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Gene sequencing used for study of structure and functioning of microbial communities in oceans

Post-doctoral Researcher Guilhem Sommeria-Klein at the Academy of Finland is developing mathematical models of microbial communities. He aims to build a unified statistical framework for describing the assembly of microbial communities. These models can then be applied to various environments, such as the ocean microbiome or the human gut microbiome. The goal is to better understand the role of microbiota in the functioning of ecosystems or human health. The research, carried out at the University of Turku, will result in open-source computing methods available for other researchers to use in their work.

 

High-throughput DNA sequencing has had a major impact on studying micro organisms. The method enables using the DNA sequence data sampled from any environment to assess the composition of the microbial community, whether it be in the soil, the ocean or the human gut.

“First we check what information can be found about the DNA sequences of the samples in the sequence databases. If a similar sequence cannot be found in the sequence databases, it will be difficult to know what the organism is. For example, the oceans have many organisms we do not know about. So in the end we are dependent on the sequence databases.”

However, Sommeria-Klein points out that not all species of plankton can possibly be included in the databases.

“We will never be able to describe and sequence all species of plankton. The huge diversity simply makes it impossible.”

However, this problem can be bypassed. Microbial communities can be classified into operational taxonomic units (OTU) using computational methods. The classification is based on DNA sequence similarity, and it is widely used in microbial research. The similarity is usually determined based on the sequence of a certain gene, chosen for its widespread occurrence and stability across the targeted microbial organisms.

“The similarity of the data derived from different ecosystems through the analysis of DNA sequences is striking. Organisms living in the human gut or in the ocean, especially bacteria, do not necessarily differ that much from each other.”

Sequenced genes of a microbiota contained in an environmental sample are analysed in bulk using the same method that is used to analyse the sequenced genes of one species. This approach, called metagenomics, is a common concept in the microbial research.

“We can use metagenomics to compare microbial communities sampled in different locations and study spatial patterns of variation, for instance. We can also determine the functions of certain genes in the microbial communities and how those functions change when the place and conditions are different.”

The ocean microbiome consists of prokaryotes, i.e. non-nucleated bacteria and archaea, and eukaryotes, i.e. nucleated microbes. Among the common kinds of phytoplankton are cyanobacteria, green algae, diatoms, dinoflagellates and cryptophyta. Plankton produces half of the oxygen we breathe.

Changes in ecosystems and plankton communities

 

Unlike on land, microbes make up most of the biomass in the ocean. Phytoplankton are a key part of  theoceanic microbial communities, since these organisms can combine water and carbon dioxide using energy from sunlight to form the organic molecules that constitute all living organisms, as plants do on land (photosynthesis).

“Since there are no plants in the open ocean, phytoplankton form the base of the whole ocean food chain,” says Sommeria-Klein.

The process also releases oxygen: phytoplankton are responsible for half of the oxygen in the atmosphere, and have a major impact on the oxygen content of sea water, thus enabling animals to live in the ocean.

“Although phytoplankton need light, they are actually often most abundant at a depth of around a hundred meters, where colder water that transport nutrients from the ocean depths meet the sunlight. The ocean is a three-dimensional environment: we miss a lot by only studying its surface. The biomass in the depths of the ocean, up to thousands of meters deep, is much larger than we thought previously. Due to darkness, there is no photosynthesis there. However, plenty of organic matter falls to the bottom, nourishing the deep ocean ecosystems.”

Guilhem Sommeria-Klein has access to enormous amounts of data on all the oceans of the world and at different depths. The research schooner Tara captured genetic material for DNA sequencing from the world’s oceans in 2009–2013. In total, 35,000 samples were collected from 210 locations around the world. The DNA analysis revealed over 40 million genes, the majority of which were new to science. About 250,000 molecular “species” of plankton were isolated from the samples based on DNA. The analysis was based on the metabarcoding approach, which is the analysis of DNA sequences in a specific gene region to identify different species or individuals.

“The ocean actually harbours a very wide range of microbes beyond phytoplankton. This view was much underappreciated until Tara expeditions. Microbial eukaryotes, in particular, are highly diversified and still poorly known. Moreover, the geographic distribution of plankton is not well known, as studying their habitat is difficult. In a recent study, we analysed the geographic distribution of different groups of eukaryotic plankton around the world and contrasted these distributions in light of the organisms’ main characteristics. ”

Sommeria-Klein’s interests lie in the functioning of these microbial communities and what they are doing in response to their environment in the oceans.

“Plankton are constantly moving with the ocean currents, which reshuffle communities and transport the organisms to different environmental conditions. I am fascinated by the way that these communities continue to interact, specialise and evolve under such challenging conditions.”

The oceans are an important carbon sink

 

The oceans also have an important role to play as a carbon sink. Plankton communities greatly contribute to it by capturing carbon dioxide from the atmosphere through photosynthesis. This carbon is then recycled in the ocean food chain and finally sequestered in the ocean floor as dead organisms sink to the bottom.

“Global warming leads to changes in water temperature but also in ocean currents. These combined changes can have profound effects on the ecosystems, with an impact on the ocean fish stocks and the effectiveness of the ocean as a carbon sink.”

The Tara Oceans Expedition (2009–2013) collected 35,000 samples of seawater and plankton. Sequencing and imaging was later applied to the samples. Research schooner Tara collected samples from 210 open ocean locations at different depths during this expedition. The schooner has since then regularly taken part in new research expeditions to document the various aquatic ecosystems worldwide.

Guilhem Sommeria-Klein wants to develop more efficient methods for analysing and interpreting the data. Rather than solely specialising in mathematics or biology, his research aims to connect various disciplines.

“This represents the core area of our research team focusing on computational analysis, and the work of Sommeria-Klein supports it well”, says Leo Lahti, Associate Professor in Data Science at University of Turku, whose team develops machine learning models for screening microbial communities.

“Microbial ecology is in desperate need of this type of basic computational studies. These models will help break complex microbial ecosystems down to a few basic structures. Ocean microbiome research could also be useful in monitoring the changes in the state of the Baltic Sea. Models based on statistical reasoning can take into account any prior information and describe the uncertainty in the results. The high-performance computing services of CSC – IT Center for Science are needed to fit these models to the data.”

In the future, Sommeria-Klein wants to continue studying ecosystems that differ from each other.

“We want the perspective on microbial ecology to be consistent across ecosystems, as it is of major importance for various societal issues, such as human health, the ocean food chain and the global carbon cycle.”

 

 

Bacteria, archaea and eukaryotes are derived from the same ancestor. However, these groups diverged from each other at a very early stage. Bacteria represent the most ancestral form of microbes, from which the ancestor of archaea and eukaryotes branched off. The split between archaea and eukaryotes occurred later, and is currently the subject of much research interest.

Ari Turunen

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More information:

University of Turku

https://www.utu.fi/en

CSC – IT Center for Science

is a non-profit, state-owned company administered by the Ministry of Education and Culture. CSC maintains and develops the state-owned, centra- lised IT infrastructure.

https://www.csc.fi/en/

https://research.csc.fi/cloud-computing

 

ELIXIR

builds infrastructure in support of the biological sector. It brings together the leading organisations of 21 Euro- pean countries and the EMBL European Molecular Bio- logy Laboratory to form a common infrastructure for biological information. CSC – IT Center for Science is the Finnish centre within this infrastructure.

https://www.elixir-finland.org