on marine biodiversity. Notably, changes in phytoplankton composition are expected to have consequences that ripple through entire food webs. Phytoplankton are photosynthetic microorganisms that account for roughly half of global net primary productivity (NPP), as well as significant CO2 drawdown from the atmosphere. As primary producers they are fundamental for marine ecosystem function and resulting ecosystem services. As a consequence, changes in phytoplankton community structure and biogeography (range shifts) as a response to climate change are currently topical issues in marine ecology. Elucidation and quantification of changes in marine plankton biodiversity require long-term observations to link biological effects to their underlying physical-chemical drivers.Despite this its great importance, the task of measuring changes in plankton diversity on a global scale is severely hampered by difficulties in maintaining regular observations of plankton on an adequate temporal and spatial scale, as well as with appropriate taxonomic resolution.As such, new automated high throughput approaches are needed to improve and facilitate long-term observations of marine plankton biodiversity.
Research processes in many fields of marine science are undergoing striking changes, becoming more and more automated and, as a consequence, facilitating much higher frequencies of observation. Two examples of emerging high throughput, and at least partly automated, technologies are (1) Flow cytometry techniques that are coupled with high frequency imaging and (2) High throughput (and other) molecular techniques.
The problem
While methodological and analytical advances in the field of imaging flow cytometry and molecular biology hold great promise for an urgently needed improvement in the understanding of marine biodiversity, the challenges are equally great in terms of computational, data storage and archival needs, as well as new approaches needed for data analysis and visualisation. Many different molecular analysis approaches and protocols, as well as optical observation systems are being developed in unconnected research projects (Figure 1). This provides the additional challenge that different data standards, storage technologies, databases and analysis pipelines will ultimately limit the comparability of data sets from these systems and also limit the usability of the individual data sets for large scale ecological analyses. As a consequence, the integration of these new approaches into long-term investigations is very challenging. Nevertheless, many of the new techniques being developed are destined to eventually be used for long-term observations, while an additional danger is that they are introduced into existing observation programmes without enough focus on the comparability of data from different measuring devices, consequently threatening the internal consistency of a given time series (in addition to limiting the comparability between time series).
The above problems are not new, but have been encountered for time series with conventional manual sampling. In some cases, it has taken several decades to overcome issues regarding the inter-calibration and standardization in the face of shifting methods. With the emerging high throughput techniques for biodiversity assessments, we have an opportunity to avoid similar problems.
It is important to emphasize that although these two methodological approaches have distinct differences there is considerable added value in addressing them together. First, the two methodologies are often used for the same time series/ observatories. Second, they provide highly complementary information. Imaging, for instance, is more rapid and can also be used to annotate sequence information, while sequencing can provide a level of taxonomic and evolutionary detail that in many cases cannot be discerned from images alone. It is therefore timely to network respective communities with the goal of harmonizing approaches and protocols as much as possible, and evaluating the synergistic potential of the two methodologies to refine and facilitate long term observation of marine plankton biodiversity.
Aims of this Symposium
There are five major aims of this symposium that, taken together, will represent a large step forward for research related to exploring and understanding global change consequences for marine plankton biodiversity (see also Figure 2):
I.Assess and discuss advantages and pitfalls of the methodologies
II.Develop a strategy for protocol standardization for the observation of marine plankton biodiversity via imaging flow cytometry and molecular methods.
III.Improve communication between scientists working with the two methodologies
IV.Identify and discuss potential synergistic effects of an application and combination of imaging flow cytometry and molecular methods in ongoing marine long term plankton observation programs.
V.Develop a roadmap to promote the integration and better exploitation of these new methodologies in marine plankton observation programs.
October 11th: Prof Chris Bowler and the TARA Oceans consortium
Ecology and Evolutionary Biology Section, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Paris, FRANCE
Tara Oceans: Eco-Systems Biology at Planetary Scale
The ocean is the largest ecosystem on Earth and yet we know very little about it. This is particularly true for the plankton that drift within. Although these organisms are at least as important for the Earth system as the forests on land, most of them are invisible to the naked eye and thus are largely uncharacterized, even though they form the base of marine food webs and are key players in Earth’s biogeochemical cycles. To increase our understanding of this underexplored world, a multidisciplinary consortium, Tara Oceans, was formed around the 110-ft research schooner Tara, which sampled plankton at more than 210 sites and multiple depth layers in all the major oceanic regions during expeditions from 2009-2013 (Karsenti et al. Plos Biol., 2011). The seminar will summarize the first foundational resources from the project (see Science special issue May 22, 2015 and Nature 28 April, 2016) and their initial analyses, illustrating several aspects of the Tara Oceans’ eco-systems biology approach to address microbial contributions to macro-ecological processes. The project provides unique resources for several scientific disciplines, capturing biodiversity of a wide range of organisms that are rarely studied together, exploring interactions between them and integrating them with environmental conditions to further our understanding of life in the ocean and beyond in the context of evolution, adaptation and ongoing climate changes.
October 12th: Prof Heidi Sosik, Woods Hole Oceanographic Institution, Woods Hole, MA USA 02543
Long-Duration High-Resolution Time Series of Plankton from Automated Flow Cytometry and Imaging
Many aspects of how and why marine plankton communities change through time remain poorly understood, in large part because traditional organism-level sampling strategies are not amenable to high-frequency, long-duration application. The combination of ocean observatories and automated sensors is now addressing this gap and accelerating the pace of discovery. Submersible flow cytometers and imaging-in-flow cytometers are capable of rapid, unattended analysis of individual cells and colonies. Over a decade of high-resolution observations in US coastal waters have provided measurements of 100s of millions of cells, which in many cases can be classified to genus or species with automated analysis. These taxon-specific, high-resolution records are revealing extraordinary detail about the biology and dynamics of plankton ecosystems, including occurrence patterns of harmful species, effects of life cycle transitions during blooms, influences of taxon-specific parasites on mortality, and climate-related impacts on phenology. In this talk, I will highlight examples of new insights and provide some perspective on the challenges in scaling these observational approaches to a more extensive network of aquatic locations.
October 13th: Prof Frank Oliver Glöckner
Challenges in Marine 'Omics: Lessons from Ocean Sampling Day
The Ocean Sampling Day (OSD) was initiated by the EU “Ocean of Tomorrow” project Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) to obtain a global snapshot of marine microbial biodiversity and function. OSDs are simultaneous, collaborative, global mega-sequencing campaigns to analyze marine microbial community composition and functional traits on a single day. On June 21st 2014, 2015 and 2016 scientists from around the world collected more than 350 ribosomal DNA (rDNA) amplicon datasets and metagenomes plus a rich set of environmental metadata. Standardized procedures, including a centralized hub for laboratory work and data processing, assured a high level of consistency and data interoperability.Since 2015 OSD was accompanied by the Citizen Science campaign MyOSD to enhance the marine microbial community snapshot resolution of the OSD and to increase environmental awareness of the general public.
OSD was an experiment, not only by its research tasks, but also by its innovative character in activating and mobilising marine researchers and citizens alike to form a virtual research community that combines many brains, questions and approaches. OSD has shown that the full potential of recent technological advances can only unfold by moving towards an immediate and free exchange of data, technology and expertise to engage many brains from the start.
The talk will provide an overview about OSD including its first scientific results. It will stress the importance of contextual data and proper research data management for integrative research following the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. It will reflect on supportive activities like the German Federation for Biological Data (www.gfbio.org) and the Council for Scientific Information Infrastructures (www.rfii.de).
Reference:
Kopf A et al. (2015) The ocean sampling day consortium. GigaScience 4:27
