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Climate change microbiology - problems and perspectives.

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PubMed ID: 31092905

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Hutchins DA, Jansson JK, Remais JV, Rich VI, Singh BK, Trivedi P

Nat Rev Microbiol. Jun 2019. doi: 10.1038/s41579-019-0178-5

COMMENT: A nice article in Q&A format, where several experts in the field discuss the effects of climate change in the composition of microbial communities from several enviroments, as well as in infectious diseases and ecosystem maintenance. 

Oceans are affected by climate change at the microbial level by inducing shifts in populations that render restructured marine nitrogen and other elements cycles. Taxa that otherwise would be less predominant, now are dominant, inducing toxin-producing phytoplankton and harmful algae blooms. Shifts in microbiomes due to water warming also produce less biologically mediated storage of carbon in deep ocean. Solutions under research include small-scale interventions by reducing pollution and nutrient in local regions. However, the size and nature of marine microorganism communities will require global solutions.

Permafrost thawing due to global warming makes microorganisms in these enviroments more active. As a consecuence, there is more organic carbon decomposition and subsequent greenhouse gases release. Grasslands are specially affected by changes in precipitation patterns that produce changes in soil moisture and have a direct impact in carbon and other nutrients cycles. To overcome these problems, research is being made to exploit the metabolic capabilities of soil microbiomes as carbon sequesters. Synthetic biology tools are also being evaluated in order to produce custom beneficiary plant-soil microorganisms combinations and microorganisms that can promote growth of plants under stress conditions. The use of naturally interacting soil microbiomes is also a possibility that is being explored.

There is a considerable heterogeneity in responses of pathogenic bacteria, protozoa, viruses and fungi to climate change. In bacteria, increased temperatures may lead to increased expression of virulence genes and increased antibiotic resistance. Apart from traditional measures such as isolation and control of dispersion, solutions that include reengineering of organisms and gene editing technologies are under research. Development of new tools for characterization of pathogen populations in soil, water, and air is key in this field. 

Inland waters are key spots in ecosystems and enviroment conservation. Postglacial lakes are affected by permafrost thawing, which become first partially thawed bogs and then fully thawed fens. This progessive thawing induces shifts in the microbial repertoire of these ecosystems, favoring a shift for carbon processing towards simpler polysaccharide degradation, fermentation and acetogenesis, directly affectig methane and carbon emissions. Some approaches to overcome these problems include the identification and utilization of key microbial lineages to reduce methane emissions. In this regard, the use of advanced statistical analyses to integrate biogeochemical and microbiome data, in order to identify lineages associated with methane emissions will be very important in the near future. Direct intervention approaches, like the use of phages against target microorganisms and ecosystem engineering are also being evaluated.

Climate change has both direct and indirect effects on soil microbiomes, generating reduced ecosystem functionality, low stability and replacement or loss of key microbial species. One major consequence of this is the loss of soil organic carbon due to microbial respiration. Manipulation of terrestrial ecosystems, such as changes in land use is establishing as an alternative to mitigate this problem. More innovative solutions that are being evaluated include the use of donor microbiomes from healthy soils, as well as the use of specific groups of microorganisms to restore degraded land. 

And understanding of how environmental microbiomes respond, adapt and evolve to climate change is central to our ability to identify climate-ecosystem feedbacks. 

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Vicente Díaz