Crucial stepping stones in freshwater microbiology

Combining long-term studies with high data volumes to generate new insights into ecosystem function.
Published in Microbiology
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Microbial communities are fundamental to ecosystem function since they participate in biogeochemical cycling and provide essential ecosystem services. Microorganisms are also very useful in ecological experimentation due to their population densities, growth rates and response to environmental stimuli. However, a core challenge to understanding natural ecosystems remains their inherent complexity.  Three articles, published today in Nature Microbiology (by Rohwer et al., Zhou et al. and Michoud et al.) showcase significant recent developments in freshwater microbiology and have, in part, overcome such challenges through long term observations in combination with high data volumes.

Scientific advances are significant but often overlooked or can be taken for granted, although if we look back across even the most recent generations, we see remarkable scientific progress, for example; in transport from horse drawn vehicles to cars, the very first flights to Mars exploration, computing from their conception to quantum computing, and in terms of energy production from wood and then fossil fuels to nuclear fusion and renewables. From a biological perspective, we are fortunate to live in an era following the molecular revolution when genetic resolution and computing power are reaching the point at which we can start to make sensible predictions and hypotheses about the behaviour of microorganisms in response to appropriate environmental stimuli.

In a Microbiology News and Views article entitled ‘Crucial stepping stones in freshwater microbiology’ published in the same edition (https://doi.org/10.1038/s41564-024-01898-1), we take a look at these three articles, how well they illustrate this and speculate about what might come next. Indeed, taken together, they offer far greater insight into freshwater aquatic ecosystems, that are not routinely investigated through a genomic lens at such resolution.

These articles illustrate the benefits of working with freshwater ecosystems, of focusing on extreme environments, once believed to be of relatively low complexity, but with strong selection pressures and of working within the developing framework of some of the broad scale biogeographic studies such as the Global Ocean Sampling Expedition, Tara Oceans and the Earth Microbiome Project. They show the importance of transition environments and what we can learn from such systems, particularly those subject to the strong effects of climate change. Perhaps more fundamentally, they show the potential return from resourcing ambitious projects in microbial ecology and highlight what might be possible through further engagement and investment.

In so doing, they also highlight some of the remaining challenges such as the field is still predominantly in the phase of hypothesis generation, and the need to address the proportion of unknowns and bias inherent in easily detectable or already known sequences in the databases. Work such as this will provide the gateway to the next phase of directed experiments that will eventually provide a full and detailed mechanistic understanding.  

In general, long-term datasets and higher data volumes are already providing vastly increased resolution, enabling greater insights into ecology, evolution and ecosystem function. Together the three studies provide good examples of the potential impact of long-term studies which buck the trend of a need for short-term and immediate impact, which have been long argued for but are still challenging to evidence; they also highlight the benefits of multiple groups focusing on the same system.

What we would add to the overall discussion is the as yet untapped potential for broader international collaboration and corporation, as shown in Antarctic research through the success of the International Geophysical and Polar Year initiatives and also in terms of expensive projects that benefit everyone such as the European Project for Ice Coring in Antarctica (EPICA).

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Environmental Microbiology
Life Sciences > Biological Sciences > Microbiology > Environmental Microbiology

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