Research project SeaLab
SeaLab is a joint research venture between the Baltic Sea Centre at Stockholm University and the Environmental Genomics group at SciLifeLab. By combining biogeochemical, ecological, molecular and meta-omic expertise and know-how, the aim is to understand the fundamental microbial processes of coastal ecosystems.
Coastal ecosystems are highly productive, biodiverse, and provide important ecosystem services, such as nurseries for fish populations and carbon sinks that mitigate the greenhouse effect.
The key players of the biogeochemical cycling of nutrients and carbon, underpinning these ecosystem services, are the microbial communities of planktonic protists, bacteria, archaea and viruses.
In SeaLab, cutting-edge meta-omics methods are used to analyse samples from water, sediment and possibly also the surfaces of macroalgae and benthic animals, to identify what microorganisms are present and the metabolic activities they are involved in. The goal is to achieve a detailed understanding of the microbial processes in coastal waters and how they vary in time and space depending on geochemical conditions.
Project description
Microbial processes of the sea
The diverse functions of coastal ecosystems are vital for human societies both for food, protection, climate mitigation and as living and recreational environments. In order to understand the ecological and biogeochemical processes catering for these ecosystem services at the very fundamental, molecular level, SeaLab will combine biogeochemical data from water and air with cutting-edge meta-omics analyses of the marine microbiome.
The aim is to identify what microbial species are present and the metabolic activities they are involved in, and how these depend on the geochemical conditions of the coastal waters.
Based on this new knowledge, experiments can be designed to simulate how eutrophication, increased temperature and other environmental changes impact the microbially driven processes. Such experiments can in their turn be used to develop models to predict potential future scenarios in a changing world. The knowledge can also be used to develop efficient DNA-based methods for environmental monitoring of coastal ecosystems.
Better understanding for better management
Coastal waters have exceptionally high biodiversity and productivity. They function, among other ways, as nurseries for fish populations and as carbon sinks that mitigate the greenhouse effect. However, they are sensitive environments and often subject to negative human impacts such as eutrophication, pollution, and global warming.
This leads to overgrowth, low oxygen levels, reduced biodiversity and declining fish stocks. Coastal ecosystems have generally been regarded as carbon sinks, but recent research shows that these ecosystems can also release significant amounts of greenhouse gases such as methane and possibly nitrous oxide.
The source of these emissions is microbiological processes, but it is not clear how they are regulated, and to what extent they occur in different parts of the marine environment. To maximise the benefits of coastal areas and achieve effective environmental management, it is essential to understand these microbiological processes in greater detail.
Meta-omics on field samples
Much is known about animals, plants and macroalgae in coastal ecosystems, but way less about microorganisms, such as planktonic protists, bacteria, archaea and viruses, despite their fundamental role in the cycling of nutrients and carbon.
Microorganisms live in complex communities where different species are often interdependent, making them difficult to cultivate in laboratories. To overcome this, DNA-based methods are used that can be applied directly to environmental samples without cultivation. This enables identification and quantification of microorganisms and even the reconstruction of genomes of new, unknown species. By analysing messenger RNA (mRNA) and proteins it is further possible to study metabolic activity and map how this activity varies over time and space in relation to environmental conditions.
Combining omics, image recognition technology and biogeochemical data
To gain a detailed understanding of how coastal ecosystems function, the SeaLab project studies microbial communities in relation to biogeochemical processes and nutrient cycles. By using metagenomics (targeting DNA), metatranscriptomics (targeting mRNA) and metaproteomics (targeting proteins) methods, we will reconstruct microbial genomes, identify functional genes and measure metabolic activities among microbial community members.
These methods will be applied to both sediment and water samples and possibly also to surfaces of plants and animals. We will also use submersible image recognition technology for the identification of microbial species. The data will then be linked to biogeochemical measurements in the water and in the air just above the sea surface, including greenhouse gases, to find out how the geochemical conditions affect and are affected by the microbiome.
Microbial climate-affecting emissions
To begin with, we will focus on microorganisms that produce and transform greenhouse gases (GHGs) and volatile organic compounds (VOCs). While the climate impacts of GHGs emissions are well studied, the drivers and effects of VOC emissions from coastal ecosystems remain less understood. We know that microbes play a key role in cycling these compounds, yet how the processes are regulated and the extent to which they occur in water, sediment and the air-sea interface is unclear. By quantifying GHGs and VOCs and linking them to microbial metabolism, we aim to better understand the air-sea exchange of carbon and the role of coastal ecosystems in atmospheric chemistry and climate regulation.
Contact us:
Are you interested in microbes and using microbial meta-omics in your research? Feel free to get in touch!
Project members
Project managers
Christoph Humborg
Professor
Anders Andersson
Professor
Members
Emma Bell
Researcher
Alexis Armando Fonseca Poza
Postdoktor
Matthew Salter
Staff scientist
Eva Lindell
Head of Asko laboratory
