Marine bacteria: Who does what, and when?
Marine bacteria play a crucial role in biogeochemical processes such as the cycling of carbon and nitrogen. They have a variety of functions, which in some species are triggered only when seasonal conditions indicate that the time is right. A Marie Curie fellow has taken a closer look at the task division among these tiny agents of change.
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Marine microbiologist Laura Alonso-Sáez has studied the composition of the bacterial communities thriving in coastal waters of the Bay of Biscay and analysed a variety of functions carried out by individual species.
Her findings indicate that the roles of the various species may not overlap as much as previously thought. She has also concluded that some species only perform their particular tasks at specific times of the year, when seasonal changes in environmental conditions kickstart these processes.
“The main problem we have as marine microbiologists is that the vast majority of the microbes that live in the seawater cannot be cultured in the lab. So it’s hard to study what they do,” Alonso-Sáez explains.
However, she adds, the advent of high-throughput technologies for genetic analyses has opened up new horizons. Taking water samples from the ocean and sequencing their genetic material has become a viable proposition.
Alonso-Sáez, then working at the Spanish Oceanographic Institute, put this possibility to good use in the Fundiversity project, for which she benefited from a Marie Curie Reintegration Grant. This funding was awarded to help her re-establish her career in her native Spain after a post-doc assignment in Sweden on a Marie Curie mobility scheme.
The two grants helped Alonso-Sáez pursue her specialisation and acquire additional scientific skills, she notes, listing the genomics expertise that underpinned Fundiversity as one example. They have also allowed her to develop the coordination know-how required to run a molecular biology laboratory, adding to the promising CV that then helped her to secure a tenure-track position in Spain.
Diversity and demarcation
Fundiversity enabled Alonso-Sáez to shed new light on the ocean’s briny bacteria. Over a period of three years, she regularly sampled the waters at a coastal station in the Bay of Biscay within the Spanish time-series programme Radiales.
Every lucky dip brought up specimens of hundreds of species. By studying their DNA and RNA – their genetic coding and the genes that are actually expressed – Alonso-Sáez managed to establish the seasonal variations in the composition and functioning of bacterial communities in this part of the Atlantic.
While some species are strongly represented at all times, others appear to come and go with the seasons. Some grow and carry out their specific functions only at particular times of the year. Alonso-Sáez cites the example of species involved in ammonia oxidation, the transformation of ammonia into nitrite as part of the marine nitrogen cycle, which only expressed the relevant genes in autumn.
A hot topic
There is still a lot to learn about individual species’ contributions to the biogeochemical processes that keep our environment going. However, says Alonso-Sáez, comparing their genes to similar ones from other, well-characterised species makes it possible to infer their functions. A key step in Fundiversity was then to see if the various copies of a particular gene in the samples belonged exclusively to related specimens, or to several types.
Understanding these roles and the vulnerability of the species performing them is crucial. Seasonality reflects a reaction to variations in environmental conditions such as temperature and the availability of nutrients. A lasting change in these parameters, for example as a result of global warming, might jeopardise seasonal species and processes.
Fundiversity ended in August 2013, having unleashed a torrent of data which Alonso-Sáez and her colleagues continue to analyse and exploit. Alonso-Sáez has since moved on to the marine research Institute AZTI, also in Spain. Her work on the functioning of marine bacteria continues in a new project (Teccam) that will explore the impact of changing environmental conditions on model marine bacteria. For this particular study, she will be focusing on species that can be cultured in the lab.
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